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= 0566.0012.p (243 letters) Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF 2,715,099 sequences; 757,237,578 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value ref|NP_243983.1| RNA polymerase ECF-type sigma factor [Bacillus ... 157 1e-37 ref|NP_962555.1| SigG [Mycobacterium avium subsp. paratuberculos... 88 2e-16 ref|NP_244499.1| RNA polymerase ECF-type sigma factor [Bacillus ... 86 1e-15 ref|NP_979124.1| RNA polymerase sigma-70 factor, ECF subfamily [... 82 8e-15 ref|NP_214696.1| sigG [Mycobacterium tuberculosis H37Rv] >gi|158... 82 1e-14 >ref|NP_243983.1| RNA polymerase ECF-type sigma factor [Bacillus halodurans] pir||E84039 RNA polymerase ECF-type sigma factor BH3117 [imported] - Bacillus halodurans (strain C-125) dbj|BAB06836.1| RNA polymerase ECF-type sigma factor [Bacillus halodurans] Length = 230 Score = 157 bits (398), Expect = 1e-37, Method: Compositional matrix adjust. Identities = 90/212 (42%), Positives = 127/212 (59%), Gaps = 11/212 (5%) Query: 2 DEQSYPPLREALFRYCLSLTRSRVEAEDLAQDTWTKTLAYKKFADSPNPEALLLRIAKNT 61 D + L + + RYCL +T+S +AEDLAQ+TW K + K NPEA LLR+AKN Sbjct: 3 DRKHLKQLHDTVSRYCLFVTKSTWDAEDLAQETWLKAIETLKKQGHQNPEAFLLRVAKNQ 62 Query: 62 WIDAMRRKTSLGRVLEHTQAVAALAQGQMSGQAPESGRSEIEMAFQALIRHLSPLQRTVF 121 WID R+K R+L+ Q + PE G E+E AF AL+ HLSPLQ +VF Sbjct: 63 WIDQSRKKAVFARILK---------QEKPEVTPPEQGLFEMERAFFALVNHLSPLQLSVF 113 Query: 122 VMRDVLDYPAGETAEMLGTTEGAVKAALHRARQALGAVRKELAEDDGPAQPQDLDFRILL 181 ++RDV Y E A+M+ TEGAVKAAL RAR++L VR +L ++ P P + + L Sbjct: 114 LLRDVFGYSTSEAAKMVEKTEGAVKAALRRARKSLALVRDDLETENSPL-PNGEEAKAWL 172 Query: 182 QALAESYEKGQLPVMLELLRRETAAEMTMAVS 213 +A+A +YE G++ +++L+ + A TM VS Sbjct: 173 RAIAVAYEAGEIDTVIDLIDQGVYAR-TMVVS 203 >ref|NP_962555.1| SigG [Mycobacterium avium subsp. paratuberculosis str. k10] gb|AAS06171.1| SigG [Mycobacterium avium subsp. paratuberculosis str. k10] Length = 366 Score = 88.2 bits (217), Expect = 2e-16, Method: Compositional matrix adjust. Identities = 71/221 (32%), Positives = 102/221 (46%), Gaps = 22/221 (9%) Query: 8 PLREALFRYCLSLTRSRVEAEDLAQDTWTKTL-AYKKFADSPNPEALLLRIAKNTWIDAM 66 P R L +C +T S +AEDL Q+T + AY +F + L RIA NT + A+ Sbjct: 51 PYRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYDRFEGKSSVRTWLHRIATNTCLSAL 110 Query: 67 ----RRKTSLG---------------RVLEHTQAVAALAQGQMSGQAPESGRSEIEMAFQ 107 RR +G R + + + AL R + +AF Sbjct: 111 EGRQRRPLPVGLGAPSADPTAELVERREVPWLEPLPALTDDPADPSVIVGSRESVRLAFV 170 Query: 108 ALIRHLSPLQRTVFVMRDVLDYPAGETAEMLGTTEGAVKAALHRARQALGAVRKELAEDD 167 A +++LSP QR V ++RDVL + A E AE +GTT AV + L RAR L AV + DD Sbjct: 171 AALQYLSPRQRAVLLLRDVLGWRAAEVAEAIGTTTAAVNSLLQRARAQLDAVGP--SADD 228 Query: 168 GPAQPQDLDFRILLQALAESYEKGQLPVMLELLRRETAAEM 208 AQP + + LL ++E + ++EL E EM Sbjct: 229 QLAQPDSAETQDLLARYIAAFESYDIDRLVELFTAEAIWEM 269 >ref|NP_244499.1| RNA polymerase ECF-type sigma factor [Bacillus halodurans] pir||H84103 RNA polymerase ECF-type sigma factor BH3632 [imported] - Bacillus halodurans (strain C-125) dbj|BAB07351.1| RNA polymerase ECF-type sigma factor [Bacillus halodurans] Length = 320 Score = 85.5 bits (210), Expect = 1e-15, Method: Compositional matrix adjust. Identities = 65/207 (31%), Positives = 100/207 (48%), Gaps = 24/207 (11%) Query: 13 LFRYCLSLTRSRVEAEDLAQDTWTKTLA--YKKFADSPNPEALLLRIAKNTWIDAMRR-K 69 L+R+C LT S + EDL Q+T K Y+++ + NP+A L RIA NTWID R+ K Sbjct: 31 LWRFCRYLTGSPWDGEDLYQETLVKAFGSLYQRWQPT-NPKAYLFRIATNTWIDQCRKAK 89 Query: 70 TSLGRVLEHTQAVAALAQGQMSGQAPE-SGRSEIEMAFQALIRHLSPLQRTVFVMRDVLD 128 +G V E M G E S E+E AF L P Q VF+++DV Sbjct: 90 RIVGTVDE------------MEGPVEEFSNDLELEHAFTRLFTLFPPRQVAVFLLKDVFA 137 Query: 129 YPAGETAEMLGTTEGAVKAALHRARQAL---GAVRKELAEDDGPAQPQDLDFRILLQALA 185 + A E A M+ +T V A R R+ L ++ +EL+ + P+ Q ++Q Sbjct: 138 FTAEEVASMVRSTSNGVYATSSRVRKKLKETASLEEELSSNGRPSPEQSE----VIQQYL 193 Query: 186 ESYEKGQLPVMLELLRRETAAEMTMAV 212 E++ G L + +L+ E + ++ Sbjct: 194 EAFNAGDLGKLFDLMSDEVHIDASLGF 220 >ref|NP_979124.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus ATCC 10987] gb|AAS41732.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus ATCC 10987] Length = 228 Score = 82.4 bits (202), Expect = 8e-15, Method: Compositional matrix adjust. Identities = 45/150 (30%), Positives = 83/150 (55%), Gaps = 13/150 (8%) Query: 13 LFRYCLSLTRSRVEAEDLAQDTWTKTLAYKKFADSPNPEALLLRIAKNTWIDAMRRKTSL 72 L RYC LT+++ + EDLAQ+T K L +K+++ L+ +IA+N W+D M+ K+ Sbjct: 30 LKRYCTFLTKNKWDGEDLAQETVCKVL--QKYSNKDICMTLVYKIARNRWLDQMKSKSVH 87 Query: 73 GRVLEHTQAVAALAQGQMSGQAPESGRSEIEMAFQALIRHLSPLQRTVFVMRDVLDYPAG 132 ++ E Q++ + P+ +++ ++ L+ Q T+ +++DV Y Sbjct: 88 EKIRE-----------QITFEEPQENIADLHEMVGKVLSSLNVQQSTILLLKDVFQYSIV 136 Query: 133 ETAEMLGTTEGAVKAALHRARQALGAVRKE 162 + A++ +EGAVKA+L R+R L V +E Sbjct: 137 DIAKVCSVSEGAVKASLFRSRNRLKTVSEE 166 >ref|NP_214696.1| sigG [Mycobacterium tuberculosis H37Rv] ref|NP_334597.1| RNA polymerase sigma-70 factor, ECF subfamily [Mycobacterium tuberculosis CDC1551] ref|NP_853853.1| PROBABLE ALTERNATIVE RNA POLYMERASE SIGMA FACTOR SIGG (RNA POLYMERASE ECF TYPE SIGMA FACTOR) [Mycobacterium bovis subsp. bovis AF2122/97] pir||A70906 probable RNA polymerase sigma subunit - Mycobacterium tuberculosis (strain H37RV) emb|CAB09733.1| PROBABLE ALTERNATIVE RNA POLYMERASE SIGMA FACTOR SIGG (RNA POLYMERASE ECF TYPE SIGMA FACTOR) [Mycobacterium tuberculosis H37Rv] gb|AAK44411.1| RNA polymerase sigma-70 factor, ECF subfamily [Mycobacterium tuberculosis CDC1551] emb|CAD93052.1| PROBABLE ALTERNATIVE RNA POLYMERASE SIGMA FACTOR SIGG (RNA POLYMERASE ECF TYPE SIGMA FACTOR) [Mycobacterium bovis subsp. bovis AF2122/97] Length = 370 Score = 82.0 bits (201), Expect = 1e-14, Method: Compositional matrix adjust. Identities = 70/222 (31%), Positives = 102/222 (45%), Gaps = 24/222 (10%) Query: 8 PLREALFRYCLSLTRSRVEAEDLAQDTWTKTL-AYKKFADSPNPEALLLRIAKNTWIDAM 66 P R L +C +T S +AEDL Q+T + AY+ FA + L RIA NT + A+ Sbjct: 64 PYRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAYEGFAGKSSLRTWLHRIATNTCLTAL 123 Query: 67 ---RRK---TSLGRV-------------LEHTQAVAALAQGQMSGQAPESGRSEIEMAFQ 107 RR+ T LGR + + + + R + +AF Sbjct: 124 EGRRRRPLPTGLGRPSADPSGELVERREVSWLEPLPDVTDDPADPSTIVGNRESVRLAFV 183 Query: 108 ALIRHLSPLQRTVFVMRDVLDYPAGETAEMLGTTEGAVKAALHRARQALGAVRKELAED- 166 A ++HLSP QR V ++RDVL + + E A+ +GT+ AV + L RAR L VR A+ Sbjct: 184 AALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSLLQRARSQLQTVRPSAADRL 243 Query: 167 DGPAQPQDLDFRILLQALAESYEKGQLPVMLELLRRETAAEM 208 P P+ D A E+Y+ +L +EL E EM Sbjct: 244 SAPDSPEAQDLLARYIAAFEAYDIDRL---VELFTAEAIWEM 282 Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF Posted date: Mar 24, 2004 1:53 AM Number of letters in database: 757,237,578 Number of sequences in database: 2,715,099 Lambda K H 0.317 0.129 0.360 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 2715099 Number of Hits to DB: 278,733,390 Number of extensions: 9787635 Number of successful extensions: 26226 Number of sequences better than 1.0e-05: 89 Number of HSP's gapped: 26315 Number of HSP's successfully gapped: 89 Length of query: 243 Length of database: 757,237,578 Length adjustment: 122 Effective length of query: 121 Effective length of database: 425,995,500 Effective search space: 51545455500 Effective search space used: 51545455500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 124 (52.4 bits)