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= 0264.0034.p (239 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KG97.1 B3KG97_9BACI RNA polymerase sigma factor 423 e-117 B1DMB2.1 B1DMB2_9BACL RNA polymerase sigma factor 415 e-114 Q9K9T9.1 Q9K9T9_BACHD RNA polymerase sigma factor 365 1e-99 Q65JW9.1 Q65JW9_BACLD RNA polymerase sigma factor 362 1e-98 Q5WFH4.1 Q5WFH4_BACSK RNA polymerase sigma factor 360 6e-98 >B3KG97.1 B3KG97_9BACI RNA polymerase sigma factor Length = 240 Score = 423 bits (1087), Expect = e-117, Method: Compositional matrix adjust. Identities = 209/238 (87%), Positives = 222/238 (93%) Query: 2 VKWKIALQLQYYRMLFLLGLKSQEIYYIGGSEALPPPLTREEEEFLLQRLSSGDAAVRAM 61 VKW++ALQLQYYR+LF+LGLKSQEIYYIGGSEALPPPLT+EEEEFLL++L +GDAA RAM Sbjct: 3 VKWRLALQLQYYRVLFMLGLKSQEIYYIGGSEALPPPLTKEEEEFLLKKLPTGDAATRAM 62 Query: 62 LIERNLRLVVYIARKFENTGINIEDLVSIGAIGLIKAVNTFDPEKKIKLATYASRCIENE 121 LIERNLRLVVYIARKFENTGINIEDLVSIGAIGLIKAVNTFDPEKKIKLATYASRCIENE Sbjct: 63 LIERNLRLVVYIARKFENTGINIEDLVSIGAIGLIKAVNTFDPEKKIKLATYASRCIENE 122 Query: 122 ILMYLRRNSKTRSEVSFDEPLNIDWDGNELLLSDVLGTENDTIYRNIEEQVDRKLLQKAL 181 ILMYLRRN+KTRSEVSFDEPLNIDWDGNELLLSDVLGTENDTIYRNIEEQVDRKLLQKAL Sbjct: 123 ILMYLRRNNKTRSEVSFDEPLNIDWDGNELLLSDVLGTENDTIYRNIEEQVDRKLLQKAL 182 Query: 182 EKLSERERLIMELRFGLRGGEEKTQKDVADLLGISQSYISXXXXXXXXXXXXXFNKMV 239 +KLS+RER+IMELRFGL+ GEEKTQKDVADLLGISQSYIS FNKMV Sbjct: 183 DKLSDRERMIMELRFGLQDGEEKTQKDVADLLGISQSYISRLEKRIIKRLRKEFNKMV 240 >B1DMB2.1 B1DMB2_9BACL RNA polymerase sigma factor Length = 240 Score = 415 bits (1066), Expect = e-114, Method: Compositional matrix adjust. Identities = 206/239 (86%), Positives = 217/239 (90%) Query: 1 MVKWKIALQLQYYRMLFLLGLKSQEIYYIGGSEALPPPLTREEEEFLLQRLSSGDAAVRA 60 +VKWK+ LQL YYR+LFL GLKS+EIYYIGGSEALPPPLTREEEE+LL +L SGD A+RA Sbjct: 2 LVKWKLVLQLYYYRVLFLFGLKSEEIYYIGGSEALPPPLTREEEEYLLDKLPSGDTAIRA 61 Query: 61 MLIERNLRLVVYIARKFENTGINIEDLVSIGAIGLIKAVNTFDPEKKIKLATYASRCIEN 120 MLIERNLRLVVYIARKFENTGI+IEDLVSIGAIGLIKAVNTFDPEKKIKLATYASRCIEN Sbjct: 62 MLIERNLRLVVYIARKFENTGIHIEDLVSIGAIGLIKAVNTFDPEKKIKLATYASRCIEN 121 Query: 121 EILMYLRRNSKTRSEVSFDEPLNIDWDGNELLLSDVLGTENDTIYRNIEEQVDRKLLQKA 180 EILMYLRRNSKTR+EVSFDEPLNIDWDGNELLLSDVLGTENDTIYRNIEEQVDRKLL KA Sbjct: 122 EILMYLRRNSKTRTEVSFDEPLNIDWDGNELLLSDVLGTENDTIYRNIEEQVDRKLLHKA 181 Query: 181 LEKLSERERLIMELRFGLRGGEEKTQKDVADLLGISQSYISXXXXXXXXXXXXXFNKMV 239 L+KLSERER+IMELRFGL GEEKTQKDVADLLGISQSYIS FNKMV Sbjct: 182 LDKLSERERIIMELRFGLADGEEKTQKDVADLLGISQSYISRLEKRIIKRLRKEFNKMV 240 >Q9K9T9.1 Q9K9T9_BACHD RNA polymerase sigma factor Length = 237 Score = 365 bits (938), Expect = 1e-99, Method: Compositional matrix adjust. Identities = 182/235 (77%), Positives = 202/235 (85%) Query: 5 KIALQLQYYRMLFLLGLKSQEIYYIGGSEALPPPLTREEEEFLLQRLSSGDAAVRAMLIE 64 K+ L +YR+L+ LG+K+ EIYYIGGSEALPPPL++EEE LL++L SGD AVR+MLIE Sbjct: 3 KLKATLIWYRLLYRLGMKADEIYYIGGSEALPPPLSKEEEAHLLKKLPSGDKAVRSMLIE 62 Query: 65 RNLRLVVYIARKFENTGINIEDLVSIGAIGLIKAVNTFDPEKKIKLATYASRCIENEILM 124 RNLRLVVYIARKFENTGINIEDL+SIG IGLIKAVNTF+PEKKIKLATYASRCIENEILM Sbjct: 63 RNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILM 122 Query: 125 YLRRNSKTRSEVSFDEPLNIDWDGNELLLSDVLGTENDTIYRNIEEQVDRKLLQKALEKL 184 YLRRN+K RSEVSFDEPLNIDWDGNELLLSDVLGT++D I R IEE+VDRKLL KAL L Sbjct: 123 YLRRNNKIRSEVSFDEPLNIDWDGNELLLSDVLGTDDDIITRGIEEKVDRKLLMKALHTL 182 Query: 185 SERERLIMELRFGLRGGEEKTQKDVADLLGISQSYISXXXXXXXXXXXXXFNKMV 239 ++RE+ IMELRFGL GGEEKTQKDVADLLGISQSYIS FNKMV Sbjct: 183 TDREKQIMELRFGLAGGEEKTQKDVADLLGISQSYISRLEKRIIKRLQKEFNKMV 237 >Q65JW9.1 Q65JW9_BACLD RNA polymerase sigma factor Length = 239 Score = 362 bits (930), Expect = 1e-98, Method: Compositional matrix adjust. Identities = 181/239 (75%), Positives = 203/239 (84%) Query: 1 MVKWKIALQLQYYRMLFLLGLKSQEIYYIGGSEALPPPLTREEEEFLLQRLSSGDAAVRA 60 M K K+ L +Y++L LGLKS EIYYIGGSEALPPPL+++EE+ LL +L GD A RA Sbjct: 1 MKKLKLRLTYLWYKLLMKLGLKSDEIYYIGGSEALPPPLSKDEEQVLLHKLPDGDQAARA 60 Query: 61 MLIERNLRLVVYIARKFENTGINIEDLVSIGAIGLIKAVNTFDPEKKIKLATYASRCIEN 120 +LIERNLRLVVYIARKFENTGINIEDL+SIG IGLIKAVNTF+PEKKIKLATYASRCIEN Sbjct: 61 ILIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIEN 120 Query: 121 EILMYLRRNSKTRSEVSFDEPLNIDWDGNELLLSDVLGTENDTIYRNIEEQVDRKLLQKA 180 EILMYLRRN+K RSEVSFDEPLNIDWDGNELLLSDVLGTEND I ++IE VD+KLL+KA Sbjct: 121 EILMYLRRNNKIRSEVSFDEPLNIDWDGNELLLSDVLGTENDIITKDIEANVDKKLLKKA 180 Query: 181 LEKLSERERLIMELRFGLRGGEEKTQKDVADLLGISQSYISXXXXXXXXXXXXXFNKMV 239 LE+L++RE+ IMELRFGL GGEEKTQKDVAD+LGISQSYIS FNKMV Sbjct: 181 LEQLNDREKQIMELRFGLVGGEEKTQKDVADMLGISQSYISRLEKRIIKRLRKEFNKMV 239 >Q5WFH4.1 Q5WFH4_BACSK RNA polymerase sigma factor Length = 237 Score = 360 bits (924), Expect = 6e-98, Method: Compositional matrix adjust. Identities = 184/235 (78%), Positives = 201/235 (85%) Query: 5 KIALQLQYYRMLFLLGLKSQEIYYIGGSEALPPPLTREEEEFLLQRLSSGDAAVRAMLIE 64 K+ LQL +YR+L LGLK+ EIYYIGGSEALPPPL++EEE LL +L SGD AVR++LIE Sbjct: 3 KLKLQLFWYRLLNKLGLKADEIYYIGGSEALPPPLSKEEEAELLGKLPSGDKAVRSVLIE 62 Query: 65 RNLRLVVYIARKFENTGINIEDLVSIGAIGLIKAVNTFDPEKKIKLATYASRCIENEILM 124 RNLRLVVYIARKFENTGINIEDL+SIG IGLIKAVNTF+PEKKIKLATYASRCIENEILM Sbjct: 63 RNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILM 122 Query: 125 YLRRNSKTRSEVSFDEPLNIDWDGNELLLSDVLGTENDTIYRNIEEQVDRKLLQKALEKL 184 YLRRN+KTRSEVSFDEPLNIDWDGNELLLSDVLGTE D I R IEE+VDR+LL KAL L Sbjct: 123 YLRRNNKTRSEVSFDEPLNIDWDGNELLLSDVLGTEEDIITRGIEERVDRRLLVKALHTL 182 Query: 185 SERERLIMELRFGLRGGEEKTQKDVADLLGISQSYISXXXXXXXXXXXXXFNKMV 239 SERE+ IMELRFGL G EEKTQKDVAD+LGISQSYIS F+KMV Sbjct: 183 SEREKQIMELRFGLAGEEEKTQKDVADMLGISQSYISRLEKRIIKRLQKEFSKMV 237 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 0.138 0.378 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: 1,230,494,422 Number of extensions: 46804515 Number of successful extensions: 157239 Number of sequences better than 1.0e-05: 4426 Number of HSP's gapped: 157155 Number of HSP's successfully gapped: 4431 Length of query: 239 Length of database: 3,060,696,203 Length adjustment: 132 Effective length of query: 107 Effective length of database: 1,817,122,223 Effective search space: 194432077861 Effective search space used: 194432077861 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 (21.7 bits) S2: 129 (54.3 bits)