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= 0112.0022.p (377 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value P52328.1 RPSD2_BACSP RNA polymerase sigma factor rpoD 625 e-177 B1DFN2.1 B1DFN2_9BACL RNA polymerase sigma factor 592 e-167 C1PEH1.1 C1PEH1_BACCO RNA polymerase, sigma 70 subunit, RpoD sub... 523 e-146 Q2YT18.1 Q2YT18_STAAB RNA polymerase sigma factor 513 e-144 Q2FGG2.1 Q2FGG2_STAA3 RNA polymerase sigma factor 513 e-144 >P52328.1 RPSD2_BACSP RNA polymerase sigma factor rpoD Length = 377 Score = 625 bits (1611), Expect = e-177, Method: Compositional matrix adjust. Identities = 319/377 (84%), Positives = 322/377 (85%) Query: 1 MANDQHTELEAEFTLDQVKDQLIEQGKKRSSLNYKDIMEKLSPFDQDPEQMEEFYEQLSD 60 MANDQHTELE EFTLDQVKDQLIEQGKKRSSLNYKDIMEKLSPFDQDPEQM+EFYE L D Sbjct: 1 MANDQHTELETEFTLDQVKDQLIEQGKKRSSLNYKDIMEKLSPFDQDPEQMDEFYEHLGD 60 Query: 61 LGIXXXXXXXXXXXTLRPXXXXXXXXXXXXXXXXXXXXPPGIKINDPVRMYLKEIGRVPL 120 LGI LR PPGIKINDPVRMYLKEIGRVPL Sbjct: 61 LGIEVVNENDEEVSNLRQGEDHDGNDNDDFNFDDDLSLPPGIKINDPVRMYLKEIGRVPL 120 Query: 121 LSADDEVELAMRIKNGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKA 180 LSADDEVELA RI NGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKA Sbjct: 121 LSADDEVELAKRIMNGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKA 180 Query: 181 VEKFDHNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELG 240 VEKFDHNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELG Sbjct: 181 VEKFDHNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELG 240 Query: 241 REPSPEEIAAEMELTVEKVREIMKIAQEPVSLETPIGEEDDSHLGDFIXXXXXXXXXXXX 300 REP+PEEIAAEMEL+VEKVREIMKIAQEPVSLETPIGEEDDSHLGDFI Sbjct: 241 REPTPEEIAAEMELSVEKVREIMKIAQEPVSLETPIGEEDDSHLGDFIEDQEALTPADAA 300 Query: 301 XXXXXKEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKAL 360 KEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKAL Sbjct: 301 AYELLKEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKAL 360 Query: 361 RKLRHPSRSKRLKDFLE 377 RKLRHPSRSKRLKDFLE Sbjct: 361 RKLRHPSRSKRLKDFLE 377 >B1DFN2.1 B1DFN2_9BACL RNA polymerase sigma factor Length = 376 Score = 592 bits (1525), Expect = e-167, Method: Compositional matrix adjust. Identities = 306/377 (81%), Positives = 318/377 (84%), Gaps = 1/377 (0%) Query: 1 MANDQHTELEAEFTLDQVKDQLIEQGKKRSSLNYKDIMEKLSPFDQDPEQMEEFYEQLSD 60 MANDQHTEL+AE LD VK+QLIEQGKKR+SL YK+IMEKLSPFDQDPEQ++EF+EQL D Sbjct: 1 MANDQHTELDAEQKLDLVKEQLIEQGKKRASLTYKEIMEKLSPFDQDPEQIDEFFEQLDD 60 Query: 61 LGIXXXXXXXXXXXTLRPXXXXXXXXXXXXXXXXXXXXPPGIKINDPVRMYLKEIGRVPL 120 LGI L PPGIKINDPVRMYLKEIGRVPL Sbjct: 61 LGIEVLNERDEDRDPLN-RGEDSERESDDFNFDDDLALPPGIKINDPVRMYLKEIGRVPL 119 Query: 121 LSADDEVELAMRIKNGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKA 180 LSADDE+ELA RI+NGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKA Sbjct: 120 LSADDEIELARRIENGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKA 179 Query: 181 VEKFDHNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELG 240 VEKFDH KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELG Sbjct: 180 VEKFDHQKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELG 239 Query: 241 REPSPEEIAAEMELTVEKVREIMKIAQEPVSLETPIGEEDDSHLGDFIXXXXXXXXXXXX 300 REP+PEEIAAEMEL+ +KVREIMKIAQEPVSLETPIGEEDDSHLGDFI Sbjct: 240 REPTPEEIAAEMELSTDKVREIMKIAQEPVSLETPIGEEDDSHLGDFIEDQEALAPADAA 299 Query: 301 XXXXXKEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKAL 360 KEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKAL Sbjct: 300 AYELLKEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKAL 359 Query: 361 RKLRHPSRSKRLKDFLE 377 RKLRHPSRSKRLKDFLE Sbjct: 360 RKLRHPSRSKRLKDFLE 376 >C1PEH1.1 C1PEH1_BACCO RNA polymerase, sigma 70 subunit, RpoD subfamily Length = 377 Score = 523 bits (1347), Expect = e-146, Method: Compositional matrix adjust. Identities = 269/368 (73%), Positives = 293/368 (79%), Gaps = 3/368 (0%) Query: 10 EAEFTLDQVKDQLIEQGKKRSSLNYKDIMEKLSPFDQDPEQMEEFYEQLSDLGIXXXXXX 69 E+EFT+++ K+QL+E+GKKR L Y I EKL FD +QM+EFYE L + GI Sbjct: 13 ESEFTVEKAKEQLVERGKKRGFLTYDTISEKLGHFDLTSDQMDEFYESLGEQGIDVTDDT 72 Query: 70 XXXXXTLRPXXXXXXXXXXXXXXXXXXXXPPGIKINDPVRMYLKEIGRVPLLSADDEVEL 129 P PPG+KINDPVRMYLKEIGRV LLSAD+E+EL Sbjct: 73 SDEDA---PSHLELEKENDEEFDLNDLSVPPGVKINDPVRMYLKEIGRVDLLSADEEIEL 129 Query: 130 AMRIKNGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDHNKG 189 A RI+ GDEEAKRRLAEANLRLVVSIAKRYVGRGM FLDLIQEGNMGLIKAVEKFD+ KG Sbjct: 130 AKRIEQGDEEAKRRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLIKAVEKFDYKKG 189 Query: 190 FKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPSPEEIA 249 +KFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRV R LLQ+LGREP+PEEIA Sbjct: 190 YKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRSLLQDLGREPTPEEIA 249 Query: 250 AEMELTVEKVREIMKIAQEPVSLETPIGEEDDSHLGDFIXXXXXXXXXXXXXXXXXKEQL 309 EM+++ +KVREI+KIAQEPVSLETPIGEEDDSHLGDFI KEQL Sbjct: 250 EEMDISPDKVREIIKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPSDHAAYELLKEQL 309 Query: 310 EDVLDTLTEREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRS 369 EDVLDTLT+REENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRS Sbjct: 310 EDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRS 369 Query: 370 KRLKDFLE 377 KRLKDFLE Sbjct: 370 KRLKDFLE 377 >Q2YT18.1 Q2YT18_STAAB RNA polymerase sigma factor Length = 368 Score = 513 bits (1322), Expect = e-144, Method: Compositional matrix adjust. Identities = 265/371 (71%), Positives = 293/371 (78%), Gaps = 17/371 (4%) Query: 9 LEAEFTLDQVKDQLIEQGKKRSSLNYKDIMEKLSPFDQDPEQMEEFYEQLSD--LGIXXX 66 ++ TL+ VK QLIE+GKK L++++I EKL FD D +QM++F++QL+D + + Sbjct: 13 IDPTLTLEDVKKQLIEKGKKEGHLSHEEIAEKLQNFDIDSDQMDDFFDQLNDNDISLVNE 72 Query: 67 XXXXXXXXTLRPXXXXXXXXXXXXXXXXXXXXPPGIKINDPVRMYLKEIGRVPLLSADDE 126 L P PPG+KINDPVRMYLKEIGRV LLSA +E Sbjct: 73 KDSSDTDEKLNPSDLSA---------------PPGVKINDPVRMYLKEIGRVNLLSAQEE 117 Query: 127 VELAMRIKNGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDH 186 +ELA RI+ GDE AK RLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFD Sbjct: 118 IELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDF 177 Query: 187 NKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPSPE 246 NKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRV RQLLQ+LGR+P+PE Sbjct: 178 NKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGRDPAPE 237 Query: 247 EIAAEMELTVEKVREIMKIAQEPVSLETPIGEEDDSHLGDFIXXXXXXXXXXXXXXXXXK 306 EI EM+L EKVREI+KIAQEPVSLETPIGEEDDSHLGDFI K Sbjct: 238 EIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAAYELLK 297 Query: 307 EQLEDVLDTLTEREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHP 366 EQLEDVLDTLT+REENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHP Sbjct: 298 EQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHP 357 Query: 367 SRSKRLKDFLE 377 SRSKRLKDF++ Sbjct: 358 SRSKRLKDFMD 368 >Q2FGG2.1 Q2FGG2_STAA3 RNA polymerase sigma factor Length = 368 Score = 513 bits (1322), Expect = e-144, Method: Compositional matrix adjust. Identities = 265/371 (71%), Positives = 293/371 (78%), Gaps = 17/371 (4%) Query: 9 LEAEFTLDQVKDQLIEQGKKRSSLNYKDIMEKLSPFDQDPEQMEEFYEQLSD--LGIXXX 66 ++ TL+ VK QLIE+GKK L++++I EKL FD D +QM++F++QL+D + + Sbjct: 13 IDPTLTLEDVKKQLIEKGKKEGHLSHEEIAEKLQNFDIDSDQMDDFFDQLNDNDISLVNE 72 Query: 67 XXXXXXXXTLRPXXXXXXXXXXXXXXXXXXXXPPGIKINDPVRMYLKEIGRVPLLSADDE 126 L P PPG+KINDPVRMYLKEIGRV LLSA +E Sbjct: 73 KDSSDTDEKLNPSDLSA---------------PPGVKINDPVRMYLKEIGRVNLLSAQEE 117 Query: 127 VELAMRIKNGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDH 186 +ELA RI+ GDE AK RLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFD Sbjct: 118 IELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDF 177 Query: 187 NKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPSPE 246 NKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRV RQLLQ+LGR+P+PE Sbjct: 178 NKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGRDPAPE 237 Query: 247 EIAAEMELTVEKVREIMKIAQEPVSLETPIGEEDDSHLGDFIXXXXXXXXXXXXXXXXXK 306 EI EM+L EKVREI+KIAQEPVSLETPIGEEDDSHLGDFI K Sbjct: 238 EIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAAYELLK 297 Query: 307 EQLEDVLDTLTEREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHP 366 EQLEDVLDTLT+REENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHP Sbjct: 298 EQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHP 357 Query: 367 SRSKRLKDFLE 377 SRSKRLKDF++ Sbjct: 358 SRSKRLKDFMD 368 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 0.136 0.375 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: 1,790,438,494 Number of extensions: 65255356 Number of successful extensions: 243627 Number of sequences better than 1.0e-05: 5687 Number of HSP's gapped: 235650 Number of HSP's successfully gapped: 5800 Length of query: 377 Length of database: 3,060,696,203 Length adjustment: 137 Effective length of query: 240 Effective length of database: 1,770,017,148 Effective search space: 424804115520 Effective search space used: 424804115520 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: 132 (55.5 bits)