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= 0530.0014.p (528 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... 92 2e-18 BS_sigW [K] COG1595 DNA-directed RNA polymerase specialized sigm... 80 1e-14 Cgl1096 [K] COG1595 DNA-directed RNA polymerase specialized sigm... 66 2e-10 CAC3267 [K] COG1595 DNA-directed RNA polymerase specialized sigm... 66 2e-10 Rv1221 [K] COG1595 DNA-directed RNA polymerase specialized sigma... 63 1e-09 >BH0263 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 187 Score = 92.0 bits (227), Expect = 2e-18, Method: Compositional matrix adjust. Identities = 60/180 (33%), Positives = 87/180 (48%), Gaps = 11/180 (6%) Query: 2 RQWVEKARQGDAEAFAQLMAHCRGMAYAVSYDMLKDVHLAEDAVQEAFLEAYLNLQKLSE 61 ++ V + R GD +AFA+L+ + Y V+Y M+ +VH A+D QEAFL AY N+ Sbjct: 6 KRLVREVRAGDEQAFAELVELYKDKVYQVAYRMVGNVHEAQDVAQEAFLRAYTNIDTYDI 65 Query: 62 PAAFPGWFRTIVVRQCQRTLRRKRHPLLPLDEALQGLQ----------NEPGAADILERK 111 F W I L RKR P L++ +QG +E D + + Sbjct: 66 QRKFSTWLFRIATNVAIDRL-RKRKPDFHLEDPVQGADGLTIESQLAADEEPVDDQVIQM 124 Query: 112 EAEQVLQSSVAALSAKLRVPVQLFYFYGYSLQEISGYLGTPVQTLKKRLHDARQKLKGTL 171 E +Q + AL K R+ V L Y SL+EIS L PV T+K R+H R+ L+ + Sbjct: 125 ETRDWIQQEIQALPPKYRMAVLLKYMEDLSLKEISDILDLPVSTVKTRIHRGREALRKRM 184 >BS_sigW [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 187 Score = 79.7 bits (195), Expect = 1e-14, Method: Compositional matrix adjust. Identities = 52/181 (28%), Positives = 83/181 (45%), Gaps = 11/181 (6%) Query: 1 MRQWVEKARQGDAEAFAQLMAHCRGMAYAVSYDMLKDVHLAEDAVQEAFLEAYLNLQKLS 60 +++ +++ ++GD +AFA ++ + Y + Y ML +VH AED QEAF+ AY+N+ Sbjct: 5 IKKRIKQVKKGDQDAFADIVDIYKDKIYQLCYRMLGNVHEAEDIAQEAFIRAYVNIDSFD 64 Query: 61 EPAAFPGWFRTIVVRQCQRTLRRKRHPLLPLDEALQGLQNEPGAADILE----------R 110 F W I +R+K+ P LD + G + + I+ Sbjct: 65 INRKFSTWLYRIATNLTIDRIRKKK-PDYYLDAEVAGTEGLTMYSQIVADGVLPEDAVVS 123 Query: 111 KEAEQVLQSSVAALSAKLRVPVQLFYFYGYSLQEISGYLGTPVQTLKKRLHDARQKLKGT 170 E +Q + L K R + L Y SL EI L PV T+K R+H R+ L+ Sbjct: 124 LELSNTIQQKILKLPDKYRTVIVLKYIDELSLIEIGEILNIPVGTVKTRIHRGREALRKQ 183 Query: 171 L 171 L Sbjct: 184 L 184 >Cgl1096 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 213 Score = 65.9 bits (159), Expect = 2e-10, Method: Compositional matrix adjust. Identities = 52/175 (29%), Positives = 79/175 (45%), Gaps = 7/175 (4%) Query: 8 ARQGDAEAFAQLMAHCRGMAYAVSYDMLKDVHLAEDAVQEAFLEAYLNLQKLSEPAAFPG 67 A Q D + +L+A Y ++Y + + H AED QE F+ + +L K +P F G Sbjct: 32 AGQADMPTWGELVAEHADSVYRLAYRLSGNQHDAEDLTQETFMRVFRSL-KSYQPGTFEG 90 Query: 68 WFRTIVVRQCQRTLRRK---RHPLLPLD-EALQGLQNEPGAADILERKEAEQVLQSSVAA 123 W I +R + R LP D E + G P A + LQ+++ Sbjct: 91 WLHRITTNLFLDMVRHRGKIRMEALPEDYERVPGNDITPEQA--YTEANLDPALQAALDE 148 Query: 124 LSAKLRVPVQLFYFYGYSLQEISGYLGTPVQTLKKRLHDARQKLKGTLPVADLAS 178 LS RV V L G S EI+ LG + T++ R+H R +L+ +L A + S Sbjct: 149 LSPDFRVAVILCDVVGMSYDEIAETLGVKMGTVRSRIHRGRSQLRASLEAAAMTS 203 >CAC3267 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 190 Score = 65.9 bits (159), Expect = 2e-10, Method: Compositional matrix adjust. Identities = 43/178 (24%), Positives = 82/178 (46%), Gaps = 8/178 (4%) Query: 2 RQWVEKARQGDAEAFAQLMAHCRGMAYAVSYDMLKDVHLAEDAVQEAFLEAYLNLQKLSE 61 ++ +++ ++ D +F+QL Y + Y ++ A D VQE +++ + N++ E Sbjct: 5 KEILKRCKKYDRASFSQLFHLYEKYLYNLCYGYTQNTSDAMDLVQEIYIKVFKNIKNFDE 64 Query: 62 PAAFPGWFRTIVVRQCQRTLRRKRHPLLPLDEALQGLQNEPG---AADILERKEA----- 113 F W R I V C R R ++ L+ + E A D +E Sbjct: 65 NLPFHPWVRKISVNTCLNFKRDNRGNVMSLNSKYYDSEFEEEDRLAEDYNMEQEVVNRIN 124 Query: 114 EQVLQSSVAALSAKLRVPVQLFYFYGYSLQEISGYLGTPVQTLKKRLHDARQKLKGTL 171 +V++ S+ L+ R+ + L Y+ S EI+ L P+ T+K +++ A+ LK +L Sbjct: 125 NEVVKESIKKLTYDYRMVIMLRYYEDLSYDEIASVLDMPIGTVKTKIYRAKNVLKKSL 182 >Rv1221 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog Length = 257 Score = 63.2 bits (152), Expect = 1e-09, Method: Compositional matrix adjust. Identities = 52/185 (28%), Positives = 81/185 (43%), Gaps = 18/185 (9%) Query: 3 QWVEKARQ----------GDA---EAFAQLMAHCRGMAYAVSYDMLKDVHLAEDAVQEAF 49 QWVE + Q GD ++ +L+ Y ++Y + + H AED QE F Sbjct: 58 QWVEPSDQLQGTAVFDATGDKATMPSWDELVRQHADRVYRLAYRLSGNQHDAEDLTQETF 117 Query: 50 LEAYLNLQKLSEPAAFPGWFRTIVVRQCQRTLRRK---RHPLLPLDEALQGLQNEPGAAD 106 + + ++Q +P F GW I +RR+ R LP D + +EP Sbjct: 118 IRVFRSVQNY-QPGTFEGWLHRITTNLFLDMVRRRARIRMEALPEDYD-RVPADEPNPEQ 175 Query: 107 ILERKEAEQVLQSSVAALSAKLRVPVQLFYFYGYSLQEISGYLGTPVQTLKKRLHDARQK 166 I LQ+++A+L + R V L G S +EI LG + T++ R+H RQ Sbjct: 176 IYHDARLGPDLQAALASLPPEFRAAVVLCDIEGLSYEEIGATLGVKLGTVRSRIHRGRQA 235 Query: 167 LKGTL 171 L+ L Sbjct: 236 LRDYL 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 0.137 0.413 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: 40,193,164 Number of extensions: 1761334 Number of successful extensions: 5578 Number of sequences better than 1.0e-05: 29 Number of HSP's gapped: 5579 Number of HSP's successfully gapped: 29 Length of query: 528 Length of database: 38,378,431 Length adjustment: 111 Effective length of query: 417 Effective length of database: 25,576,357 Effective search space: 10665340869 Effective search space used: 10665340869 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: 118 (50.1 bits)