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= 0112.0022.p (377 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value CAC1300 [K] COG0568 DNA-directed RNA polymerase, sigma subunit (... 449 e-126 ML0139 [Q] COG3321 Polyketide synthase modules and related proteins 412 e-115 Rv2703 [K] COG0568 DNA-directed RNA polymerase, sigma subunit (s... 358 8e-99 MT2777 [K] COG0568 DNA-directed RNA polymerase, sigma subunit (s... 358 8e-99 MT2777.1 [J] COG0251 Putative translation initiation inhibitor, ... 358 8e-99 >CAC1300 [K] COG0568 DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) Length = 378 Score = 449 bits (1155), Expect = e-126, Method: Compositional matrix adjust. Identities = 245/357 (68%), Positives = 273/357 (76%), Gaps = 15/357 (4%) Query: 21 QLIEQGKKRSSLNYKDIMEKLSPFDQDPEQMEEFYEQLSDLGIXXXXXXXXXXXTLRPXX 80 LI++GKK SL YK+IM++L D PEQ+E+ YE L +G+ Sbjct: 37 NLIDKGKKSGSLTYKEIMDELQEVDLGPEQIEKIYEVLESVGVDVVGDMHEIEV------ 90 Query: 81 XXXXXXXXXXXXXXXXXXPPGIKINDPVRMYLKEIGRVPLLSADDEVELAMRIKNGDEEA 140 P GI I+DPVRMYLKEIG+VPLLS ++E++LA RIKNGD A Sbjct: 91 ---------EEEDLDLTIPEGIAIDDPVRMYLKEIGKVPLLSPEEEIDLAQRIKNGDRSA 141 Query: 141 KRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDHNKGFKFSTYATWWI 200 +++LAEANLRLVVSIAKRYVGRGMLFLDLIQEGN+GLIKAVEKFD KGFKFSTYATWWI Sbjct: 142 RKKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDFKKGFKFSTYATWWI 201 Query: 201 RQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPSPEEIAAEMELTVEKVR 260 RQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREP PEEIA M++ V+KVR Sbjct: 202 RQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPQPEEIAKIMDMPVDKVR 261 Query: 261 EIMKIAQEPVSLETPIGEEDDSHLGDFIXXXXXXXXXXXXXXXXXKEQLEDVLDTLTERE 320 EIMKIAQEPVSLETPIGEE+DSHLGDFI KEQL +L+TLT RE Sbjct: 262 EIMKIAQEPVSLETPIGEEEDSHLGDFIPDDEAPAPADAAAFRMLKEQLLKILNTLTPRE 321 Query: 321 ENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFLE 377 E VLRLRFGLDDGR RTLEEVGK F VTRERIRQIEAKALRKLRHPSRSK+LKD+L+ Sbjct: 322 EKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSKKLKDYLD 378 >ML0139 [Q] COG3321 Polyketide synthase modules and related proteins Length = 447 Score = 412 bits (1058), Expect = e-115, Method: Compositional matrix adjust. Identities = 206/279 (73%), Positives = 232/279 (83%), Gaps = 3/279 (1%) Query: 101 GIKINDPVRMYLKEIGRVPLLSADDEVELAMRIKNGDEEA---KRRLAEANLRLVVSIAK 157 ++I+DPVRMYLKEIGR PL+S D+E +LA I G E A K+ LAEANLRLVVSIAK Sbjct: 169 NVRIDDPVRMYLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAK 228 Query: 158 RYVGRGMLFLDLIQEGNMGLIKAVEKFDHNKGFKFSTYATWWIRQAITRAIADQARTIRI 217 RY GRGM FLDLIQEGNMGL+KAV+KFDH KGFKFSTYATWWIRQAITRAIADQARTIRI Sbjct: 229 RYSGRGMQFLDLIQEGNMGLMKAVDKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRI 288 Query: 218 PVHMVETINKLIRVSRQLLQELGREPSPEEIAAEMELTVEKVREIMKIAQEPVSLETPIG 277 PVHMVETINKLIRV R LLQELGR+PSPEEI E+ + +KVRE++KIAQEPVSLETPIG Sbjct: 289 PVHMVETINKLIRVQRNLLQELGRDPSPEEIGKELHMAPDKVREVLKIAQEPVSLETPIG 348 Query: 278 EEDDSHLGDFIXXXXXXXXXXXXXXXXXKEQLEDVLDTLTEREENVLRLRFGLDDGRTRT 337 EEDDSHLGDFI +EQL++V+DTLT+REENVLR+RFGLDDGR T Sbjct: 349 EEDDSHLGDFIEDDVIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLDDGRMHT 408 Query: 338 LEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFL 376 LE+VGK F VTRERIRQIEAKA++KLRHP RSK L+DF+ Sbjct: 409 LEDVGKQFKVTRERIRQIEAKAIKKLRHPRRSKPLRDFM 447 >Rv2703 [K] COG0568 DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) Length = 528 Score = 358 bits (919), Expect = 8e-99, Method: Compositional matrix adjust. Identities = 181/303 (59%), Positives = 222/303 (73%), Gaps = 31/303 (10%) Query: 106 DPVRMYLKEIGRVPLLSADDEVELAMRIKNG----------------------------- 136 D VR YLK+IG+V LL+A++EVELA RI+ G Sbjct: 226 DSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKLPAAQRRDMMWIC 285 Query: 137 --DEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDHNKGFKFST 194 + AK L EANLRLVVS+AKRY GRGM FLDLIQEGN+GLI+AVEKFD+ KG+KFST Sbjct: 286 RDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFST 345 Query: 195 YATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPSPEEIAAEMEL 254 YATWWIRQAITRA+ADQARTIRIPVHMVE INKL R+ R+LLQ+LGREP+PEE+A EM++ Sbjct: 346 YATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDI 405 Query: 255 TVEKVREIMKIAQEPVSLETPIGEEDDSHLGDFIXXXXXXXXXXXXXXXXXKEQLEDVLD 314 T EKV EI + A+EP+SL+ IG+E DS LGDFI ++QL+ VLD Sbjct: 406 TPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLD 465 Query: 315 TLTEREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKD 374 TL+ERE V+RLRFGL DG+ RTL+E+G+V+GVTRERIRQIE+K + KLRHPSRS+ L+D Sbjct: 466 TLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRD 525 Query: 375 FLE 377 +L+ Sbjct: 526 YLD 528 >MT2777 [K] COG0568 DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) Length = 528 Score = 358 bits (919), Expect = 8e-99, Method: Compositional matrix adjust. Identities = 181/303 (59%), Positives = 222/303 (73%), Gaps = 31/303 (10%) Query: 106 DPVRMYLKEIGRVPLLSADDEVELAMRIKNG----------------------------- 136 D VR YLK+IG+V LL+A++EVELA RI+ G Sbjct: 226 DSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKLPAAQRRDMMWIC 285 Query: 137 --DEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDHNKGFKFST 194 + AK L EANLRLVVS+AKRY GRGM FLDLIQEGN+GLI+AVEKFD+ KG+KFST Sbjct: 286 RDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFST 345 Query: 195 YATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPSPEEIAAEMEL 254 YATWWIRQAITRA+ADQARTIRIPVHMVE INKL R+ R+LLQ+LGREP+PEE+A EM++ Sbjct: 346 YATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDI 405 Query: 255 TVEKVREIMKIAQEPVSLETPIGEEDDSHLGDFIXXXXXXXXXXXXXXXXXKEQLEDVLD 314 T EKV EI + A+EP+SL+ IG+E DS LGDFI ++QL+ VLD Sbjct: 406 TPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVVAVDAVSFTLLQDQLQSVLD 465 Query: 315 TLTEREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKD 374 TL+ERE V+RLRFGL DG+ RTL+E+G+V+GVTRERIRQIE+K + KLRHPSRS+ L+D Sbjct: 466 TLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRD 525 Query: 375 FLE 377 +L+ Sbjct: 526 YLD 528 >MT2777.1 [J] COG0251 Putative translation initiation inhibitor, yjgF family Length = 141 Score = 358 bits (919), Expect = 8e-99, Method: Compositional matrix adjust. Identities = 0/303 (0%), Positives = 0/303 (0%), Gaps = 31/303 (10%) Query: 106 DPVRMYLKEIGRVPLLSADDEVELAMRIKNG----------------------------- 136 Sbjct: 226 285 Query: 137 --DEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDHNKGFKFST 194 Sbjct: 286 345 Query: 195 YATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPSPEEIAAEMEL 254 Sbjct: 346 405 Query: 255 TVEKVREIMKIAQEPVSLETPIGEEDDSHLGDFIXXXXXXXXXXXXXXXXXKEQLEDVLD 314 Sbjct: 406 465 Query: 315 TLTEREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKD 374 Sbjct: 466 525 Query: 375 FLE 377 Sbjct: 526 528 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 0.317 0.136 0.375 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: 22,839,890 Number of extensions: 851469 Number of successful extensions: 3733 Number of sequences better than 1.0e-05: 113 Number of HSP's gapped: 3562 Number of HSP's successfully gapped: 114 Length of query: 377 Length of database: 38,378,431 Length adjustment: 108 Effective length of query: 269 Effective length of database: 25,922,359 Effective search space: 6973114571 Effective search space used: 6973114571 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 117 (49.7 bits)