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= 0291.0037.p (230 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value A9KRY5.1 A9KRY5_CLOPH RNA polymerase sigma factor 134 4e-30 B9XPW8.1 B9XPW8_9BACT RNA polymerase sigma factor 87 8e-16 Q24ZK5.1 Q24ZK5_DESHY Putative uncharacterized protein 83 2e-14 B8FW34.1 B8FW34_DESHD RNA polymerase, sigma-24 subunit, ECF subf... 82 3e-14 B2A648.1 B2A648_NATTJ RNA polymerase, sigma-24 subunit, ECF subf... 77 1e-12 >A9KRY5.1 A9KRY5_CLOPH RNA polymerase sigma factor Length = 204 Score = 134 bits (338), Expect = 4e-30, Method: Compositional matrix adjust. Identities = 76/220 (34%), Positives = 122/220 (55%), Gaps = 27/220 (12%) Query: 1 VGTDSSSPRPNSKDKGPPDEEAAMLLRFRQGEREAFEWLVRKYRQPAVHFAHHLTGDYHL 60 VG D SS K+ +++ + F G+ EAFE LV K++ ++F L + + Sbjct: 10 VGKDISS-----KEGVQSEQDKIIYQNFLDGDMEAFEELVIKHKDRLIYFIQRLVNNLTI 64 Query: 61 AEDLAQDCFAHLLVYPEKYDFRASFKTYLYTLLRHKCIDAWRKSRRTLPGEAGGRNESGR 120 AEDLAQD F +LV+ E+Y F+ SFKTYL+T+ R+K ID RK++R + E Sbjct: 65 AEDLAQDAFVEVLVHKERYHFQVSFKTYLFTIGRNKAIDYIRKNKRMMLVED-------- 116 Query: 121 MSPEDHPDDGQMSGRYISPYALDDPARLAIVREEDREWHRRMRMLKPDYRLAVYLVDIAQ 180 PE + ++ +M I +EE + + M+ LKPDY+ A+ L+D+ Q Sbjct: 117 -YPESYDEENRMEENIIR-------------KEESKLLYDAMKKLKPDYKAAISLIDLEQ 162 Query: 181 LSYEEASSIMQRSTVSFRVLLHRARKKLRQIYEGEEWDCE 220 +SY EA+ ++++S +VL++RARK L ++ E E + E Sbjct: 163 MSYAEAAKVLKKSDAQMKVLIYRARKSLAKLMEKEGYSYE 202 >B9XPW8.1 B9XPW8_9BACT RNA polymerase sigma factor Length = 205 Score = 87.4 bits (215), Expect = 8e-16, Method: Compositional matrix adjust. Identities = 57/195 (29%), Positives = 99/195 (50%), Gaps = 14/195 (7%) Query: 19 DEEAAMLLRFRQGEREAFEWLVRKYRQPAVHFAHHLTGDYHLAEDLAQDCFAHLLVYPEK 78 D + A++LR ++G+ +AF LV KY+QP ++ + D AEDLAQ+ F + + Sbjct: 6 DPDVALMLRVKRGDSDAFAELVEKYKQPVINVVFRILRDATEAEDLAQNVFIQVYKSAHR 65 Query: 79 YDFRASFKTYLYTLLRHKCIDAWRKSRRTLPG---EAGGRNESGRMSPEDHPDDGQMSGR 135 Y+ A F T+L+T+ R+ C++ R+ R P EA N P +D ++ Sbjct: 66 YEVSAKFSTWLFTIARNLCLNEIRRRSRH-PADSLEANFTNSDNEDLPSRQFEDVKV--- 121 Query: 136 YISPYALDDPARLAIVREEDREWHRRMRMLKPDYRLAVYLVDIAQLSYEEASSIMQRSTV 195 Y +P L + E + E + ++ L + R A+ L +SYEE + ++ S Sbjct: 122 YSAPDTL-------LQHELEHEVEQALKELPENQRTAILLCRQEDMSYEEIAKVIGCSLS 174 Query: 196 SFRVLLHRARKKLRQ 210 + + L+HR R+ L+Q Sbjct: 175 ATKSLIHRGRETLKQ 189 >Q24ZK5.1 Q24ZK5_DESHY Putative uncharacterized protein Length = 182 Score = 82.8 bits (203), Expect = 2e-14, Method: Compositional matrix adjust. Identities = 61/199 (30%), Positives = 97/199 (48%), Gaps = 30/199 (15%) Query: 20 EEAAMLLRFRQGEREAFEWLVRKYRQPAVHFAHHLTGDYHLAEDLAQDCF----AHLLVY 75 E+A ++ + +G E + LV++Y++P +HF + G D AQ+ F +L Y Sbjct: 2 EDAELIQQVLKGRHEQYGLLVQRYQEPLIHFLRGILGAEDEVFDCAQEAFLAAYGNLWRY 61 Query: 76 PEKYDFRASFKTYLYTLLRHKCIDAWRKSRRTLPGEAGGRNESGRMSPEDHPDDGQMSGR 135 +KY FRA +LY + R+K ID RK +R +P +S ++ D QM Sbjct: 62 SDKYTFRA----WLYAIARNKAIDLMRKRKREIP-----------LSIDESLVDRQMG-- 104 Query: 136 YISPYALDDPARLAIVREEDREWHRRMRMLKPDYRLAVYLVDIAQLSYEEASSIMQRSTV 195 P + +E+ + + L YR A+YL +LSYEE S+++ Sbjct: 105 ---------PEEAYLAKEQALDVRTILEELPEHYRQALYLRYQQELSYEEISTVLNIPIS 155 Query: 196 SFRVLLHRARKKLRQIYEG 214 S + LHR ++KLRQI EG Sbjct: 156 SVKTHLHRGKEKLRQIMEG 174 >B8FW34.1 B8FW34_DESHD RNA polymerase, sigma-24 subunit, ECF subfamily Length = 182 Score = 82.4 bits (202), Expect = 3e-14, Method: Compositional matrix adjust. Identities = 61/199 (30%), Positives = 97/199 (48%), Gaps = 30/199 (15%) Query: 20 EEAAMLLRFRQGEREAFEWLVRKYRQPAVHFAHHLTGDYHLAEDLAQDCF----AHLLVY 75 E+A ++ + +G E + LV++Y++P +HF + G D AQ+ F +L Y Sbjct: 2 EDAELIQQVLKGRHEQYGLLVQRYQEPLIHFLRGILGAEDEVFDCAQEAFLAAYGNLWRY 61 Query: 76 PEKYDFRASFKTYLYTLLRHKCIDAWRKSRRTLPGEAGGRNESGRMSPEDHPDDGQMSGR 135 +KY FRA +LY + R+K ID RK +R +P +S ++ D QM Sbjct: 62 SDKYTFRA----WLYAIARNKAIDLMRKRKREIP-----------LSIDESLVDRQMG-- 104 Query: 136 YISPYALDDPARLAIVREEDREWHRRMRMLKPDYRLAVYLVDIAQLSYEEASSIMQRSTV 195 P + +E+ + + L YR A+YL +LSYEE S+++ Sbjct: 105 ---------PEEAYLAKEQALDVRAILEELPEHYRQALYLRYQQELSYEEISTVLNIPIS 155 Query: 196 SFRVLLHRARKKLRQIYEG 214 S + LHR ++KLRQI EG Sbjct: 156 SVKTHLHRGKEKLRQIMEG 174 >B2A648.1 B2A648_NATTJ RNA polymerase, sigma-24 subunit, ECF subfamily Length = 206 Score = 76.6 bits (187), Expect = 1e-12, Method: Compositional matrix adjust. Identities = 51/183 (27%), Positives = 92/183 (50%), Gaps = 11/183 (6%) Query: 29 RQGEREAFEWLVRKYRQPAVHFAHHLTGDYHLAEDLAQDCFAHLLVYPEKYDFRASFKTY 88 + G +AFE LV KY Q + +G++ A DLAQ+ F + K+ F+++F T+ Sbjct: 16 QNGHLDAFEELVHKYHQKVYSLCYRFSGNHDDANDLAQEAFIRVYHSINKFHFKSAFSTW 75 Query: 89 LYTLLRHKCIDAWRKSRRTLPGEAGGRNESGRMSPEDHPDDGQMSGRYISPYALDDPARL 148 LY + + C+D RK +R ++ SP + DDG++ + P +P + Sbjct: 76 LYRVTSNVCLDEMRKRKR--------KSSVSLDSPME-TDDGEL--YFNLPDQKFNPELM 124 Query: 149 AIVREEDREWHRRMRMLKPDYRLAVYLVDIAQLSYEEASSIMQRSTVSFRVLLHRARKKL 208 A ++ H+ ++ L D +L + L ++ SY+E + +M S + + L RAR L Sbjct: 125 AERKDVQEIVHKAIQELPKDQKLTLLLREMEGFSYDEMAEVMNVSVGTVKSRLSRARNNL 184 Query: 209 RQI 211 ++I Sbjct: 185 KEI 187 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 0.321 0.135 0.416 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: 1,467,597,644 Number of extensions: 60695190 Number of successful extensions: 135306 Number of sequences better than 1.0e-05: 565 Number of HSP's gapped: 135773 Number of HSP's successfully gapped: 565 Length of query: 230 Length of database: 3,060,696,203 Length adjustment: 131 Effective length of query: 99 Effective length of database: 1,826,543,238 Effective search space: 180827780562 Effective search space used: 180827780562 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: 129 (54.3 bits)