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= 0560.0020.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 B3K602.1 B3K602_9BACI RNA polymerase sigma factor, sigma-70 family 313 4e-84 B3KKX3.1 B3KKX3_9BACI RNA polymerase sigma factor, sigma-70 family 130 9e-29 B1DA07.1 B1DA07_9BACL RNA polymerase sigma factor 125 1e-27 C0ZKR6.1 C0ZKR6_BREBN RNA polymerase ECF-type sigma factor 125 2e-27 C0Z8S7.1 C0Z8S7_BREBN RNA polymerase ECF-type sigma factor 117 6e-25 >B3K602.1 B3K602_9BACI RNA polymerase sigma factor, sigma-70 family Length = 197 Score = 313 bits (803), Expect = 4e-84, Method: Compositional matrix adjust. Identities = 150/197 (76%), Positives = 171/197 (86%) Query: 1 LQPTIPGDKEAKRNAVEAAVERVKAGDKQAYGAVISQFERQMYTYCYYILKNHAETEDAV 60 +QPTIPG+ E KR A+E +E+VKAGDK AY A+I QFERQMYTYCYYILKNHAETEDAV Sbjct: 1 MQPTIPGEAEGKRKAIEEVIEQVKAGDKHAYQAIIVQFERQMYTYCYYILKNHAETEDAV 60 Query: 61 QEIFVRAYENLQHYNRQVSFSAWLYKMAYHHLINLKKKQSRWLKLVEKYKEQQPVMQIFE 120 QEIF+RAYE+L Y RQVSFSAWLYKMAYHHLIN+K+KQ+R+L L+E KEQQPVMQI + Sbjct: 61 QEIFIRAYEHLHLYKRQVSFSAWLYKMAYHHLINIKRKQNRFLNLIEHCKEQQPVMQISQ 120 Query: 121 HESTVYELLVYLTTEERHILLLKAVEQYTFEEIGDIIGLKPATIRKKYERLRHKLVERMN 180 HE VYELL YLT EERHILLLKAVEQYTFEEI I+GLK ATIRKKYERLRHKL++R++ Sbjct: 121 HEPVVYELLTYLTAEERHILLLKAVEQYTFEEISGIMGLKSATIRKKYERLRHKLMDRIS 180 Query: 181 QKGERTHGTIAETHGVR 197 QKGE GTIA T+G+R Sbjct: 181 QKGEVARGTIAGTNGIR 197 >B3KKX3.1 B3KKX3_9BACI RNA polymerase sigma factor, sigma-70 family Length = 204 Score = 130 bits (326), Expect = 9e-29, Method: Compositional matrix adjust. Identities = 72/192 (37%), Positives = 117/192 (60%), Gaps = 11/192 (5%) Query: 1 LQPTIPGDKEAKRNAVEAAVERVKAGDKQAYGAVISQFERQMYTYCYYILKNHAETEDAV 60 +QPT P E K +E +ERV GD+QA+ ++ F++Q++ YC+ +L + EDAV Sbjct: 3 IQPTKP---EMKELDIEVTIERVLNGDRQAFVHIVEAFQQQIFMYCWRLLNQRQDAEDAV 59 Query: 61 QEIFVRAYENLQHYNRQVSFSAWLYKMAYHHLINLKKKQSRWLKLVEKYKEQQPVMQIFE 120 QEI V+AY+ L+ Y + SFSAWLYKMAYHH +N+ +++ + +V K + + + E Sbjct: 60 QEIMVKAYQKLETYKPETSFSAWLYKMAYHHCLNMLRRKRYFQNIVPKLRADKEHAESAE 119 Query: 121 HESTVYEL-------LVYLTTEERHILLLKAVEQYTFEEIGDIIGLKPATIRKKYERLRH 173 E+ Y + L L+ +ER++L+L+ E+ +F EIG I+ T +K+Y RL Sbjct: 120 QEAQKYIISEPMERALRRLSHDERNLLILRIFEEKSFAEIGQILDKTKDTAKKRYSRLIQ 179 Query: 174 KLVERM-NQKGE 184 KL + M +++GE Sbjct: 180 KLKKWMHDREGE 191 >B1DA07.1 B1DA07_9BACL RNA polymerase sigma factor Length = 191 Score = 125 bits (315), Expect = 1e-27, Method: Compositional matrix adjust. Identities = 66/171 (38%), Positives = 105/171 (61%), Gaps = 6/171 (3%) Query: 14 NAVEAAVERVKAGDKQAYGAVISQFERQMYTYCYYILKNHAETEDAVQEIFVRAYENLQH 73 + +E V+ V+AG + Y A++ F+R+++ YCYY++ + AE+ED VQE+F+RAY + Sbjct: 13 DRIENLVKAVQAGQVEPYRAIVLHFQRRLHLYCYYMIGDRAESEDIVQEVFLRAYREIGK 72 Query: 74 YNRQVSFSAWLYKMAYHHLINLKKK---QSRWLKLVEKYKEQQPVMQIFEHESTVYELLV 130 Y VSFSAWLYK+ Y +N KK Q R L L+++ P E LL Sbjct: 73 YQPTVSFSAWLYKIGYRLCLNALKKHKGQHRLLSLIQQQWLTAPATSSDESADC---LLK 129 Query: 131 YLTTEERHILLLKAVEQYTFEEIGDIIGLKPATIRKKYERLRHKLVERMNQ 181 L+ EER +++ +++E+ +F EI ++ G A +RKKYER+R KL ++M + Sbjct: 130 GLSPEERQLVIFRSLEERSFAEIAELTGSNAAALRKKYERIRKKLRKQMRE 180 >C0ZKR6.1 C0ZKR6_BREBN RNA polymerase ECF-type sigma factor Length = 189 Score = 125 bits (314), Expect = 2e-27, Method: Compositional matrix adjust. Identities = 65/189 (34%), Positives = 120/189 (63%), Gaps = 12/189 (6%) Query: 16 VEAAVERVKAGDKQAYGAVISQFERQMYTYCYYILKNHAETEDAVQEIFVRAYENLQHYN 75 +E ++ V+AGD + +G +I ++Q++ YCY++L + E EDAVQE+F++A+E L Y Sbjct: 1 MEQVLKEVRAGDIEQFGLIIDAMQKQLFVYCYHMLGHRQEAEDAVQEVFLKAFEQLDSYR 60 Query: 76 RQVSFSAWLYKMAYHHLINL--KKKQSR-------WLKLVEKYKEQQPVMQIFEHESTVY 126 VSFSAW+YK+AYHH +NL + K +R ++ V +++ ++ + + ++ Sbjct: 61 HNVSFSAWMYKIAYHHCLNLLNRAKLNRVVTFLRAGIQTVSRHEGEKKIEDTEYLNNPLH 120 Query: 127 ELLVYLTTEERHILLLKAVEQYTFEEIGDIIGLKPATIRKKYERLRHKLVERM--NQKGE 184 + L+ +ER++L+L+ VE+ +++E+ + +KPAT+RK+YER K M ++ G+ Sbjct: 121 VAISKLSVKERNLLILRVVEERSYDELALLFDIKPATLRKQYERALKKCKSYMLVSEGGD 180 Query: 185 RTHGTIAET 193 R H +I+ T Sbjct: 181 R-HDSISAT 188 >C0Z8S7.1 C0Z8S7_BREBN RNA polymerase ECF-type sigma factor Length = 195 Score = 117 bits (292), Expect = 6e-25, Method: Compositional matrix adjust. Identities = 63/167 (37%), Positives = 100/167 (59%), Gaps = 8/167 (4%) Query: 16 VEAAVERVKAGDKQAYGAVISQFERQMYTYCYYILKNHAETEDAVQEIFVRAYENLQHYN 75 +E V+ + G Y ++ ++ ++ YCY+IL N E EDA QE+F +AY NL+ Y+ Sbjct: 6 IEELVDEIIQGADDRYAIIMKSYQTPIFHYCYHILGNRCEAEDATQEVFFKAYRNLKKYS 65 Query: 76 RQVSFSAWLYKMAYHHLINL--KKKQSRWLKLVEKYKEQQP-----VMQIFEHESTVYEL 128 + F+AWLYK+AYHH I+L K+K ++ L + + KE Q + ++ E V+ Sbjct: 66 PIMPFAAWLYKIAYHHCIDLIRKRKWTKLLPFLMQDKESQSDIERHIENVYFSED-VFLA 124 Query: 129 LVYLTTEERHILLLKAVEQYTFEEIGDIIGLKPATIRKKYERLRHKL 175 + L+ EER +LLL+ VE+ T+EEI I+ A++RKK+ER K Sbjct: 125 MQTLSVEERTLLLLRGVEEKTYEEISLIMNKNAASLRKKFERTASKF 171 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 0.133 0.382 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: 1,111,310,293 Number of extensions: 41315010 Number of successful extensions: 154637 Number of sequences better than 1.0e-05: 2101 Number of HSP's gapped: 155213 Number of HSP's successfully gapped: 2101 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)