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= 0002.0005.p (146 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3K602.1 B3K602_9BACI RNA polymerase sigma factor, sigma-70 family 89 1e-16 C0Z8S7.1 C0Z8S7_BREBN RNA polymerase ECF-type sigma factor 89 1e-16 B3KKX3.1 B3KKX3_9BACI RNA polymerase sigma factor, sigma-70 family 89 2e-16 C0ZKR6.1 C0ZKR6_BREBN RNA polymerase ECF-type sigma factor 88 3e-16 B3K626.1 B3K626_9BACI RNA polymerase sigma factor, sigma-70 family 87 4e-16 >B3K602.1 B3K602_9BACI RNA polymerase sigma factor, sigma-70 family Length = 197 Score = 89.4 bits (220), Expect = 1e-16, Method: Compositional matrix adjust. Identities = 54/146 (36%), Positives = 75/146 (51%), Gaps = 1/146 (0%) Query: 1 LKSREEAEDAVQDIFVKVYRELERYRKVESFSAWLYKVAYHHCLDQIXXXXXXXXXXXXY 60 LK+ E EDAVQ+IF++ Y L Y++ SFSAWLYK+AYHH ++ Sbjct: 50 LKNHAETEDAVQEIFIRAYEHLHLYKRQVSFSAWLYKMAYHHLINIKRKQNRFLNLIEHC 109 Query: 61 KEQHPKAYYEPNGEGPVQLLMDSLSAEESNLLILKVVEQYSFEEIGQIMDCNPAAXXXXX 120 KEQ P + E V L+ L+AEE ++L+LK VEQY+FEEI IM A Sbjct: 110 KEQQPVMQISQH-EPVVYELLTYLTAEERHILLLKAVEQYTFEEISGIMGLKSATIRKKY 168 Query: 121 XXXXXXXXXQKMNEGGGSHGEVARSN 146 + +G + G +A +N Sbjct: 169 ERLRHKLMDRISQKGEVARGTIAGTN 194 >C0Z8S7.1 C0Z8S7_BREBN RNA polymerase ECF-type sigma factor Length = 195 Score = 89.0 bits (219), Expect = 1e-16, Method: Compositional matrix adjust. Identities = 52/148 (35%), Positives = 78/148 (52%), Gaps = 7/148 (4%) Query: 1 LKSREEAEDAVQDIFVKVYRELERYRKVESFSAWLYKVAYHHCLDQIXXXXXXXXXXXXY 60 L +R EAEDA Q++F K YR L++Y + F+AWLYK+AYHHC+D I Sbjct: 40 LGNRCEAEDATQEVFFKAYRNLKKYSPIMPFAAWLYKIAYHHCIDLIRKRKWTKLLPFLM 99 Query: 61 KEQHPKAYYEPNGEG-----PVQLLMDSLSAEESNLLILKVVEQYSFEEIGQIMDCNPAA 115 +++ ++ E + E V L M +LS EE LL+L+ VE+ ++EEI IM+ N A+ Sbjct: 100 QDKESQSDIERHIENVYFSEDVFLAMQTLSVEERTLLLLRGVEEKTYEEISLIMNKNAAS 159 Query: 116 XXXX--XXXXXXXXXXQKMNEGGGSHGE 141 + +GG +H E Sbjct: 160 LRKKFERTASKFRSAYSPLGKGGSAHDE 187 >B3KKX3.1 B3KKX3_9BACI RNA polymerase sigma factor, sigma-70 family Length = 204 Score = 88.6 bits (218), Expect = 2e-16, Method: Compositional matrix adjust. Identities = 50/119 (42%), Positives = 69/119 (57%), Gaps = 12/119 (10%) Query: 1 LKSREEAEDAVQDIFVKVYRELERYRKVESFSAWLYKVAYHHCLDQIXXXXXXXXXXXXY 60 L R++AEDAVQ+I VK Y++LE Y+ SFSAWLYK+AYHHCL+ + Sbjct: 49 LNQRQDAEDAVQEIMVKAYQKLETYKPETSFSAWLYKMAYHHCLNMLRRKRYFQNIVPKL 108 Query: 61 K---------EQHPKAYYEPNGEGPVQLLMDSLSAEESNLLILKVVEQYSFEEIGQIMD 110 + EQ + Y P++ + LS +E NLLIL++ E+ SF EIGQI+D Sbjct: 109 RADKEHAESAEQEAQKYI---ISEPMERALRRLSHDERNLLILRIFEEKSFAEIGQILD 164 >C0ZKR6.1 C0ZKR6_BREBN RNA polymerase ECF-type sigma factor Length = 189 Score = 87.8 bits (216), Expect = 3e-16, Method: Compositional matrix adjust. Identities = 49/154 (31%), Positives = 78/154 (50%), Gaps = 9/154 (5%) Query: 1 LKSREEAEDAVQDIFVKVYRELERYRKVESFSAWLYKVAYHHCLDQIXXXXXXXXXXXXY 60 L R+EAEDAVQ++F+K + +L+ YR SFSAW+YK+AYHHCL+ + Sbjct: 35 LGHRQEAEDAVQEVFLKAFEQLDSYRHNVSFSAWMYKIAYHHCLNLLNRAKLNRVVTFLR 94 Query: 61 KEQHPKAYYEPNGE--------GPVQLLMDSLSAEESNLLILKVVEQYSFEEIGQIMDCN 112 + +E + P+ + + LS +E NLLIL+VVE+ S++E+ + D Sbjct: 95 AGIQTVSRHEGEKKIEDTEYLNNPLHVAISKLSVKERNLLILRVVEERSYDELALLFDIK 154 Query: 113 PAAXXXXXXXXXXXXXXQKM-NEGGGSHGEVARS 145 PA + +EGG H ++ + Sbjct: 155 PATLRKQYERALKKCKSYMLVSEGGDRHDSISAT 188 >B3K626.1 B3K626_9BACI RNA polymerase sigma factor, sigma-70 family Length = 193 Score = 87.4 bits (215), Expect = 4e-16, Method: Compositional matrix adjust. Identities = 49/123 (39%), Positives = 67/123 (54%), Gaps = 11/123 (8%) Query: 1 LKSREEAEDAVQDIFVKVYRELERYRKVESFSAWLYKVAYHHCLDQIXXXXXXXXXXXXY 60 L +++A+DAVQDIF+K + +L Y SFS+WLYK+AYHHCL+ + Sbjct: 38 LGCKQDAQDAVQDIFIKAFTKLYTYEAKVSFSSWLYKIAYHHCLNILRKRRVRMRVSRLI 97 Query: 61 KEQHPKAYYEPNGEG--------PVQLLMDSLSAEESNLLILKVVEQYSFEEIGQIMDCN 112 K P Y + E P++ M LS EE NLL+L+V E F EI QI+D N Sbjct: 98 K---PAGYADSVEETLERKWFSEPLEYAMTKLSVEERNLLVLRVFEDKPFTEIAQILDKN 154 Query: 113 PAA 115 +A Sbjct: 155 LSA 157 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 0.314 0.132 0.379 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: 686,610,338 Number of extensions: 20307858 Number of successful extensions: 40156 Number of sequences better than 1.0e-05: 58 Number of HSP's gapped: 40530 Number of HSP's successfully gapped: 58 Length of query: 146 Length of database: 3,060,696,203 Length adjustment: 109 Effective length of query: 37 Effective length of database: 2,033,805,568 Effective search space: 75250806016 Effective search space used: 75250806016 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 125 (52.8 bits)