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= 0290.0072.p (187 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value BH0263 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 80 2e-15 BS_sigW [K] COG1595 DNA-directed RNA polymerase specialized sigm... 79 4e-15 CAC3267 [K] COG1595 DNA-directed RNA polymerase specialized sigm... 78 9e-15 BS_sigX [K] COG1595 DNA-directed RNA polymerase specialized sigm... 76 3e-14 Rv1221 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 75 5e-14 >BH0263 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 187 Score = 80.1 bits (196), Expect = 2e-15, Method: Compositional matrix adjust. Identities = 47/161 (29%), Positives = 86/161 (53%), Gaps = 10/161 (6%) Query: 6 ELFETYNKDVYRTCYYMVHDAADAEDLCQEIFITVFRS--NWQSVEYLKSWMMKITVNTC 63 EL E Y VY+ Y MV + +A+D+ QE F+ + + + +W+ +I N Sbjct: 22 ELVELYKDKVYQVAYRMVGNVHEAQDVAQEAFLRAYTNIDTYDIQRKFSTWLFRIATNVA 81 Query: 64 LNHLKRRRS---LQQKV-AANLHFFQGKSVVN--TVEGLIEQKETSREWMIH-LSRLPVK 116 ++ L++R+ L+ V A+ + + + V+ + Q ET R+W+ + LP K Sbjct: 82 IDRLRKRKPDFHLEDPVQGADGLTIESQLAADEEPVDDQVIQMET-RDWIQQEIQALPPK 140 Query: 117 IRAVLTLRYMHDFSLAEVSEALSIPLGTAKSRLHKGLKLMK 157 R + L+YM D SL E+S+ L +P+ T K+R+H+G + ++ Sbjct: 141 YRMAVLLKYMEDLSLKEISDILDLPVSTVKTRIHRGREALR 181 >BS_sigW [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 187 Score = 79.0 bits (193), Expect = 4e-15, Method: Compositional matrix adjust. Identities = 44/158 (27%), Positives = 83/158 (52%), Gaps = 14/158 (8%) Query: 6 ELFETYNKDVYRTCYYMVHDAADAEDLCQEIFITVFRSNWQSVEY---LKSWMMKITVNT 62 ++ + Y +Y+ CY M+ + +AED+ QE FI + N S + +W+ +I N Sbjct: 22 DIVDIYKDKIYQLCYRMLGNVHEAEDIAQEAFIRAY-VNIDSFDINRKFSTWLYRIATNL 80 Query: 63 CLNHLKRRRS---LQQKVAANLHFFQGKSVVNTVEGLIEQK-----ETSREWMIHLSRLP 114 ++ +++++ L +VA +V +G++ + E S + +LP Sbjct: 81 TIDRIRKKKPDYYLDAEVAGTEGLTMYSQIV--ADGVLPEDAVVSLELSNTIQQKILKLP 138 Query: 115 VKIRAVLTLRYMHDFSLAEVSEALSIPLGTAKSRLHKG 152 K R V+ L+Y+ + SL E+ E L+IP+GT K+R+H+G Sbjct: 139 DKYRTVIVLKYIDELSLIEIGEILNIPVGTVKTRIHRG 176 >CAC3267 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 190 Score = 77.8 bits (190), Expect = 9e-15, Method: Compositional matrix adjust. Identities = 54/172 (31%), Positives = 84/172 (48%), Gaps = 27/172 (15%) Query: 6 ELFETYNKDVYRTCYYMVHDAADAEDLCQEIFITVFRS--NWQSVEYLKSWMMKITVNTC 63 +LF Y K +Y CY + +DA DL QEI+I VF++ N+ W+ KI+VNTC Sbjct: 21 QLFHLYEKYLYNLCYGYTQNTSDAMDLVQEIYIKVFKNIKNFDENLPFHPWVRKISVNTC 80 Query: 64 LNHLKRRR----SLQQK-----------VAANLHFFQGKSVVNTVEGLIEQKETSREWMI 108 LN + R SL K +A + + Q VVN + E +E Sbjct: 81 LNFKRDNRGNVMSLNSKYYDSEFEEEDRLAEDYNMEQ--EVVNRINN-----EVVKE--- 130 Query: 109 HLSRLPVKIRAVLTLRYMHDFSLAEVSEALSIPLGTAKSRLHKGLKLMKNVL 160 + +L R V+ LRY D S E++ L +P+GT K+++++ ++K L Sbjct: 131 SIKKLTYDYRMVIMLRYYEDLSYDEIASVLDMPIGTVKTKIYRAKNVLKKSL 182 >BS_sigX [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 194 Score = 75.9 bits (185), Expect = 3e-14, Method: Compositional matrix adjust. Identities = 48/186 (25%), Positives = 95/186 (51%), Gaps = 8/186 (4%) Query: 7 LFETYNKDVYRTCYYMVHDAADAEDLCQEIFITVFRS--NWQSVEYLKSWMMKITVNTCL 64 L++TY++D+Y+ +YMV D EDL QE++I V S ++ K+W++ I + + Sbjct: 8 LYDTYHQDLYQFLFYMVKDKNQTEDLLQEVYIRVLNSYHTFEGRSSEKTWLLSIARHVAI 67 Query: 65 NHLKRRRSLQQKVAANLHFFQGKSVVNT---VEGLIEQKETSREWMIHLSRLPVKIRAVL 121 + +++++++Q++ + + V + + L Q E RE L + + RAV+ Sbjct: 68 DWFRKQQTIRQRILGTFD-WDTQDVRDQQLLPDELAVQHENVREISCALDQCTIDQRAVI 126 Query: 122 TLRYMHDFSLAEVSEALSIPLGTAKSRLHKGLKLMKN--VLLETGIPEQEWKGEHYEQAG 179 LR++ +S+ E ++AL K+ H+GLK+++ LL + + E + E G Sbjct: 127 ILRFIQGYSIQETAKALRFSESKVKTTQHRGLKVLRKHMELLREELMDDEVRMERRTDKG 186 Query: 180 ACTQAS 185 S Sbjct: 187 VVKSTS 192 >Rv1221 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 257 Score = 75.5 bits (184), Expect = 5e-14, Method: Compositional matrix adjust. Identities = 47/157 (29%), Positives = 79/157 (50%), Gaps = 4/157 (2%) Query: 6 ELFETYNKDVYRTCYYMVHDAADAEDLCQEIFITVFRS--NWQSVEYLKSWMMKITVNTC 63 EL + VYR Y + + DAEDL QE FI VFRS N+Q + + W+ +IT N Sbjct: 86 ELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSVQNYQPGTF-EGWLHRITTNLF 144 Query: 64 LNHLKRRRSLQQKVAANLHFFQGKSVVNTVEGLIEQKETSREWMIHLSRLPVKIRAVLTL 123 L+ ++RR ++ + A + + + E + + L+ LP + RA + L Sbjct: 145 LDMVRRRARIRME-ALPEDYDRVPADEPNPEQIYHDARLGPDLQAALASLPPEFRAAVVL 203 Query: 124 RYMHDFSLAEVSEALSIPLGTAKSRLHKGLKLMKNVL 160 + S E+ L + LGT +SR+H+G + +++ L Sbjct: 204 CDIEGLSYEEIGATLGVKLGTVRSRIHRGRQALRDYL 240 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 0.132 0.392 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: 12,674,906 Number of extensions: 451985 Number of successful extensions: 843 Number of sequences better than 1.0e-05: 49 Number of HSP's gapped: 804 Number of HSP's successfully gapped: 49 Length of query: 187 Length of database: 38,378,431 Length adjustment: 100 Effective length of query: 87 Effective length of database: 26,845,031 Effective search space: 2335517697 Effective search space used: 2335517697 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 (21.9 bits) S2: 112 (47.8 bits)