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= 0470.0011.p (233 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 pir||A55249 transcription initiation factor sigma K precursor - ... 347 2e-94 ref|NP_242151.1| RNA polymerase sigma factor (sigma K) precursor... 345 4e-94 ref|NP_834048.1| RNA polymerase sigma-K factor [Bacillus cereus ... 337 1e-91 ref|NP_658369.1| sigma70, Sigma-70 factor [Bacillus anthracis A2... 337 2e-91 ref|NP_980714.1| RNA polymerase sigma-27 factor [Bacillus cereus... 336 2e-91 >pir||A55249 transcription initiation factor sigma K precursor - Bacillus subtilis Length = 242 Score = 347 bits (889), Expect = 2e-94, Method: Compositional matrix adjust. Identities = 168/229 (73%), Positives = 196/229 (85%), Gaps = 1/229 (0%) Query: 1 LPGIISTIALLIKELTLLVSYVRNNAFPQPLSEQDESKYLGRMAEGDAKARNLLIEHNLR 60 + G+ + + ++KEL LVSYV+NNAFPQPLS +E KYL MA+GD ARN+LIEHNLR Sbjct: 2 VTGVFAALGFVVKELVFLVSYVKNNAFPQPLSSSEEKKYLELMAKGDEHARNMLIEHNLR 61 Query: 61 LVAHIVKKFDNTGEDMEDLISIGTIGLIKAIESYRPNKGTKLATFAARCIENEILMHLRS 120 LVAHIVKKF+NTGED EDLISIGTIGLIK IESY KGTK+AT+AARCIENEILMHLR+ Sbjct: 62 LVAHIVKKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKVATYAARCIENEILMHLRA 121 Query: 121 LKKTRKDVSLHDPIGTDKEGNEITLIDILGSETDDVIKEVDLKIEKSKIYRNLDILDDRE 180 LKKT+KDVSLHDPIG DKEGNEI+LID+L SE +DVI + L +E K+ + +DILDDRE Sbjct: 122 LKKTKKDVSLHDPIGQDKEGNEISLIDVLKSENEDVIDTIQLNMELEKVKQYIDILDDRE 181 Query: 181 KEVVVGRFGLDTGGEERTQREIAKELGISRSYVSRIEKRALMKLYHEFY 229 KEV+VGRFGLD +E+TQREIAKELGISRSYVSRIEKRALMK++HEFY Sbjct: 182 KEVIVGRFGLDL-KKEKTQREIAKELGISRSYVSRIEKRALMKMFHEFY 229 >ref|NP_242151.1| RNA polymerase sigma factor (sigma K) precursor [Bacillus halodurans] pir||E83810 RNA polymerase sigma factor (sigma K) precursor sigK [imported] - Bacillus halodurans (strain C-125) dbj|BAB05004.1| RNA polymerase sigma factor (sigma K) precursor [Bacillus halodurans] Length = 235 Score = 345 bits (885), Expect = 4e-94, Method: Compositional matrix adjust. Identities = 169/230 (73%), Positives = 196/230 (85%), Gaps = 1/230 (0%) Query: 1 LPGIISTIALLIKELTLLVSYVRNNAFPQPLSEQDESKYLGRMAEGDAKARNLLIEHNLR 60 + II+ + KE+ + VSYV+NNAFPQPLS+++E YL RMAEGD +ARN LIEHNLR Sbjct: 1 MSSIIAALTYFFKEVLVFVSYVKNNAFPQPLSKEEERHYLKRMAEGDEEARNRLIEHNLR 60 Query: 61 LVAHIVKKFDNTGEDMEDLISIGTIGLIKAIESYRPNKGTKLATFAARCIENEILMHLRS 120 LVAHIVKKF+NT E EDLISIGTIGLIKAIES+ KGTKLAT+AARCIENEILMHLR+ Sbjct: 61 LVAHIVKKFENTREHTEDLISIGTIGLIKAIESFSEGKGTKLATYAARCIENEILMHLRA 120 Query: 121 LKKTRKDVSLHDPIGTDKEGNEITLIDILGSETDDVIKEVDLKIEKSKIYRNLDILDDRE 180 LKK +KDVSLHDPIGTDKEGNEITLID+L +++D+ + LK+EK +IY + +LDDRE Sbjct: 121 LKKVKKDVSLHDPIGTDKEGNEITLIDVLQEDSEDIADSIQLKMEKKQIYEYIHVLDDRE 180 Query: 181 KEVVVGRFGLDTGGEERTQREIAKELGISRSYVSRIEKRALMKLYHEFYK 230 KEV+VGRFGLD EERTQREIAKELGISRSYVSRIEKRALMKL+HEFYK Sbjct: 181 KEVIVGRFGLDL-EEERTQREIAKELGISRSYVSRIEKRALMKLFHEFYK 229 >ref|NP_834048.1| RNA polymerase sigma-K factor [Bacillus cereus ATCC 14579] gb|AAP11249.1| RNA polymerase sigma-K factor [Bacillus cereus ATCC 14579] Length = 240 Score = 337 bits (863), Expect = 1e-91, Method: Compositional matrix adjust. Identities = 167/231 (72%), Positives = 195/231 (84%), Gaps = 1/231 (0%) Query: 3 GIISTIALLIKELTLLVSYVRNNAFPQPLSEQDESKYLGRMAEGDAKARNLLIEHNLRLV 62 + + I +++E+ + VSYV+NNAFPQPLS DE KYL M +GDA+ARNLLIEHNLRLV Sbjct: 5 SLFAAIGYMVREVFVFVSYVKNNAFPQPLSSDDERKYLELMEQGDAQARNLLIEHNLRLV 64 Query: 63 AHIVKKFDNTGEDMEDLISIGTIGLIKAIESYRPNKGTKLATFAARCIENEILMHLRSLK 122 AHIVKKF+NTGED EDLISIGTIGLIKAIESY KGTKLAT+AARCIENEILMHLR LK Sbjct: 65 AHIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLATYAARCIENEILMHLRVLK 124 Query: 123 KTRKDVSLHDPIGTDKEGNEITLIDILGSETDDVIKEVDLKIEKSKIYRNLDILDDREKE 182 KT+KDVSLHDPIG DKEGNEI+LIDIL SE++DVI + L +E KI +DILD+REKE Sbjct: 125 KTKKDVSLHDPIGQDKEGNEISLIDILKSESEDVIDMIQLSMELEKIKEYIDILDEREKE 184 Query: 183 VVVGRFGLDTGGEERTQREIAKELGISRSYVSRIEKRALMKLYHEFYKAKR 233 V+V RFGL +E+TQREIAK LGISRSYVSRIEKRALMK++HEF +A++ Sbjct: 185 VIVKRFGLGL-DKEKTQREIAKALGISRSYVSRIEKRALMKMFHEFVRAEK 234 >ref|NP_658369.1| sigma70, Sigma-70 factor [Bacillus anthracis A2012] ref|NP_846788.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. Ames] sp|P26765|RP28_BACAA RNA polymerase sigma-28 factor precursor pir||A39441 transcription initiation factor sigma 28 precursor - Bacillus thuringiensis subsp. kurstaki emb|CAA40024.1| sigma factor 28 [Bacillus thuringiensis] gb|AAL99379.1| sigma factor 28 [Bacillus thuringiensis serovar israelensis] gb|AAP28274.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. Ames] Length = 237 Score = 337 bits (863), Expect = 2e-91, Method: Compositional matrix adjust. Identities = 167/231 (72%), Positives = 195/231 (84%), Gaps = 1/231 (0%) Query: 3 GIISTIALLIKELTLLVSYVRNNAFPQPLSEQDESKYLGRMAEGDAKARNLLIEHNLRLV 62 + + I +++E+ + VSYV+NNAFPQPLS DE KYL M +GDA+ARNLLIEHNLRLV Sbjct: 2 SLFAAIGYMVREVFVFVSYVKNNAFPQPLSSDDERKYLELMEQGDAQARNLLIEHNLRLV 61 Query: 63 AHIVKKFDNTGEDMEDLISIGTIGLIKAIESYRPNKGTKLATFAARCIENEILMHLRSLK 122 AHIVKKF+NTGED EDLISIGTIGLIKAIESY KGTKLAT+AARCIENEILMHLR LK Sbjct: 62 AHIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLATYAARCIENEILMHLRVLK 121 Query: 123 KTRKDVSLHDPIGTDKEGNEITLIDILGSETDDVIKEVDLKIEKSKIYRNLDILDDREKE 182 KT+KDVSLHDPIG DKEGNEI+LIDIL SE++DVI + L +E KI +DILD+REKE Sbjct: 122 KTKKDVSLHDPIGQDKEGNEISLIDILKSESEDVIDMIQLSMELEKIKEYIDILDEREKE 181 Query: 183 VVVGRFGLDTGGEERTQREIAKELGISRSYVSRIEKRALMKLYHEFYKAKR 233 V+V RFGL +E+TQREIAK LGISRSYVSRIEKRALMK++HEF +A++ Sbjct: 182 VIVKRFGLGL-DKEKTQREIAKALGISRSYVSRIEKRALMKMFHEFVRAEK 231 >ref|NP_980714.1| RNA polymerase sigma-27 factor [Bacillus cereus ATCC 10987] gb|AAS43322.1| RNA polymerase sigma-27 factor [Bacillus cereus ATCC 10987] Length = 265 Score = 336 bits (862), Expect = 2e-91, Method: Compositional matrix adjust. Identities = 167/231 (72%), Positives = 195/231 (84%), Gaps = 1/231 (0%) Query: 3 GIISTIALLIKELTLLVSYVRNNAFPQPLSEQDESKYLGRMAEGDAKARNLLIEHNLRLV 62 + + I +++E+ + VSYV+NNAFPQPLS DE KYL M +GDA+ARNLLIEHNLRLV Sbjct: 30 SLFAAIGYMVREVFVFVSYVKNNAFPQPLSSDDERKYLELMEQGDAQARNLLIEHNLRLV 89 Query: 63 AHIVKKFDNTGEDMEDLISIGTIGLIKAIESYRPNKGTKLATFAARCIENEILMHLRSLK 122 AHIVKKF+NTGED EDLISIGTIGLIKAIESY KGTKLAT+AARCIENEILMHLR LK Sbjct: 90 AHIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLATYAARCIENEILMHLRVLK 149 Query: 123 KTRKDVSLHDPIGTDKEGNEITLIDILGSETDDVIKEVDLKIEKSKIYRNLDILDDREKE 182 KT+KDVSLHDPIG DKEGNEI+LIDIL SE++DVI + L +E KI +DILD+REKE Sbjct: 150 KTKKDVSLHDPIGQDKEGNEISLIDILKSESEDVIDMIQLSMELEKIKEYIDILDEREKE 209 Query: 183 VVVGRFGLDTGGEERTQREIAKELGISRSYVSRIEKRALMKLYHEFYKAKR 233 V+V RFGL +E+TQREIAK LGISRSYVSRIEKRALMK++HEF +A++ Sbjct: 210 VIVKRFGLGL-DKEKTQREIAKALGISRSYVSRIEKRALMKMFHEFVRAEK 259 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 0.137 0.372 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: 334,020,194 Number of extensions: 13978597 Number of successful extensions: 51855 Number of sequences better than 1.0e-05: 1278 Number of HSP's gapped: 51833 Number of HSP's successfully gapped: 1342 Length of query: 233 Length of database: 757,237,578 Length adjustment: 122 Effective length of query: 111 Effective length of database: 425,995,500 Effective search space: 47285500500 Effective search space used: 47285500500 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 (21.6 bits) S2: 124 (52.4 bits)