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= 0331.0005.p (317 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B1D828.1 B1D828_9BACL RNA polymerase, sigma-24 subunit, ECF subf... 324 8e-87 B3KCX3.1 B3KCX3_9BACI RNA polymerase sigma factor, sigma-70 family 316 2e-84 Q9KF25.1 Q9KF25_BACHD RNA polymerase ECF-type sigma factor 236 2e-60 C0Z641.1 C0Z641_BREBN RNA polymerase ECF-type sigma factor 230 1e-58 B3K3T9.1 B3K3T9_9BACI RNA polymerase sigma factor, sigma-70 family 221 1e-55 >B1D828.1 B1D828_9BACL RNA polymerase, sigma-24 subunit, ECF subfamily Length = 284 Score = 324 bits (830), Expect = 8e-87, Method: Compositional matrix adjust. Identities = 160/281 (56%), Positives = 201/281 (71%) Query: 33 MEELYQKYKGLLFKLAYQLTGSVTDAEDVVHDVFLKIVDVPPEKLAEPKAYLCKMVTNRC 92 M ELY++YKGLLF LAYQLTGS DAED V DVFLK+ ++ PEKL EPKAYLCKM+TNRC Sbjct: 1 MIELYERYKGLLFSLAYQLTGSAADAEDAVQDVFLKVQNMNPEKLHEPKAYLCKMITNRC 60 Query: 93 RDLQKSARRKREQYYGEWLPEPLHSMNDDAIDAVVRDDLLSYAMLVLLERLSPTERVVFV 152 D +SAR +REQY G WLPEP+ DD ++ VVR DLLSYAML LLERLSP+ER VFV Sbjct: 61 LDHLRSARVRREQYVGPWLPEPIAQYYDDGLEEVVRHDLLSYAMLALLERLSPSERAVFV 120 Query: 153 LREALGFDYHEIAELVEKSEVNCRKLFSRANAKMGITSEQLVHSEGATPELVHGFLSALK 212 LREALGFDY IAEL KSE NCRKL SRA AKMG+T E+L+ ++ F++AL Sbjct: 121 LREALGFDYPAIAELTGKSEQNCRKLMSRARAKMGLTEEELLTGGTIEQAWINRFVAALS 180 Query: 213 QGNLNQILSILDQEVVLVSDGGGKVSAVVEPLSTRELVAQFLVGPLHRASTIDGVHIEVV 272 +G ++ +LS+L ++ VLVSDGGGK SA V P+ TRE VAQFL+G ++ + +E+ Sbjct: 181 EGEVDIVLSMLAEDAVLVSDGGGKASAAVRPIETRERVAQFLLGIFRKSQITSHMTVELK 240 Query: 273 QMNRQPAFILRSSEGIHTVGIFHVEKNRIRNIYIVRNPDKL 313 +N +PAF+ R + +V + + I+IVRNPDKL Sbjct: 241 PLNGEPAFVFRQEGIVDSVVFLEQREEVLHRIFIVRNPDKL 281 >B3KCX3.1 B3KCX3_9BACI RNA polymerase sigma factor, sigma-70 family Length = 286 Score = 316 bits (810), Expect = 2e-84, Method: Compositional matrix adjust. Identities = 157/283 (55%), Positives = 200/283 (70%), Gaps = 2/283 (0%) Query: 33 MEELYQKYKGLLFKLAYQLTGSVTDAEDVVHDVFLKIVDVPPEKLAEPKAYLCKMVTNRC 92 M ELY++YKG+LF LAYQ+TG+VTDAED V DVF+K+ +P +++ EPKAYLCKMVTNRC Sbjct: 1 MLELYEQYKGVLFHLAYQMTGTVTDAEDAVQDVFVKVQSLPIKQIREPKAYLCKMVTNRC 60 Query: 93 RDLQKSARRKREQYYGEWLPEPLHSMNDDAIDAVVRDDLLSYAMLVLLERLSPTERVVFV 152 D KSAR +REQY+G WLPEP+ + + + +LLSYAMLVLLERLSP+ER VFV Sbjct: 61 LDEIKSARNRREQYFGPWLPEPIPESYSETYETIENQELLSYAMLVLLERLSPSERAVFV 120 Query: 153 LREALGFDYHEIAELVEKSEVNCRKLFSRANAKMGITSEQLVHSEGATPELVHGFLSALK 212 LREALGFDY EIA L++K+E NCRKL SRA KMGIT E L+ E V F +AL Sbjct: 121 LREALGFDYPEIAGLIDKTEANCRKLMSRARGKMGITEEDLIGVGSVEEEWVKRFFTALS 180 Query: 213 QGNLNQILSILDQEVVLVSDGGGKVSAVVEPLSTRELVAQFLVGPLHRASTIDGV--HIE 270 +GN +LS+L + VL++DGGGKV A P+ TRE VA+FL G L +A DGV IE Sbjct: 181 EGNAEHVLSLLADDAVLLADGGGKVIAAARPVETRERVARFLSGILRQALLEDGVAPEIE 240 Query: 271 VVQMNRQPAFILRSSEGIHTVGIFHVEKNRIRNIYIVRNPDKL 313 V ++N Q + R + + V F++ +++IYIVRNPDKL Sbjct: 241 VRELNHQTGVVFRQAGNVTGVVFFNIRNGLLQDIYIVRNPDKL 283 >Q9KF25.1 Q9KF25_BACHD RNA polymerase ECF-type sigma factor Length = 285 Score = 236 bits (603), Expect = 2e-60, Method: Compositional matrix adjust. Identities = 125/286 (43%), Positives = 178/286 (62%), Gaps = 7/286 (2%) Query: 28 IGSEDMEELYQKYKGLLFKLAYQLTGSVTDAEDVVHDVFLKIVDVPPEKLAEPKAYLCKM 87 I +ED E+L K LLF L Y+L GSVTDAED+V + FL+ ++ KAYLCKM Sbjct: 3 ISNEDYEQL----KPLLFSLGYRLLGSVTDAEDLVQETFLRAYQAEEREINNKKAYLCKM 58 Query: 88 VTNRCRDLQKSARRKREQYYGEWLPEPLHSMNDDAIDAVVRDDLLSYAMLVLLERLSPTE 147 +TNRC D+ KSARRKREQY G WLPEPL +DD +A+++ + LS A L ++E L+P E Sbjct: 59 MTNRCLDVLKSARRKREQYVGPWLPEPLLITSDDPSEAILQKEGLSMAYLRMMEHLTPHE 118 Query: 148 RVVFVLREALGFDYHEIAELVEKSEVNCRKLFSRANAKMGITSEQLVHSEGATPELVHGF 207 R VF+LRE F Y EIA ++EK E NCRKL+SRA K+ + +H E +V F Sbjct: 119 RAVFLLREVFTFSYREIASMMEKKEDNCRKLYSRAKEKLSAVKGESLHYEN-NRSVVDRF 177 Query: 208 LSALKQGNLNQILSILDQEVVLVSDGGGKVSAVVEPLSTRELVAQFLVGPLHRASTIDGV 267 + + + + +L +L V L +DGGGKV A + P+ T++ VA FL G + + Sbjct: 178 IHSFQTEDQGDLLELLSDHVTLYTDGGGKVRAALRPIYTKDHVAAFLFGIAKKRP--NDF 235 Query: 268 HIEVVQMNRQPAFILRSSEGIHTVGIFHVEKNRIRNIYIVRNPDKL 313 ++EV +N QPA I + ++ V F++ +I++IYI+ NP+KL Sbjct: 236 YVEVKNVNGQPALISYADSKLYNVICFYIVGGQIQDIYIIMNPEKL 281 >C0Z641.1 C0Z641_BREBN RNA polymerase ECF-type sigma factor Length = 295 Score = 230 bits (586), Expect = 1e-58, Method: Compositional matrix adjust. Identities = 122/289 (42%), Positives = 179/289 (61%), Gaps = 6/289 (2%) Query: 33 MEELYQKYKGLLFKLAYQLTGSVTDAEDVVHDVFLKIVDVPPEKLAEPKAYLCKMVTNRC 92 ME++Y++YK LLF LAY++TGSVT+AED+V D FL + + + K+YLCK VTNRC Sbjct: 5 MEDVYREYKSLLFSLAYRMTGSVTEAEDIVQDTFLALAGTEIQDIHHVKSYLCKAVTNRC 64 Query: 93 RDLQKSARRKREQYYGEWLPEPL--HSMNDDAIDAVVRDDLLSYAMLVLLERLSPTERVV 150 D+ KSAR KREQY GEWLPEP+ S +D + V+ ++ +SY +LVLLE+L T R V Sbjct: 65 LDVLKSARWKREQYVGEWLPEPMLDASETNDPLQTVIAEEAVSYGLLVLLEKLPSTLRAV 124 Query: 151 FVLREALGFDYHEIAELVEKSEVNCRKLFSRANAKMGITSEQ-LVHSEGATPELVHGFLS 209 FVLR AL ++Y EIA ++ +EVNCRK FS A K+ Q +V T LV + Sbjct: 125 FVLRTALDYEYSEIAAMLGMTEVNCRKKFSLARKKLAEAGYQAIVPQPSRTSSLVEQLMQ 184 Query: 210 ALKQGNLNQILSILDQEVVLVSDGGGKVSAVVEPLSTRELVAQFLVGPLHRASTIDGVHI 269 A+ + + ++ +L ++ V VSDGGGKV A + P+ + E + F +G R ++ + Sbjct: 185 AISKSDAKSLIGLLTKDAVFVSDGGGKVRAAIHPIFSDERITAFWMGVWPRWAS--HATM 242 Query: 270 EVVQMNRQPAFILRSSEGIHTV-GIFHVEKNRIRNIYIVRNPDKLKHAQ 317 ++ +N Q + S + T+ I E++RI +Y++ NPDKL H Q Sbjct: 243 QIRSINGQDGIAVYSEGQLKTIMQITMNEEDRIARLYMMVNPDKLAHLQ 291 >B3K3T9.1 B3K3T9_9BACI RNA polymerase sigma factor, sigma-70 family Length = 299 Score = 221 bits (562), Expect = 1e-55, Method: Compositional matrix adjust. Identities = 124/290 (42%), Positives = 174/290 (60%), Gaps = 14/290 (4%) Query: 34 EELYQKYKGLLFKLAYQLTGSVTDAEDVVHDVFLKIVDVPPEKLAEPKAYLCKMVTNRCR 93 +++Y +YK ++F LAY++ GS DAED+V DVF + V + ++ KAYL KM TNRC Sbjct: 4 DQIYIEYKPMMFGLAYRMLGSAADAEDIVQDVFSQFVQMDRGEVQNEKAYLAKMTTNRCI 63 Query: 94 DLQKSARRKREQYYGEWLPEPLHSMNDDAI---DAVVRDDLLSYAMLVLLERLSPTERVV 150 +L KS+RRKRE Y G WLPEP+ D I D R + + YA LVLL+RL+P ER + Sbjct: 64 NLLKSSRRKRETYTGPWLPEPMPDY--DMIQRSDPAERRENIGYAYLVLLQRLTPLERAI 121 Query: 151 FVLREALGFDYHEIAELVEKSEVNCRKLFSRANAKMGITSEQLVHSEGATPE----LVHG 206 ++ ++ LG +YHEI+E++ K+E++CRK FSRA KMG +E+ V EG E V Sbjct: 122 YIAKDTLGLEYHEISEMLGKTEISCRKTFSRAQQKMGRHTERPV-GEGTRTEKQERFVEA 180 Query: 207 FLSALKQGNLNQILSILDQEVVLVSDGGGKVSAVVEPLSTRELVAQFLVGPLHRASTIDG 266 FL A GN +LS L +EV L+SDGGGK A + P+ E V F G + S +G Sbjct: 181 FLRASDMGNFKPLLSFLKEEVTLLSDGGGKAKAAINPILGVERVRAFFEGLSAKGSFREG 240 Query: 267 VHIEVVQMNRQPAFILRSSEGIHTVGIFHVEKN--RIRNIYIVRNPDKLK 314 E V +N +P +L+ + V E + RI I++V NPDKL+ Sbjct: 241 --FEPVSINGEPGVLLKREGRVSMVLTAEWEPDLSRISRIFLVVNPDKLQ 288 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 0.320 0.137 0.390 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: 1,800,780,099 Number of extensions: 71576992 Number of successful extensions: 189412 Number of sequences better than 1.0e-05: 658 Number of HSP's gapped: 188858 Number of HSP's successfully gapped: 660 Length of query: 317 Length of database: 3,060,696,203 Length adjustment: 135 Effective length of query: 182 Effective length of database: 1,788,859,178 Effective search space: 325572370396 Effective search space used: 325572370396 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: 131 (55.1 bits)