Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_010531251.1 ON01_RS11790 acetate--CoA ligase
Query= SwissProt::P39062 (572 letters) >NCBI__GCF_000224785.1:WP_010531251.1 Length = 571 Score = 815 bits (2105), Expect = 0.0 Identities = 376/573 (65%), Positives = 467/573 (81%), Gaps = 3/573 (0%) Query: 1 MNLKALPAIEGDHNLKNYEETYRHFDWAEAEKHFSWHETGKLNAAYEAIDRHAES-FRKN 59 M+++ +PA +G +NL+NYE + F W +KHFSW++TGK+N AYEA+DRHAE +K Sbjct: 1 MDMQRIPAQDGTYNLQNYENMRKTFSWDNVKKHFSWNDTGKVNMAYEAVDRHAEDPSKKV 60 Query: 60 KVALYYKDAKRDEKYTFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGA 119 K AL + R+EK TF E++++SN+ NVL++ G VEKGDR+F+F+PRSPE Y G Sbjct: 61 KAALLFSSPDREEKVTFDELRKQSNQFANVLKKNG-VEKGDRIFMFLPRSPEFYATFFGI 119 Query: 120 IKIGAIAGPLFEAFMEGAVKDRLENSEAKVVVTTPELLERIPVDKLPHLQHVFVVGGEAE 179 +K GAIAGPLFEAFME AV+DRLE+SEA ++TTP+LLER+P D LP L+ + +VG E Sbjct: 120 LKTGAIAGPLFEAFMEQAVRDRLEDSEASTLITTPDLLERVPQDDLPDLKKIVLVGENNE 179 Query: 180 SGTNIINYDEAAKQESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGK 239 + I+Y + K+ ST DIEW+D +DG L+HYTSGSTG PKGV HVH AMIQ Y T + Sbjct: 180 TSDKYIDYQQEMKEASTDFDIEWVDLEDGMLIHYTSGSTGKPKGVYHVHNAMIQHYATAE 239 Query: 240 WVLDLKEEDIYWCTADPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNV 299 WVLDL+E+D+YWCTADPGWVTGT YGIFAPWL+G TNV+ GGRFSP++WYGTI++ V+V Sbjct: 240 WVLDLREDDVYWCTADPGWVTGTSYGIFAPWLHGVTNVVRGGRFSPDAWYGTIDKYNVSV 299 Query: 300 WYSAPTAFRMLMGAGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMT 359 WY+APTA R L+ AG+++ K+D++SLRH++SVGEPLNPEVI WG + F+ RIHDTWWMT Sbjct: 300 WYTAPTALRKLVSAGEDVVKKHDMSSLRHIMSVGEPLNPEVITWGLQAFDLRIHDTWWMT 359 Query: 360 ETGSQLICNYPCMDIKPGSMGKPIPGVEAAIVDNQGNELPPYRMGNLAIKKGWPSMMHTI 419 ETG+QLI N P +I+PGSMGKPIPGVEA+IVDN+GNELP +MGNLAIK WP+MM I Sbjct: 360 ETGAQLIVNLPSQEIRPGSMGKPIPGVEASIVDNEGNELPANQMGNLAIKAPWPAMMRQI 419 Query: 420 WNNPEKYESYFMPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEH 479 W PEKYESYF+ GWYVSGDSAY DE+GYFWFQGR+DDVI TSGERVGPFEVESKL+EH Sbjct: 420 WKRPEKYESYFI-NGWYVSGDSAYKDEDGYFWFQGRLDDVINTSGERVGPFEVESKLIEH 478 Query: 480 PAIAEAGVIGKPDPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFK 539 PA+AEAGVIGKPDP RGEI+KAFI L +G+E S++L EE+R FVK GL+AHAAPRE+E K Sbjct: 479 PAVAEAGVIGKPDPERGEIVKAFITLNDGYEDSEELLEEVRQFVKTGLSAHAAPRELEIK 538 Query: 540 DKLPKTRSGKIMRRVLKAWELNLPAGDLSTMED 572 D +PKTRSGKIMRR+LK+WEL LP GD ST+E+ Sbjct: 539 DAIPKTRSGKIMRRLLKSWELGLPTGDTSTLEE 571 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: 1128 Number of extensions: 38 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: 572 Length of database: 571 Length adjustment: 36 Effective length of query: 536 Effective length of database: 535 Effective search space: 286760 Effective search space used: 286760 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