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: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value BH0672 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 236 3e-62 SMb20030 [K] COG1595 DNA-directed RNA polymerase specialized sig... 147 3e-35 Rv1189 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 103 3e-22 MT1226 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 103 3e-22 Rv0182c [K] COG1595 DNA-directed RNA polymerase specialized sigm... 60 4e-09 >BH0672 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 285 Score = 236 bits (603), Expect = 3e-62, 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 >SMb20030 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 285 Score = 147 bits (370), Expect = 3e-35, Method: Compositional matrix adjust. Identities = 88/274 (32%), Positives = 146/274 (53%), Gaps = 12/274 (4%) Query: 44 LFKLAYQLTGSVTDAEDVVHDVFLKIVDVPPEKLAEPKAYLCKMVTNRCRDLQKSARRKR 103 L ++AY++ GSV DAED+V + F++ + ++ EP+A+L + VT C D KSARR+R Sbjct: 20 LMRVAYRMLGSVADAEDMVQEAFIRWMGADRAEVREPEAFLRRTVTRLCLDQLKSARRQR 79 Query: 104 EQYYGEWLPEPLHSMNDDAIDAVVRDDLLSYAMLVLLERLSPTERVVFVLREALGFDYHE 163 E Y G WLP+P+ + ++ +++ LERLSP ER F+L + G + E Sbjct: 80 ETYVGPWLPDPVVEEEEVED--------VTLPLMLALERLSPLERAAFLLHDVFGLGFEE 131 Query: 164 IAELVEKSEVNCRKLFSRANAKMGITSEQLVHSEGATPELVHGFLSALKQGNLNQILSIL 223 +A +++ CR+L +RA + + + EL F A + G++N ++L Sbjct: 132 VAATIQRDAAACRQLAARARTHVREARPRFHVEKERGLELAEAFFKASRSGDMNAFGAML 191 Query: 224 DQEVVLVSDGGGKVSAVVEPLSTRELVAQF--LVGPLHRASTIDGVHIEVVQMNRQPAFI 281 +V + +DGGGK SA + P+ + V + + L RA+ + + V N P FI Sbjct: 192 AADVSIHADGGGKRSAAIMPIIGFDAVMKVHEKLAALFRANGSKLLRVGFV--NGLPGFI 249 Query: 282 LRSSEGIHTVGIFHVEKNRIRNIYIVRNPDKLKH 315 ++G +E ++ IY+VRNPDKL+H Sbjct: 250 TMEADGEIQTTALEIEGGKVAAIYVVRNPDKLRH 283 >Rv1189 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 301 Score = 103 bits (257), Expect = 3e-22, Method: Compositional matrix adjust. Identities = 17/291 (5%), Positives = 52/291 (17%), Gaps = 35/291 (12%) Query: 37 YQKYKGLLFKLAYQLTGSVTDAEDVVHDVFLKIVDVPPEKLAEPKAYLCKMVTNRCRDLQ 96 + L + + E + T + Sbjct: 11 IAIVGRPNVGKSTLLNKLLGQKISITSRKAQTTRHRIVGIHTEGAYQAIYVDTPGLHMEE 70 Query: 97 KSA--RRKREQYYGEWLPEPLHSMNDDAIDAVVRDDLLSYAMLVLLERLSPTERVVFVLR 154 K A R + L + D+++ + + V ++ Sbjct: 71 KRAINRLMNKAASSSIGDVELVIFVVEGTRWTPDDEMVLNKLREGKAPVILAVNKVDNVQ 130 Query: 155 EALGFDYHEIAELVEKSEVNCRKLFSRANAKMGITSEQLVHSEGATPELV-HGFLSALKQ 213 E H + + ++ + + + T +V + Sbjct: 131 EKADLLPHLQFLASQMNFLDIVPISAETGLNVD-TIAAIVRKHLPEATHHFPEDYITDRS 189 Query: 214 GNLNQILSILDQEVVLVSDGGGKVSAV----VEPLSTRE-------LVAQFLVGPLHRAS 262 I ++ + + V LV + Sbjct: 190 QRFMASEIIREKLMRFLGAELPYSVTVEIERFVSNERGGYDINGLILVEREGQK------ 243 Query: 263 TIDGVHIEVVQMNRQPAFILRSSEGIHTVGIFHVEKNRIRNIYIVRNPDKL 313 + + ++ + + + Sbjct: 244 --------------KMVIGNKGAKIKTIGIEARKDMQEMFEAPVHLELWVK 280 >MT1226 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 290 Score = 103 bits (257), Expect = 3e-22, Method: Compositional matrix adjust. Identities = 83/291 (28%), Positives = 127/291 (43%), Gaps = 35/291 (12%) Query: 37 YQKYKGLLFKLAYQLTGSVTDAEDVVHDVFLKIVDVPPEKLAEPKAYLCKMVTNRCRDLQ 96 ++ ++ L LA+++ G + AED+V + F +++ P + + + +L + + C D Sbjct: 11 WRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGDIDDERGWLIVVTSRLCLDHI 70 Query: 97 KSA--RRKREQYYGEWLPEPLHSMNDDAIDAVVRDDLLSYAMLVLLERLSPTERVVFVLR 154 KSA RR+R Q W + D D V DD + A+L++LERL P ERVVFVL Sbjct: 71 KSASTRRERPQDIAAWHDGDASVSSVDPADRVTLDDEVRLALLIMLERLGPAERVVFVLH 130 Query: 155 EALGFDYHEIAELVEKSEVNCRKLFSRANAKMGITSEQLVHSEGATPELV-HGFLSALKQ 213 E G Y +IA + CR+L RA K+ S E A +V F+ A Sbjct: 131 EIFGLPYQQIATTIGSQASTCRQLAHRARRKIN-ESRIAASVEPAQHRVVTRAFIEACSN 189 Query: 214 GNLNQILSILDQEVVLVSDGGGKVSAV----VEPLSTRE-------LVAQFLVGPLHRAS 262 G+L+ +L +LD V D V V V P R LVAQ + G Sbjct: 190 GDLDTLLEVLDPGVAGEIDARKGVVVVGADRVGPTILRHWSHPATVLVAQPVCG------ 243 Query: 263 TIDGVHIEVVQMNRQPAFILRSSEGIHTVGIFHVEKNRIRNIYIVRNPDKL 313 QPA + + + V +E +I I+++ P L Sbjct: 244 --------------QPAVLAFVNRALAGVLALSIEAGKITKIHVLVQPSTL 280 >Rv0182c [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 370 Score = 60.5 bits (145), Expect = 4e-09, Method: Compositional matrix adjust. Identities = 56/225 (24%), Positives = 97/225 (43%), Gaps = 30/225 (13%) Query: 32 DMEELYQKYKGLLFKLAYQLTGSVTDAEDVVHDVFLKIVDVPPEKLAEP---KAYLCKMV 88 D + Y+ L Y++TGS+ DAED+V + L+ E A + +L ++ Sbjct: 57 DFSAHTEPYRRELLAHCYRMTGSLHDAEDLVQETLLRAWKAY-EGFAGKSSLRTWLHRIA 115 Query: 89 TNRC---------RDLQKSARRKREQYYGE--------WLPEPLHSMNDDAIDA---VVR 128 TN C R L R GE WL EPL + DD D V Sbjct: 116 TNTCLTALEGRRRRPLPTGLGRPSADPSGELVERREVSWL-EPLPDVTDDPADPSTIVGN 174 Query: 129 DDLLSYAMLVLLERLSPTERVVFVLREALGFDYHEIAELVEKSEVNCRKLFSRANAKMGI 188 + + A + L+ LSP +R V +LR+ L + E+A+ + S V L RA +++ Sbjct: 175 RESVRLAFVAALQHLSPRQRAVLLLRDVLQWKSAEVADAIGTSTVAVNSLLQRARSQLQT 234 Query: 189 TSEQLVHSEGA--TPE---LVHGFLSALKQGNLNQILSILDQEVV 228 A +PE L+ +++A + ++++++ + E + Sbjct: 235 VRPSAADRLSAPDSPEAQDLLARYIAAFEAYDIDRLVELFTAEAI 279 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 0.320 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: 115334 Number of Hits to DB: 22,977,648 Number of extensions: 974627 Number of successful extensions: 1968 Number of sequences better than 1.0e-05: 10 Number of HSP's gapped: 1973 Number of HSP's successfully gapped: 10 Length of query: 317 Length of database: 38,378,431 Length adjustment: 106 Effective length of query: 211 Effective length of database: 26,153,027 Effective search space: 5518288697 Effective search space used: 5518288697 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: 116 (49.3 bits)