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= 0370.0041.p (195 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 168 3e-40 B3KKX3.1 B3KKX3_9BACI RNA polymerase sigma factor, sigma-70 family 153 9e-36 C0ZKR6.1 C0ZKR6_BREBN RNA polymerase ECF-type sigma factor 127 6e-28 C0Z8S7.1 C0Z8S7_BREBN RNA polymerase ECF-type sigma factor 124 6e-27 C0Z4U4.1 C0Z4U4_BREBN RNA polymerase ECF-type sigma factor 114 5e-24 >B3K626.1 B3K626_9BACI RNA polymerase sigma factor, sigma-70 family Length = 193 Score = 168 bits (425), Expect = 3e-40, Method: Compositional matrix adjust. Identities = 83/173 (47%), Positives = 110/173 (63%) Query: 3 LDWIEQAVARVQAGEVEPYAQIVEAYQKPIHRYCSRLLGSRSEAEDAVQDILVKAYLNIA 62 +D IE+ V RV+AGEV+ + IVE Y+K I+ YC R+LG + +A+DAVQDI +KA+ + Sbjct: 1 MDSIEEYVGRVKAGEVDCFEPIVETYKKQIYLYCCRMLGCKQDAQDAVQDIFIKAFTKLY 60 Query: 63 AYRSVASFSSWLYKIAYHHCXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMDRNIFSEPLA 122 Y + SFSSWLYKIAYHHC ++R FSEPL Sbjct: 61 TYEAKVSFSSWLYKIAYHHCLNILRKRRVRMRVSRLIKPAGYADSVEETLERKWFSEPLE 120 Query: 123 KALSRLSTEERNLLVLRIFEEQSFPEIAGILDKNMEAVKKKYRRTLMKLAKMM 175 A+++LS EERNLLVLR+FE++ F EIA ILDKN+ AVKKKY R K+ K++ Sbjct: 121 YAMTKLSVEERNLLVLRVFEDKPFTEIAQILDKNLSAVKKKYARMKQKVIKLI 173 >B3KKX3.1 B3KKX3_9BACI RNA polymerase sigma factor, sigma-70 family Length = 204 Score = 153 bits (386), Expect = 9e-36, Method: Compositional matrix adjust. Identities = 80/181 (44%), Positives = 103/181 (56%), Gaps = 1/181 (0%) Query: 6 IEQAVARVQAGEVEPYAQIVEAYQKPIHRYCSRLLGSRSEAEDAVQDILVKAYLNIAAYR 65 IE + RV G+ + + IVEA+Q+ I YC RLL R +AEDAVQ+I+VKAY + Y+ Sbjct: 15 IEVTIERVLNGDRQAFVHIVEAFQQQIFMYCWRLLNQRQDAEDAVQEIMVKAYQKLETYK 74 Query: 66 SVASFSSWLYKIAYHHCXXXXXXXX-XXXXXXXXXXXXXXXXXXXXXMDRNIFSEPLAKA 124 SFS+WLYK+AYHHC + I SEP+ +A Sbjct: 75 PETSFSAWLYKMAYHHCLNMLRRKRYFQNIVPKLRADKEHAESAEQEAQKYIISEPMERA 134 Query: 125 LSRLSTEERNLLVLRIFEEQSFPEIAGILDKNMEAVKKKYRRTLMKLAKMMSAHKGGSEW 184 L RLS +ERNLL+LRIFEE+SF EI ILDK + KK+Y R + KL K M +G W Sbjct: 135 LRRLSHDERNLLILRIFEEKSFAEIGQILDKTKDTAKKRYSRLIQKLKKWMHDREGEPRW 194 Query: 185 N 185 N Sbjct: 195 N 195 >C0ZKR6.1 C0ZKR6_BREBN RNA polymerase ECF-type sigma factor Length = 189 Score = 127 bits (318), Expect = 6e-28, Method: Compositional matrix adjust. Identities = 66/184 (35%), Positives = 99/184 (53%), Gaps = 3/184 (1%) Query: 6 IEQAVARVQAGEVEPYAQIVEAYQKPIHRYCSRLLGSRSEAEDAVQDILVKAYLNIAAYR 65 +EQ + V+AG++E + I++A QK + YC +LG R EAEDAVQ++ +KA+ + +YR Sbjct: 1 MEQVLKEVRAGDIEQFGLIIDAMQKQLFVYCYHMLGHRQEAEDAVQEVFLKAFEQLDSYR 60 Query: 66 SVASFSSWLYKIAYHHCXXXXXXXXXXXXXXXXXXXXXXXXXXXXXM---DRNIFSEPLA 122 SFS+W+YKIAYHHC D + PL Sbjct: 61 HNVSFSAWMYKIAYHHCLNLLNRAKLNRVVTFLRAGIQTVSRHEGEKKIEDTEYLNNPLH 120 Query: 123 KALSRLSTEERNLLVLRIFEEQSFPEIAGILDKNMEAVKKKYRRTLMKLAKMMSAHKGGS 182 A+S+LS +ERNLL+LR+ EE+S+ E+A + D ++K+Y R L K M +GG Sbjct: 121 VAISKLSVKERNLLILRVVEERSYDELALLFDIKPATLRKQYERALKKCKSYMLVSEGGD 180 Query: 183 EWNG 186 + Sbjct: 181 RHDS 184 >C0Z8S7.1 C0Z8S7_BREBN RNA polymerase ECF-type sigma factor Length = 195 Score = 124 bits (310), Expect = 6e-27, Method: Compositional matrix adjust. Identities = 68/178 (38%), Positives = 97/178 (54%), Gaps = 1/178 (0%) Query: 6 IEQAVARVQAGEVEPYAQIVEAYQKPIHRYCSRLLGSRSEAEDAVQDILVKAYLNIAAYR 65 IE+ V + G + YA I+++YQ PI YC +LG+R EAEDA Q++ KAY N+ Y Sbjct: 6 IEELVDEIIQGADDRYAIIMKSYQTPIFHYCYHILGNRCEAEDATQEVFFKAYRNLKKYS 65 Query: 66 SVASFSSWLYKIAYHHCXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMDRNIFSEPLAKAL 125 + F++WLYKIAYHHC ++ FSE + A+ Sbjct: 66 PIMPFAAWLYKIAYHHCIDLIRKRKWTKLLPFLMQDKESQSDIERHIENVYFSEDVFLAM 125 Query: 126 SRLSTEERNLLVLRIFEEQSFPEIAGILDKNMEAVKKKYRRTLMKLAKMMSA-HKGGS 182 LS EER LL+LR EE+++ EI+ I++KN +++KK+ RT K S KGGS Sbjct: 126 QTLSVEERTLLLLRGVEEKTYEEISLIMNKNAASLRKKFERTASKFRSAYSPLGKGGS 183 >C0Z4U4.1 C0Z4U4_BREBN RNA polymerase ECF-type sigma factor Length = 190 Score = 114 bits (284), Expect = 5e-24, Method: Compositional matrix adjust. Identities = 68/186 (36%), Positives = 102/186 (54%), Gaps = 2/186 (1%) Query: 6 IEQAVARVQAGEVEPYAQIVEAYQKPIHRYCSRLLGSRSEAEDAVQDILVKAYLNIAAYR 65 IE+ + ++AG +E Y I++ YQ+PI YC +LG R +AEDAVQ++L +AY ++ Y Sbjct: 6 IERLLIEIKAGSLEQYELIIDYYQQPIFTYCYHMLGHRQDAEDAVQEVLFRAYEHLDQYT 65 Query: 66 SVASFSSWLYKIAYHHCXXXXXXXXXXXXXXXXXXXXXX-XXXXXXXMDRNIFSEPLAKA 124 SFS+WLY+IAY+HC +D N EPL + Sbjct: 66 YSLSFSAWLYRIAYNHCANVLKRRKLSRVLPFLYNRDQDGRNYVEESIDSNYLGEPLEQI 125 Query: 125 LSRLSTEERNLLVLRIFEEQSFPEIAGILDKNMEAVKKKYRRTLMKLAKMMSAHKGGSEW 184 RLS EER L+ LR+ EE+ + EIA ++DK A++K++ R L K + + GG Sbjct: 126 WKRLSAEERTLIFLRVLEEREYEEIAELMDKKSAALRKQFERILKKCKRYLPT-MGGVAA 184 Query: 185 NGKGSL 190 NG+ S+ Sbjct: 185 NGQKSV 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 0.319 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: 885,710,801 Number of extensions: 26362637 Number of successful extensions: 86128 Number of sequences better than 1.0e-05: 350 Number of HSP's gapped: 86454 Number of HSP's successfully gapped: 351 Length of query: 195 Length of database: 3,060,696,203 Length adjustment: 128 Effective length of query: 67 Effective length of database: 1,854,806,283 Effective search space: 124272020961 Effective search space used: 124272020961 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)