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= 0545.0026.p (219 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value Q9K7Z1.1 Q9K7Z1_BACHD RNA polymerase ECF-type sigma factor 144 6e-33 B3KFV2.1 B3KFV2_9BACI RNA polymerase sigma factor, sigma-70 family 143 1e-32 C3J1S4.1 C3J1S4_9BACI RNA polymerase, sigma-24 subunit, ECF subf... 137 6e-31 B7YAZ4.1 B7YAZ4_9BACI RNA polymerase, sigma-24 subunit, ECF subf... 137 6e-31 B6C1Z5.1 B6C1Z5_9GAMM RNA polymerase sigma factor, sigma-70 family 92 3e-17 >Q9K7Z1.1 Q9K7Z1_BACHD RNA polymerase ECF-type sigma factor Length = 193 Score = 144 bits (363), Expect = 6e-33, Method: Compositional matrix adjust. Identities = 74/187 (39%), Positives = 113/187 (60%), Gaps = 2/187 (1%) Query: 21 NEAMAAALAKMCEGSTAAFDEFYGWGGXXXVMQIAYRQTQDWMEAEDICHDIFLEVLRKG 80 N+ L K+ GS AFD FY V I+ +D EAED+ HD+FLEV +K Sbjct: 4 NQESLQLLQKIQNGSRLAFDTFYKMH-YPLVFNISLNILKDHSEAEDVSHDVFLEVFQKI 62 Query: 81 RAYDASRGTVKAWLAVMTRSRCIDRLRRKARTEPLANPETQLRNQDGPQEDAAVRKLQCE 140 YDA++G+V++WLAVMT+SR +DRLR+K R + E L++++ + + +LQ Sbjct: 63 EHYDATKGSVRSWLAVMTKSRSLDRLRKK-RPLLINRLEYLLKDEEKGADLQFLSELQRH 121 Query: 141 ALGDALQSLPANQKKAILGSYYAAHTHQELADSWSVPLGTVKSWIKYGVANMRRQFIKQG 200 + DAL+ +P Q++AI+ SY+ TH E+A + PLG++KS I+YG+ N+R+Q Sbjct: 122 LIVDALKQIPTEQREAIIRSYFRGETHSEIATTMDKPLGSIKSLIRYGLNNLRKQKSLLN 181 Query: 201 WIEQPEG 207 W+E G Sbjct: 182 WVESEGG 188 >B3KFV2.1 B3KFV2_9BACI RNA polymerase sigma factor, sigma-70 family Length = 199 Score = 143 bits (361), Expect = 1e-32, Method: Compositional matrix adjust. Identities = 78/181 (43%), Positives = 113/181 (62%), Gaps = 6/181 (3%) Query: 21 NEAMAAALAKMCEGSTAAFDEFYGWGGXXXVMQIAYRQTQDWMEAEDICHDIFLEVLRKG 80 N+ A L ++ EGS AAF FY V ++A + T+D EAED+C DIF+EVL K Sbjct: 2 NDHSALWLEEIAEGSAAAFRRFYD-AYARLVYRLALQMTKDPAEAEDVCQDIFMEVLHKA 60 Query: 81 RAYDASRGTVKAWLAVMTRSRCIDRLRRKARTEPL-----ANPETQLRNQDGPQEDAAVR 135 YD +RG+V+AWLAV TR R +DRLR++ R A PET + E AA+R Sbjct: 61 DQYDPARGSVEAWLAVRTRCRAMDRLRKRQRIAAAEWNGEALPETVWSEEQESVELAALR 120 Query: 136 KLQCEALGDALQSLPANQKKAILGSYYAAHTHQELADSWSVPLGTVKSWIKYGVANMRRQ 195 +++ E + +ALQ +P Q+ A+ GSY +H+E+A+ + P+GTVKS I+YG+ N+RR+ Sbjct: 121 RVELEQVKEALQGIPPLQRMAVYGSYVEQRSHREMAELLNRPVGTVKSLIRYGILNVRRR 180 Query: 196 F 196 Sbjct: 181 L 181 >C3J1S4.1 C3J1S4_9BACI RNA polymerase, sigma-24 subunit, ECF subfamily Length = 193 Score = 137 bits (345), Expect = 6e-31, Method: Compositional matrix adjust. Identities = 77/185 (41%), Positives = 114/185 (61%), Gaps = 3/185 (1%) Query: 28 LAKMCEGSTAAFDEFYGWGGXXXVMQIAYRQTQDWMEAEDICHDIFLEVLRKGRAYDASR 87 L K+ EGS AAFD FY V IA R + +EAED+ HD+FLE+L+K +D R Sbjct: 11 LEKIAEGSRAAFDRFYEKYAPM-VYHIALRIVGNEVEAEDVSHDVFLEILQKPHQFDPKR 69 Query: 88 GTVKAWLAVMTRSRCIDRLRRKARTEPLANPETQLRNQDGPQEDAAVRKLQCEALGDALQ 147 G+V+A+LAV T+SR +DRLR+K R ++ E + G E +R+L+ + + DAL Sbjct: 70 GSVQAFLAVKTKSRSLDRLRKK-RDLLVSRLEEAALKEKGA-EFYFLRQLEQQVILDALT 127 Query: 148 SLPANQKKAILGSYYAAHTHQELADSWSVPLGTVKSWIKYGVANMRRQFIKQGWIEQPEG 207 LP Q++AI+ Y+ T +E+A + + PLG+VKS I+YG+ N+R+Q W+E G Sbjct: 128 HLPEEQRQAIIHFYFHGETQREIAAAMNKPLGSVKSLIRYGLRNLRKQKELFHWMEAGRG 187 Query: 208 DISHE 212 + HE Sbjct: 188 EEQHE 192 >B7YAZ4.1 B7YAZ4_9BACI RNA polymerase, sigma-24 subunit, ECF subfamily Length = 193 Score = 137 bits (345), Expect = 6e-31, Method: Compositional matrix adjust. Identities = 77/185 (41%), Positives = 114/185 (61%), Gaps = 3/185 (1%) Query: 28 LAKMCEGSTAAFDEFYGWGGXXXVMQIAYRQTQDWMEAEDICHDIFLEVLRKGRAYDASR 87 L K+ EGS AAFD FY V IA R + +EAED+ HD+FLE+L+K +D R Sbjct: 11 LEKIAEGSRAAFDRFYEKYAPM-VYHIALRIVGNEVEAEDVSHDVFLEILQKPHQFDPKR 69 Query: 88 GTVKAWLAVMTRSRCIDRLRRKARTEPLANPETQLRNQDGPQEDAAVRKLQCEALGDALQ 147 G+V+A+LAV T+SR +DRLR+K R ++ E + G E +R+L+ + + DAL Sbjct: 70 GSVQAFLAVKTKSRSLDRLRKK-RDLLVSRLEEAALKEKGA-EFYFLRQLEQQVILDALT 127 Query: 148 SLPANQKKAILGSYYAAHTHQELADSWSVPLGTVKSWIKYGVANMRRQFIKQGWIEQPEG 207 LP Q++AI+ Y+ T +E+A + + PLG+VKS I+YG+ N+R+Q W+E G Sbjct: 128 HLPEEQRQAIIHFYFHGETQREIAAAMNKPLGSVKSLIRYGLRNLRKQKELFHWMEAGRG 187 Query: 208 DISHE 212 + HE Sbjct: 188 EEQHE 192 >B6C1Z5.1 B6C1Z5_9GAMM RNA polymerase sigma factor, sigma-70 family Length = 157 Score = 92.4 bits (228), Expect = 3e-17, Method: Compositional matrix adjust. Identities = 49/137 (35%), Positives = 78/137 (56%), Gaps = 2/137 (1%) Query: 64 EAEDICHDIFLEVLRKGRAYDASRGTVKAWLAVMTRSRCIDRLRRKARTEPLANPETQLR 123 EAED+ H++F+E+ RK YD RG+V+AWL + RSR +DRLR T + PET L Sbjct: 11 EAEDVLHNVFMEIWRKASQYDGRRGSVRAWLILRMRSRSLDRLRSAPYTRSIPIPETVLE 70 Query: 124 NQ-DGPQEDAAVRKLQCEALGDALQSLPANQKKAILGSYYAAHTHQELADSWSVPLGTVK 182 N +G +D A+ C+A+ A+ L Q+ + +Y+ + E+A +PLGT+K Sbjct: 71 NTANGMSQDPAL-AWDCQAVRKAMSKLSREQRTIMELAYFQGLSASEIASHVGLPLGTIK 129 Query: 183 SWIKYGVANMRRQFIKQ 199 S ++ + +R + Q Sbjct: 130 SRMRGALNVLRTHYRTQ 146 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 0.131 0.403 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: 1,323,641,109 Number of extensions: 49249526 Number of successful extensions: 113161 Number of sequences better than 1.0e-05: 781 Number of HSP's gapped: 113611 Number of HSP's successfully gapped: 781 Length of query: 219 Length of database: 3,060,696,203 Length adjustment: 130 Effective length of query: 89 Effective length of database: 1,835,964,253 Effective search space: 163400818517 Effective search space used: 163400818517 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: 128 (53.9 bits)