BLASTP 2.2.17 [Aug-26-2007] 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 composition-based statistics: 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= 0001.5135.p (496 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... 858 0.0 ref|ZP_08274231.1| sigma N (sigma 54) factor of RNA polymerase [... 731 0.0 ref|YP_001355042.1| RNA polymerase factor sigma-54 [Janthinobact... 725 0.0 ref|YP_001101339.1| RNA polymerase factor sigma-54 [Herminiimona... 722 0.0 ref|YP_004751122.1| sigma N (sigma 54) factor of RNA polymerase ... 711 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 = 858 bits (2216), Expect = 0.0, Method: Composition-based stats. Identities = 470/497 (94%), Positives = 488/497 (98%), Gaps = 2/497 (0%) Query: 1 MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQILSDNPLLERLDDALDNSVRL 60 MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQIL+DNPLLERLDDALDNSVRL Sbjct: 1 MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQILTDNPLLERLDDALDNSVRL 60 Query: 61 LADGAVSSSPSSGVAETS-HEGSGEAAPAASDGDSSFDYQDNTPETGVTGDADWSFDDVA 119 LADGAVS++PSSGV+ET+ E S EAAPAA+DG+SSF+YQD PE GV+GD+DWSFDDVA Sbjct: 61 LADGAVSAAPSSGVSETTGSEASSEAAPAAADGESSFEYQDTAPE-GVSGDSDWSFDDVA 119 Query: 120 RSGKSPDDDDARPQLEAHELTLREHLLEQIRVTARTLRDRALLELLTDALDESGYLEEPL 179 RSGKSPDD+DARPQLEAHE+TLREHLLEQIRVTART RDRALLELLTDALD+SGYLEEPL Sbjct: 120 RSGKSPDDEDARPQLEAHEITLREHLLEQIRVTARTQRDRALLELLTDALDDSGYLEEPL 179 Query: 180 EDIHARLPEELGIDMEELSISLKLLQSLDPAGVGARSAGECLALQIRRLPKIPFVTRKLA 239 EDI ARLPEELG+D+EELSISLKLLQSLDPAGVGARSAGECLALQIRRLPK+PFVTR+LA Sbjct: 180 EDILARLPEELGVDLEELSISLKLLQSLDPAGVGARSAGECLALQIRRLPKVPFVTRRLA 239 Query: 240 LRIVEDYLPLFAQRDFNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDASDYVVPDV 299 L+IVEDYLPLFAQRDFNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDASDYVVPDV Sbjct: 240 LKIVEDYLPLFAQRDFNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDASDYVVPDV 299 Query: 300 IVKQTKNGWQVMLNHEVMPKLRVNAMYASALKQAKGEGSLSSQLQEAKWLIKNMRQRFDT 359 IVKQTKNGWQVMLNHEVMPKLRVNAMYASALKQAKGEGSLSSQLQEAKWLIKNMRQRFDT Sbjct: 300 IVKQTKNGWQVMLNHEVMPKLRVNAMYASALKQAKGEGSLSSQLQEAKWLIKNMRQRFDT 359 Query: 360 ILRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFEL 419 ILRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFEL Sbjct: 360 ILRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFEL 419 Query: 420 KYFFGSHVATETGGEASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTVA 479 KYFFGSHVATETGGEASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTVA Sbjct: 420 KYFFGSHVATETGGEASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTVA 479 Query: 480 KYREVLKIPPVNLRKSL 496 KYREVLKIPPVNLRKSL Sbjct: 480 KYREVLKIPPVNLRKSL 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 = 731 bits (1887), Expect = 0.0, Method: Composition-based stats. Identities = 389/496 (78%), Positives = 435/496 (87%), Gaps = 3/496 (0%) Query: 1 MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQILSDNPLLERLDDALDNSVRL 60 MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQ+L+DNPLLERLDD LD+SVRL Sbjct: 1 MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQMLTDNPLLERLDDPLDHSVRL 60 Query: 61 LADGAVSSSPSSGVAETSHEGSGEAAPAASDGDSSFDYQDNTPETGVTGDADWSFDDVAR 120 LADGA+ + G+ + AAP+ S+ D+ Q++ + + DADWSFDDVAR Sbjct: 61 LADGALGAE---GIRQEGASEDANAAPSPSEPDAPAPDQNDAGDATPSTDADWSFDDVAR 117 Query: 121 SGKSPDDDDARPQLEAHELTLREHLLEQIRVTARTLRDRALLELLTDALDESGYLEEPLE 180 + K+P+DDDARPQLEAHE TLRE LLEQ+RVT R RDRAL+EL+ DAL+++GYL++ LE Sbjct: 118 TSKAPEDDDARPQLEAHESTLREFLLEQMRVTVRNPRDRALVELMIDALNDNGYLDDTLE 177 Query: 181 DIHARLPEELGIDMEELSISLKLLQSLDPAGVGARSAGECLALQIRRLPKIPFVTRKLAL 240 + RLP EL ++ EEL+I+LKLLQS DP GVGAR+A ECLALQIRR P I VTR++AL Sbjct: 178 AMLERLPAELEVEPEELTIALKLLQSFDPPGVGARNAAECLALQIRRFPGIAMVTRRMAL 237 Query: 241 RIVEDYLPLFAQRDFNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDASDYVVPDVI 300 IVEDYLPLFAQRDF+K+KKALDCDDEDLREAQ+VIRQC PHPGA F SDYVVPDVI Sbjct: 238 TIVEDYLPLFAQRDFSKLKKALDCDDEDLREAQSVIRQCNPHPGAIFGGGTSDYVVPDVI 297 Query: 301 VKQTKNGWQVMLNHEVMPKLRVNAMYASALKQAKGEGSLSSQLQEAKWLIKNMRQRFDTI 360 VK+TK GWQVMLNH+VMP+LRVNAMYA+ LKQ+KG+GSL+SQLQEAKWLIKNMRQRFDTI Sbjct: 298 VKRTKAGWQVMLNHDVMPRLRVNAMYANILKQSKGDGSLTSQLQEAKWLIKNMRQRFDTI 357 Query: 361 LRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELK 420 LRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELK Sbjct: 358 LRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELK 417 Query: 421 YFFGSHVATETGGEASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTVAK 480 YFFGSHVATETGGEASSTAIRALIKQLIGAE+P+ P SDSKIADML EQGMVVARRTVAK Sbjct: 418 YFFGSHVATETGGEASSTAIRALIKQLIGAEDPKIPFSDSKIADMLGEQGMVVARRTVAK 477 Query: 481 YREVLKIPPVNLRKSL 496 YRE LKIPPVNLRK+L Sbjct: 478 YREALKIPPVNLRKAL 493 >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 = 725 bits (1872), Expect = 0.0, Method: Composition-based stats. Identities = 396/496 (79%), Positives = 441/496 (88%), Gaps = 7/496 (1%) Query: 1 MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQILSDNPLLERLDDALDNSVRL 60 MKQSLQLR SQHLALTPQLQQSIRLLQLSTLELHQELEQIL+DNP+LER DD LD++VRL Sbjct: 1 MKQSLQLRVSQHLALTPQLQQSIRLLQLSTLELHQELEQILADNPMLERTDDPLDHAVRL 60 Query: 61 LADGAVSSSPSSGVAETSHEGSGEAAPAASDGDSSFDYQDNTPETGVTGDADWSFDDVAR 120 LADGA+ +S T S EA + ++SF+ D PE GD++WSFDDVAR Sbjct: 61 LADGAIGAS-----GTTPEGASVEANTQTPESETSFEAPD-LPEAS-NGDSEWSFDDVAR 113 Query: 121 SGKSPDDDDARPQLEAHELTLREHLLEQIRVTARTLRDRALLELLTDALDESGYLEEPLE 180 + K+P+DDDARPQLEAHE TLREHLLEQ+RVT R RDRALLEL+ DAL+++GYLEE LE Sbjct: 114 TSKAPEDDDARPQLEAHETTLREHLLEQMRVTVREHRDRALLELIIDALNDNGYLEEELE 173 Query: 181 DIHARLPEELGIDMEELSISLKLLQSLDPAGVGARSAGECLALQIRRLPKIPFVTRKLAL 240 +IHARLPEEL I++EEL ISLK+LQS DP GVGAR A ECLALQI+R+PK+ VTR++AL Sbjct: 174 EIHARLPEELEIELEELQISLKMLQSFDPPGVGARDAAECLALQIKRMPKVAMVTRRMAL 233 Query: 241 RIVEDYLPLFAQRDFNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDASDYVVPDVI 300 IVE++LPLFAQRDFNK++KALDCDDEDLREAQA+I+QC PHPG+ FA DASDYVVPDVI Sbjct: 234 AIVENHLPLFAQRDFNKLRKALDCDDEDLREAQAIIKQCNPHPGSIFATDASDYVVPDVI 293 Query: 301 VKQTKNGWQVMLNHEVMPKLRVNAMYASALKQAKGEGSLSSQLQEAKWLIKNMRQRFDTI 360 VK+T+NGWQVMLNH+VMP+LRVN+MYA+ LKQ+KGEGSL SQLQEAKWLIKNMRQRFDTI Sbjct: 294 VKRTRNGWQVMLNHDVMPRLRVNSMYANILKQSKGEGSLGSQLQEAKWLIKNMRQRFDTI 353 Query: 361 LRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELK 420 LRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELK Sbjct: 354 LRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELK 413 Query: 421 YFFGSHVATETGGEASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTVAK 480 YFFGSHVATE GGEASSTAIRALIKQLIGAE+P+ P SDSKIADMLAEQGMVVARRTVAK Sbjct: 414 YFFGSHVATEAGGEASSTAIRALIKQLIGAEDPKIPFSDSKIADMLAEQGMVVARRTVAK 473 Query: 481 YREVLKIPPVNLRKSL 496 YRE LKIPPVNLRKSL Sbjct: 474 YREALKIPPVNLRKSL 489 >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 = 722 bits (1864), Expect = 0.0, Method: Composition-based stats. Identities = 396/497 (79%), Positives = 439/497 (88%), Gaps = 9/497 (1%) Query: 1 MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQILSDNPLLERLDDALDNSVRL 60 MKQSLQLR SQHLALTPQLQQSIRLLQLSTLELHQELEQIL+DNPLLER DD LD+++RL Sbjct: 1 MKQSLQLRVSQHLALTPQLQQSIRLLQLSTLELHQELEQILADNPLLERTDDPLDHAIRL 60 Query: 61 LADGAVSSSPSSGVAETSHEGSG-EAAPAASDGDSSFDYQDNTPETGVTGDADWSFDDVA 119 LADGA+ G A T+ EG+ EA + D+S + + P GDA+WSFDDVA Sbjct: 61 LADGAI------GSAGTTPEGASVEANAQTPESDTSVEAPE--PAEASNGDAEWSFDDVA 112 Query: 120 RSGKSPDDDDARPQLEAHELTLREHLLEQIRVTARTLRDRALLELLTDALDESGYLEEPL 179 R+ K+PDDDDARPQLEAHE TLREHLLEQ+RVT R RDRALLEL+ DAL+++GYLEE L Sbjct: 113 RTSKAPDDDDARPQLEAHETTLREHLLEQMRVTVRERRDRALLELIIDALNDNGYLEETL 172 Query: 180 EDIHARLPEELGIDMEELSISLKLLQSLDPAGVGARSAGECLALQIRRLPKIPFVTRKLA 239 E+IHARLPEEL I+ EEL I+L LLQS DPAGVGAR+A ECLALQI+R+PK+ VTR++A Sbjct: 173 EEIHARLPEELEIEPEELQIALNLLQSFDPAGVGARNASECLALQIKRMPKVAMVTRRMA 232 Query: 240 LRIVEDYLPLFAQRDFNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDASDYVVPDV 299 L IVE +L LFAQRDFNK++KALDCDDEDLREAQ VI+QC PHPG+ FA D SDYVVPDV Sbjct: 233 LAIVEHHLGLFAQRDFNKLRKALDCDDEDLREAQVVIKQCNPHPGSIFATDTSDYVVPDV 292 Query: 300 IVKQTKNGWQVMLNHEVMPKLRVNAMYASALKQAKGEGSLSSQLQEAKWLIKNMRQRFDT 359 IVK+T+NGWQVMLNH+VMP+LRVN+MYA+ LKQ+KGEGSL SQLQEAKWLIKNMRQRFDT Sbjct: 293 IVKRTRNGWQVMLNHDVMPRLRVNSMYANILKQSKGEGSLGSQLQEAKWLIKNMRQRFDT 352 Query: 360 ILRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFEL 419 ILRV+QAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFEL Sbjct: 353 ILRVSQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFEL 412 Query: 420 KYFFGSHVATETGGEASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTVA 479 KYFFGSHVATETGGEASSTAIRALIKQLIGAEN +TP SDSKIA+MLAEQGMVVARRTVA Sbjct: 413 KYFFGSHVATETGGEASSTAIRALIKQLIGAENQKTPFSDSKIAEMLAEQGMVVARRTVA 472 Query: 480 KYREVLKIPPVNLRKSL 496 KYRE LKIPPVNLRKSL Sbjct: 473 KYREALKIPPVNLRKSL 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 = 711 bits (1834), Expect = 0.0, Method: Composition-based stats. Identities = 386/496 (77%), Positives = 432/496 (87%), Gaps = 3/496 (0%) Query: 1 MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQILSDNPLLERLDDALDNSVRL 60 MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQILSDNPLLER+DD LDNSVRL Sbjct: 1 MKQSLQLRTSQHLALTPQLQQSIRLLQLSTLELHQELEQILSDNPLLERVDDPLDNSVRL 60 Query: 61 LADGAVSSSPSSGVAETSHEGSGEAAPAASDGDSSFDYQDNTPETGVTGDADWSFDDVAR 120 LADGA+S + S+ A + + G + +N PE G D++WSFDDVAR Sbjct: 61 LADGAISGATSTMDAPVGDSEVSSSPSESEAGLDTPPAAENGPENG---DSEWSFDDVAR 117 Query: 121 SGKSPDDDDARPQLEAHELTLREHLLEQIRVTARTLRDRALLELLTDALDESGYLEEPLE 180 S K+PDD+DARPQLEAHE TLREHLL+Q+R T +RDRAL+EL DALD++GYLEE LE Sbjct: 118 SSKTPDDEDARPQLEAHECTLREHLLQQMRETLNDIRDRALVELTIDALDDNGYLEESLE 177 Query: 181 DIHARLPEELGIDMEELSISLKLLQSLDPAGVGARSAGECLALQIRRLPKIPFVTRKLAL 240 +I RLP EL I +EELS +LK++QS DPAGVGAR+A ECL LQI+R K+PFVTR+LAL Sbjct: 178 EILERLPPELEIAIEELSTALKMVQSFDPAGVGARNAAECLGLQIKRFIKVPFVTRRLAL 237 Query: 241 RIVEDYLPLFAQRDFNKIKKALDCDDEDLREAQAVIRQCRPHPGAEFARDASDYVVPDVI 300 IV+D+L LFAQRDFNKIKKALDCDDEDLREAQAVI+QC PHPGA FA +ASDYVVPDVI Sbjct: 238 AIVQDHLMLFAQRDFNKIKKALDCDDEDLREAQAVIKQCNPHPGAPFAANASDYVVPDVI 297 Query: 301 VKQTKNGWQVMLNHEVMPKLRVNAMYASALKQAKGEGSLSSQLQEAKWLIKNMRQRFDTI 360 V+++K GWQVMLN++VMP+LRVN +YA+ LKQ+KG+G+L+SQLQEAKWLIKNMRQRFDTI Sbjct: 298 VRRSKQGWQVMLNNDVMPRLRVNVLYANILKQSKGDGALTSQLQEAKWLIKNMRQRFDTI 357 Query: 361 LRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELK 420 LRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELK Sbjct: 358 LRVAQAIVERQRNFFSHGAVAMRPLVLREIADTLGLHESTISRVTTQKYMLTPHGMFELK 417 Query: 421 YFFGSHVATETGGEASSTAIRALIKQLIGAENPQTPLSDSKIADMLAEQGMVVARRTVAK 480 YFFGSHVATE GGEASSTAIRALIKQLIGAE+ + P SDSKIADMLAEQGMVVARRTVAK Sbjct: 418 YFFGSHVATEAGGEASSTAIRALIKQLIGAEDTKNPFSDSKIADMLAEQGMVVARRTVAK 477 Query: 481 YREVLKIPPVNLRKSL 496 YRE LKIP VNLRK+L Sbjct: 478 YREALKIPSVNLRKAL 493