BLASTP 2.2.21 [Jun-14-2009] 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. Query= 0094.0006.p (426 letters) Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF excluding environmental samples from WGS projects 15,459,386 sequences; 5,307,515,862 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value ref|NP_774135.1| hypothetical protein bll7495 [Bradyrhizobium ja... 307 2e-81 ref|YP_001237816.1| putative pseudouridine synthase, Rsu [Bradyr... 261 1e-67 ref|YP_578366.1| pseudouridine synthase, Rsu [Nitrobacter hambur... 241 2e-61 ref|YP_001207948.1| putative pseudouridine synthase, Rsu:RNA-bin... 227 3e-57 ref|YP_530796.1| pseudouridine synthase Rsu [Rhodopseudomonas pa... 210 3e-52 >ref|NP_774135.1| hypothetical protein bll7495 [Bradyrhizobium japonicum USDA 110] dbj|BAC52760.1| bll7495 [Bradyrhizobium japonicum USDA 110] Length = 696 Score = 307 bits (787), Expect = 2e-81, Method: Compositional matrix adjust. Identities = 250/460 (54%), Positives = 286/460 (62%), Gaps = 103/460 (22%) Query: 1 MPRDSDKNNDSPRGRRDRGAPGKGRPSGSRGSDKPFGKRSFGGKPDR--GKGDRDKRAFG 58 MPRDSDK+NDS RGRRDRG P KGR +RG +K F KR F GK D +GDR Sbjct: 5 MPRDSDKDNDS-RGRRDRG-PAKGRSGKARGPEKKFAKRGFEGKGDSRPPRGDR------ 56 Query: 59 DKGEGRSFRRREDGDAPRRDYGDRPHFKRDDRGGE---------------------GGGK 97 EGR FRRRE+GDAPRRD+ DRP FKRDDRGGE G K Sbjct: 57 ---EGRPFRRREEGDAPRRDFSDRPRFKRDDRGGEERGERSFKPRGDRPFSDRGARDGEK 113 Query: 98 RPFKPRGERRDFDAGDRPQRG----GARSEGRSSDRKFGEKRSYGDREKRPYTPRGERDG 153 RPFKPRG+R + DRP R +R+ GR+ DRKFG+KR Sbjct: 114 RPFKPRGDRPSYGRDDRPPRSRDRDDSRAAGRTGDRKFGDKRPS---------------- 157 Query: 154 EKRTFAPRGERAERKFD-DRKFSRGDRDKGS-FRDKGE---GRPFRRREDGD----APRR 204 APRG+R ERKFD +RKFSRG D+ RD+GE +P+++R+ G PR+ Sbjct: 158 -----APRGDRPERKFDGERKFSRGAPDRSDRPRDRGERSDSKPWQKRDAGPRGDRPPRK 212 Query: 205 DFGDRPRFKRDRDFEGRDRSDEKPWQKRDRTPREDYKSGDDRGGDERPRFSRSRDDRSGG 264 DF PR +DF GRDRS++KPWQKR+ GGD+RPRFSRSRDDR G Sbjct: 213 DFSKGPR----KDFGGRDRSEDKPWQKRE-------------GGDDRPRFSRSRDDRPSG 255 Query: 265 DRP----------RFSRSRDDREQGDRPKFGRPRWSRD-EDAGDR-RDNR-XERPEGRTD 311 DRP +F R + DR + DRPKF RPR D E GDR + NR ER EGR+D Sbjct: 256 DRPFRERPKFDRPKFDRPKFDRPRDDRPKFDRPRRDGDGERGGDRPKFNRPRERSEGRSD 315 Query: 312 WQEHPRSEGRFSDRPRRDNEDDSRIFAKRPAFGGRGAYRERASD----DRRERPEPKPKK 367 W EHPRSEGRF DRPRR+NED+SRIF KRPAFGGRGAYRER D RRE PKPKK Sbjct: 316 WHEHPRSEGRFGDRPRRENEDESRIFEKRPAFGGRGAYRERDRDFEGRPRRED-APKPKK 374 Query: 368 SGERIAKVLARAGLASRRDAEEIVTQGRVTVNGRVINXTA 407 +GERIAK LARAGLASRRDAEE+VTQGRV VNGRVIN A Sbjct: 375 AGERIAKALARAGLASRRDAEEMVTQGRVAVNGRVINSPA 414 >ref|YP_001237816.1| putative pseudouridine synthase, Rsu [Bradyrhizobium sp. BTAi1] gb|ABQ33910.1| Putative Pseudouridine synthase, Rsu [Bradyrhizobium sp. BTAi1] Length = 690 Score = 261 bits (668), Expect = 1e-67, Method: Compositional matrix adjust. Identities = 227/468 (48%), Positives = 260/468 (55%), Gaps = 118/468 (25%) Query: 1 MPRDSDKNNDSPRGRRDRGAP----GKGRPSGSRGSDKPFGKRSFGGKPDRGKGDRDKRA 56 MPRD+DK+NDS R GKGR +RG +K F KR FG D+ G + KR+ Sbjct: 1 MPRDTDKDNDSRGRRGGAPRGRSEGGKGRSGAARGPEKKFAKRGFG---DKDAGAKGKRS 57 Query: 57 FGDKGEGRSFRRREDGDAPRRDYGDRPHFKRDDR------------GGEGGGKRPFKPRG 104 F D GR+ RRR+DGDAPR+ YGD+P F RD+R G KR FKPRG Sbjct: 58 FDD---GRAPRRRDDGDAPRKSYGDKPRFNRDERPRGDRPFAARPARAADGEKRAFKPRG 114 Query: 105 ERRDFD----------AGDRPQRGGARSEGRSSDRKFGEKRSYGDRE----KRPYTPRGE 150 +R FD R R AR GRSS+RKFGE++ Y RE KRPYTPRGE Sbjct: 115 DRPKFDRDERSGEKRPYTPRANRDEARPAGRSSERKFGERKPYAARERDGDKRPYTPRGE 174 Query: 151 -------RDGEKRTFAPR----GERAERKFD-DRKFSRGDRDKGSFRDKGEGRPFRRRED 198 R R+F R G+R ERKF +RKFSRG R G G Sbjct: 175 GARDRGDRPRADRSFGDRPPRTGDRPERKFGGERKFSRGAEGDRGERKFGAG-------- 226 Query: 199 GDAPRRDFGDRPRFKRDRDFEGRDRSDEKPWQKR----------DRTPREDYKSGDDRGG 248 PR++FGDRP+ R + KPWQKR R PRE +S D Sbjct: 227 PRGPRKEFGDRPQ-----------RGETKPWQKRGADGDRPERSPRAPREGGRSFD---- 271 Query: 249 DERPRFSRSRDDRSGGDRPRFSRSRDDREQGDRPKFGRPRWSRDEDAGDRRDNRXERPEG 308 RPR R R+DR DRP+F D+PKF RPR RPEG Sbjct: 272 --RPRSDRPREDRPKFDRPKF----------DKPKFDRPR----------------RPEG 303 Query: 309 RTDWQEHPRSE---GRFSDRPRRDNEDDSRIFAKRPAFGGRGAYRER--ASDDRRERP-- 361 RTDWQEHPRSE G F DRPRRDNEDDSR+FAKRPAFGGRGAYRER +D R +R Sbjct: 304 RTDWQEHPRSERRGGDFGDRPRRDNEDDSRVFAKRPAFGGRGAYRERKPETDKRVKRVVP 363 Query: 362 --EPKPKKSGERIAKVLARAGLASRRDAEEIVTQGRVTVNGRVINXTA 407 PKP K+G+RIAKVLARAGLASRRDAEE+VTQGRVTVNGRVIN A Sbjct: 364 DEAPKPGKAGDRIAKVLARAGLASRRDAEEMVTQGRVTVNGRVINSPA 411 >ref|YP_578366.1| pseudouridine synthase, Rsu [Nitrobacter hamburgensis X14] gb|ABE63906.1| Pseudouridine synthase, Rsu [Nitrobacter hamburgensis X14] Length = 687 Score = 241 bits (614), Expect = 2e-61, Method: Compositional matrix adjust. Identities = 212/459 (46%), Positives = 247/459 (53%), Gaps = 121/459 (26%) Query: 1 MPRDSDKNNDSPRGRRDRGAPGKGRPSGSRGSDKPFGKRSFGGKPDRGKGDRDKRAFGDK 60 MPRD+DK+N S RGRRDR + GKGR +RG +K F KR GK D KGD DKR + K Sbjct: 8 MPRDNDKDNASSRGRRDRPSGGKGRSGAARGPEKKFAKRGLAGKTD--KGDGDKRPYAGK 65 Query: 61 -----------------GEGRSFRRREDGDAPRRDYGDRPHFKRDDRGGEGGGKRPFKPR 103 G G+ + + DGDA R P F RD G KRP+ PR Sbjct: 66 SDGTKPYAKKPYARKPYGAGKPYASKRDGDAAR------PRFNRDG----GSEKRPYAPR 115 Query: 104 G-----ERRDF---DAGDRPQRGGARSEGRSSDRKFGEKRSYGDREKRPYTPRGERDGEK 155 G ER F D R RG R GR +D+KFGEKRSY Sbjct: 116 GDSPRSERPAFKRDDRAPRADRGDTRPAGRPADKKFGEKRSY------------------ 157 Query: 156 RTFAPRGERAERKFDDRKFSRGDRDKGSFRDKGEGRPFRRREDGDAPRRDFGDRPRFKRD 215 APRG+R F D+KFSRG D+G PR++FGDR Sbjct: 158 ---APRGDRP---FGDKKFSRGAPDRG-------------------PRKEFGDRA----- 187 Query: 216 RDFEGRDRSDEKPWQKRDRTPREDYK-----SGDDRGGDERPRFSRSRDDRSGGDRPRFS 270 DR + KPW+KR+ PR+D + S D G ++PRF R RDDR G RPRFS Sbjct: 188 ------DRGESKPWEKREARPRDDARRESRPSRDGAGRFDKPRFDRPRDDRGGSGRPRFS 241 Query: 271 RSRDDRE----------------QGDRPKFGRPRWSR---DEDAGDRRDNRXERPEG-RT 310 + R+DR QGDRP++ RP R D DR D +RP G R Sbjct: 242 KPREDRPERTAGGDRGPRKFDRPQGDRPRYERPTGDRPRFDRPRQDRPDG--DRPGGSRN 299 Query: 311 DWQEHPRSEGRFSDRPRRDNEDDSRIFAKRPAFGGRGAYRERASDDRR--ERPEPKPKKS 368 WQE PR R +RPRRDNEDDSR+FAKRPAFGGRGAYRER DD R RPEP+ KK+ Sbjct: 300 AWQERPRRNDR-DERPRRDNEDDSRVFAKRPAFGGRGAYRERKPDDDRRGARPEPRSKKT 358 Query: 369 GERIAKVLARAGLASRRDAEEIVTQGRVTVNGRVINXTA 407 GERIAKV+ARAG+ASRRDAEE VTQGRV VNGRVIN A Sbjct: 359 GERIAKVMARAGVASRRDAEEWVTQGRVAVNGRVINSPA 397 >ref|YP_001207948.1| putative pseudouridine synthase, Rsu:RNA-binding S4:pseudouridine synthase [Bradyrhizobium sp. ORS 278] emb|CAL79733.1| Putative Pseudouridine synthase, Rsu:RNA-binding S4:Pseudouridine synthase [Bradyrhizobium sp. ORS 278] Length = 683 Score = 227 bits (579), Expect = 3e-57, Method: Compositional matrix adjust. Identities = 218/462 (47%), Positives = 254/462 (54%), Gaps = 114/462 (24%) Query: 1 MPRDSDKNNDSPRGRR------DRGAPGK--GRPSGSRGSDKPFGKRSFGGKPDRGKGDR 52 MPR +DK+NDS R G G GR +RG +K F KRSF Sbjct: 1 MPRTTDKDNDSRGRRGGAPRGRSEGGKGSKAGRSGAARGPEKKFAKRSFD---------- 50 Query: 53 DKRAFGDKGEGRSFRRREDGDAPRRDYGDRPHFKRDDR----------GGEGGGKRPFKP 102 +GR+ RRR+DGDAPR+ YG +P F RD+R GEG KR FKP Sbjct: 51 ---------DGRAPRRRDDGDAPRKSYGGKPRFNRDERPRGDRPYAARSGEGE-KRAFKP 100 Query: 103 RGERRDFDAGDRP----------QRGGARSEGRSSDRKFGEKRSYGDRE----KRPYTPR 148 RG+R FD DR R AR GRSS+RKFGE++ Y RE KRPYTPR Sbjct: 101 RGDRPKFDRDDRGGEKRPYTPRGNRDDARPAGRSSERKFGERKPYAPRERDGEKRPYTPR 160 Query: 149 GER-----DGEKRTFAPR----GERAERKFD-DRKFSRGDRDKGSFRDKGEGRPFRRRED 198 GE D R+F R G+R ERKF +RKFSRG D+GE R+ Sbjct: 161 GEGARDRGDRPARSFGDRPSRGGDRPERKFGGERKFSRGAEG-----DRGE-----RKFG 210 Query: 199 GDA--PRRDFGDRPRFKRDRDFEGRDRSDEKPWQKRDRTPREDYKSGDDRGGDERPRFSR 256 G A PR++FGDRP R + KPWQKR G E R R Sbjct: 211 GGARGPRKEFGDRP-----------PRGESKPWQKR---------------GAEGERAER 244 Query: 257 S-RDDRSGG---DRPRFSRSRDDREQGDRPKFGRPRWSRDEDAGDRRDNRXERPEGRTDW 312 R R GG DRPR R+R+DR + DRPKF R SRD + RPEG TDW Sbjct: 245 GPRATREGGRSYDRPRSDRTREDRPKFDRPKFDR---SRDRGDDRGFNKPRRRPEGPTDW 301 Query: 313 QEHPRSEGR-FSDRPRRDNEDDSRIFAKRPAFGGRGAYRERASD----DRRERPE--PKP 365 QEHPRSE R F DRPRRDNE+D IFA+RPAFGGRG YR R + +R P+ PKP Sbjct: 302 QEHPRSERREFGDRPRRDNENDGEIFARRPAFGGRGPYRARKPEPEKRSKRVVPDEAPKP 361 Query: 366 KKSGERIAKVLARAGLASRRDAEEIVTQGRVTVNGRVINXTA 407 +K+GERIAKVLARAGLASRRDAEE+VTQGRV+VNGR+IN A Sbjct: 362 RKTGERIAKVLARAGLASRRDAEEMVTQGRVSVNGRIINSPA 403 >ref|YP_530796.1| pseudouridine synthase Rsu [Rhodopseudomonas palustris BisB18] gb|ABD86477.1| Pseudouridine synthase, Rsu [Rhodopseudomonas palustris BisB18] Length = 743 Score = 210 bits (535), Expect = 3e-52, Method: Compositional matrix adjust. Identities = 219/499 (43%), Positives = 260/499 (52%), Gaps = 131/499 (26%) Query: 1 MPRDSDKNNDSPRGRRDRGAPGKG------RPSGSRGSDKPFGKR-------------SF 41 MPRD+DKNN RGRRDR + GKG R +RG +K F KR SF Sbjct: 1 MPRDNDKNNGPARGRRDRPSGGKGAAGHKGRSGAARGPEKKFAKRAGATDGAFGGEKKSF 60 Query: 42 GGKPDRGKG-----------------------------------DRDKRAFGDK------ 60 G KP G G DR R+ GD+ Sbjct: 61 GSKPYAGPGKPYAGKREGPPPRRDDDRAPRRDFSDAPRPRFNKDDRPARSGGDRPDRGPR 120 Query: 61 ---GEGRSFRRREDGD-----APRRDYG--DRPHFKRDDRGGEGGGKRPFKPRG-----E 105 GE R++ RE G PR + G RP+ R R G G KRP+ PRG E Sbjct: 121 KEFGEKRAYAPREGGGEKRPYTPRGEGGGDKRPYSPRPPREG-GYEKRPYTPRGDAPRGE 179 Query: 106 RRDF-DAGDRPQRGGARSEGRSSDRKFGEKRSYGDRE----KRPYTPRGERDGEKRTFAP 160 R +F D G R RGG R SD+KFG+KR Y RE KRPYTPRGE G+KR ++P Sbjct: 180 RSNFNDRGPRQDRGGDARPARFSDKKFGDKRPYTPREGGGEKRPYTPRGEGGGDKRPYSP 239 Query: 161 RGER-AERKFDDRKFSRGDRDKGSFRDKGEGRPFRRREDGDAPRRDFGDRPRFKRDRDFE 219 R R +R F R +G+R G + G G P R PR++FG RP DR Sbjct: 240 RPSRDGDRPFSAR--PQGERKFGGEKKFGRGAPDR------GPRKEFGSRP----DR--- 284 Query: 220 GRDRSDEKPWQKRDRT----------PREDYKSGDDRGGDERPRFSRSRDDRSGGDRPRF 269 G DR + KPWQKRD + P D DR ++PRF R R++ S G+RPRF Sbjct: 285 GADRGEAKPWQKRDASAPDHVGRNARPARDGARNFDRPDFDKPRFDRPREEGSSGERPRF 344 Query: 270 SRSRDDREQGDRPKFGRPRWSRDEDAGDRRDNRXERPEGRTDWQEHPRSE-GRFSDRPRR 328 SR R+DR PKF RPR E R+ WQEHPRSE +RPRR Sbjct: 345 SRPREDR-----PKFDRPR------------------EARSAWQEHPRSEPSEAGERPRR 381 Query: 329 DNEDDSRIFAKRPAFGGRGAYRERASDDRRERPEPKPKKSGERIAKVLARAGLASRRDAE 388 DNEDDS++FAKRPAFGGRGA+RER D+RR P PKK+GERIAKV++RAGL SRRDAE Sbjct: 382 DNEDDSKVFAKRPAFGGRGAFRERKPDERRPPRPPAPKKAGERIAKVVSRAGLCSRRDAE 441 Query: 389 EIVTQGRVTVNGRVINXTA 407 E VTQGRV VNGR+IN A Sbjct: 442 EWVTQGRVAVNGRIINSPA 460