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= 0168.0011.p (256 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KDJ3.1 B3KDJ3_9BACI RNA polymerase sigma factor, sigma-70 family 444 e-123 B1D884.1 B1D884_9BACL RNA polymerase, sigma 28 subunit, FliA/Whi... 285 2e-75 Q5KUC7.1 Q5KUC7_GEOKA DNA-directed RNA polymerase sigma-37 facto... 284 6e-75 C3IZB1.1 C3IZB1_9BACI RNA polymerase, sigma 28 subunit, FliA/Whi... 283 1e-74 B7Y780.1 B7Y780_9BACI RNA polymerase, sigma 28 subunit, FliA/Whi... 283 1e-74 >B3KDJ3.1 B3KDJ3_9BACI RNA polymerase sigma factor, sigma-70 family Length = 256 Score = 444 bits (1142), Expect = e-123, Method: Compositional matrix adjust. Identities = 215/256 (83%), Positives = 231/256 (90%) Query: 1 MNEKVTPPESMNEAVSLIWEYQQTKDNEIATALIRKYEPMVKMAAGKIARNRPDLYEDLY 60 M++K TP ES +EAV LI +YQQTKDN+IAT LI+KYEPMVKMAAGKIARNRPDLYEDLY Sbjct: 1 MSDKATPQESRDEAVHLIEQYQQTKDNDIATVLIKKYEPMVKMAAGKIARNRPDLYEDLY 60 Query: 61 QVGQMALIRLLQQYDISLGIPFEPYAMKSMIGHMKNFLRDKSWYIQVPRRIKEKGALVQQ 120 QVGQMALIRLLQQYDISLGIPFEPYAMKSMIGHMKNFLRDKSWYIQVPRRIKEKGALVQQ Sbjct: 61 QVGQMALIRLLQQYDISLGIPFEPYAMKSMIGHMKNFLRDKSWYIQVPRRIKEKGALVQQ 120 Query: 121 AIDELTIRLERSPAVEEIAHYLDLTVEETVEVLAGRECYHYVSLDSPLSQEETGATLGEL 180 AIDEL ++LERSP V EIA YLDL+VEETVEVLAGRECYHYVSLDSPLSQEETGATLGEL Sbjct: 121 AIDELMVKLERSPDVNEIASYLDLSVEETVEVLAGRECYHYVSLDSPLSQEETGATLGEL 180 Query: 181 ISSEANDYETVEKRMDLQQAXXXXXXXXXXXXXXAFQDGQSQRAIAQKLGVSQMSVSRIQ 240 ISS+ ND+++VEKRMDLQQA AFQ+GQSQRAIAQ+LGVSQMSVSRIQ Sbjct: 181 ISSDVNDFDSVEKRMDLQQAMSQLKEQEQKVLLLAFQEGQSQRAIAQRLGVSQMSVSRIQ 240 Query: 241 KRATEKLKQIMANSSY 256 KRATEKLKQIM+NSSY Sbjct: 241 KRATEKLKQIMSNSSY 256 >B1D884.1 B1D884_9BACL RNA polymerase, sigma 28 subunit, FliA/WhiG family Length = 258 Score = 285 bits (730), Expect = 2e-75, Method: Compositional matrix adjust. Identities = 135/235 (57%), Positives = 177/235 (75%) Query: 17 LIWEYQQTKDNEIATALIRKYEPMVKMAAGKIARNRPDLYEDLYQVGQMALIRLLQQYDI 76 L+ Y++ N+ ATAL++ +E +V+MA KI+RNRPDLYEDLYQVGQM+++RL +QYD Sbjct: 16 LLQRYKEMSCNDAATALLQHFESLVRMAVSKISRNRPDLYEDLYQVGQMSMLRLFKQYDS 75 Query: 77 SLGIPFEPYAMKSMIGHMKNFLRDKSWYIQVPRRIKEKGALVQQAIDELTIRLERSPAVE 136 G+PFE YAMKS+IG +KN+LRDKSWYIQVPR +KEKG L+Q+AIDELT +LERSP ++ Sbjct: 76 DKGVPFEGYAMKSVIGQLKNYLRDKSWYIQVPRNMKEKGLLIQKAIDELTTKLERSPKMD 135 Query: 137 EIAHYLDLTVEETVEVLAGRECYHYVSLDSPLSQEETGATLGELISSEANDYETVEKRMD 196 EIA YL L+VEET+EVL+ RE Y YVSLD+PLS E AT+G++IS ++ Y V+ ++ Sbjct: 136 EIAAYLGLSVEETIEVLSSRESYQYVSLDTPLSSEGDSATIGDVISDHSDKYSHVDNQIA 195 Query: 197 LQQAXXXXXXXXXXXXXXAFQDGQSQRAIAQKLGVSQMSVSRIQKRATEKLKQIM 251 L A +Q GQSQR IA +LGVSQMSVSR QKRA +KL+Q++ Sbjct: 196 LSDAMAQLKEEERKVLVLVYQHGQSQREIADQLGVSQMSVSRFQKRALDKLRQLL 250 >Q5KUC7.1 Q5KUC7_GEOKA DNA-directed RNA polymerase sigma-37 factor (Sigma-B) Length = 256 Score = 284 bits (726), Expect = 6e-75, Method: Compositional matrix adjust. Identities = 136/250 (54%), Positives = 190/250 (76%), Gaps = 1/250 (0%) Query: 7 PPESMNEAVSLIWEYQQTKDNEIATALIRKYEPMVKMAAGKIARNRPDLYEDLYQVGQMA 66 PP S ++ +LI YQQTK E ATAL+ ++EP++ AA K+AR+RPD YEDL+Q+G+++ Sbjct: 6 PPLSKSKLDALISAYQQTKTEEAATALLVRFEPLIAAAAKKMARSRPDFYEDLFQIGRLS 65 Query: 67 LIRLLQQYDISLGIPFEPYAMKSMIGHMKNFLRDKSWYIQVPRRIKEKGALVQQAIDELT 126 +RLL YD S G FE YAMKS+IG+MKN+LRDK+WYIQVPR++KEKG+ VQQAIDELT Sbjct: 66 FLRLLDHYDPSQGASFESYAMKSLIGYMKNYLRDKAWYIQVPRKVKEKGSKVQQAIDELT 125 Query: 127 IRLERSPAVEEIAHYLDLTVEETVEVLAGRECYHYVSLDSPLSQEETGA-TLGELISSEA 185 ++LERSP ++EIA +L L+VEET+E+LAGR+ Y +SLD+P+ E A T+GE ++ EA Sbjct: 126 VKLERSPNIDEIAAHLGLSVEETIEILAGRDHYQAISLDAPVQDGEKDATTIGEFVADEA 185 Query: 186 NDYETVEKRMDLQQAXXXXXXXXXXXXXXAFQDGQSQRAIAQKLGVSQMSVSRIQKRATE 245 N+ E++ +RMDL+QA F+ G++QR++A++LGVSQM++SRIQKRA Sbjct: 186 NEIESLIERMDLEQAIGKLSEQEQIVIDAVFRRGETQRSLAERLGVSQMTISRIQKRAIA 245 Query: 246 KLKQIMANSS 255 KLK+ +A S Sbjct: 246 KLKRQLAAYS 255 >C3IZB1.1 C3IZB1_9BACI RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily Length = 256 Score = 283 bits (724), Expect = 1e-74, Method: Compositional matrix adjust. Identities = 136/250 (54%), Positives = 189/250 (75%), Gaps = 1/250 (0%) Query: 7 PPESMNEAVSLIWEYQQTKDNEIATALIRKYEPMVKMAAGKIARNRPDLYEDLYQVGQMA 66 PP S ++ +LI YQQTK E ATAL+ ++EP++ AA K+AR+RPD YEDL+Q+G+++ Sbjct: 6 PPLSKSKLDALISAYQQTKTEEAATALLVRFEPLIAAAAKKMARSRPDFYEDLFQIGRLS 65 Query: 67 LIRLLQQYDISLGIPFEPYAMKSMIGHMKNFLRDKSWYIQVPRRIKEKGALVQQAIDELT 126 +RLL YD G FE YAMKS+IG+MKN+LRDK+WYIQVPR++KEKG+ VQQAIDELT Sbjct: 66 FLRLLDHYDPKQGTSFESYAMKSLIGYMKNYLRDKAWYIQVPRKVKEKGSKVQQAIDELT 125 Query: 127 IRLERSPAVEEIAHYLDLTVEETVEVLAGRECYHYVSLDSPLSQEETGA-TLGELISSEA 185 ++LERSP ++EIA +L L+VEET+E+LAGR+ Y VSLD+P+ E A T+GE ++ EA Sbjct: 126 VKLERSPTIDEIAGHLGLSVEETIEILAGRDHYQAVSLDAPVQDGEKDATTIGEFVADEA 185 Query: 186 NDYETVEKRMDLQQAXXXXXXXXXXXXXXAFQDGQSQRAIAQKLGVSQMSVSRIQKRATE 245 N+ E++ +RMDL+QA F+ G++QR++A++LGVSQM++SRIQKRA Sbjct: 186 NEIESLIERMDLEQAIGKLSEQEQIVIDAIFRRGETQRSLAERLGVSQMTISRIQKRAIA 245 Query: 246 KLKQIMANSS 255 KLK+ +A S Sbjct: 246 KLKRQLAAYS 255 >B7Y780.1 B7Y780_9BACI RNA polymerase, sigma 28 subunit, FliA/WhiG family Length = 256 Score = 283 bits (724), Expect = 1e-74, Method: Compositional matrix adjust. Identities = 136/250 (54%), Positives = 189/250 (75%), Gaps = 1/250 (0%) Query: 7 PPESMNEAVSLIWEYQQTKDNEIATALIRKYEPMVKMAAGKIARNRPDLYEDLYQVGQMA 66 PP S ++ +LI YQQTK E ATAL+ ++EP++ AA K+AR+RPD YEDL+Q+G+++ Sbjct: 6 PPLSKSKLDALISAYQQTKTEEAATALLVRFEPLIAAAAKKMARSRPDFYEDLFQIGRLS 65 Query: 67 LIRLLQQYDISLGIPFEPYAMKSMIGHMKNFLRDKSWYIQVPRRIKEKGALVQQAIDELT 126 +RLL YD G FE YAMKS+IG+MKN+LRDK+WYIQVPR++KEKG+ VQQAIDELT Sbjct: 66 FLRLLDHYDPKQGTSFESYAMKSLIGYMKNYLRDKAWYIQVPRKVKEKGSKVQQAIDELT 125 Query: 127 IRLERSPAVEEIAHYLDLTVEETVEVLAGRECYHYVSLDSPLSQEETGA-TLGELISSEA 185 ++LERSP ++EIA +L L+VEET+E+LAGR+ Y VSLD+P+ E A T+GE ++ EA Sbjct: 126 VKLERSPTIDEIAGHLGLSVEETIEILAGRDHYQAVSLDAPVQDGEKDATTIGEFVADEA 185 Query: 186 NDYETVEKRMDLQQAXXXXXXXXXXXXXXAFQDGQSQRAIAQKLGVSQMSVSRIQKRATE 245 N+ E++ +RMDL+QA F+ G++QR++A++LGVSQM++SRIQKRA Sbjct: 186 NEIESLIERMDLEQAIGKLSEQEQIVIDAIFRRGETQRSLAERLGVSQMTISRIQKRAIA 245 Query: 246 KLKQIMANSS 255 KLK+ +A S Sbjct: 246 KLKRQLAAYS 255 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 0.315 0.129 0.354 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: 1,250,234,402 Number of extensions: 45217631 Number of successful extensions: 136889 Number of sequences better than 1.0e-05: 2138 Number of HSP's gapped: 136343 Number of HSP's successfully gapped: 2138 Length of query: 256 Length of database: 3,060,696,203 Length adjustment: 133 Effective length of query: 123 Effective length of database: 1,807,701,208 Effective search space: 222347248584 Effective search space used: 222347248584 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 130 (54.7 bits)