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= 0322.0001.p (178 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3K4I8.1 B3K4I8_9BACI RNA polymerase sigma factor, sigma-70 family 180 4e-44 C0ZBE3.1 C0ZBE3_BREBN RNA polymerase ECF-type sigma factor 160 4e-38 B1D9J1.1 B1D9J1_9BACL RNA polymerase, sigma-24 subunit, ECF subf... 150 4e-35 B1DKW3.1 B1DKW3_9BACL RNA polymerase, sigma-24 subunit, ECF subf... 149 8e-35 Q2BC17.1 Q2BC17_9BACI Possible RNA polymerase sigma factor, ECF ... 125 1e-27 >B3K4I8.1 B3K4I8_9BACI RNA polymerase sigma factor, sigma-70 family Length = 176 Score = 180 bits (457), Expect = 4e-44, Method: Compositional matrix adjust. Identities = 93/169 (55%), Positives = 118/169 (69%), Gaps = 2/169 (1%) Query: 7 EMKKLTGAVPREDN-AFYDAVMEHSDQLYHIAYSYLRNRSDALEAVQEATCRAWIKRATL 65 E K+L A R D AFY V EH +LY IAYSYL N SDALEA+QE CRAW+K L Sbjct: 3 ETKELAAAACRGDEEAFYALVTEHRRRLYGIAYSYLHNESDALEALQETVCRAWMKCRKL 62 Query: 66 KDPQAFKPWIIRILIYVCIDEQRRRKRSVPTPEAAMREPVMQ-DSSSKLEMLWAVEQVKP 124 K P+AF PW+IRILI C+DEQ+R+KR +P E RE + S SKL++ A+ ++KP Sbjct: 63 KHPEAFVPWLIRILINCCVDEQKRKKRMLPVEEVRSRETAAEMVSDSKLDLERALSRMKP 122 Query: 125 KYRHVLLLKYYNDMTLTEIADLLGKPEGTIKTWQHKGLKQLRTIMKNRG 173 KYRHVL+LKYY DMT+++IA +L PEGT+KT H+GLK LR ++ G Sbjct: 123 KYRHVLILKYYQDMTISDIAHILDVPEGTVKTRLHQGLKLLRQKIEPGG 171 >C0ZBE3.1 C0ZBE3_BREBN RNA polymerase ECF-type sigma factor Length = 181 Score = 160 bits (406), Expect = 4e-38, Method: Compositional matrix adjust. Identities = 73/154 (47%), Positives = 110/154 (71%), Gaps = 5/154 (3%) Query: 18 EDNAFYDAVMEHSDQLYHIAYSYLRNRSDALEAVQEATCRAWIKRATLKDPQAFKPWIIR 77 +D+AF+ V H DQLY IAY++LRN +DALEA+QEATCR+++K A LK F+ W+ R Sbjct: 21 DDDAFFQLVSLHKDQLYKIAYAFLRNETDALEAIQEATCRSYLKLARLKQTAYFRTWLTR 80 Query: 78 ILIYVCIDEQRRRKRSVPTP-----EAAMREPVMQDSSSKLEMLWAVEQVKPKYRHVLLL 132 ILI++C+DEQ+RRKR + + E+ P+ + ++++ A+ +++P YRH+++L Sbjct: 81 ILIHICLDEQKRRKRIILSAMEDDIESRASIPMDDQNVERIQIEEALARLRPNYRHIIIL 140 Query: 133 KYYNDMTLTEIADLLGKPEGTIKTWQHKGLKQLR 166 KY+ D T+ +IA++LG PEGTIKTW HK L LR Sbjct: 141 KYFEDRTIRDIAEVLGHPEGTIKTWLHKALGALR 174 >B1D9J1.1 B1D9J1_9BACL RNA polymerase, sigma-24 subunit, ECF subfamily Length = 179 Score = 150 bits (380), Expect = 4e-35, Method: Compositional matrix adjust. Identities = 82/181 (45%), Positives = 110/181 (60%), Gaps = 23/181 (12%) Query: 11 LTGAVPREDNA-FYDAVMEHSDQLYHIAYSYLRNRSDALEAVQEATCRAWIKRATLKDPQ 69 L A R D+A FY + + +++Y IAYSYL+N +DALEAVQEATCRA+++ LK+P+ Sbjct: 6 LVAAAKRGDDAAFYSLITQQKEKMYRIAYSYLKNETDALEAVQEATCRAYMQIHKLKEPE 65 Query: 70 AFKPWIIRILIYVCIDEQRRRKR--------------SVPTPEAAMREPVMQDSSSKLEM 115 F W+IRIL+ C DE +R+ R + E+A+ E VM +S Sbjct: 66 FFGSWLIRILMNYCADEAKRKARRTDGQQAAAAALDLHATSGESALLERVMLES------ 119 Query: 116 LWAVEQVKPKYRHVLLLKYYNDMTLTEIADLLGKPEGTIKTWQHKGLKQLRTIMKNRGEW 175 AVEQ+ Y+ V+ LKYY+D+T+TEIA L KPEGTIKTW HK L LR + GE Sbjct: 120 --AVEQLDANYQKVIQLKYYHDLTITEIARTLQKPEGTIKTWLHKALGGLRQRLGKEGEP 177 Query: 176 N 176 N Sbjct: 178 N 178 >B1DKW3.1 B1DKW3_9BACL RNA polymerase, sigma-24 subunit, ECF subfamily Length = 180 Score = 149 bits (377), Expect = 8e-35, Method: Compositional matrix adjust. Identities = 71/158 (44%), Positives = 106/158 (67%), Gaps = 3/158 (1%) Query: 13 GAVPREDNAFYDAVMEHSDQLYHIAYSYLRNRSDALEAVQEATCRAWIKRATLKDPQAFK 72 A+ +D+A + ++LY IAYSY+RN +DALEA+QE T R W KR +L+DP+ F Sbjct: 9 AAIKGDDDALIARIQMDQNRLYGIAYSYMRNETDALEAIQETTVRVWNKRRSLRDPKVFT 68 Query: 73 PWIIRILIYVCIDEQRRRKRSVPTPEAAMR---EPVMQDSSSKLEMLWAVEQVKPKYRHV 129 W+ RILI VC+DE++++ R P + + + +++M ++++ KYR V Sbjct: 69 TWVTRILIRVCLDERKKQLRERPLRNELLERDAQTANEHGIDRMDMAVQLKKLPSKYRMV 128 Query: 130 LLLKYYNDMTLTEIADLLGKPEGTIKTWQHKGLKQLRT 167 ++LKYY DMT+TEIA+LL KP+GTI+TW H+ LKQLRT Sbjct: 129 IVLKYYRDMTITEIAELLEKPDGTIRTWLHQALKQLRT 166 >Q2BC17.1 Q2BC17_9BACI Possible RNA polymerase sigma factor, ECF subfamily protein Length = 173 Score = 125 bits (315), Expect = 1e-27, Method: Compositional matrix adjust. Identities = 75/163 (46%), Positives = 104/163 (63%), Gaps = 5/163 (3%) Query: 18 EDNAFYDAVMEHSDQLYHIAYSYLRNRSDALEAVQEATCRAWIKRATLKDPQAFKPWIIR 77 +D AFY+ + H QL IAYSYLRN +ALEA+QE T RA+ +LK F W+IR Sbjct: 14 DDEAFYELMQAHKVQLLKIAYSYLRNEEEALEALQEVTFRAYRSIRSLKKADYFSTWLIR 73 Query: 78 ILIYVCIDEQRRRKRSVPTPEAAMREPVMQ--DSSSKLEMLWAVEQVKPKYRHVLLLKYY 135 I++ C D+ R++KR+ P + E + + + S LE+ A+E++ K R V++LKYY Sbjct: 74 IMLNYCHDQSRKKKRAAPLD---LTESLAETYNYSQALEIEEALEKIDSKCREVIILKYY 130 Query: 136 NDMTLTEIADLLGKPEGTIKTWQHKGLKQLRTIMKNRGEWNDQ 178 +DM + EIA+LL PE TIKTW +KGLK LR + RGE N Q Sbjct: 131 HDMKIKEIANLLESPESTIKTWLYKGLKALREQLGERGEANVQ 173 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 0.319 0.132 0.400 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: 1,063,296,843 Number of extensions: 38566549 Number of successful extensions: 109521 Number of sequences better than 1.0e-05: 1578 Number of HSP's gapped: 110265 Number of HSP's successfully gapped: 1578 Length of query: 178 Length of database: 3,060,696,203 Length adjustment: 127 Effective length of query: 51 Effective length of database: 1,864,227,298 Effective search space: 95075592198 Effective search space used: 95075592198 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 126 (53.1 bits)