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: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value BH0529 [K] COG1191 DNA-directed RNA polymerase specialized sigma... 167 2e-41 BS_sigB [K] COG1191 DNA-directed RNA polymerase specialized sigm... 163 2e-40 all3853 [K] COG1191 DNA-directed RNA polymerase specialized sigm... 98 1e-20 BH1538 [K] COG1191 DNA-directed RNA polymerase specialized sigma... 91 1e-18 BS_sigF [K] COG1191 DNA-directed RNA polymerase specialized sigm... 85 1e-16 >BH0529 [K] COG1191 DNA-directed RNA polymerase specialized sigma subunit Length = 261 Score = 167 bits (423), Expect = 2e-41, Method: Compositional matrix adjust. Identities = 92/239 (38%), Positives = 140/239 (58%), Gaps = 3/239 (1%) Query: 12 NEAVSLIWEYQQTKDNEIATALIRKYEPMVKMAAGKIARNRPDLYEDLYQVGQMALIRLL 71 +E I YQQ D EI T L++ YEP+V A K +R+R +DL QVG + L+ Sbjct: 13 DEVYDWIESYQQGADEEIQTKLVKHYEPLVHSLARKFSRSRAH-DDDLIQVGMVGLLAAF 71 Query: 72 QQYDISLGIPFEPYAMKSMIGHMKNFLRDKSWYIQVPRRIKEKGALVQQAIDELTIRLER 131 ++YD G FE +A+ ++IG +K F+RDK+W + VPRRIKE G +++A DEL L+R Sbjct: 72 ERYDPKYGRSFESFAVPTIIGEIKRFIRDKTWSVHVPRRIKELGPKIKKAADELASELQR 131 Query: 132 SPAVEEIAHYLDLTVEETVEVLAGRECYHYVSLDSPLSQEETGA--TLGELISSEANDYE 189 SP VEEIA +L ++ EE +E + + Y +S+D L + G TL +L+ E YE Sbjct: 132 SPRVEEIADFLGVSEEEVLETMEMGKSYQALSVDRSLEADPEGGEVTLLDLVGQEDGGYE 191 Query: 190 TVEKRMDLQQAXXXXXXXXXXXXXXAFQDGQSQRAIAQKLGVSQMSVSRIQKRATEKLK 248 +++M L++A + + SQ+ +LG+SQM VSR+Q+RA +KL+ Sbjct: 192 KADQQMLLEKAFQVLDEREKQILLCTYFEHLSQKETGHRLGISQMHVSRLQRRALKKLR 250 >BS_sigB [K] COG1191 DNA-directed RNA polymerase specialized sigma subunit Length = 264 Score = 163 bits (413), Expect = 2e-40, Method: Compositional matrix adjust. Identities = 85/242 (35%), Positives = 144/242 (59%), Gaps = 3/242 (1%) Query: 12 NEAVSLIWEYQQTKDNEIATALIRKYEPMVKMAAGKIARNRPDLYEDLYQVGQMALIRLL 71 +E LI +YQ +D + L+R Y +V M A K ++ + +EDL QVG + L+ + Sbjct: 15 DEVDRLISDYQTKQDEQAQETLVRVYTNLVDMLAKKYSKGKS-FHEDLRQVGMIGLLGAI 73 Query: 72 QQYDISLGIPFEPYAMKSMIGHMKNFLRDKSWYIQVPRRIKEKGALVQQAIDELTIRLER 131 ++YD +G FE +A+ ++IG +K FLRDK+W + VPRRIKE G ++ A+D+LT +R Sbjct: 74 KRYDPVVGKSFEAFAIPTIIGEIKRFLRDKTWSVHVPRRIKELGPRIKMAVDQLTTETQR 133 Query: 132 SPAVEEIAHYLDLTVEETVEVLAGRECYHYVSLDSPLSQEETGATLG--ELISSEANDYE 189 SP VEEIA +LD++ EE +E + + Y +S+D + + G+T+ +++ S+ + YE Sbjct: 134 SPKVEEIAEFLDVSEEEVLETMEMGKSYQALSVDHSIEADSDGSTVTILDIVGSQEDGYE 193 Query: 190 TVEKRMDLQQAXXXXXXXXXXXXXXAFQDGQSQRAIAQKLGVSQMSVSRIQKRATEKLKQ 249 V +++ LQ + +SQ+ LG+SQM VSR+Q++A +KL++ Sbjct: 194 RVNQQLMLQSVLHVLSDREKQIIDLTYIQNKSQKETGDILGISQMHVSRLQRKAVKKLRE 253 Query: 250 IM 251 + Sbjct: 254 AL 255 >all3853 [K] COG1191 DNA-directed RNA polymerase specialized sigma subunit Length = 258 Score = 98.2 bits (243), Expect = 1e-20, Method: Compositional matrix adjust. Identities = 74/258 (28%), Positives = 131/258 (50%), Gaps = 17/258 (6%) Query: 7 PPESMNEAVSLIW----EYQQTKDNEIATALIRKYEPMVKMAAGKIARNRPDLYEDLYQV 62 P + NE IW EYQQ++ + L++ +V+ A + Y+DL QV Sbjct: 2 PTTATNELKYEIWQLLREYQQSRSETVRNQLVKLNLGLVRKEAHYWMNQCRENYDDLVQV 61 Query: 63 GQMALIRLLQQYDISLGIPFEPYAMKSMIGHMKNFLRDKSWYIQVPRR---IKEKGALVQ 119 G + LIR +++++I+ G F +A+ + G ++++LRDK +++PRR I+++ V Sbjct: 62 GCLGLIRAIERFEIAKGHAFSSFAIPYIRGEIQHYLRDKGVTVRIPRRYLAIQQRAIGVS 121 Query: 120 QAIDELTIRLERSPAVEEIAHYLDLTVEETVEVLAGRECYHYVSLDSPLSQEETGAT-LG 178 +++ E + R P E+A L+++ +E E+ +SLD P+ E GAT LG Sbjct: 122 RSLRE---QYNRQPTDSELATALEISPDEWQEIKLAWVNRAPLSLDVPVQDGEEGATSLG 178 Query: 179 ELISSEANDYETV----EKRMDLQQAXXXXXXXXXXXXXXAFQDGQSQRAIAQKLGVSQM 234 EL+ + Y + E ++ LQQA F +Q+ +A+ LG+S + Sbjct: 179 ELVPD--HHYRSFQLAQEDQIRLQQALFQLEQRTREVLECVFLQDLTQKQVAEHLGISVV 236 Query: 235 SVSRIQKRATEKLKQIMA 252 +VSR K+ + LK +M Sbjct: 237 TVSRRVKKGLDLLKHLMC 254 >BH1538 [K] COG1191 DNA-directed RNA polymerase specialized sigma subunit Length = 252 Score = 91.3 bits (225), Expect = 1e-18, Method: Compositional matrix adjust. Identities = 63/202 (31%), Positives = 105/202 (51%), Gaps = 4/202 (1%) Query: 51 NRPDLYEDLYQVGQMALIRLLQQYDISLGIPFEPYAMKSMIGHMKNFLRDKSWYIQVPRR 110 NR +DL+Q+G + LI+ + ++D+S + F YA+ +IG ++ FLRD ++V R Sbjct: 54 NRGYEADDLFQIGCIGLIKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRS 112 Query: 111 IKEKGALVQQAIDELTIRLERSPAVEEIAHYLDLTVEETVEVLAGRECYHYVSLDSPLSQ 170 IKE G +++ D++T L R+P V EIA L++T EE V AG S+ + Sbjct: 113 IKELGNKIRKLKDDMTKTLGRTPTVNEIAEQLEITPEEV--VFAGDASRSLSSIHETVY- 169 Query: 171 EETGATLGELISSEANDYETVEKRMDLQQAXXXXXXXXXXXXXXAFQDGQSQRAIAQKLG 230 E G + L E ++ L++A + Q+Q +AQ+LG Sbjct: 170 ENDGDPITLLDQLEDQSETRWFDKIALKEAIHNLEERERLIVYLRYYKDQTQSEVAQRLG 229 Query: 231 VSQMSVSRIQKRATEKLKQIMA 252 +SQ+ VSR++K+ E +K +A Sbjct: 230 ISQVQVSRLEKKILETMKANIA 251 >BS_sigF [K] COG1191 DNA-directed RNA polymerase specialized sigma subunit Length = 255 Score = 85.1 bits (209), Expect = 1e-16, Method: Compositional matrix adjust. Identities = 55/199 (27%), Positives = 106/199 (53%), Gaps = 4/199 (2%) Query: 57 EDLYQVGQMALIRLLQQYDISLGIPFEPYAMKSMIGHMKNFLRDKSWYIQVPRRIKEKGA 116 +DL+Q+G + L++ + ++D++ + F YA+ +IG ++ F+RD ++V R +KE G Sbjct: 60 DDLFQIGCIGLLKSVDKFDLTYDVRFSTYAVPMIIGEIQRFIRDDG-TVKVSRSLKELGN 118 Query: 117 LVQQAIDELTIRLERSPAVEEIAHYLDLTVEETVEVLAGRECYHYVSLDSPLSQEETGAT 176 +++A DEL+ L R P V+EIA +L++ E +V+ +E S E G Sbjct: 119 KIRRAKDELSKTLGRVPTVQEIADHLEIEAE---DVVLAQEAVRAPSSIHETVYENDGDP 175 Query: 177 LGELISSEANDYETVEKRMDLQQAXXXXXXXXXXXXXXAFQDGQSQRAIAQKLGVSQMSV 236 + L N E ++ L++A + Q+Q +A++LG+SQ+ V Sbjct: 176 ITLLDQIADNSEEKWFDKIALKEAISDLEEREKLIVYLRYYKDQTQSEVAERLGISQVQV 235 Query: 237 SRIQKRATEKLKQIMANSS 255 SR++K+ +++K M ++ Sbjct: 236 SRLEKKILKQIKVQMDHTD 254 Database: COG Posted date: Aug 3, 2010 9:58 AM Number of letters in database: 38,378,431 Number of sequences in database: 115,334 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: 115334 Number of Hits to DB: 15,869,591 Number of extensions: 584832 Number of successful extensions: 1365 Number of sequences better than 1.0e-05: 39 Number of HSP's gapped: 1358 Number of HSP's successfully gapped: 39 Length of query: 256 Length of database: 38,378,431 Length adjustment: 104 Effective length of query: 152 Effective length of database: 26,383,695 Effective search space: 4010321640 Effective search space used: 4010321640 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: 114 (48.5 bits)