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= 0430.0005.p (251 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value O32722.1 O32722_PAEPO RNA polymerase sigma factor 452 e-125 B1DJB7.1 B1DJB7_9BACL RNA polymerase sigma factor 448 e-124 B3KK84.1 B3KK84_9BACI RNA polymerase sigma-70 factor, sigma-B/F/... 397 e-109 P35145.1 RPSF_BACME RNA polymerase sigma-F factor 392 e-107 C0ZC64.1 C0ZC64_BREBN RNA polymerase sigma-F factor 390 e-107 >O32722.1 O32722_PAEPO RNA polymerase sigma factor Length = 251 Score = 452 bits (1163), Expect = e-125, Method: Compositional matrix adjust. Identities = 218/251 (86%), Positives = 235/251 (93%) Query: 1 MDAESKKAPPTYLDDAEVKRLIALSQAGDNLARDTLVNCNIRLVWSVVQRFMNRGYEPDD 60 M+A KK +YL+D EVKRLIALSQ+GDN AR+TL+N NIRLVWSVVQRFMNRGYEPDD Sbjct: 1 MEAGGKKTSHSYLEDTEVKRLIALSQSGDNDARETLINSNIRLVWSVVQRFMNRGYEPDD 60 Query: 61 LFQIGCIGLLKSVDKFDLSYEVKFSTYAVPMIIGEIQRFLRDDGTLKVSRSLKEMANRVR 120 LFQIGCIGLLKSVDKFDLSYEVKFSTYAVPMIIGEIQRFLRDDGTLKVSRSLKE AN+VR Sbjct: 61 LFQIGCIGLLKSVDKFDLSYEVKFSTYAVPMIIGEIQRFLRDDGTLKVSRSLKETANKVR 120 Query: 121 KMKDEMSKTLDRLPTIGEVAEALGVTPEEIVFAQEANKPPTSIHETVFENDGDPITLIDQ 180 KMKDE+SK L+RLPT+ EVA+ LGVTPE++VFAQEANKPPTSIHETVFENDGDPITL+DQ Sbjct: 121 KMKDELSKPLNRLPTVKEVADELGVTPEDVVFAQEANKPPTSIHETVFENDGDPITLMDQ 180 Query: 181 IADETQERWFDKLALNEAIGALTERERLIVYLRYYRDQTQSEVASRLGISQVQVSRLEKK 240 IADE+QERWFDKLALNEAI L+ERERLIVYLRYYRDQTQSEVASRLGISQVQVSRLEKK Sbjct: 181 IADESQERWFDKLALNEAIDGLSERERLIVYLRYYRDQTQSEVASRLGISQVQVSRLEKK 240 Query: 241 ILASIREQIAQ 251 IL IR+QIAQ Sbjct: 241 ILQQIRDQIAQ 251 >B1DJB7.1 B1DJB7_9BACL RNA polymerase sigma factor Length = 251 Score = 448 bits (1153), Expect = e-124, Method: Compositional matrix adjust. Identities = 216/251 (86%), Positives = 235/251 (93%) Query: 1 MDAESKKAPPTYLDDAEVKRLIALSQAGDNLARDTLVNCNIRLVWSVVQRFMNRGYEPDD 60 MD + K+ YLDDAEVKRLIALSQ+GD +ARDTLV CNIRLVWSVVQRF+NRGYEP+D Sbjct: 1 MDVDLKQTAQPYLDDAEVKRLIALSQSGDTIARDTLVQCNIRLVWSVVQRFINRGYEPED 60 Query: 61 LFQIGCIGLLKSVDKFDLSYEVKFSTYAVPMIIGEIQRFLRDDGTLKVSRSLKEMANRVR 120 LFQIGCIGLLKSVDKFDLSY+VKFSTYAVPMIIGEIQRFLRDDGTLKVSRSLKE AN+VR Sbjct: 61 LFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDGTLKVSRSLKETANKVR 120 Query: 121 KMKDEMSKTLDRLPTIGEVAEALGVTPEEIVFAQEANKPPTSIHETVFENDGDPITLIDQ 180 KMKDE+SKTL RLPT+ EVA+ LG+TPE++VFAQEANKPPTSIHETVFENDGDPITL+DQ Sbjct: 121 KMKDELSKTLGRLPTVSEVADRLGITPEDVVFAQEANKPPTSIHETVFENDGDPITLMDQ 180 Query: 181 IADETQERWFDKLALNEAIGALTERERLIVYLRYYRDQTQSEVASRLGISQVQVSRLEKK 240 IAD++QERWFDKLAL EAI L+ERERLIVYLRYYRD+TQSEVASRLGISQVQVSRLEKK Sbjct: 181 IADDSQERWFDKLALIEAIEGLSERERLIVYLRYYRDKTQSEVASRLGISQVQVSRLEKK 240 Query: 241 ILASIREQIAQ 251 IL SIREQIAQ Sbjct: 241 ILQSIREQIAQ 251 >B3KK84.1 B3KK84_9BACI RNA polymerase sigma-70 factor, sigma-B/F/G subfamily Length = 277 Score = 397 bits (1020), Expect = e-109, Method: Compositional matrix adjust. Identities = 189/210 (90%), Positives = 201/210 (95%) Query: 1 MDAESKKAPPTYLDDAEVKRLIALSQAGDNLARDTLVNCNIRLVWSVVQRFMNRGYEPDD 60 MDA+ KK TYLDDAEVKRLIALSQ+GDN+ARDTLVNCNIRLVWSVVQRFMNRGYEPDD Sbjct: 1 MDADVKKTSQTYLDDAEVKRLIALSQSGDNVARDTLVNCNIRLVWSVVQRFMNRGYEPDD 60 Query: 61 LFQIGCIGLLKSVDKFDLSYEVKFSTYAVPMIIGEIQRFLRDDGTLKVSRSLKEMANRVR 120 LFQIGCIGLLKSVDKFDLSY+VKFSTYAVPMIIGEIQRFLRDDGTLKVSRSLKEMAN+VR Sbjct: 61 LFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDGTLKVSRSLKEMANKVR 120 Query: 121 KMKDEMSKTLDRLPTIGEVAEALGVTPEEIVFAQEANKPPTSIHETVFENDGDPITLIDQ 180 K +DE+SK LDRLPT+ EVAE LGVTPEE+VFAQEANKPPTSIHETVFENDGDPITL+DQ Sbjct: 121 KKRDELSKQLDRLPTVKEVAEELGVTPEEVVFAQEANKPPTSIHETVFENDGDPITLMDQ 180 Query: 181 IADETQERWFDKLALNEAIGALTERERLIV 210 IAD++QERWFDKLALNEAIG LTERERLIV Sbjct: 181 IADDSQERWFDKLALNEAIGGLTERERLIV 210 >P35145.1 RPSF_BACME RNA polymerase sigma-F factor Length = 253 Score = 392 bits (1007), Expect = e-107, Method: Compositional matrix adjust. Identities = 188/247 (76%), Positives = 215/247 (87%), Gaps = 1/247 (0%) Query: 1 MDAESKKAP-PTYLDDAEVKRLIALSQAGDNLARDTLVNCNIRLVWSVVQRFMNRGYEPD 59 MD E KK YL D EVK LI SQ GD +ARDT+V N+RLVWSVVQRF+NRGYEPD Sbjct: 1 MDVEVKKNKNEPYLKDHEVKDLIKRSQQGDQIARDTIVQKNMRLVWSVVQRFINRGYEPD 60 Query: 60 DLFQIGCIGLLKSVDKFDLSYEVKFSTYAVPMIIGEIQRFLRDDGTLKVSRSLKEMANRV 119 DLFQIGCIGLLKSVDKFDLSY+VKFSTYAVPMIIGEIQRF+RDDGT+KVSRSLKEM+N++ Sbjct: 61 DLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFIRDDGTVKVSRSLKEMSNKI 120 Query: 120 RKMKDEMSKTLDRLPTIGEVAEALGVTPEEIVFAQEANKPPTSIHETVFENDGDPITLID 179 RK KDE+SK L R+PT+ EVAE L +TPEE+V AQEAN+ P+SIHETV+ENDGDPITL+D Sbjct: 121 RKAKDELSKLLGRVPTVAEVAEHLDLTPEEVVLAQEANRAPSSIHETVYENDGDPITLLD 180 Query: 180 QIADETQERWFDKLALNEAIGALTERERLIVYLRYYRDQTQSEVASRLGISQVQVSRLEK 239 QIAD T+ +WFDK+AL EAI L ERE+LIVYLRYY+DQTQSEVA+RLGISQVQVSRLEK Sbjct: 181 QIADHTEAKWFDKIALKEAIEELDEREKLIVYLRYYKDQTQSEVAARLGISQVQVSRLEK 240 Query: 240 KILASIR 246 KIL ++ Sbjct: 241 KILKQMK 247 >C0ZC64.1 C0ZC64_BREBN RNA polymerase sigma-F factor Length = 251 Score = 390 bits (1001), Expect = e-107, Method: Compositional matrix adjust. Identities = 187/249 (75%), Positives = 217/249 (87%) Query: 1 MDAESKKAPPTYLDDAEVKRLIALSQAGDNLARDTLVNCNIRLVWSVVQRFMNRGYEPDD 60 M A+ K A +L + +VK LIA SQAGD AR+ LVN NIRLVWSVVQRF+NRGYE DD Sbjct: 1 MGADIKNASQPFLTNDQVKELIAKSQAGDTEARELLVNSNIRLVWSVVQRFINRGYEADD 60 Query: 61 LFQIGCIGLLKSVDKFDLSYEVKFSTYAVPMIIGEIQRFLRDDGTLKVSRSLKEMANRVR 120 LFQIGCIGLLK+VDKFDLSY+V+FSTYAVPMIIGEIQRFLRDDGT+KVSRSLKE AN+VR Sbjct: 61 LFQIGCIGLLKAVDKFDLSYDVRFSTYAVPMIIGEIQRFLRDDGTVKVSRSLKETANKVR 120 Query: 121 KMKDEMSKTLDRLPTIGEVAEALGVTPEEIVFAQEANKPPTSIHETVFENDGDPITLIDQ 180 + KDE+ K R PTI EVA+A+G+TPEE+VFAQEAN+ P+SIHETVFENDGDPITLIDQ Sbjct: 121 RTKDELYKQFGRAPTIAEVADAVGITPEEVVFAQEANRAPSSIHETVFENDGDPITLIDQ 180 Query: 181 IADETQERWFDKLALNEAIGALTERERLIVYLRYYRDQTQSEVASRLGISQVQVSRLEKK 240 IADE +WF+K+AL +AI L+ERE+LIVYLRYY+DQTQSEVA RLGISQVQVSRLEK+ Sbjct: 181 IADEGVNKWFEKIALKDAISRLSEREQLIVYLRYYKDQTQSEVAERLGISQVQVSRLEKR 240 Query: 241 ILASIREQI 249 IL +I++QI Sbjct: 241 ILQTIKDQI 249 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 0.318 0.134 0.373 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: 1,357,592,270 Number of extensions: 53086174 Number of successful extensions: 200003 Number of sequences better than 1.0e-05: 5577 Number of HSP's gapped: 195254 Number of HSP's successfully gapped: 5608 Length of query: 251 Length of database: 3,060,696,203 Length adjustment: 132 Effective length of query: 119 Effective length of database: 1,817,122,223 Effective search space: 216237544537 Effective search space used: 216237544537 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: 129 (54.3 bits)