Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_007152779.1 MDG893_RS05680 AMP-binding protein
Query= SwissProt::P39062 (572 letters) >NCBI__GCF_000170835.1:WP_007152779.1 Length = 549 Score = 330 bits (845), Expect = 1e-94 Identities = 206/554 (37%), Positives = 303/554 (54%), Gaps = 26/554 (4%) Query: 14 NLKNYEETYRHFDWAEAEKHF-SWHETGKLNAAYEAIDRHAESFRKNKVALYYKDAKRDE 72 +L +Y+ Y +FD A E + LN E D+ A + +VALYY+ A Sbjct: 2 SLPDYQSVYDNFDPASLEAEILEGNLQDGLNVCTEICDKWA--YDPQRVALYYEKADGGS 59 Query: 73 -KYTFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFE 131 K TF E+KE+S R N L G + KGDRV +PRSPEL ++ GA++ GA+ PLF Sbjct: 60 GKLTFAELKEQSARFANYLTSQG-IGKGDRVAALLPRSPELLIVIAGALRAGAVYQPLFT 118 Query: 132 AFMEGAVKDRLENSEAKVVVTTPELLERIPVDKLPHLQHV--FVVGGEAESGTNIINYDE 189 AF GA++ R E + K+VVT P + KL ++ V AE ++ ++D+ Sbjct: 119 AFGPGAIEYRFERASTKLVVTDP-----VNYPKLTEVKDCAPVVCVNAAEVSGDVPDFDK 173 Query: 190 AAKQESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGKWVLDLKEEDI 249 ++S + + + D FL +TSG+ G KGV +A++ Y K+ +DL+++D+ Sbjct: 174 TLAEQSGQFEPVLIKGGDPFLQMFTSGTVGKSKGVAVPAKALLAFYVYMKYAIDLRDDDV 233 Query: 250 YWCTADPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNVWYSAPTAFRM 309 +W ADPGW G Y + P L G G F+PE+ Y I + + +APTA+R+ Sbjct: 234 FWNVADPGWAYGLYYAVVGPLLMGHATHFNPGAFTPETTYDMIRKYKITNLAAAPTAYRL 293 Query: 310 LMGAGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQLICNY 369 L A D + + + LR S GEPLNPEV+ W K + D + TETG CN+ Sbjct: 294 LK-ANDHVLPEGENLGLRVASSAGEPLNPEVVSWIEKRHFCPVKDHYGQTETG-MTCCNF 351 Query: 370 PCMD--IKPGSMGKPIPGVEAAIVDNQGNELPPYRMGNLAIKKGWPSMMHT---IWNNPE 424 +D ++ GSMG PG ++ + E+ +G +A+ + H W + Sbjct: 352 HGLDHPVRQGSMGYSSPGHRVVALNEKNEEVGEGEIGQVAVDVKASPLFHFDGYTWGEKD 411 Query: 425 KYESYFMPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHPAIAE 484 + G+Y++GD A +G F F GR DD+I T+G RVGP +VES L+EH A+AE Sbjct: 412 PFVK-----GYYLTGDMAVCHGDGCFSFSGRDDDIITTAGYRVGPADVESTLLEHKAVAE 466 Query: 485 AGVIGKPDPVRGEIIKAFIALREGFEP--SDKLKEEIRLFVKQGLAAHAAPREIEFKDKL 542 +GV+ KPD RG IIKA++ ++ EP D LK+E++ V+ L+AHA PREIEF D+L Sbjct: 467 SGVVAKPDEKRGSIIKAYVVIKGDQEPESEDALKDELQELVRHRLSAHAYPREIEFVDEL 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: 46 Number of successful extensions: 7 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 24 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