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: pfamseq 15,929,002 sequences; 5,169,768,107 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value D8ISM8.1 D8ISM8_HERSS RNA polymerase sigma-N (Sigma-54) factor t... 824 0.0 F1VYM1.1 F1VYM1_9BURK Sigma N (Sigma 54) factor of RNA polymerase 812 0.0 A4G9N1.1 A4G9N1_HERAR RNA polymerase, sigma 54 (Sigma N) factor 787 0.0 A6T3E5.1 A6T3E5_JANMA RNA polymerase sigma-54 factor 782 0.0 E5ALV1.1 E5ALV1_BURRH RNA polymerase sigma-54 factor rpoN 592 e-167 >D8ISM8.1 D8ISM8_HERSS RNA polymerase sigma-N (Sigma-54) factor transcription regulator protein 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 >F1VYM1.1 F1VYM1_9BURK Sigma N (Sigma 54) factor of RNA polymerase 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 >A4G9N1.1 A4G9N1_HERAR RNA polymerase, sigma 54 (Sigma N) factor 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 >A6T3E5.1 A6T3E5_JANMA RNA polymerase sigma-54 factor 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 >E5ALV1.1 E5ALV1_BURRH RNA polymerase sigma-54 factor rpoN Length = 504 Score = 592 bits (1525), Expect = e-167, Method: Compositional matrix adjust. Identities = 311/506 (61%), Positives = 370/506 (73%), Gaps = 15/506 (2%) Query: 1 MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQILSDNPLLERLDDALDNSVRL 60 MK SLQLR SQHLALTPQLQQSIRLLQLSTLEL QE+ ++ NPLLE +D + + +R+ Sbjct: 1 MKASLQLRLSQHLALTPQLQQSIRLLQLSTLELQQEVATAIAQNPLLENENDWIASPLRV 60 Query: 61 LADGALSSSPSAQAEPVENSAPSAAPA--EGEAGDPQDSPAGDEHAGSDAD-------WS 111 ADG+L S S+ AP+ P+ GE + A DE+ G +D W+ Sbjct: 61 AADGSLVPSQSSALPTGMAEAPAPVPSGVNGERAQSAEPAAVDEYDGMSSDSGTDTASWN 120 Query: 112 FDDVARTGKTPDDEDSRP-QLEAHDVTLREHLQEQTRLTVRSLRDRALIELIVDAIDDHG 170 DD R G DD+D P QL V+LREHL Q RLT S RDRAL+ +++++DD G Sbjct: 121 LDDYVRPGGASDDDDMPPLQLHESTVSLREHLSTQLRLTQASPRDRALVTFLIESLDDDG 180 Query: 171 YLEEPLEEIHARLPEELEIELDELTIALKLLQSFDPAGVGARSASECLALQIRRLPKVAF 230 YL +EI A LP ELE++ DEL AL LL SFDPAGVGARSASECL LQ+ RL A Sbjct: 181 YLSASCDEILADLPAELEVDADELNAALALLHSFDPAGVGARSASECLKLQLLRLEPSA- 239 Query: 231 VTRRLALTIVEDYLALFAQRDFNKIKKALGCDDEDLREAQAVIRQCHPHPGAVFASGRSD 290 TR LAL IV +YL L A RDF +++K L D+ LR+A A+IR P PGA + +D Sbjct: 240 -TRTLALEIVSNYLELLAARDFTRLRKHLKASDDALRDAHALIRSLEPFPGAAYGKAEAD 298 Query: 291 YVVPDVIVKASKDGWQVLLNHDVMPRLRVNAMYANALKQTKGD---GSLGSQLQEAKWLI 347 YVVPD+IVK + GWQ LN +V+PRLRVN +YAN L+ +GD GSL QLQEA+WLI Sbjct: 299 YVVPDIIVKKTSQGWQAELNPEVVPRLRVNHLYANILRSNRGDPSSGSLRQQLQEARWLI 358 Query: 348 KNMRQRFDTILRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYM 407 KN++QRFDTILRVAQAIVERQR+FF+HG +AMRPLVLREIADTLGLHEST+SRVTT KYM Sbjct: 359 KNIQQRFDTILRVAQAIVERQRSFFAHGEIAMRPLVLREIADTLGLHESTVSRVTTGKYM 418 Query: 408 LTPHGMFELKYFFGSHVATETGGEASSTAIRALIKQLIGAEDPKNPLSDSKIADMLAEQG 467 LTP G E KYFFGSHV+T+TGG ASSTAIRALIKQLIGAEDPK+PLSDS+IA++LAEQG Sbjct: 419 LTPFGTLEFKYFFGSHVSTDTGGAASSTAIRALIKQLIGAEDPKSPLSDSRIAELLAEQG 478 Query: 468 MVVARRTVAKYREVLKIPPVNLRKSL 493 VVARRTVAKYRE LKIP V++RKSL Sbjct: 479 FVVARRTVAKYREALKIPAVSMRKSL 504