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= 0044.0003.p (197 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value C0Z8S7.1 C0Z8S7_BREBN RNA polymerase ECF-type sigma factor 164 5e-39 C0ZKR6.1 C0ZKR6_BREBN RNA polymerase ECF-type sigma factor 138 2e-31 B3K626.1 B3K626_9BACI RNA polymerase sigma factor, sigma-70 family 124 4e-27 C0Z4U4.1 C0Z4U4_BREBN RNA polymerase ECF-type sigma factor 124 4e-27 B3KKX3.1 B3KKX3_9BACI RNA polymerase sigma factor, sigma-70 family 112 2e-23 >C0Z8S7.1 C0Z8S7_BREBN RNA polymerase ECF-type sigma factor Length = 195 Score = 164 bits (414), Expect = 5e-39, Method: Compositional matrix adjust. Identities = 79/184 (42%), Positives = 117/184 (63%) Query: 1 LNDAELRRIIADVLEGNIERFEEIMRTYQKAILLYCYHMLGHYSEAEDSGQEVFLKAFRA 60 ++ ++ ++ ++++G +R+ IM++YQ I YCYH+LG+ EAED+ QEVF KA+R Sbjct: 1 MDTKQIEELVDEIIQGADDRYAIIMKSYQTPIFHYCYHILGNRCEAEDATQEVFFKAYRN 60 Query: 61 LGKYNPDIPFGAWLYTIAYNQCIDVIXXXXXXXXXXXXXXDERDNRHVDQQIEGKYLDEA 120 L KY+P +PF AWLY IAY+ CID+I D+ +++ IE Y E Sbjct: 61 LKKYSPIMPFAAWLYKIAYHHCIDLIRKRKWTKLLPFLMQDKESQSDIERHIENVYFSED 120 Query: 121 VQQALSKLSIEERNLLILRCVEEMSYQEISLILHHSTSKLRKKYERSAKKFRRYYAYAKG 180 V A+ LS+EER LL+LR VEE +Y+EISLI++ + + LRKK+ER+A KFR Y+ Sbjct: 121 VFLAMQTLSVEERTLLLLRGVEEKTYEEISLIMNKNAASLRKKFERTASKFRSAYSPLGK 180 Query: 181 EGSC 184 GS Sbjct: 181 GGSA 184 >C0ZKR6.1 C0ZKR6_BREBN RNA polymerase ECF-type sigma factor Length = 189 Score = 138 bits (348), Expect = 2e-31, Method: Compositional matrix adjust. Identities = 74/178 (41%), Positives = 113/178 (63%), Gaps = 3/178 (1%) Query: 6 LRRIIADVLEGNIERFEEIMRTYQKAILLYCYHMLGHYSEAEDSGQEVFLKAFRALGKYN 65 + +++ +V G+IE+F I+ QK + +YCYHMLGH EAED+ QEVFLKAF L Y Sbjct: 1 MEQVLKEVRAGDIEQFGLIIDAMQKQLFVYCYHMLGHRQEAEDAVQEVFLKAFEQLDSYR 60 Query: 66 PDIPFGAWLYTIAYNQCIDVIXXXXXXXXXXXXXXD-ERDNRHV-DQQIE-GKYLDEAVQ 122 ++ F AW+Y IAY+ C++++ + +RH +++IE +YL+ + Sbjct: 61 HNVSFSAWMYKIAYHHCLNLLNRAKLNRVVTFLRAGIQTVSRHEGEKKIEDTEYLNNPLH 120 Query: 123 QALSKLSIEERNLLILRCVEEMSYQEISLILHHSTSKLRKKYERSAKKFRRYYAYAKG 180 A+SKLS++ERNLLILR VEE SY E++L+ + LRK+YER+ KK + Y ++G Sbjct: 121 VAISKLSVKERNLLILRVVEERSYDELALLFDIKPATLRKQYERALKKCKSYMLVSEG 178 >B3K626.1 B3K626_9BACI RNA polymerase sigma factor, sigma-70 family Length = 193 Score = 124 bits (311), Expect = 4e-27, Method: Compositional matrix adjust. Identities = 64/180 (35%), Positives = 101/180 (56%) Query: 10 IADVLEGNIERFEEIMRTYQKAILLYCYHMLGHYSEAEDSGQEVFLKAFRALGKYNPDIP 69 + V G ++ FE I+ TY+K I LYC MLG +A+D+ Q++F+KAF L Y + Sbjct: 8 VGRVKAGEVDCFEPIVETYKKQIYLYCCRMLGCKQDAQDAVQDIFIKAFTKLYTYEAKVS 67 Query: 70 FGAWLYTIAYNQCIDVIXXXXXXXXXXXXXXDERDNRHVDQQIEGKYLDEAVQQALSKLS 129 F +WLY IAY+ C++++ V++ +E K+ E ++ A++KLS Sbjct: 68 FSSWLYKIAYHHCLNILRKRRVRMRVSRLIKPAGYADSVEETLERKWFSEPLEYAMTKLS 127 Query: 130 IEERNLLILRCVEEMSYQEISLILHHSTSKLRKKYERSAKKFRRYYAYAKGEGSCEIRQG 189 +EERNLL+LR E+ + EI+ IL + S ++KKY R +K + + G CEIR Sbjct: 128 VEERNLLVLRVFEDKPFTEIAQILDKNLSAVKKKYARMKQKVIKLIQEKEVTGLCEIRDS 187 >C0Z4U4.1 C0Z4U4_BREBN RNA polymerase ECF-type sigma factor Length = 190 Score = 124 bits (311), Expect = 4e-27, Method: Compositional matrix adjust. Identities = 68/181 (37%), Positives = 108/181 (59%), Gaps = 1/181 (0%) Query: 1 LNDAELRRIIADVLEGNIERFEEIMRTYQKAILLYCYHMLGHYSEAEDSGQEVFLKAFRA 60 + E+ R++ ++ G++E++E I+ YQ+ I YCYHMLGH +AED+ QEV +A+ Sbjct: 1 MEKTEIERLLIEIKAGSLEQYELIIDYYQQPIFTYCYHMLGHRQDAEDAVQEVLFRAYEH 60 Query: 61 LGKYNPDIPFGAWLYTIAYNQCIDVIXXXXXXXXXXXXXXDERDNR-HVDQQIEGKYLDE 119 L +Y + F AWLY IAYN C +V+ ++D R +V++ I+ YL E Sbjct: 61 LDQYTYSLSFSAWLYRIAYNHCANVLKRRKLSRVLPFLYNRDQDGRNYVEESIDSNYLGE 120 Query: 120 AVQQALSKLSIEERNLLILRCVEEMSYQEISLILHHSTSKLRKKYERSAKKFRRYYAYAK 179 ++Q +LS EER L+ LR +EE Y+EI+ ++ ++ LRK++ER KK +RY Sbjct: 121 PLEQIWKRLSAEERTLIFLRVLEEREYEEIAELMDKKSAALRKQFERILKKCKRYLPTMG 180 Query: 180 G 180 G Sbjct: 181 G 181 >B3KKX3.1 B3KKX3_9BACI RNA polymerase sigma factor, sigma-70 family Length = 204 Score = 112 bits (280), Expect = 2e-23, Method: Compositional matrix adjust. Identities = 59/195 (30%), Positives = 107/195 (54%), Gaps = 1/195 (0%) Query: 1 LNDAELRRIIADVLEGNIERFEEIMRTYQKAILLYCYHMLGHYSEAEDSGQEVFLKAFRA 60 + + ++ I VL G+ + F I+ +Q+ I +YC+ +L +AED+ QE+ +KA++ Sbjct: 10 MKELDIEVTIERVLNGDRQAFVHIVEAFQQQIFMYCWRLLNQRQDAEDAVQEIMVKAYQK 69 Query: 61 LGKYNPDIPFGAWLYTIAYNQCIDVIXXXXXXXXXXXXXXDERDNRHVDQQIEGKY-LDE 119 L Y P+ F AWLY +AY+ C++++ ++++ +Q KY + E Sbjct: 70 LETYKPETSFSAWLYKMAYHHCLNMLRRKRYFQNIVPKLRADKEHAESAEQEAQKYIISE 129 Query: 120 AVQQALSKLSIEERNLLILRCVEEMSYQEISLILHHSTSKLRKKYERSAKKFRRYYAYAK 179 +++AL +LS +ERNLLILR EE S+ EI IL + +K+Y R +K +++ + Sbjct: 130 PMERALRRLSHDERNLLILRIFEEKSFAEIGQILDKTKDTAKKRYSRLIQKLKKWMHDRE 189 Query: 180 GEGSCEIRQGSGFEG 194 GE + + +G Sbjct: 190 GEPRWNFNEMTWRKG 204 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 0.320 0.136 0.393 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: 1,009,720,209 Number of extensions: 34856411 Number of successful extensions: 106196 Number of sequences better than 1.0e-05: 1103 Number of HSP's gapped: 107031 Number of HSP's successfully gapped: 1103 Length of query: 197 Length of database: 3,060,696,203 Length adjustment: 129 Effective length of query: 68 Effective length of database: 1,845,385,268 Effective search space: 125486198224 Effective search space used: 125486198224 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 (21.8 bits) S2: 127 (53.5 bits)