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= 0007.0126.p (177 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313796|ref|YP_003777888.1| RNA polymerase sigma-70 factor,... 132 2e-32 gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor ... 120 7e-29 gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor,... 119 1e-28 gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor,... 117 7e-28 gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor ... 97 6e-22 >gi|300313796|ref|YP_003777888.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 178 Score = 132 bits (332), Expect = 2e-32, Method: Compositional matrix adjust. Identities = 76/166 (45%), Positives = 103/166 (62%), Gaps = 11/166 (6%) Query: 10 MHSFYSSHHGWLFGWLRKKLGCTHNAADVAQDTFVRIIAXADVAQDTFVRILLGVQEPRA 69 + + Y HHGWL WLR+KLGCT AAD+A DTF+R++A DV L ++EPRA Sbjct: 12 LETLYRDHHGWLRAWLRRKLGCTEQAADLAHDTFLRLLATRDV--------LSALKEPRA 63 Query: 70 YLTATAKRLLVDRARRQMIEQSYLAELALTM---EQTEGYPGPEEILLAVEALEQISAAL 126 YL A+ LL+DR+RRQ I Q+YL +L + P E IL AV+A+E + AL Sbjct: 64 YLVTAARHLLIDRSRRQQIRQAYLDQLERQFGACPELMHAPSAETILQAVQAIEALGRAL 123 Query: 127 QSVAAKAREAFLLHYLDGRTHAEVAAALGVSTRMVGKYLVQVLVKC 172 Q+ A+A EAF+LHY+ GR E+A+ VS R V +L Q L++C Sbjct: 124 QAARAEAAEAFILHYVQGRRQEELASHFNVSLRTVQGWLAQALIQC 169 >gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor protein [Herbaspirillum seropedicae SmR1] Length = 181 Score = 120 bits (301), Expect = 7e-29, Method: Compositional matrix adjust. Identities = 69/167 (41%), Positives = 99/167 (59%), Gaps = 10/167 (5%) Query: 9 DMHSFYSSHHGWLFGWLRKKLGCTHNAADVAQDTFVRIIAXADVAQDTFVRILLGVQEPR 68 + + Y HH WL GWL+++LG + AAD+AQDTF+R++ R+ + EPR Sbjct: 19 SIEALYCDHHSWLKGWLQRRLGNSEQAADLAQDTFLRLLGSE--------RVPSVIHEPR 70 Query: 69 AYLTATAKRLLVDRARRQMIEQSYLAELALTMEQTEGYPGPEEILLAVEALEQISAALQS 128 AYLT A+RL+ + RR+ +EQ+YL AL P P+E + +E L ++ L Sbjct: 71 AYLTTVAQRLVSNLWRREKLEQAYLE--ALAQAPVALAPSPQEQAILLETLLELDQLLDE 128 Query: 129 VAAKAREAFLLHYLDGRTHAEVAAALGVSTRMVGKYLVQVLVKCRLA 175 + + R AFLL LDG THA+VAAALG+S V +YLV+ L +C A Sbjct: 129 LPSIVRRAFLLSQLDGLTHAQVAAALGISIPTVKRYLVKALQRCYFA 175 >gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 174 Score = 119 bits (298), Expect = 1e-28, Method: Compositional matrix adjust. Identities = 68/165 (41%), Positives = 98/165 (59%), Gaps = 10/165 (6%) Query: 10 MHSFYSSHHGWLFGWLRKKLGCTHNAADVAQDTFVRIIAXADVAQDTFVRILLGVQEPRA 69 H+ YS HHGWL WLR+++G + +AAD+AQDTF+R++ L GV+EPRA Sbjct: 12 FHTLYSEHHGWLQQWLRRRVGSSFDAADLAQDTFLRVLGKPGA--------LDGVREPRA 63 Query: 70 YLTATAKRLLVDRARRQMIEQSYLAELALTMEQTEGYPGPEEILLAVEALEQISAALQSV 129 +L+ A L+VD+ RR+ +E++ L +A E PE L+ VEAL I A L+ + Sbjct: 64 WLSRIAHGLVVDKLRREEVERTCLEAIAHLPEPE--VVSPEARLILVEALCMIDALLEGL 121 Query: 130 AAKAREAFLLHYLDGRTHAEVAAALGVSTRMVGKYLVQVLVKCRL 174 +AR+AFLL LD ++ E+A LGVS V KY+ + C L Sbjct: 122 GERARQAFLLSRLDEMSYPEIARHLGVSLSSVEKYMAAAIRHCYL 166 >gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 169 Score = 117 bits (292), Expect = 7e-28, Method: Compositional matrix adjust. Identities = 65/164 (39%), Positives = 92/164 (56%), Gaps = 11/164 (6%) Query: 9 DMHSFYSSHHGWLFGWLRKKLGCTHNAADVAQDTFVRIIAXADVAQDTFVRILLGVQEPR 68 ++ Y HHGWL WL ++L C H AD+AQDTFVR++ R ++EPR Sbjct: 13 EIGGLYREHHGWLVAWLSRRLACRHLGADLAQDTFVRLLGH---------RPPPDLREPR 63 Query: 69 AYLTATAKRLLVDRARRQMIEQSYLAELALTMEQTEGYPGPEEILLAVEALEQISAALQS 128 AYLT AK L+ RR+ +E +YL LA E ++ P EE LL ++ L +I L Sbjct: 64 AYLTTIAKGLVASHLRRRQLETAYLEALAALPEPSQ--PSAEERLLVLDTLCEIDRILDQ 121 Query: 129 VAAKAREAFLLHYLDGRTHAEVAAALGVSTRMVGKYLVQVLVKC 172 + A+AR+ FLL LDG +A +A LG+S V +++V L C Sbjct: 122 LPARARQVFLLAQLDGLPYASIAGLLGISLSTVKRHMVLALRHC 165 >gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor protein [Herbaspirillum seropedicae SmR1] Length = 173 Score = 97.4 bits (241), Expect = 6e-22, Method: Compositional matrix adjust. Identities = 67/170 (39%), Positives = 95/170 (55%), Gaps = 15/170 (8%) Query: 7 QPDMHSF----YSSHHGWLFGWLRKKLGCTHNAADVAQDTFVRIIAXADVAQDTFVRILL 62 QP H F +++ + WL +LR+++ +A DVA FV + + DV+ Sbjct: 11 QPFRHDFLVTEFTNSYSWLKQYLRRQVKSLADAEDVASAAFVEMASLPDVS--------- 61 Query: 63 GVQEPRAYLTATAKRLLVDRARRQMIEQSYLAELALTMEQTEGYPGPEEILLAVEALEQI 122 ++EPRA LT ++RL+ D RR+ +E +YLA LA T E T P PE +L V+ L I Sbjct: 62 IIREPRALLTTISQRLVFDLWRRRDLEAAYLAALATTEEATT--PSPEVVLEVVQTLVNI 119 Query: 123 SAALQSVAAKAREAFLLHYLDGRTHAEVAAALGVSTRMVGKYLVQVLVKC 172 L ++ AR+AFL LDG T+ E+A LGVS MV KY+ Q L KC Sbjct: 120 DRLLYGLSKNARQAFLYSQLDGLTYREIAELLGVSVSMVRKYIAQALAKC 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 0.322 0.132 0.378 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: 502,354 Number of extensions: 17734 Number of successful extensions: 128 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 111 Number of HSP's successfully gapped: 7 Length of query: 177 Length of database: 1,619,870 Length adjustment: 79 Effective length of query: 98 Effective length of database: 1,245,805 Effective search space: 122088890 Effective search space used: 122088890 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 127 (53.5 bits)