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: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value BH3117 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 157 1e-38 Rv0182c [K] COG1595 DNA-directed RNA polymerase specialized sigm... 82 8e-16 MT0191 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 82 8e-16 mll1867 [K] COG1595 DNA-directed RNA polymerase specialized sigm... 74 2e-13 Cgl0743 [K] COG1595 DNA-directed RNA polymerase specialized sigm... 70 4e-12 >BH3117 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 230 Score = 157 bits (398), Expect = 1e-38, 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 >Rv0182c [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 370 Score = 82.0 bits (201), Expect = 8e-16, 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 >MT0191 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 370 Score = 82.0 bits (201), Expect = 8e-16, 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 >mll1867 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 301 Score = 73.9 bits (180), Expect = 2e-13, Method: Compositional matrix adjust. Identities = 5/172 (2%), Positives = 25/172 (14%), Gaps = 31/172 (18%) Query: 9 LREALFRYCLSLTRSRVEAEDLAQDTWTKTLAYKKFADSPNPEAL---LLRIAKNTWIDA 65 L ++ + R+ + Sbjct: 28 LLGQKISITSRKAQTTRHRIVGIHTEGAY--QAIYVDTPGLHMEEKRAINRLMNKAASSS 85 Query: 66 MR-RKTSLGRVLEHTQAVAALAQGQM----SGQAPESGRSEIEMAFQALIRHLSPLQRTV 120 + + + V + E + + +Q Sbjct: 86 IGDVELVI-------FVVEGTRWTPDDEMVLNKLREGKA-----PVILAVNKVDNVQEKA 133 Query: 121 FVMRDVLDYPAGETAEMLGTTEGAVKAALHRARQALGAVRKELAEDDGPAQP 172 ++ + + + + + + Sbjct: 134 DLLPHLQFLASQMNFLDIVPISAETGLNVDTIAAIVRKH---------LPEA 176 >Cgl0743 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 206 Score = 69.7 bits (169), Expect = 4e-12, Method: Compositional matrix adjust. Identities = 53/170 (31%), Positives = 85/170 (50%), Gaps = 10/170 (5%) Query: 8 PLREALFRYCLSLTRSRVEAEDLAQDTWTKTL-AYKKFADSPNPEALLLRIAKNTWIDAM 66 PL + L+ L +TR+ +AEDL QDT+ K A+ F N +A L RI NT+I+ Sbjct: 24 PLLDQLYGGALRMTRNPADAEDLVQDTYIKAYQAFASFKPGTNLKAWLYRIMTNTYINMY 83 Query: 67 RRK------TSLGRVLEH--TQAVAALAQGQMSGQAPESGRSEIEMAFQALIRHLSPLQR 118 R+K TS + ++ ++ + + G S + E+ ++ + + LSP R Sbjct: 84 RKKQRQPSQTSADEITDYQLVESQSHTSTGLESAEV-EALKNLPDGKIGDAMNQLSPEYR 142 Query: 119 TVFVMRDVLDYPAGETAEMLGTTEGAVKAALHRARQALGAVRKELAEDDG 168 V DV D E AE++ G V + LHR R+ L + KE+A++ G Sbjct: 143 MVVYYADVEDLAYKEIAEIMDVPLGTVMSRLHRGRKQLRGMLKEVAKEQG 192 Database: COG Posted date: Aug 3, 2010 9:58 AM Number of letters in database: 38,378,431 Number of sequences in database: 115,334 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: 115334 Number of Hits to DB: 14,773,216 Number of extensions: 593385 Number of successful extensions: 1155 Number of sequences better than 1.0e-05: 21 Number of HSP's gapped: 1160 Number of HSP's successfully gapped: 21 Length of query: 243 Length of database: 38,378,431 Length adjustment: 103 Effective length of query: 140 Effective length of database: 26,499,029 Effective search space: 3709864060 Effective search space used: 3709864060 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: 114 (48.5 bits)