Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_033099083.1 JG50_RS0100120 acetate--CoA ligase
Query= SwissProt::P39062 (572 letters) >NCBI__GCF_000763315.1:WP_033099083.1 Length = 572 Score = 857 bits (2214), Expect = 0.0 Identities = 400/571 (70%), Positives = 470/571 (82%), Gaps = 1/571 (0%) Query: 2 NLKALPAIEGDHNLKNYEETYRHFDWAEAEKHFSWHETGKLNAAYEAIDRHAESFRKNKV 61 N + +P +NL+NYEETY FDW + E+ FSW++TGK+NAAYEAIDRH E + K Sbjct: 3 NTERIPVQTNGNNLQNYEETYASFDWKQVEQEFSWYKTGKVNAAYEAIDRHVEQGKGEKT 62 Query: 62 ALYYKDAKRDEKYTFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIK 121 AL Y R+E YTF+++KE+SN+ ++L+R G + KGDRVFIFMPR+P+LY LG IK Sbjct: 63 ALIYSAPDREETYTFRQLKEKSNQFAHLLKRIG-IHKGDRVFIFMPRTPDLYVSFLGTIK 121 Query: 122 IGAIAGPLFEAFMEGAVKDRLENSEAKVVVTTPELLERIPVDKLPHLQHVFVVGGEAESG 181 IGAI GPLFEAFME AV+DRLENSEA +VTTP LLER+PVD LPHL+H+ +VG + E Sbjct: 122 IGAIVGPLFEAFMEAAVRDRLENSEAVALVTTPTLLERVPVDDLPHLKHIILVGAKGELT 181 Query: 182 TNIINYDEAAKQESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGKWV 241 ++++ + T L+ W+D++D L+HYTSGSTG PKGV+H H AMIQ YQTGKWV Sbjct: 182 DGYYSFEKELAKSPTELEPVWVDREDPMLIHYTSGSTGKPKGVVHAHNAMIQHYQTGKWV 241 Query: 242 LDLKEEDIYWCTADPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNVWY 301 LDL+E DIYWCT DPGWVTGT YGIFAPWLNG TNV+ GGRFSP+ WY T+E+ V VWY Sbjct: 242 LDLQEGDIYWCTVDPGWVTGTSYGIFAPWLNGVTNVVRGGRFSPDDWYQTLEKYKVTVWY 301 Query: 302 SAPTAFRMLMGAGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTET 361 SAPTAFRMLM AG+++ KYD++S+RHVLSVGEPLNPEV+RWG +V+ KRIHD WWMTET Sbjct: 302 SAPTAFRMLMAAGEDLVKKYDISSVRHVLSVGEPLNPEVVRWGLQVYGKRIHDNWWMTET 361 Query: 362 GSQLICNYPCMDIKPGSMGKPIPGVEAAIVDNQGNELPPYRMGNLAIKKGWPSMMHTIWN 421 G LI NYP M+IKPGSMGKP PG+ AAI+D+QGNELPPY MGNLAIK WPS+M IW Sbjct: 362 GGILISNYPQMEIKPGSMGKPFPGIYAAILDDQGNELPPYEMGNLAIKTPWPSIMRKIWK 421 Query: 422 NPEKYESYFMPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHPA 481 NPEKY+ YF GWYVSGDSAY DE+GYFWFQGR+DDVI TSGERVGPFEVESKLVEHPA Sbjct: 422 NPEKYQEYFRIPGWYVSGDSAYKDEDGYFWFQGRLDDVINTSGERVGPFEVESKLVEHPA 481 Query: 482 IAEAGVIGKPDPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFKDK 541 +AEAGVIGKPDP+RGEIIKAFI+LR G++PS++LKEEIR FVK LAAHAAPREIEFKDK Sbjct: 482 VAEAGVIGKPDPLRGEIIKAFISLRAGYKPSEELKEEIRQFVKTRLAAHAAPREIEFKDK 541 Query: 542 LPKTRSGKIMRRVLKAWELNLPAGDLSTMED 572 LPKTRSGKIMRRVLKAWEL+LP GDLSTMED Sbjct: 542 LPKTRSGKIMRRVLKAWELDLPVGDLSTMED 572 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: 1206 Number of extensions: 45 Number of successful extensions: 2 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: 572 Length adjustment: 36 Effective length of query: 536 Effective length of database: 536 Effective search space: 287296 Effective search space used: 287296 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