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= 0254.0024.p (194 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value C2W7F8.1 C2W7F8_BACCE RNA polymerase sigma subunit, ECF subfamily 226 8e-58 C2MK24.1 C2MK24_BACCE RNA polymerase sigma subunit, ECF subfamily 224 3e-57 C2XTD8.1 C2XTD8_BACCE RNA polymerase sigma subunit, ECF subfamily 221 2e-56 A9VSU9.1 A9VSU9_BACWK RNA polymerase, sigma-24 subunit, ECF subf... 221 3e-56 C2SJ94.1 C2SJ94_BACCE RNA polymerase sigma subunit, ECF subfamily 221 3e-56 >C2W7F8.1 C2W7F8_BACCE RNA polymerase sigma subunit, ECF subfamily Length = 192 Score = 226 bits (576), Expect = 8e-58, Method: Compositional matrix adjust. Identities = 102/191 (53%), Positives = 151/191 (79%) Query: 1 MEDQTEYSQLITRTLAGSREAYGELYEATIRDVYRTVHFLVSEPSDADDVVQDIYLELHR 60 M+++ +Y LI R L+G++EAY ELY+ TI+D+YRT HFL+ E +D DDVVQ+IY++L++ Sbjct: 1 MDEEIDYCDLIERILSGNQEAYSELYDKTIQDIYRTAHFLIEEKTDVDDVVQEIYIQLYQ 60 Query: 61 SLKQYNESRAFRPWLMGLVMRQVHAYRRKGWRQLRISKKAEHTSEIQDADVAGEVIDRLS 120 SL +YN R FRPWLMGL +RQ+H+YRRK W +LRI KKAE + + D + +V++++S Sbjct: 61 SLSKYNRERPFRPWLMGLAIRQIHSYRRKRWMRLRIVKKAEEHKKPIEFDFSSDVVNKIS 120 Query: 121 SRMLMDKVNSLPYKLRQVIVLHYLQEYSQEEAAAILGIPLGTVKSRIHAALQKLRRKQKA 180 ++ L+ ++ LPYKL+QVI+L YL +YSQEE A IL IP+GTVKSRIHAAL+KLR++++ Sbjct: 121 NQKLIALIHKLPYKLKQVIILRYLHDYSQEEVADILHIPIGTVKSRIHAALKKLRQQEQV 180 Query: 181 DTIRIGKVEDL 191 + I +G+V ++ Sbjct: 181 EEIFLGEVGEM 191 >C2MK24.1 C2MK24_BACCE RNA polymerase sigma subunit, ECF subfamily Length = 192 Score = 224 bits (572), Expect = 3e-57, Method: Compositional matrix adjust. Identities = 100/191 (52%), Positives = 153/191 (80%) Query: 1 MEDQTEYSQLITRTLAGSREAYGELYEATIRDVYRTVHFLVSEPSDADDVVQDIYLELHR 60 M+D+T Y+ LI TL+G++EAY ELY+ TI +VY+T HFL+++ +D DDVVQ+IY++L+ Sbjct: 1 MKDETVYTDLIQLTLSGNKEAYSELYDVTIHEVYKTAHFLINDKADVDDVVQEIYIQLYE 60 Query: 61 SLKQYNESRAFRPWLMGLVMRQVHAYRRKGWRQLRISKKAEHTSEIQDADVAGEVIDRLS 120 SL++Y+ + FRPWL+GLV++Q+H+YRRK W +LRI KKAE + +D + +V+ ++S Sbjct: 61 SLRKYDSEKPFRPWLIGLVIKQIHSYRRKRWMRLRIIKKAEEQRKPVQSDFSNDVVSKIS 120 Query: 121 SRMLMDKVNSLPYKLRQVIVLHYLQEYSQEEAAAILGIPLGTVKSRIHAALQKLRRKQKA 180 +R L++ ++ LPYKL+QVI+L YL +YSQEE A IL IP+GTVKSRIH+AL+KLR+K++ Sbjct: 121 NRKLIELIHKLPYKLKQVIILRYLHDYSQEEVAEILHIPIGTVKSRIHSALKKLRQKEQV 180 Query: 181 DTIRIGKVEDL 191 + I +G+V ++ Sbjct: 181 EEIFLGEVGNV 191 >C2XTD8.1 C2XTD8_BACCE RNA polymerase sigma subunit, ECF subfamily Length = 192 Score = 221 bits (564), Expect = 2e-56, Method: Compositional matrix adjust. Identities = 99/191 (51%), Positives = 152/191 (79%) Query: 1 MEDQTEYSQLITRTLAGSREAYGELYEATIRDVYRTVHFLVSEPSDADDVVQDIYLELHR 60 M+D+T Y++LI TL+G++EAY ELY+ TI++VY+T HFL+ + +D DDVVQ+IY++L+ Sbjct: 1 MKDETVYTELIQLTLSGNKEAYSELYDKTIQEVYKTAHFLIEDKADIDDVVQEIYIQLYE 60 Query: 61 SLKQYNESRAFRPWLMGLVMRQVHAYRRKGWRQLRISKKAEHTSEIQDADVAGEVIDRLS 120 SL++Y+ + FRPWL+GL ++Q+H+YRRK W +LRI KKAE + D + +V+ ++S Sbjct: 61 SLRKYDSEKPFRPWLIGLAIKQIHSYRRKRWMRLRIVKKAEEQRKPVQIDFSSDVVSKIS 120 Query: 121 SRMLMDKVNSLPYKLRQVIVLHYLQEYSQEEAAAILGIPLGTVKSRIHAALQKLRRKQKA 180 ++ L++ ++ LPYKL+QVI+L YL +YSQEE A IL IP+GTVKSRIHAAL+KLR+K++ Sbjct: 121 NQKLIELIHKLPYKLKQVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLRQKEQV 180 Query: 181 DTIRIGKVEDL 191 + I +G+V ++ Sbjct: 181 EEIFLGEVGNV 191 >A9VSU9.1 A9VSU9_BACWK RNA polymerase, sigma-24 subunit, ECF subfamily Length = 192 Score = 221 bits (563), Expect = 3e-56, Method: Compositional matrix adjust. Identities = 99/191 (51%), Positives = 152/191 (79%) Query: 1 MEDQTEYSQLITRTLAGSREAYGELYEATIRDVYRTVHFLVSEPSDADDVVQDIYLELHR 60 M+D+T Y+ LI TL+G++EAY ELY+ TI++VY+T HFL+ + +D DDVVQ+IY++L+ Sbjct: 1 MKDETVYTDLIQLTLSGNKEAYSELYDKTIQEVYKTAHFLIEDKADIDDVVQEIYIQLYE 60 Query: 61 SLKQYNESRAFRPWLMGLVMRQVHAYRRKGWRQLRISKKAEHTSEIQDADVAGEVIDRLS 120 SL++Y+ + FRPWL+GL ++Q+H+YRRK W +LRI KKAE + + D + +V+ ++S Sbjct: 61 SLRKYDSEKPFRPWLIGLAIKQIHSYRRKRWMRLRIVKKAEEQRKPVEIDFSSDVVSKIS 120 Query: 121 SRMLMDKVNSLPYKLRQVIVLHYLQEYSQEEAAAILGIPLGTVKSRIHAALQKLRRKQKA 180 ++ L++ ++ LPYKL+QVI+L YL +YSQEE A IL IP+GTVKSRIHAAL+KLR+K++ Sbjct: 121 NQKLIELIHKLPYKLKQVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLRQKEQV 180 Query: 181 DTIRIGKVEDL 191 + I +G+V ++ Sbjct: 181 EEIFLGEVGNV 191 >C2SJ94.1 C2SJ94_BACCE RNA polymerase sigma subunit, ECF subfamily Length = 192 Score = 221 bits (563), Expect = 3e-56, Method: Compositional matrix adjust. Identities = 99/191 (51%), Positives = 152/191 (79%) Query: 1 MEDQTEYSQLITRTLAGSREAYGELYEATIRDVYRTVHFLVSEPSDADDVVQDIYLELHR 60 M+D+T Y+ LI TL+G++EAY ELY+ TI++VY+T HFL+ + +D DDVVQ+IY++L+ Sbjct: 1 MKDETVYTDLIQLTLSGNKEAYSELYDKTIQEVYKTAHFLIEDKADIDDVVQEIYIQLYE 60 Query: 61 SLKQYNESRAFRPWLMGLVMRQVHAYRRKGWRQLRISKKAEHTSEIQDADVAGEVIDRLS 120 SL++Y+ + FRPWL+GL ++Q+H+YRRK W +LRI KKAE + + D + +V+ ++S Sbjct: 61 SLRKYDSEKPFRPWLIGLAIKQIHSYRRKRWMRLRIVKKAEEQRKPVEIDFSSDVVSKIS 120 Query: 121 SRMLMDKVNSLPYKLRQVIVLHYLQEYSQEEAAAILGIPLGTVKSRIHAALQKLRRKQKA 180 ++ L++ ++ LPYKL+QVI+L YL +YSQEE A IL IP+GTVKSRIHAAL+KLR+K++ Sbjct: 121 NQKLIELIHKLPYKLKQVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLRQKEQV 180 Query: 181 DTIRIGKVEDL 191 + I +G+V ++ Sbjct: 181 EEIFLGEVGNV 191 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 0.371 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: 1,034,226,914 Number of extensions: 37787788 Number of successful extensions: 131139 Number of sequences better than 1.0e-05: 3386 Number of HSP's gapped: 130805 Number of HSP's successfully gapped: 3386 Length of query: 194 Length of database: 3,060,696,203 Length adjustment: 128 Effective length of query: 66 Effective length of database: 1,854,806,283 Effective search space: 122417214678 Effective search space used: 122417214678 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)