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= 0587.0010.p (205 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3K626.1 B3K626_9BACI RNA polymerase sigma factor, sigma-70 family 179 9e-44 B3KKX3.1 B3KKX3_9BACI RNA polymerase sigma factor, sigma-70 family 167 6e-40 B1DA07.1 B1DA07_9BACL RNA polymerase sigma factor 139 1e-31 C0Z8S7.1 C0Z8S7_BREBN RNA polymerase ECF-type sigma factor 139 2e-31 C0ZKR6.1 C0ZKR6_BREBN RNA polymerase ECF-type sigma factor 132 2e-29 >B3K626.1 B3K626_9BACI RNA polymerase sigma factor, sigma-70 family Length = 193 Score = 179 bits (455), Expect = 9e-44, Method: Compositional matrix adjust. Identities = 80/177 (45%), Positives = 131/177 (74%) Query: 21 VDSIEEKIKRIQAGEVYLFSDVIRLYQQRIYVYCFRLLNSREEAEDAVQDIFIKAYQNIW 80 +DSIEE + R++AGEV F ++ Y+++IY+YC R+L +++A+DAVQDIFIKA+ ++ Sbjct: 1 MDSIEEYVGRVKAGEVDCFEPIVETYKKQIYLYCCRMLGCKQDAQDAVQDIFIKAFTKLY 60 Query: 81 DFKLQANFTSWLYRVSYHHCLNQLRRQKFQNQLRRLLRQDVTAKSAEQVVENRLFSESVA 140 ++ + +F+SWLY+++YHHCLN LR+++ + ++ RL++ A S E+ +E + FSE + Sbjct: 61 TYEAKVSFSSWLYKIAYHHCLNILRKRRVRMRVSRLIKPAGYADSVEETLERKWFSEPLE 120 Query: 141 AALQKLSIEERNLVILRIFEDKSFAEIAEILGKSTVTVRKRYERTRSKLRESIVRRE 197 A+ KLS+EERNL++LR+FEDK F EIA+IL K+ V+K+Y R + K+ + I +E Sbjct: 121 YAMTKLSVEERNLLVLRVFEDKPFTEIAQILDKNLSAVKKKYARMKQKVIKLIQEKE 177 >B3KKX3.1 B3KKX3_9BACI RNA polymerase sigma factor, sigma-70 family Length = 204 Score = 167 bits (422), Expect = 6e-40, Method: Compositional matrix adjust. Identities = 84/178 (47%), Positives = 127/178 (71%), Gaps = 1/178 (0%) Query: 23 SIEEKIKRIQAGEVYLFSDVIRLYQQRIYVYCFRLLNSREEAEDAVQDIFIKAYQNIWDF 82 IE I+R+ G+ F ++ +QQ+I++YC+RLLN R++AEDAVQ+I +KAYQ + + Sbjct: 14 DIEVTIERVLNGDRQAFVHIVEAFQQQIFMYCWRLLNQRQDAEDAVQEIMVKAYQKLETY 73 Query: 83 KLQANFTSWLYRVSYHHCLNQLRRQK-FQNQLRRLLRQDVTAKSAEQVVENRLFSESVAA 141 K + +F++WLY+++YHHCLN LRR++ FQN + +L A+SAEQ + + SE + Sbjct: 74 KPETSFSAWLYKMAYHHCLNMLRRKRYFQNIVPKLRADKEHAESAEQEAQKYIISEPMER 133 Query: 142 ALQKLSIEERNLVILRIFEDKSFAEIAEILGKSTVTVRKRYERTRSKLRESIVRREKQ 199 AL++LS +ERNL+ILRIFE+KSFAEI +IL K+ T +KRY R KL++ + RE + Sbjct: 134 ALRRLSHDERNLLILRIFEEKSFAEIGQILDKTKDTAKKRYSRLIQKLKKWMHDREGE 191 >B1DA07.1 B1DA07_9BACL RNA polymerase sigma factor Length = 191 Score = 139 bits (351), Expect = 1e-31, Method: Compositional matrix adjust. Identities = 73/191 (38%), Positives = 121/191 (63%), Gaps = 10/191 (5%) Query: 14 DSRKETVVDSIEEKIKRIQAGEVYLFSDVIRLYQQRIYVYCFRLLNSREEAEDAVQDIFI 73 +S + D IE +K +QAG+V + ++ +Q+R+++YC+ ++ R E+ED VQ++F+ Sbjct: 5 ESMEPLSADRIENLVKAVQAGQVEPYRAIVLHFQRRLHLYCYYMIGDRAESEDIVQEVFL 64 Query: 74 KAYQNIWDFKLQANFTSWLYRVSYHHCLNQLRRQKFQNQLRRLLRQD-VTAKSAEQVVEN 132 +AY+ I ++ +F++WLY++ Y CLN L++ K Q++L L++Q +TA + Sbjct: 65 RAYREIGKYQPTVSFSAWLYKIGYRLCLNALKKHKGQHRLLSLIQQQWLTAPATSS---- 120 Query: 133 RLFSESVAAALQKLSIEERNLVILRIFEDKSFAEIAEILGKSTVTVRKRYERTRSKLRES 192 ES L+ LS EER LVI R E++SFAEIAE+ G + +RK+YER R KLR+ Sbjct: 121 ---DESADCLLKGLSPEERQLVIFRSLEERSFAEIAELTGSNAAALRKKYERIRKKLRKQ 177 Query: 193 IVRREKQLCAR 203 + RE++L R Sbjct: 178 M--REEKLDER 186 >C0Z8S7.1 C0Z8S7_BREBN RNA polymerase ECF-type sigma factor Length = 195 Score = 139 bits (349), Expect = 2e-31, Method: Compositional matrix adjust. Identities = 66/169 (39%), Positives = 111/169 (65%) Query: 24 IEEKIKRIQAGEVYLFSDVIRLYQQRIYVYCFRLLNSREEAEDAVQDIFIKAYQNIWDFK 83 IEE + I G ++ +++ YQ I+ YC+ +L +R EAEDA Q++F KAY+N+ + Sbjct: 6 IEELVDEIIQGADDRYAIIMKSYQTPIFHYCYHILGNRCEAEDATQEVFFKAYRNLKKYS 65 Query: 84 LQANFTSWLYRVSYHHCLNQLRRQKFQNQLRRLLRQDVTAKSAEQVVENRLFSESVAAAL 143 F +WLY+++YHHC++ +R++K+ L L++ + E+ +EN FSE V A+ Sbjct: 66 PIMPFAAWLYKIAYHHCIDLIRKRKWTKLLPFLMQDKESQSDIERHIENVYFSEDVFLAM 125 Query: 144 QKLSIEERNLVILRIFEDKSFAEIAEILGKSTVTVRKRYERTRSKLRES 192 Q LS+EER L++LR E+K++ EI+ I+ K+ ++RK++ERT SK R + Sbjct: 126 QTLSVEERTLLLLRGVEEKTYEEISLIMNKNAASLRKKFERTASKFRSA 174 >C0ZKR6.1 C0ZKR6_BREBN RNA polymerase ECF-type sigma factor Length = 189 Score = 132 bits (332), Expect = 2e-29, Method: Compositional matrix adjust. Identities = 64/178 (35%), Positives = 117/178 (65%), Gaps = 5/178 (2%) Query: 24 IEEKIKRIQAGEVYLFSDVIRLYQQRIYVYCFRLLNSREEAEDAVQDIFIKAYQNIWDFK 83 +E+ +K ++AG++ F +I Q++++VYC+ +L R+EAEDAVQ++F+KA++ + ++ Sbjct: 1 MEQVLKEVRAGDIEQFGLIIDAMQKQLFVYCYHMLGHRQEAEDAVQEVFLKAFEQLDSYR 60 Query: 84 LQANFTSWLYRVSYHHCLNQLRRQKFQNQLRRLLR---QDVTAKSAEQVVEN-RLFSESV 139 +F++W+Y+++YHHCLN L R K N++ LR Q V+ E+ +E+ + + Sbjct: 61 HNVSFSAWMYKIAYHHCLNLLNRAKL-NRVVTFLRAGIQTVSRHEGEKKIEDTEYLNNPL 119 Query: 140 AAALQKLSIEERNLVILRIFEDKSFAEIAEILGKSTVTVRKRYERTRSKLRESIVRRE 197 A+ KLS++ERNL+ILR+ E++S+ E+A + T+RK+YER K + ++ E Sbjct: 120 HVAISKLSVKERNLLILRVVEERSYDELALLFDIKPATLRKQYERALKKCKSYMLVSE 177 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 0.324 0.134 0.377 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: 974,767,058 Number of extensions: 33603447 Number of successful extensions: 166595 Number of sequences better than 1.0e-05: 3594 Number of HSP's gapped: 166187 Number of HSP's successfully gapped: 3594 Length of query: 205 Length of database: 3,060,696,203 Length adjustment: 129 Effective length of query: 76 Effective length of database: 1,845,385,268 Effective search space: 140249280368 Effective search space used: 140249280368 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 128 (53.9 bits)