BLASTP 2.2.18 [Mar-02-2008] 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= 0257.0023.p (157 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor ... 146 6e-37 gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor,... 145 2e-36 gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor,... 134 4e-33 gi|300313796|ref|YP_003777888.1| RNA polymerase sigma-70 factor,... 105 2e-24 gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor ... 103 6e-24 >gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor protein [Herbaspirillum seropedicae SmR1] Length = 181 Score = 146 bits (369), Expect = 6e-37, Method: Compositional matrix adjust. Identities = 82/152 (53%), Positives = 114/152 (75%), Gaps = 1/152 (0%) Query: 1 MYRDHHRWLLGWLHKRLGNAFDAADLAQDAFMRILLKNDDFRV-KEPRALLTTIAQGIVA 59 +Y DHH WL GWL +RLGN+ AADLAQD F+R+L V EPRA LTT+AQ +V+ Sbjct: 23 LYCDHHSWLKGWLQRRLGNSEQAADLAQDTFLRLLGSERVPSVIHEPRAYLTTVAQRLVS 82 Query: 60 NLRRRQEIERSYLDALALMPEAHAPSPESRMIMLETLVALDRMLGVLPALTKEAFLLSQL 119 NL RR+++E++YL+ALA P A APSP+ + I+LETL+ LD++L LP++ + AFLLSQL Sbjct: 83 NLWRREKLEQAYLEALAQAPVALAPSPQEQAILLETLLELDQLLDELPSIVRRAFLLSQL 142 Query: 120 EGLRQTEIAERLNISVPTVKRHIARALEQCCF 151 +GL ++A L IS+PTVKR++ +AL++C F Sbjct: 143 DGLTHAQVAAALGISIPTVKRYLVKALQRCYF 174 >gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 169 Score = 145 bits (365), Expect = 2e-36, Method: Compositional matrix adjust. Identities = 74/149 (49%), Positives = 103/149 (69%) Query: 1 MYRDHHRWLLGWLHKRLGNAFDAADLAQDAFMRILLKNDDFRVKEPRALLTTIAQGIVAN 60 +YR+HH WL+ WL +RL ADLAQD F+R+L ++EPRA LTTIA+G+VA+ Sbjct: 17 LYREHHGWLVAWLSRRLACRHLGADLAQDTFVRLLGHRPPPDLREPRAYLTTIAKGLVAS 76 Query: 61 LRRRQEIERSYLDALALMPEAHAPSPESRMIMLETLVALDRMLGVLPALTKEAFLLSQLE 120 RR+++E +YL+ALA +PE PS E R+++L+TL +DR+L LPA ++ FLL+QL+ Sbjct: 77 HLRRRQLETAYLEALAALPEPSQPSAEERLLVLDTLCEIDRILDQLPARARQVFLLAQLD 136 Query: 121 GLRQTEIAERLNISVPTVKRHIARALEQC 149 GL IA L IS+ TVKRH+ AL C Sbjct: 137 GLPYASIAGLLGISLSTVKRHMVLALRHC 165 >gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 174 Score = 134 bits (337), Expect = 4e-33, Method: Compositional matrix adjust. Identities = 67/150 (44%), Positives = 104/150 (69%), Gaps = 1/150 (0%) Query: 1 MYRDHHRWLLGWLHKRLGNAFDAADLAQDAFMRILLKNDDF-RVKEPRALLTTIAQGIVA 59 +Y +HH WL WL +R+G++FDAADLAQD F+R+L K V+EPRA L+ IA G+V Sbjct: 15 LYSEHHGWLQQWLRRRVGSSFDAADLAQDTFLRVLGKPGALDGVREPRAWLSRIAHGLVV 74 Query: 60 NLRRRQEIERSYLDALALMPEAHAPSPESRMIMLETLVALDRMLGVLPALTKEAFLLSQL 119 + RR+E+ER+ L+A+A +PE SPE+R+I++E L +D +L L ++AFLLS+L Sbjct: 75 DKLRREEVERTCLEAIAHLPEPEVVSPEARLILVEALCMIDALLEGLGERARQAFLLSRL 134 Query: 120 EGLRQTEIAERLNISVPTVKRHIARALEQC 149 + + EIA L +S+ +V++++A A+ C Sbjct: 135 DEMSYPEIARHLGVSLSSVEKYMAAAIRHC 164 >gi|300313796|ref|YP_003777888.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 178 Score = 105 bits (262), Expect = 2e-24, Method: Compositional matrix adjust. Identities = 67/155 (43%), Positives = 94/155 (60%), Gaps = 6/155 (3%) Query: 1 MYRDHHRWLLGWLHKRLGNAFDAADLAQDAFMRILLKNDDFR-VKEPRALLTTIAQGIVA 59 +YRDHH WL WL ++LG AADLA D F+R+L D +KEPRA L T A+ ++ Sbjct: 15 LYRDHHGWLRAWLRRKLGCTEQAADLAHDTFLRLLATRDVLSALKEPRAYLVTAARHLLI 74 Query: 60 NLRRRQEIERSYLDAL----ALMPE-AHAPSPESRMIMLETLVALDRMLGVLPALTKEAF 114 + RRQ+I ++YLD L PE HAPS E+ + ++ + AL R L A EAF Sbjct: 75 DRSRRQQIRQAYLDQLERQFGACPELMHAPSAETILQAVQAIEALGRALQAARAEAAEAF 134 Query: 115 LLSQLEGLRQTEIAERLNISVPTVKRHIARALEQC 149 +L ++G RQ E+A N+S+ TV+ +A+AL QC Sbjct: 135 ILHYVQGRRQEELASHFNVSLRTVQGWLAQALIQC 169 >gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor protein [Herbaspirillum seropedicae SmR1] Length = 173 Score = 103 bits (257), Expect = 6e-24, Method: Compositional matrix adjust. Identities = 64/148 (43%), Positives = 99/148 (66%) Query: 2 YRDHHRWLLGWLHKRLGNAFDAADLAQDAFMRILLKNDDFRVKEPRALLTTIAQGIVANL 61 + + + WL +L +++ + DA D+A AF+ + D ++EPRALLTTI+Q +V +L Sbjct: 22 FTNSYSWLKQYLRRQVKSLADAEDVASAAFVEMASLPDVSIIREPRALLTTISQRLVFDL 81 Query: 62 RRRQEIERSYLDALALMPEAHAPSPESRMIMLETLVALDRMLGVLPALTKEAFLLSQLEG 121 RR+++E +YL ALA EA PSPE + +++TLV +DR+L L ++AFL SQL+G Sbjct: 82 WRRRDLEAAYLAALATTEEATTPSPEVVLEVVQTLVNIDRLLYGLSKNARQAFLYSQLDG 141 Query: 122 LRQTEIAERLNISVPTVKRHIARALEQC 149 L EIAE L +SV V+++IA+AL +C Sbjct: 142 LTYREIAELLGVSVSMVRKYIAQALAKC 169 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.325 0.136 0.404 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 435,965 Number of extensions: 14828 Number of successful extensions: 111 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 107 Number of HSP's successfully gapped: 7 Length of query: 157 Length of database: 1,619,870 Length adjustment: 78 Effective length of query: 79 Effective length of database: 1,250,540 Effective search space: 98792660 Effective search space used: 98792660 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 126 (53.1 bits)