Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate GFF944 HP15_923 acetyl-coA synthetase/AMP-(fatty) acid ligase
Query= SwissProt::P39062 (572 letters) >FitnessBrowser__Marino:GFF944 Length = 549 Score = 319 bits (817), Expect = 2e-91 Identities = 204/554 (36%), Positives = 300/554 (54%), Gaps = 26/554 (4%) Query: 14 NLKNYEETYRHFDWAEAEKHF-SWHETGKLNAAYEAIDRHAESFRKNKVALYYK-DAKRD 71 +L Y + Y +FD A E LN +E D+ A+ ++VALYY+ + D Sbjct: 2 SLPEYTDVYNNFDPAALEADILDGRLDSGLNVCHEICDKWADD--PSRVALYYETEDGGD 59 Query: 72 EKYTFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFE 131 TF E+KE S R N L+ G + KGDRV +PR+PEL ++ G ++ GA+ PLF Sbjct: 60 GTLTFAELKEASARFANYLKSQG-IGKGDRVAALLPRTPELLIVIAGTLRAGAVYQPLFT 118 Query: 132 AFMEGAVKDRLENSEAKVVVTTPELLERI-PVDKLPHLQHVFVVGGEA-ESGTNIINYDE 189 AF GA++ R E + K+VVT PE ++ V P VVG A E G +I +++E Sbjct: 119 AFGSGAIEYRFERASTKLVVTNPENYPKLNDVKVCPP-----VVGVNASEIGADIPDFEE 173 Query: 190 AAKQESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGKWVLDLKEEDI 249 +S+ + + D FL +TSG+ G KGV +A++ Y K+ +DL++ D Sbjct: 174 TLAAQSSDFEPVMIKGDDPFLQMFTSGTVGKSKGVAVPAKALLAFYVYMKYAIDLQDGDR 233 Query: 250 YWCTADPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNVWYSAPTAFRM 309 +W ADPGW G Y + P L G G F+PES Y I + + +APTA+R+ Sbjct: 234 FWNVADPGWAYGLYYAVVGPLLMGHATHFNPGGFTPESTYDMIRKYKITNLAAAPTAYRL 293 Query: 310 LMGAGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQLICNY 369 L A D + + + LR S GEPLNPEV+ W + D + TETG CN+ Sbjct: 294 LK-ANDHVLPEGENLGLRVASSAGEPLNPEVVNWIRNRHYCPVKDHYGQTETG-MTCCNF 351 Query: 370 PCM--DIKPGSMGKPIPGVEAAIVDNQGNELPPYRMGNLAIKKGWPSMMHT---IWNNPE 424 + ++ GSMG PG + ++ + + +G LA+ + H W + Sbjct: 352 HGLAHPVREGSMGYASPGHKVVALNEKNEVVGEGEVGQLAVDVKASPLFHFDGYTWGEKD 411 Query: 425 KYESYFMPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHPAIAE 484 + + G+Y++GD G F F GR DD+I T+G RVGP +VES L+EH A+AE Sbjct: 412 PFVN-----GYYLTGDMVINHGNGNFSFSGRDDDIITTAGYRVGPADVESTLLEHAAVAE 466 Query: 485 AGVIGKPDPVRGEIIKAFIALREGFEPSDK--LKEEIRLFVKQGLAAHAAPREIEFKDKL 542 +GV+GKPD RG IIKA++ ++ + D+ LK+E++ V++ L+ HA PREIEF D+L Sbjct: 467 SGVVGKPDEKRGSIIKAYVVIKGDYALGDEQALKDELQELVRRRLSTHAFPREIEFVDEL 526 Query: 543 PKTRSGKIMRRVLK 556 PKT SGKI R VL+ Sbjct: 527 PKTPSGKIQRFVLR 540 Lambda K H 0.318 0.136 0.425 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: 899 Number of extensions: 41 Number of successful extensions: 6 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: 572 Length of database: 549 Length adjustment: 36 Effective length of query: 536 Effective length of database: 513 Effective search space: 274968 Effective search space used: 274968 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: 53 (25.0 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