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= 0264.0033.p (260 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value BH2554 [K] COG1191 DNA-directed RNA polymerase specialized sigma... 446 e-125 BS_sigG [K] COG1191 DNA-directed RNA polymerase specialized sigm... 428 e-120 CAC1696 [K] COG1191 DNA-directed RNA polymerase specialized sigm... 402 e-112 BS_sigF [K] COG1191 DNA-directed RNA polymerase specialized sigm... 237 2e-62 BH1538 [K] COG1191 DNA-directed RNA polymerase specialized sigma... 234 8e-62 >BH2554 [K] COG1191 DNA-directed RNA polymerase specialized sigma subunit Length = 261 Score = 446 bits (1148), Expect = e-125, Method: Compositional matrix adjust. Identities = 219/262 (83%), Positives = 238/262 (90%), Gaps = 3/262 (1%) Query: 1 MTRNKVEICGVDTAKLPVLTNVEMRELFTSLQQQGERSAREKLVNGNLRLVLSVIQRFNN 60 MTRNKVEICGVDT+KLPVL N EMRELF LQ G+ SARE LVNGNLRLVLSVIQRFNN Sbjct: 1 MTRNKVEICGVDTSKLPVLKNQEMRELFARLQS-GDTSARETLVNGNLRLVLSVIQRFNN 59 Query: 61 RGEFVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLR 120 RGE+VDDLFQVGCIGLMK+IDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLR Sbjct: 60 RGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLR 119 Query: 121 DIAYKALQVRDSLTNQNSRE--PTIFEISEALGVPKEDVVFALDAIQDPVSLFEPIYHDG 178 DIAYKALQVRD L + RE PT+ EI++ LGVPKEDVVFALDAIQDPVSLFEPIY+DG Sbjct: 120 DIAYKALQVRDQLMGEKQREKEPTVQEIAKELGVPKEDVVFALDAIQDPVSLFEPIYNDG 179 Query: 179 GDPIYVMDQISDDKNKDVSWIEEIALREAMQRLGQREKRILSMRFFEGKTQMEVADEIGI 238 GDPIYVMDQISDD+NKDV W++EIAL+EAM RL REK IL+MRF++GKTQMEVA+EIGI Sbjct: 180 GDPIYVMDQISDDRNKDVQWVDEIALKEAMVRLNDREKLILNMRFYQGKTQMEVAEEIGI 239 Query: 239 SQAQVSRLEKSAIQQMQKHVKS 260 SQAQVSRLEK+AIQQM KH +S Sbjct: 240 SQAQVSRLEKAAIQQMSKHAQS 261 >BS_sigG [K] COG1191 DNA-directed RNA polymerase specialized sigma subunit Length = 260 Score = 428 bits (1100), Expect = e-120, Method: Compositional matrix adjust. Identities = 205/258 (79%), Positives = 233/258 (90%) Query: 1 MTRNKVEICGVDTAKLPVLTNVEMRELFTSLQQQGERSAREKLVNGNLRLVLSVIQRFNN 60 M+RNKVEICGVDT+KLPVL N EMR+LF LQ +G+ SAREKLVNGNLRLVLSVIQRFNN Sbjct: 1 MSRNKVEICGVDTSKLPVLKNEEMRKLFRQLQDEGDDSAREKLVNGNLRLVLSVIQRFNN 60 Query: 61 RGEFVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLR 120 RGE+VDDLFQVGCIGLMK+IDNFDLS NVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLR Sbjct: 61 RGEYVDDLFQVGCIGLMKSIDNFDLSHNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLR 120 Query: 121 DIAYKALQVRDSLTNQNSREPTIFEISEALGVPKEDVVFALDAIQDPVSLFEPIYHDGGD 180 DIAYKALQVR+ L ++ S+EPT +I++ L VP E++VFALDAIQDPVSLFEPIY+DGGD Sbjct: 121 DIAYKALQVRERLISETSKEPTAEDIAKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGGD 180 Query: 181 PIYVMDQISDDKNKDVSWIEEIALREAMQRLGQREKRILSMRFFEGKTQMEVADEIGISQ 240 PIYVMDQISD++N D WIEE+AL+E M+RL REK IL RFF+GKTQMEVA+EIGISQ Sbjct: 181 PIYVMDQISDERNTDSQWIEELALKEGMRRLNDREKMILRKRFFQGKTQMEVAEEIGISQ 240 Query: 241 AQVSRLEKSAIQQMQKHV 258 AQVSRLEK+AI+QM K++ Sbjct: 241 AQVSRLEKAAIKQMNKNI 258 >CAC1696 [K] COG1191 DNA-directed RNA polymerase specialized sigma subunit Length = 257 Score = 402 bits (1032), Expect = e-112, Method: Compositional matrix adjust. Identities = 190/258 (73%), Positives = 228/258 (88%), Gaps = 1/258 (0%) Query: 1 MTRNKVEICGVDTAKLPVLTNVEMRELFTSLQQQGERSAREKLVNGNLRLVLSVIQRFNN 60 M NKVEICGV+T+KLPVL EMREL S++ G +AREK + GNLRLVLSVIQRFNN Sbjct: 1 MVINKVEICGVNTSKLPVLKEKEMRELLISMRN-GNTTAREKFIKGNLRLVLSVIQRFNN 59 Query: 61 RGEFVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLR 120 RGE DDLFQVGCIGL+K+IDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN IRVSRSLR Sbjct: 60 RGENADDLFQVGCIGLIKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNSIRVSRSLR 119 Query: 121 DIAYKALQVRDSLTNQNSREPTIFEISEALGVPKEDVVFALDAIQDPVSLFEPIYHDGGD 180 DIAY+ALQVRD L ++N++EPT+ +I++ L +P+E+V+FALDAIQDP+SLFEPIYHD GD Sbjct: 120 DIAYRALQVRDRLISKNNKEPTVSQIAKELKIPREEVIFALDAIQDPISLFEPIYHDDGD 179 Query: 181 PIYVMDQISDDKNKDVSWIEEIALREAMQRLGQREKRILSMRFFEGKTQMEVADEIGISQ 240 IYVMDQISD+KN D SW++ I+++EAM++L REK IL+MRFF+G+TQMEVADEIGISQ Sbjct: 180 AIYVMDQISDNKNLDDSWLQNISIKEAMKKLSDREKMILNMRFFDGRTQMEVADEIGISQ 239 Query: 241 AQVSRLEKSAIQQMQKHV 258 AQVSRLEK+A++ M+K+V Sbjct: 240 AQVSRLEKTALKHMKKYV 257 >BS_sigF [K] COG1191 DNA-directed RNA polymerase specialized sigma subunit Length = 255 Score = 237 bits (604), Expect = 2e-62, Method: Compositional matrix adjust. Identities = 115/237 (48%), Positives = 174/237 (73%), Gaps = 3/237 (1%) Query: 19 LTNVEMRELFTSLQQQGERSAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCIGLMK 78 L + E++EL Q G++ AR+ L+ N+RLV SV+QRF NRG DDLFQ+GCIGL+K Sbjct: 14 LKDHEVKELIKQ-SQNGDQQARDLLIEKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLK 72 Query: 79 AIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVRDSLTNQNS 138 ++D FDL+ +V+FSTYAVPMIIGEI+R++RD+ ++VSRSL+++ K + +D L+ Sbjct: 73 SVDKFDLTYDVRFSTYAVPMIIGEIQRFIRDDGTVKVSRSLKELGNKIRRAKDELSKTLG 132 Query: 139 REPTIFEISEALGVPKEDVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDDKNKDVSW 198 R PT+ EI++ L + EDVV A +A++ P S+ E +Y + GDPI ++DQI+D N + W Sbjct: 133 RVPTVQEIADHLEIEAEDVVLAQEAVRAPSSIHETVYENDGDPITLLDQIAD--NSEEKW 190 Query: 199 IEEIALREAMQRLGQREKRILSMRFFEGKTQMEVADEIGISQAQVSRLEKSAIQQMQ 255 ++IAL+EA+ L +REK I+ +R+++ +TQ EVA+ +GISQ QVSRLEK ++Q++ Sbjct: 191 FDKIALKEAISDLEEREKLIVYLRYYKDQTQSEVAERLGISQVQVSRLEKKILKQIK 247 >BH1538 [K] COG1191 DNA-directed RNA polymerase specialized sigma subunit Length = 252 Score = 234 bits (598), Expect = 8e-62, Method: Compositional matrix adjust. Identities = 114/240 (47%), Positives = 173/240 (72%), Gaps = 3/240 (1%) Query: 19 LTNVEMRELFTSLQQQGERSAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCIGLMK 78 T+ E+++L Q G++ AR+++V+ N RLV SV+QRF NRG DDLFQ+GCIGL+K Sbjct: 14 FTDEEIKQLIAQ-SQAGDQEARDQIVSRNTRLVWSVVQRFLNRGYEADDLFQIGCIGLIK 72 Query: 79 AIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVRDSLTNQNS 138 ++D FDLS +VKFSTYAVPMIIGEI+R+LRD+ ++VSRS++++ K +++D +T Sbjct: 73 SVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDGTVKVSRSIKELGNKIRKLKDDMTKTLG 132 Query: 139 REPTIFEISEALGVPKEDVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDDKNKDVSW 198 R PT+ EI+E L + E+VVFA DA + S+ E +Y + GDPI ++DQ+ D + W Sbjct: 133 RTPTVNEIAEQLEITPEEVVFAGDASRSLSSIHETVYENDGDPITLLDQLED--QSETRW 190 Query: 199 IEEIALREAMQRLGQREKRILSMRFFEGKTQMEVADEIGISQAQVSRLEKSAIQQMQKHV 258 ++IAL+EA+ L +RE+ I+ +R+++ +TQ EVA +GISQ QVSRLEK ++ M+ ++ Sbjct: 191 FDKIALKEAIHNLEERERLIVYLRYYKDQTQSEVAQRLGISQVQVSRLEKKILETMKANI 250 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 0.136 0.374 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: 17,219,654 Number of extensions: 635833 Number of successful extensions: 2058 Number of sequences better than 1.0e-05: 112 Number of HSP's gapped: 1926 Number of HSP's successfully gapped: 115 Length of query: 260 Length of database: 38,378,431 Length adjustment: 104 Effective length of query: 156 Effective length of database: 26,383,695 Effective search space: 4115856420 Effective search space used: 4115856420 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: 115 (48.9 bits)