Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate BWI76_RS17800 BWI76_RS17800 long-chain-fatty-acid--CoA ligase
Query= SwissProt::P39062 (572 letters) >FitnessBrowser__Koxy:BWI76_RS17800 Length = 572 Score = 157 bits (398), Expect = 8e-43 Identities = 137/521 (26%), Positives = 236/521 (45%), Gaps = 53/521 (10%) Query: 72 EKYTFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFE 131 E T+++++E S L+ ++KGDRV + MP + + G ++ G I + Sbjct: 58 EVMTYRKLEERSRAFAAYLQEGLGLQKGDRVALMMPNLLQYPVALFGILRAGMIVVNVNP 117 Query: 132 AFMEGAVKDRLENSEAKVVVTTPEL---LERIPVDKLPHLQHVFV--VGGEAESGTN-II 185 + ++ +L +S A +V LE++ VDK ++HV + +G + ++ Sbjct: 118 LYTPRELEHQLNDSGAAAIVIVSNFAHTLEKV-VDKT-QVKHVILTRMGDQLSPAKGTVV 175 Query: 186 NYD-------------------EAAKQESTRLDIEWMD--KKDGFLLHYTSGSTGTPKGV 224 N+ +A Q R+ + +D L YT G+TG KG Sbjct: 176 NFVVKYIKRLVPKYHLPDAISFRSALQHGYRMQYIKPEIVPQDLAFLQYTGGTTGVAKGA 235 Query: 225 LHVHEAMIQQYQ--TGKWVLDLKEEDIYWCTADPGWVTGTVYGIFAPWLNGATNVIVGGR 282 + H M+ + G + L TA P +Y IFA +N + +GG+ Sbjct: 236 MLTHRNMLANLEQVNGTYGPLLHRGKELVVTALP------LYHIFALTMNCLLFIELGGQ 289 Query: 283 ----FSPESWYGTIEQLGVNVWYSAPTAFRMLMGA--GDEMAAKYDLTSLRHVLSVGEPL 336 +P G +++L ++A T L A ++ + D +SL G P+ Sbjct: 290 NLLITNPRDIPGLVKELA-KYPFTAMTGVNTLFNALLNNKEFQQLDFSSLHLSAGGGMPV 348 Query: 337 NPEVIRWGHKVFNKRIHDTWWMTETGSQLICNYPCMDIKPGSMGKPIPGVEAAIVDNQGN 396 V K+ + + + + +TE + N +D GS+G P+P EA +VD+ N Sbjct: 349 QQVVAERWVKLTGQYLLEGYGLTECAPLVSVNPHDIDYHSGSIGLPVPSTEAKLVDDDDN 408 Query: 397 ELPPYRMGNLAIKKGWPSMMHTIWNNPEKYESYFMPGGWYVSGDSAYMDEEGYFWFQGRV 456 E+PP G L +K P +M W P+ + + GW +GD A MDEEG+ R Sbjct: 409 EVPPGEPGELCVKG--PQVMLGYWQRPDA-TAEIIKDGWLHTGDIAVMDEEGFLRIVDRK 465 Query: 457 DDVIMTSGERVGPFEVESKLVEHPAIAEAGVIGKPDPVRGEIIKAFIALREGFEPSDKLK 516 D+I+ SG V P E+E +++H + E +G P GE +K F+ ++ L Sbjct: 466 KDMILVSGFNVYPNEIEDVVMQHAGVQEVAAVGVPSGSSGEAVKIFVVKKD-----PTLT 520 Query: 517 EEIRL-FVKQGLAAHAAPREIEFKDKLPKTRSGKIMRRVLK 556 EE+ + F ++ L + P+ +EF+D+LPK+ GKI+RR L+ Sbjct: 521 EEMLITFCRRQLTGYKVPKHVEFRDELPKSNVGKILRRELR 561 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: 812 Number of extensions: 51 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: 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 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