Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate Ac3H11_951 Acetyl-coenzyme A synthetase (EC 6.2.1.1)
Query= SwissProt::P31638 (660 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_951 Length = 664 Score = 1038 bits (2684), Expect = 0.0 Identities = 495/659 (75%), Positives = 568/659 (86%), Gaps = 2/659 (0%) Query: 2 SAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPF 61 SAIESV+ E+RVF P + A + M Y ALC EA++D+EGFWAR ARE ++WTKPF Sbjct: 6 SAIESVLVENRVFPPSDAVVKAARVSGMAGYDALCAEADKDFEGFWARLARENVNWTKPF 65 Query: 62 TKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHG 121 + LD SNAPF+KWF+DGELNAS NCLDR++ +K AIVFEADDG+VTR+TY+EL Sbjct: 66 NRTLDTSNAPFFKWFDDGELNASANCLDRHIGTPTENKTAIVFEADDGTVTRITYKELLA 125 Query: 122 KVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERL 181 +V +FAN LKA G+ KGDRV+IYMPM++EGV+AMQACAR+GATHSVVFGGFSAK++QER+ Sbjct: 126 RVSQFANALKAHGVTKGDRVLIYMPMTIEGVIAMQACARIGATHSVVFGGFSAKAVQERI 185 Query: 182 VDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDR 241 +D GAVA+ITA+ QMRGGK LPLKAI D+ALA+GGC+ +RNV VY+RT GRD+ Sbjct: 186 IDAGAVAVITANYQMRGGKELPLKAIIDEALAMGGCDTIRNVFVYQRTATACNMVAGRDK 245 Query: 242 WMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDI 301 ++ AGQ C PV AEHPLF+LYTSGSTGKPKGVQH+TGGYLLWA +TM WTFD+ Sbjct: 246 TFGEMLAGQSTECAPVPVGAEHPLFILYTSGSTGKPKGVQHATGGYLLWAKLTMDWTFDL 305 Query: 302 KPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFY 361 + DD+FWCTADIGW+TGHTY+AYGPLAAGATQ++FEGVPT+PNAGRFW MI +HK +IFY Sbjct: 306 RADDVFWCTADIGWITGHTYVAYGPLAAGATQIIFEGVPTFPNAGRFWQMIEKHKCTIFY 365 Query: 362 TAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVD 421 TAPTAIRSLIKAAE D +HP + DLSSLR+LG+VGEPINPEAWMWY+KN+G ERCPIVD Sbjct: 366 TAPTAIRSLIKAAEGDAAVHPARSDLSSLRILGSVGEPINPEAWMWYHKNVGGERCPIVD 425 Query: 422 TFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWP 481 TFWQTETGGH+ITPLPGATPLVPGSCTLPLPGI AAIVDE G+DV NG GGILV+K+PWP Sbjct: 426 TFWQTETGGHVITPLPGATPLVPGSCTLPLPGISAAIVDEMGNDVANGAGGILVIKKPWP 485 Query: 482 AMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMG 541 +MIRTIW DPERF+K+YFPEEL G YLAGDG++R D GYF I GRIDDVLNVSGHRMG Sbjct: 486 SMIRTIWNDPERFKKAYFPEELKG-YYLAGDGAVRSADRGYFRITGRIDDVLNVSGHRMG 544 Query: 542 TMEIESALVS-NPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVG 600 TMEIESALVS LVAEAAVVGRPDD+TGEAICAFVVLKRSRPTGEEA +IA ELRNWV Sbjct: 545 TMEIESALVSKTDLVAEAAVVGRPDDVTGEAICAFVVLKRSRPTGEEAKQIANELRNWVA 604 Query: 601 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQA 659 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRS+AKGE ITQDTSTLENPAIL+QL +A Sbjct: 605 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSIAKGEAITQDTSTLENPAILDQLAKA 663 Lambda K H 0.319 0.136 0.422 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1493 Number of extensions: 73 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 660 Length of database: 664 Length adjustment: 38 Effective length of query: 622 Effective length of database: 626 Effective search space: 389372 Effective search space used: 389372 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 (21.7 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory