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: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KFW0.1 B3KFW0_9BACI RNA polymerase sigma factor 421 e-116 B1DAQ8.1 B1DAQ8_9BACL RNA polymerase sigma factor 399 e-109 Q2B1A2.1 Q2B1A2_9BACI RNA polymerase sigma factor 356 9e-97 C5D4X5.1 C5D4X5_9BACI RNA polymerase, sigma 28 subunit, SigK 356 1e-96 A7Z6Y8.1 A7Z6Y8_BACA2 RNA polymerase sigma factor 353 5e-96 >B3KFW0.1 B3KFW0_9BACI RNA polymerase sigma factor Length = 233 Score = 421 bits (1081), Expect = e-116, Method: Compositional matrix adjust. Identities = 203/233 (87%), Positives = 221/233 (94%) Query: 1 LPGIISTIALLIKELTLLVSYVRNNAFPQPLSEQDESKYLGRMAEGDAKARNLLIEHNLR 60 +PG+ + IAL IKELTLLVSYV+NNAFPQPL+E++E+K+L RMAEGD ++RN LIEHNLR Sbjct: 1 MPGLFTAIALFIKELTLLVSYVKNNAFPQPLTEEEEAKHLQRMAEGDPQSRNKLIEHNLR 60 Query: 61 LVAHIVKKFDNTGEDMEDLISIGTIGLIKAIESYRPNKGTKLATFAARCIENEILMHLRS 120 LVAHIVKKFDNTGED+EDLISIGTIGLIKAIES+RPNKGTKLATFAARCIENEILMHLRS Sbjct: 61 LVAHIVKKFDNTGEDLEDLISIGTIGLIKAIESFRPNKGTKLATFAARCIENEILMHLRS 120 Query: 121 LKKTRKDVSLHDPIGTDKEGNEITLIDILGSETDDVIKEVDLKIEKSKIYRNLDILDDRE 180 LKKTRKDVSLHDPIGTDKEGNEITLIDILG+E DD++ V LKIEKSKIYRNLDILDDRE Sbjct: 121 LKKTRKDVSLHDPIGTDKEGNEITLIDILGTEADDIVDAVQLKIEKSKIYRNLDILDDRE 180 Query: 181 KEVVVGRFGLDTGGEERTQREIAKELGISRSYVSRIEKRALMKLYHEFYKAKR 233 KEVV+GRFGL+ GGEERTQREIAKELGISRSYVSRIEKRALMKLYHEFYK KR Sbjct: 181 KEVVIGRFGLEAGGEERTQREIAKELGISRSYVSRIEKRALMKLYHEFYKQKR 233 >B1DAQ8.1 B1DAQ8_9BACL RNA polymerase sigma factor Length = 232 Score = 399 bits (1025), Expect = e-109, Method: Compositional matrix adjust. Identities = 195/231 (84%), Positives = 215/231 (93%) Query: 3 GIISTIALLIKELTLLVSYVRNNAFPQPLSEQDESKYLGRMAEGDAKARNLLIEHNLRLV 62 G+ + IAL IK+L+LLVSYV+NNAFPQPL E++E K+L MAEG+A +RNLLIEHNLRLV Sbjct: 2 GLFAAIALFIKQLSLLVSYVKNNAFPQPLHEEEEMKHLQLMAEGNAHSRNLLIEHNLRLV 61 Query: 63 AHIVKKFDNTGEDMEDLISIGTIGLIKAIESYRPNKGTKLATFAARCIENEILMHLRSLK 122 AHIVKKFDNTGED+EDLISIGTIGLIKAIES++ KGTKLATFAARCIENEILMHLRSLK Sbjct: 62 AHIVKKFDNTGEDLEDLISIGTIGLIKAIESFQTGKGTKLATFAARCIENEILMHLRSLK 121 Query: 123 KTRKDVSLHDPIGTDKEGNEITLIDILGSETDDVIKEVDLKIEKSKIYRNLDILDDREKE 182 KTRKDVSLHDPIGTDKEGNEITLIDILG+E DDV+ V LKIEKSKIYRNLDILD+RE+E Sbjct: 122 KTRKDVSLHDPIGTDKEGNEITLIDILGTEADDVVDRVQLKIEKSKIYRNLDILDEREQE 181 Query: 183 VVVGRFGLDTGGEERTQREIAKELGISRSYVSRIEKRALMKLYHEFYKAKR 233 V+ GRFGLD GG+ERTQREIAKELGISRSYVSRIEKRALMKLYHEFYKAK+ Sbjct: 182 VIRGRFGLDHGGDERTQREIAKELGISRSYVSRIEKRALMKLYHEFYKAKK 232 >Q2B1A2.1 Q2B1A2_9BACI RNA polymerase sigma factor Length = 240 Score = 356 bits (913), Expect = 9e-97, Method: Compositional matrix adjust. Identities = 173/233 (74%), Positives = 202/233 (86%), Gaps = 1/233 (0%) Query: 1 LPGIISTIALLIKELTLLVSYVRNNAFPQPLSEQDESKYLGRMAEGDAKARNLLIEHNLR 60 + GI + + L+KE+ LVSYV+NNAFPQPLS DE KYL MAEGDA ARN+LIEHNLR Sbjct: 1 MSGIATALGYLVKEIVFLVSYVKNNAFPQPLSAADERKYLRLMAEGDAHARNMLIEHNLR 60 Query: 61 LVAHIVKKFDNTGEDMEDLISIGTIGLIKAIESYRPNKGTKLATFAARCIENEILMHLRS 120 LVAHIVKKF+NTGED EDLISIGTIGLIKAIESY KGTKLAT+AARCIENEILMHLR+ Sbjct: 61 LVAHIVKKFENTGEDSEDLISIGTIGLIKAIESYSEGKGTKLATYAARCIENEILMHLRA 120 Query: 121 LKKTRKDVSLHDPIGTDKEGNEITLIDILGSETDDVIKEVDLKIEKSKIYRNLDILDDRE 180 LKKT+KDVSLHDPIG DKEGNEI+LID+L SE++DVI + L +E K+ +D+LDDRE Sbjct: 121 LKKTKKDVSLHDPIGQDKEGNEISLIDVLKSESEDVINTIQLNMELEKVKEYIDVLDDRE 180 Query: 181 KEVVVGRFGLDTGGEERTQREIAKELGISRSYVSRIEKRALMKLYHEFYKAKR 233 KEV++GRFGLD +E+TQREIAKELGISRSYVSRIEKRALMK++HEFY+A++ Sbjct: 181 KEVIIGRFGLDL-KKEKTQREIAKELGISRSYVSRIEKRALMKMFHEFYRAEK 232 >C5D4X5.1 C5D4X5_9BACI RNA polymerase, sigma 28 subunit, SigK Length = 236 Score = 356 bits (913), Expect = 1e-96, Method: Compositional matrix adjust. Identities = 170/233 (72%), Positives = 203/233 (87%), Gaps = 1/233 (0%) Query: 1 LPGIISTIALLIKELTLLVSYVRNNAFPQPLSEQDESKYLGRMAEGDAKARNLLIEHNLR 60 + GI+S LIKEL LVSY++NNAFPQPLS ++E KYL MA+GD +ARN+LIEHNLR Sbjct: 1 MSGILSAFTFLIKELVFLVSYIKNNAFPQPLSAKEEEKYLQLMAKGDEQARNILIEHNLR 60 Query: 61 LVAHIVKKFDNTGEDMEDLISIGTIGLIKAIESYRPNKGTKLATFAARCIENEILMHLRS 120 LVAHIVKKF+NTGED EDLISIGTIGLIKAIESY P KGTKLAT+AARCIENEILMHLRS Sbjct: 61 LVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSPGKGTKLATYAARCIENEILMHLRS 120 Query: 121 LKKTRKDVSLHDPIGTDKEGNEITLIDILGSETDDVIKEVDLKIEKSKIYRNLDILDDRE 180 LKKTRKDVSLH+PIG DKEGNEI+LID+L SE +D+I E+ L +E ++ + +D+LD+RE Sbjct: 121 LKKTRKDVSLHEPIGQDKEGNEISLIDVLKSEGNDIIDEIQLNMELEQVKKYIDVLDERE 180 Query: 181 KEVVVGRFGLDTGGEERTQREIAKELGISRSYVSRIEKRALMKLYHEFYKAKR 233 KEV++ RFGLD +E+TQREIAKELGISRSYVSRIEKRALMK++HEFY+ ++ Sbjct: 181 KEVIISRFGLDM-QQEKTQREIAKELGISRSYVSRIEKRALMKMFHEFYRNEK 232 >A7Z6Y8.1 A7Z6Y8_BACA2 RNA polymerase sigma factor Length = 240 Score = 353 bits (907), Expect = 5e-96, Method: Compositional matrix adjust. Identities = 171/231 (74%), Positives = 199/231 (86%), Gaps = 1/231 (0%) Query: 1 LPGIISTIALLIKELTLLVSYVRNNAFPQPLSEQDESKYLGRMAEGDAKARNLLIEHNLR 60 + G+ + + ++KEL LVSYV+NNAFPQPLS +E KYL MAEGD ARN+LIEHNLR Sbjct: 1 MTGVFAALGFIVKELVFLVSYVKNNAFPQPLSNNEEKKYLDLMAEGDEHARNMLIEHNLR 60 Query: 61 LVAHIVKKFDNTGEDMEDLISIGTIGLIKAIESYRPNKGTKLATFAARCIENEILMHLRS 120 LVAHIVKKF+NTGED EDLISIGTIGLIK IESY KGTKLAT+AARCIENEILMHLR+ Sbjct: 61 LVAHIVKKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYAARCIENEILMHLRA 120 Query: 121 LKKTRKDVSLHDPIGTDKEGNEITLIDILGSETDDVIKEVDLKIEKSKIYRNLDILDDRE 180 LKKT+KDVSLHDPIG DKEGNEI+LID+L SE++DVI + L +E K+ + +DILDDRE Sbjct: 121 LKKTKKDVSLHDPIGQDKEGNEISLIDVLKSESEDVIDTIQLNMELEKVKKYIDILDDRE 180 Query: 181 KEVVVGRFGLDTGGEERTQREIAKELGISRSYVSRIEKRALMKLYHEFYKA 231 KEV+VGRFGLD +E+TQREIAKELGISRSYVSRIEKRALMK++HEFY+A Sbjct: 181 KEVIVGRFGLDL-KKEKTQREIAKELGISRSYVSRIEKRALMKMFHEFYRA 230 Database: pfamseq Posted date: Aug 5, 2010 3:22 PM Number of letters in database: 3,060,696,203 Number of sequences in database: 9,421,015 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: 9421015 Number of Hits to DB: 1,324,545,986 Number of extensions: 54891318 Number of successful extensions: 190633 Number of sequences better than 1.0e-05: 3992 Number of HSP's gapped: 189450 Number of HSP's successfully gapped: 4273 Length of query: 233 Length of database: 3,060,696,203 Length adjustment: 131 Effective length of query: 102 Effective length of database: 1,826,543,238 Effective search space: 186307410276 Effective search space used: 186307410276 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: 129 (54.3 bits)