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= 0153.0010.p (189 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value Q897R6.1 Q897R6_CLOTE RNA polymerase sigma factor 126 9e-28 A8MKG5.1 A8MKG5_ALKOO RNA polymerase, sigma-24 subunit, ECF subf... 123 7e-27 Q65P51.1 Q65P51_BACLD RNA polymerase sigma factor 108 2e-22 C4KZK8.1 C4KZK8_EXISA RNA polymerase, sigma-24 subunit, ECF subf... 105 1e-21 A8F9E2.1 A8F9E2_BACP2 RNA polymerase sigma factor 105 2e-21 >Q897R6.1 Q897R6_CLOTE RNA polymerase sigma factor Length = 198 Score = 126 bits (317), Expect = 9e-28, Method: Compositional matrix adjust. Identities = 64/184 (34%), Positives = 111/184 (60%), Gaps = 3/184 (1%) Query: 2 VTDKQLIEGYRTGRREMLELLVERYKDDLYRFCRHLTLNALEAEDLFQEVWVRVIRKLDR 61 + +K + E Y + L+++++ YKD LYRF +L N++E++DLFQ+ WV+VI+ + + Sbjct: 10 LDEKYIYEIYLKDKSLALKMIIDEYKDFLYRFSFYLCKNSMESDDLFQDTWVKVIKNIHK 69 Query: 62 YDPERSFKAWLFQVTLNMYRDSYRK---WKKLYERLTGEASCRVPLLELRDGAPLTEEQI 118 Y +F+ W+ + LN Y+D YRK W + + E ++ L E++ Sbjct: 70 YTWNETFQPWIRTICLNTYKDKYRKSKRWLNIIKDYFDEEKKEREIINFPSKNNLPEKET 129 Query: 119 LRNERYARLEEGLCKLPKRYLSPLVLYYYEEFSYEEIGKMLDIPIGTVKSRLNQGKKLLQ 178 ++NE L++ + L Y P++LYY+E SY+EI +++ IP GT+KSRLN+ +KLL+ Sbjct: 130 IKNEEKKILKKAVDNLKDEYRIPIILYYFERLSYKEISEIISIPEGTIKSRLNKARKLLK 189 Query: 179 KAVE 182 + VE Sbjct: 190 EYVE 193 >A8MKG5.1 A8MKG5_ALKOO RNA polymerase, sigma-24 subunit, ECF subfamily Length = 171 Score = 123 bits (309), Expect = 7e-27, Method: Compositional matrix adjust. Identities = 60/167 (35%), Positives = 105/167 (62%), Gaps = 3/167 (1%) Query: 19 LELLVERYKDDLYRFCRHLTLNALEAEDLFQEVWVRVIRKLDRYDPERSFKAWLFQVTLN 78 +E +++ YKDD+Y+ C LT N ++A+DLFQ+ W+++ + + ++++K W++ + +N Sbjct: 3 IETMIDIYKDDVYKLCLKLTNNKIDADDLFQDTWLKLYSNFHKLNDQKTYKNWIYTICIN 62 Query: 79 MYRDSYRKWKKLYERLTGEASCRVP--LLELRDGAPLTEEQILRNERYARLEEGLCK-LP 135 Y+DSY K K+ +T +V ++E + E I+ N + + L K L Sbjct: 63 TYKDSYSKKKRWLNIITDFFDSKVQHEVMEHQSSTIDETEFIIFNTIEKKTIQNLIKDLD 122 Query: 136 KRYLSPLVLYYYEEFSYEEIGKMLDIPIGTVKSRLNQGKKLLQKAVE 182 ++Y P++LYYY ++SY +I +L+IPIGT+K RLNQGKKLL+ +E Sbjct: 123 EKYKLPIILYYYLDYSYVDIASILNIPIGTLKYRLNQGKKLLKTKLE 169 >Q65P51.1 Q65P51_BACLD RNA polymerase sigma factor Length = 187 Score = 108 bits (271), Expect = 2e-22, Method: Compositional matrix adjust. Identities = 59/178 (33%), Positives = 104/178 (58%), Gaps = 4/178 (2%) Query: 5 KQLIEGYRTGRREMLELLVERYKDDLYRFCRHLTLNALEAEDLFQEVWVRVIRKLDRYDP 64 K+ I+ + G R +V+ YKD +Y+ C + NA EAED+ QE ++R +D +D Sbjct: 6 KKRIKQVKKGDRNAFADIVDIYKDKIYQLCYRMLGNAHEAEDIAQEAFIRAYVNIDSFDI 65 Query: 65 ERSFKAWLFQVTLNMYRDSYRKWKKLYERLTGEASCRVPLL---ELRDGAPLTEEQILRN 121 R F WL+++ N+ D RK K Y L E + L ++ L E++++ Sbjct: 66 NRKFSTWLYRIATNLTIDRIRKKKPDY-YLDAEVAGTEGLTMYSQVAADVALPEDEVVSL 124 Query: 122 ERYARLEEGLCKLPKRYLSPLVLYYYEEFSYEEIGKMLDIPIGTVKSRLNQGKKLLQK 179 E ++ ++E + +LP +Y + +VL Y +E S EI ++L+IP+GTVK+R+++G++ L+K Sbjct: 125 ELHSTIQEKILRLPDKYRTVIVLKYIDELSLIEISEILNIPVGTVKTRIHRGREALRK 182 >C4KZK8.1 C4KZK8_EXISA RNA polymerase, sigma-24 subunit, ECF subfamily Length = 191 Score = 105 bits (263), Expect = 1e-21, Method: Compositional matrix adjust. Identities = 58/176 (32%), Positives = 99/176 (56%), Gaps = 4/176 (2%) Query: 6 QLIEGYRTGRREMLELLVERYKDDLYRFCRHLTLNALEAEDLFQEVWVRVIRKLDRYDPE 65 +L++ R G + LVE YKD ++ + + EAED QE ++R ++D YD + Sbjct: 7 RLVDELRAGNHDSFAELVELYKDGVFAIAYKILYDRGEAEDAAQEAFIRAYTRIDTYDAQ 66 Query: 66 RSFKAWLFQVTLNMYRDSYRKWKKLYERLTGEASCRVPLL---ELRDGAPLTEEQILRNE 122 FK WL+++T N+ D RK K Y + E + L L D AP + Q++ E Sbjct: 67 YKFKTWLYRITTNVAIDRLRKRKPEYS-MDAEIAGTDGLTYQDHLADEAPQPDAQVVHRE 125 Query: 123 RYARLEEGLCKLPKRYLSPLVLYYYEEFSYEEIGKMLDIPIGTVKSRLNQGKKLLQ 178 + + E + +LP +Y PL+L Y ++ S +EI M+D+P+ TVK+R+ +G+++L+ Sbjct: 126 IRSEMHEAIKQLPDKYRIPLLLKYVDDLSLKEISVMIDMPVATVKTRIFRGREMLK 181 >A8F9E2.1 A8F9E2_BACP2 RNA polymerase sigma factor Length = 195 Score = 105 bits (263), Expect = 2e-21, Method: Compositional matrix adjust. Identities = 58/178 (32%), Positives = 103/178 (57%), Gaps = 4/178 (2%) Query: 5 KQLIEGYRTGRREMLELLVERYKDDLYRFCRHLTLNALEAEDLFQEVWVRVIRKLDRYDP 64 K+ I+ + G + +V+ YKD +Y+ C + NA EAED+ QE ++R ++ +D Sbjct: 14 KKRIKQLKKGDQNAFADIVDLYKDKIYQLCYRMLGNAHEAEDIAQEAFIRAYVNIESFDV 73 Query: 65 ERSFKAWLFQVTLNMYRDSYRKWKKLY---ERLTGEASCRVPLLELRDGAPLTEEQILRN 121 R F WL+++ N+ D RK K Y + G + DG L EE+++ Sbjct: 74 NRKFSTWLYRIATNLTIDRIRKKKPDYYLDAEVAGTEGLNMYSQIAADGI-LPEEEVVSL 132 Query: 122 ERYARLEEGLCKLPKRYLSPLVLYYYEEFSYEEIGKMLDIPIGTVKSRLNQGKKLLQK 179 E + +++ + +LP +Y S +VL Y +E S +EI ++L+IP+GTVK+R+++G++ L+K Sbjct: 133 ELSSTIQQKILRLPDKYRSVIVLKYIDELSLKEISEILNIPVGTVKTRIHRGREALRK 190 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 0.322 0.140 0.422 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: 1,152,126,705 Number of extensions: 47506871 Number of successful extensions: 144630 Number of sequences better than 1.0e-05: 3841 Number of HSP's gapped: 142849 Number of HSP's successfully gapped: 3841 Length of query: 189 Length of database: 3,060,696,203 Length adjustment: 128 Effective length of query: 61 Effective length of database: 1,854,806,283 Effective search space: 113143183263 Effective search space used: 113143183263 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 (21.9 bits) S2: 127 (53.5 bits)