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= 0002.0249.p (493 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|YP_003777352.1| RNA polymerase sigma-N (sigma-54) factor tra... 824 0.0 ref|ZP_08274231.1| sigma N (sigma 54) factor of RNA polymerase [... 812 0.0 ref|YP_001101339.1| RNA polymerase factor sigma-54 [Herminiimona... 787 0.0 ref|YP_001355042.1| RNA polymerase factor sigma-54 [Janthinobact... 782 0.0 ref|YP_004751122.1| sigma N (sigma 54) factor of RNA polymerase ... 775 0.0 >ref|YP_003777352.1| RNA polymerase sigma-N (sigma-54) factor transcription regulator protein [Herbaspirillum seropedicae SmR1] gb|ADJ65444.1| RNA polymerase sigma-N (sigma-54) factor transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 496 Score = 824 bits (2129), Expect = 0.0, Method: Compositional matrix adjust. Identities = 413/498 (82%), Positives = 449/498 (90%), Gaps = 7/498 (1%) Query: 1 MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQILSDNPLLERLDDALDNSVRL 60 MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQIL+DNPLLERLDDALDNSVRL Sbjct: 1 MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQILTDNPLLERLDDALDNSVRL 60 Query: 61 LADGALSSSPSAQAEPVENSAPSAAPA----EGEAG-DPQDSPAGDEHAGSDADWSFDDV 115 LADGA+S++PS+ S S+ A +GE+ + QD+ E D+DWSFDDV Sbjct: 61 LADGAVSAAPSSGVSETTGSEASSEAAPAAADGESSFEYQDT--APEGVSGDSDWSFDDV 118 Query: 116 ARTGKTPDDEDSRPQLEAHDVTLREHLQEQTRLTVRSLRDRALIELIVDAIDDHGYLEEP 175 AR+GK+PDDED+RPQLEAH++TLREHL EQ R+T R+ RDRAL+EL+ DA+DD GYLEEP Sbjct: 119 ARSGKSPDDEDARPQLEAHEITLREHLLEQIRVTARTQRDRALLELLTDALDDSGYLEEP 178 Query: 176 LEEIHARLPEELEIELDELTIALKLLQSFDPAGVGARSASECLALQIRRLPKVAFVTRRL 235 LE+I ARLPEEL ++L+EL+I+LKLLQS DPAGVGARSA ECLALQIRRLPKV FVTRRL Sbjct: 179 LEDILARLPEELGVDLEELSISLKLLQSLDPAGVGARSAGECLALQIRRLPKVPFVTRRL 238 Query: 236 ALTIVEDYLALFAQRDFNKIKKALGCDDEDLREAQAVIRQCHPHPGAVFASGRSDYVVPD 295 AL IVEDYL LFAQRDFNKIKKAL CDDEDLREAQAVIRQC PHPGA FA SDYVVPD Sbjct: 239 ALKIVEDYLPLFAQRDFNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDASDYVVPD 298 Query: 296 VIVKASKDGWQVLLNHDVMPRLRVNAMYANALKQTKGDGSLGSQLQEAKWLIKNMRQRFD 355 VIVK +K+GWQV+LNH+VMP+LRVNAMYA+ALKQ KG+GSL SQLQEAKWLIKNMRQRFD Sbjct: 299 VIVKQTKNGWQVMLNHEVMPKLRVNAMYASALKQAKGEGSLSSQLQEAKWLIKNMRQRFD 358 Query: 356 TILRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFE 415 TILRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFE Sbjct: 359 TILRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFE 418 Query: 416 LKYFFGSHVATETGGEASSTAIRALIKQLIGAEDPKNPLSDSKIADMLAEQGMVVARRTV 475 LKYFFGSHVATETGGEASSTAIRALIKQLIGAE+P+ PLSDSKIADMLAEQGMVVARRTV Sbjct: 419 LKYFFGSHVATETGGEASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTV 478 Query: 476 AKYREVLKIPPVNLRKSL 493 AKYREVLKIPPVNLRKSL Sbjct: 479 AKYREVLKIPPVNLRKSL 496 >ref|ZP_08274231.1| sigma N (sigma 54) factor of RNA polymerase [Oxalobacteraceae bacterium IMCC9480] gb|EGF32299.1| sigma N (sigma 54) factor of RNA polymerase [Oxalobacteraceae bacterium IMCC9480] Length = 493 Score = 812 bits (2097), Expect = 0.0, Method: Compositional matrix adjust. Identities = 398/493 (80%), Positives = 440/493 (89%) Query: 1 MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQILSDNPLLERLDDALDNSVRL 60 MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQ+L+DNPLLERLDD LD+SVRL Sbjct: 1 MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQMLTDNPLLERLDDPLDHSVRL 60 Query: 61 LADGALSSSPSAQAEPVENSAPSAAPAEGEAGDPQDSPAGDEHAGSDADWSFDDVARTGK 120 LADGAL + Q E++ + +P+E +A P + AGD +DADWSFDDVART K Sbjct: 61 LADGALGAEGIRQEGASEDANAAPSPSEPDAPAPDQNDAGDATPSTDADWSFDDVARTSK 120 Query: 121 TPDDEDSRPQLEAHDVTLREHLQEQTRLTVRSLRDRALIELIVDAIDDHGYLEEPLEEIH 180 P+D+D+RPQLEAH+ TLRE L EQ R+TVR+ RDRAL+EL++DA++D+GYL++ LE + Sbjct: 121 APEDDDARPQLEAHESTLREFLLEQMRVTVRNPRDRALVELMIDALNDNGYLDDTLEAML 180 Query: 181 ARLPEELEIELDELTIALKLLQSFDPAGVGARSASECLALQIRRLPKVAFVTRRLALTIV 240 RLP ELE+E +ELTIALKLLQSFDP GVGAR+A+ECLALQIRR P +A VTRR+ALTIV Sbjct: 181 ERLPAELEVEPEELTIALKLLQSFDPPGVGARNAAECLALQIRRFPGIAMVTRRMALTIV 240 Query: 241 EDYLALFAQRDFNKIKKALGCDDEDLREAQAVIRQCHPHPGAVFASGRSDYVVPDVIVKA 300 EDYL LFAQRDF+K+KKAL CDDEDLREAQ+VIRQC+PHPGA+F G SDYVVPDVIVK Sbjct: 241 EDYLPLFAQRDFSKLKKALDCDDEDLREAQSVIRQCNPHPGAIFGGGTSDYVVPDVIVKR 300 Query: 301 SKDGWQVLLNHDVMPRLRVNAMYANALKQTKGDGSLGSQLQEAKWLIKNMRQRFDTILRV 360 +K GWQV+LNHDVMPRLRVNAMYAN LKQ+KGDGSL SQLQEAKWLIKNMRQRFDTILRV Sbjct: 301 TKAGWQVMLNHDVMPRLRVNAMYANILKQSKGDGSLTSQLQEAKWLIKNMRQRFDTILRV 360 Query: 361 AQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKYFF 420 AQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKYFF Sbjct: 361 AQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKYFF 420 Query: 421 GSHVATETGGEASSTAIRALIKQLIGAEDPKNPLSDSKIADMLAEQGMVVARRTVAKYRE 480 GSHVATETGGEASSTAIRALIKQLIGAEDPK P SDSKIADML EQGMVVARRTVAKYRE Sbjct: 421 GSHVATETGGEASSTAIRALIKQLIGAEDPKIPFSDSKIADMLGEQGMVVARRTVAKYRE 480 Query: 481 VLKIPPVNLRKSL 493 LKIPPVNLRK+L Sbjct: 481 ALKIPPVNLRKAL 493 >ref|YP_001101339.1| RNA polymerase factor sigma-54 [Herminiimonas arsenicoxydans] emb|CAL63218.1| RNA polymerase, sigma 54 (sigma N) factor [Herminiimonas arsenicoxydans] Length = 489 Score = 787 bits (2033), Expect = 0.0, Method: Compositional matrix adjust. Identities = 395/498 (79%), Positives = 439/498 (88%), Gaps = 14/498 (2%) Query: 1 MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQILSDNPLLERLDDALDNSVRL 60 MKQSLQLR SQHLALTPQLQQSIRLLQLSTLELHQELEQIL+DNPLLER DD LD+++RL Sbjct: 1 MKQSLQLRVSQHLALTPQLQQSIRLLQLSTLELHQELEQILADNPLLERTDDPLDHAIRL 60 Query: 61 LADGALSSSPSAQAEPVENSAPSAAPAEGEAGDPQ-----DSPAGDEHAGSDADWSFDDV 115 LADGA+ S+ + P A E A P+ ++P E + DA+WSFDDV Sbjct: 61 LADGAIGSA---------GTTPEGASVEANAQTPESDTSVEAPEPAEASNGDAEWSFDDV 111 Query: 116 ARTGKTPDDEDSRPQLEAHDVTLREHLQEQTRLTVRSLRDRALIELIVDAIDDHGYLEEP 175 ART K PDD+D+RPQLEAH+ TLREHL EQ R+TVR RDRAL+ELI+DA++D+GYLEE Sbjct: 112 ARTSKAPDDDDARPQLEAHETTLREHLLEQMRVTVRERRDRALLELIIDALNDNGYLEET 171 Query: 176 LEEIHARLPEELEIELDELTIALKLLQSFDPAGVGARSASECLALQIRRLPKVAFVTRRL 235 LEEIHARLPEELEIE +EL IAL LLQSFDPAGVGAR+ASECLALQI+R+PKVA VTRR+ Sbjct: 172 LEEIHARLPEELEIEPEELQIALNLLQSFDPAGVGARNASECLALQIKRMPKVAMVTRRM 231 Query: 236 ALTIVEDYLALFAQRDFNKIKKALGCDDEDLREAQAVIRQCHPHPGAVFASGRSDYVVPD 295 AL IVE +L LFAQRDFNK++KAL CDDEDLREAQ VI+QC+PHPG++FA+ SDYVVPD Sbjct: 232 ALAIVEHHLGLFAQRDFNKLRKALDCDDEDLREAQVVIKQCNPHPGSIFATDTSDYVVPD 291 Query: 296 VIVKASKDGWQVLLNHDVMPRLRVNAMYANALKQTKGDGSLGSQLQEAKWLIKNMRQRFD 355 VIVK +++GWQV+LNHDVMPRLRVN+MYAN LKQ+KG+GSLGSQLQEAKWLIKNMRQRFD Sbjct: 292 VIVKRTRNGWQVMLNHDVMPRLRVNSMYANILKQSKGEGSLGSQLQEAKWLIKNMRQRFD 351 Query: 356 TILRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFE 415 TILRV+QAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFE Sbjct: 352 TILRVSQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFE 411 Query: 416 LKYFFGSHVATETGGEASSTAIRALIKQLIGAEDPKNPLSDSKIADMLAEQGMVVARRTV 475 LKYFFGSHVATETGGEASSTAIRALIKQLIGAE+ K P SDSKIA+MLAEQGMVVARRTV Sbjct: 412 LKYFFGSHVATETGGEASSTAIRALIKQLIGAENQKTPFSDSKIAEMLAEQGMVVARRTV 471 Query: 476 AKYREVLKIPPVNLRKSL 493 AKYRE LKIPPVNLRKSL Sbjct: 472 AKYREALKIPPVNLRKSL 489 >ref|YP_001355042.1| RNA polymerase factor sigma-54 [Janthinobacterium sp. Marseille] gb|ABR88962.1| RNA polymerase sigma-54 factor [Janthinobacterium sp. Marseille] Length = 489 Score = 782 bits (2019), Expect = 0.0, Method: Compositional matrix adjust. Identities = 393/498 (78%), Positives = 440/498 (88%), Gaps = 14/498 (2%) Query: 1 MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQILSDNPLLERLDDALDNSVRL 60 MKQSLQLR SQHLALTPQLQQSIRLLQLSTLELHQELEQIL+DNP+LER DD LD++VRL Sbjct: 1 MKQSLQLRVSQHLALTPQLQQSIRLLQLSTLELHQELEQILADNPMLERTDDPLDHAVRL 60 Query: 61 LADGALSSSPSAQAEPVENSAPSAAPAEGEAGDPQ-----DSPAGDEHAGSDADWSFDDV 115 LADGA+ +S + P A E P+ ++P E + D++WSFDDV Sbjct: 61 LADGAIGAS---------GTTPEGASVEANTQTPESETSFEAPDLPEASNGDSEWSFDDV 111 Query: 116 ARTGKTPDDEDSRPQLEAHDVTLREHLQEQTRLTVRSLRDRALIELIVDAIDDHGYLEEP 175 ART K P+D+D+RPQLEAH+ TLREHL EQ R+TVR RDRAL+ELI+DA++D+GYLEE Sbjct: 112 ARTSKAPEDDDARPQLEAHETTLREHLLEQMRVTVREHRDRALLELIIDALNDNGYLEEE 171 Query: 176 LEEIHARLPEELEIELDELTIALKLLQSFDPAGVGARSASECLALQIRRLPKVAFVTRRL 235 LEEIHARLPEELEIEL+EL I+LK+LQSFDP GVGAR A+ECLALQI+R+PKVA VTRR+ Sbjct: 172 LEEIHARLPEELEIELEELQISLKMLQSFDPPGVGARDAAECLALQIKRMPKVAMVTRRM 231 Query: 236 ALTIVEDYLALFAQRDFNKIKKALGCDDEDLREAQAVIRQCHPHPGAVFASGRSDYVVPD 295 AL IVE++L LFAQRDFNK++KAL CDDEDLREAQA+I+QC+PHPG++FA+ SDYVVPD Sbjct: 232 ALAIVENHLPLFAQRDFNKLRKALDCDDEDLREAQAIIKQCNPHPGSIFATDASDYVVPD 291 Query: 296 VIVKASKDGWQVLLNHDVMPRLRVNAMYANALKQTKGDGSLGSQLQEAKWLIKNMRQRFD 355 VIVK +++GWQV+LNHDVMPRLRVN+MYAN LKQ+KG+GSLGSQLQEAKWLIKNMRQRFD Sbjct: 292 VIVKRTRNGWQVMLNHDVMPRLRVNSMYANILKQSKGEGSLGSQLQEAKWLIKNMRQRFD 351 Query: 356 TILRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFE 415 TILRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFE Sbjct: 352 TILRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFE 411 Query: 416 LKYFFGSHVATETGGEASSTAIRALIKQLIGAEDPKNPLSDSKIADMLAEQGMVVARRTV 475 LKYFFGSHVATE GGEASSTAIRALIKQLIGAEDPK P SDSKIADMLAEQGMVVARRTV Sbjct: 412 LKYFFGSHVATEAGGEASSTAIRALIKQLIGAEDPKIPFSDSKIADMLAEQGMVVARRTV 471 Query: 476 AKYREVLKIPPVNLRKSL 493 AKYRE LKIPPVNLRKSL Sbjct: 472 AKYREALKIPPVNLRKSL 489 >ref|YP_004751122.1| sigma N (sigma 54) factor of RNA polymerase [Collimonas fungivorans Ter331] gb|AEK60299.1| sigma N (sigma 54) factor of RNA polymerase [Collimonas fungivorans Ter331] Length = 493 Score = 775 bits (2001), Expect = 0.0, Method: Compositional matrix adjust. Identities = 398/495 (80%), Positives = 439/495 (88%), Gaps = 4/495 (0%) Query: 1 MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQILSDNPLLERLDDALDNSVRL 60 MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQILSDNPLLER+DD LDNSVRL Sbjct: 1 MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQILSDNPLLERVDDPLDNSVRL 60 Query: 61 LADGALSSSPSAQAEPVENSAPSAAPAEGEAGDPQDSPAGDEHA--GSDADWSFDDVART 118 LADGA+S + S PV +S S++P+E EAG D+P E+ D++WSFDDVAR+ Sbjct: 61 LADGAISGATSTMDAPVGDSEVSSSPSESEAG--LDTPPAAENGPENGDSEWSFDDVARS 118 Query: 119 GKTPDDEDSRPQLEAHDVTLREHLQEQTRLTVRSLRDRALIELIVDAIDDHGYLEEPLEE 178 KTPDDED+RPQLEAH+ TLREHL +Q R T+ +RDRAL+EL +DA+DD+GYLEE LEE Sbjct: 119 SKTPDDEDARPQLEAHECTLREHLLQQMRETLNDIRDRALVELTIDALDDNGYLEESLEE 178 Query: 179 IHARLPEELEIELDELTIALKLLQSFDPAGVGARSASECLALQIRRLPKVAFVTRRLALT 238 I RLP ELEI ++EL+ ALK++QSFDPAGVGAR+A+ECL LQI+R KV FVTRRLAL Sbjct: 179 ILERLPPELEIAIEELSTALKMVQSFDPAGVGARNAAECLGLQIKRFIKVPFVTRRLALA 238 Query: 239 IVEDYLALFAQRDFNKIKKALGCDDEDLREAQAVIRQCHPHPGAVFASGRSDYVVPDVIV 298 IV+D+L LFAQRDFNKIKKAL CDDEDLREAQAVI+QC+PHPGA FA+ SDYVVPDVIV Sbjct: 239 IVQDHLMLFAQRDFNKIKKALDCDDEDLREAQAVIKQCNPHPGAPFAANASDYVVPDVIV 298 Query: 299 KASKDGWQVLLNHDVMPRLRVNAMYANALKQTKGDGSLGSQLQEAKWLIKNMRQRFDTIL 358 + SK GWQV+LN+DVMPRLRVN +YAN LKQ+KGDG+L SQLQEAKWLIKNMRQRFDTIL Sbjct: 299 RRSKQGWQVMLNNDVMPRLRVNVLYANILKQSKGDGALTSQLQEAKWLIKNMRQRFDTIL 358 Query: 359 RVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKY 418 RVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKY Sbjct: 359 RVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELKY 418 Query: 419 FFGSHVATETGGEASSTAIRALIKQLIGAEDPKNPLSDSKIADMLAEQGMVVARRTVAKY 478 FFGSHVATE GGEASSTAIRALIKQLIGAED KNP SDSKIADMLAEQGMVVARRTVAKY Sbjct: 419 FFGSHVATEAGGEASSTAIRALIKQLIGAEDTKNPFSDSKIADMLAEQGMVVARRTVAKY 478 Query: 479 REVLKIPPVNLRKSL 493 RE LKIP VNLRK+L Sbjct: 479 REALKIPSVNLRKAL 493