Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_089754212.1 BMZ06_RS17975 acetate--CoA ligase
Query= SwissProt::P39062 (572 letters) >NCBI__GCF_900113125.1:WP_089754212.1 Length = 569 Score = 859 bits (2219), Expect = 0.0 Identities = 403/573 (70%), Positives = 480/573 (83%), Gaps = 5/573 (0%) Query: 1 MNLKALPAIEGDHNLKNYEETYRHFDWAEAEKHFSWHETGKLNAAYEAIDRHAES-FRKN 59 M++K +PA G+HN++NY+ETY F+W + + +F+W +TG +N AYEAID+HAE +KN Sbjct: 1 MDMKPIPARSGNHNMENYKETYEQFNWEDVKTNFTWSKTGNVNIAYEAIDKHAEDPQKKN 60 Query: 60 KVALYYKDAKRDEKYTFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGA 119 + AL Y +R+EK TF+++K +SN+ NVLR++ N+EKGDRVF+FM RSPE Y G Sbjct: 61 QAALIYTSPEREEKLTFEDLKVKSNQFANVLRKH-NIEKGDRVFLFMHRSPEFYVAFFGI 119 Query: 120 IKIGAIAGPLFEAFMEGAVKDRLENSEAKVVVTTPELLERIPVDKLPHLQHVFVVGGEAE 179 +KIGAIAGPLFEAFME AV+DRLE+SEA ++VTTPELL+R+P+D LP+L+ + +VGG+A Sbjct: 120 LKIGAIAGPLFEAFMEQAVRDRLEDSEATMLVTTPELLDRVPIDDLPNLKQIVLVGGDAP 179 Query: 180 SGTNIINYDEAAKQESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGK 239 N I+++E Q S DIEW+D +DG LLHYTSGSTG PKGV HVH AMIQ YQTGK Sbjct: 180 G--NYISFEEEMDQASEEFDIEWVDLEDGMLLHYTSGSTGKPKGVYHVHNAMIQHYQTGK 237 Query: 240 WVLDLKEEDIYWCTADPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNV 299 WVLDLKE D+YWCTADPGWVTGT YGIFAPWLNG TNVI GGRFSP+ WYGTI + V+V Sbjct: 238 WVLDLKEGDVYWCTADPGWVTGTSYGIFAPWLNGVTNVIRGGRFSPDDWYGTIAEQNVSV 297 Query: 300 WYSAPTAFRMLMGAGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMT 359 WYSAPTAFR L+ AG+E AAK+DL+SLRHVLSVGEPLNPEVI WG K F+ RIHDTWWMT Sbjct: 298 WYSAPTAFRKLLSAGEEAAAKHDLSSLRHVLSVGEPLNPEVITWGLKAFDLRIHDTWWMT 357 Query: 360 ETGSQLICNYPCMDIKPGSMGKPIPGVEAAIVDNQGNELPPYRMGNLAIKKGWPSMMHTI 419 ETG+ LICNYP MDI+PGSMGKP PG+ AAIVDN+GNELPP +MGNLAIK+GWPSMM I Sbjct: 358 ETGAMLICNYPAMDIRPGSMGKPFPGIVAAIVDNEGNELPPNQMGNLAIKEGWPSMMRAI 417 Query: 420 WNNPEKYESYFMPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEH 479 WNNP K+ESYF+ GWYVSGDSAY DEEGYFWFQGR+DDVI TSGERVGPFEVESKL+EH Sbjct: 418 WNNPGKFESYFL-NGWYVSGDSAYQDEEGYFWFQGRLDDVINTSGERVGPFEVESKLIEH 476 Query: 480 PAIAEAGVIGKPDPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFK 539 A+AEAGVIGKPDP RGEIIKAF+ LR+G+E SD L E+IR FVK+GL+AHAAPREIE K Sbjct: 477 EAVAEAGVIGKPDPERGEIIKAFVTLRDGYEESDDLLEDIRQFVKKGLSAHAAPREIEIK 536 Query: 540 DKLPKTRSGKIMRRVLKAWELNLPAGDLSTMED 572 D +PKTRSGKIMRR+LK+WEL LP GD ST+E+ Sbjct: 537 DTIPKTRSGKIMRRLLKSWELGLPTGDTSTLEE 569 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: 1232 Number of extensions: 51 Number of successful extensions: 5 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: 569 Length adjustment: 36 Effective length of query: 536 Effective length of database: 533 Effective search space: 285688 Effective search space used: 285688 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