Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate 15923 b1805 acyl-CoA synthase (NCBI)
Query= SwissProt::P39062 (572 letters) >FitnessBrowser__Keio:15923 Length = 561 Score = 162 bits (409), Expect = 4e-44 Identities = 139/522 (26%), Positives = 237/522 (45%), Gaps = 55/522 (10%) Query: 72 EKYTFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFE 131 E TF++++E S L++ ++KGDRV + MP + + G ++ G I + Sbjct: 47 EVMTFRKLEERSRAFAAYLQQGLGLKKGDRVALMMPNLLQYPVALFGILRAGMIVVNVNP 106 Query: 132 AFMEGAVKDRLENSEAKVVVTTPEL---LERIPVDKLPHLQHVFVVGGEAESGT---NII 185 + ++ +L +S A +V LE++ VDK +QHV + + T ++ Sbjct: 107 LYTPRELEHQLNDSGASAIVIVSNFAHTLEKV-VDKTA-VQHVILTRMGDQLSTAKGTVV 164 Query: 186 NYD-------------------EAAKQESTRLDIEWMD--KKDGFLLHYTSGSTGTPKGV 224 N+ +A R+ + +D L YT G+TG KG Sbjct: 165 NFVVKYIKRLVPKYHLPDAISFRSALHNGYRMQYVKPELVPEDLAFLQYTGGTTGVAKGA 224 Query: 225 LHVHEAMIQQYQTGKWVLDLKEEDIYWCTADPGW---VTGT-VYGIFAPWLNGATNVIVG 280 + H M+ + + Y PG VT +Y IFA +N + +G Sbjct: 225 MLTHRNMLANLE--------QVNATYGPLLHPGKELVVTALPLYHIFALTINCLLFIELG 276 Query: 281 GR----FSPESWYGTIEQLGVNVWYSAPTAFRMLMGA--GDEMAAKYDLTSLRHVLSVGE 334 G+ +P G +++L ++A T L A ++ + D +SL G Sbjct: 277 GQNLLITNPRDIPGLVKELA-KYPFTAITGVNTLFNALLNNKEFQQLDFSSLHLSAGGGM 335 Query: 335 PLNPEVIRWGHKVFNKRIHDTWWMTETGSQLICNYPCMDIKPGSMGKPIPGVEAAIVDNQ 394 P+ V K+ + + + + +TE + N +D GS+G P+P EA +VD+ Sbjct: 336 PVQQVVAERWVKLTGQYLLEGYGLTECAPLVSVNPYDIDYHSGSIGLPVPSTEAKLVDDD 395 Query: 395 GNELPPYRMGNLAIKKGWPSMMHTIWNNPEKYESYFMPGGWYVSGDSAYMDEEGYFWFQG 454 NE+PP + G L +K P +M W P+ + + GW +GD A MDEEG+ Sbjct: 396 DNEVPPGQPGELCVKG--PQVMLGYWQRPDATDE-IIKNGWLHTGDIAVMDEEGFLRIVD 452 Query: 455 RVDDVIMTSGERVGPFEVESKLVEHPAIAEAGVIGKPDPVRGEIIKAFIALREGFEPSDK 514 R D+I+ SG V P E+E +++HP + E +G P GE +K F+ + +PS Sbjct: 453 RKKDMILVSGFNVYPNEIEDVVMQHPGVQEVAAVGVPSGSSGEAVKIFVVKK---DPS-L 508 Query: 515 LKEEIRLFVKQGLAAHAAPREIEFKDKLPKTRSGKIMRRVLK 556 +E + F ++ L + P+ +EF+D+LPK+ GKI+RR L+ Sbjct: 509 TEESLVTFCRRQLTGYKVPKLVEFRDELPKSNVGKILRRELR 550 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: 797 Number of extensions: 50 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 572 Length of database: 561 Length adjustment: 36 Effective length of query: 536 Effective length of database: 525 Effective search space: 281400 Effective search space used: 281400 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