Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_083763599.1 AMB_RS07195 acetate--CoA ligase
Query= SwissProt::P27550 (652 letters) >NCBI__GCF_000009985.1:WP_083763599.1 Length = 526 Score = 292 bits (748), Expect = 2e-83 Identities = 181/520 (34%), Positives = 270/520 (51%), Gaps = 31/520 (5%) Query: 108 ISYKELHRDVCRFANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFS 167 ++Y +L R A L +LG++ G+ VA+ + P+ A L + G ++ +F F Sbjct: 13 VTYGQLAEQSGRIARVLADLGLQPGETVAVLLGRTPDLYSAALGIWKAGGIYCPLFAAFG 72 Query: 168 PEAVAGRIIDSNSRLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKI 227 P + R+ + ++ITSD+ + A + + + + D + HV+V+ G Sbjct: 73 PGPIKARLDLGKAAVLITSDD-LYARKVVASRSALPD---------LRHVLVVGGEEGAT 122 Query: 228 DWQEG-RDLWWHDLVEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAA 286 EG DL + A+ +A E P F+ +TSG+TG PKGVLH L + Sbjct: 123 P--EGCADL---RSLASAAQPMEAVPTAPEAPAFLHFTSGTTGTPKGVLHPHRAVLAHL- 176 Query: 287 LTFKYVFDYHPGDIYWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVV 346 +T + VF D++WCTAD GWVT SY + PLACGAT + E P R ++ Sbjct: 177 VTGRKVFGLSDSDVFWCTADPGWVTSTSYGIIAPLACGATLIADEAELE---PRRWYGIL 233 Query: 347 DKHQVNILYTAPTAIRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEK 406 +V YT PTAIR +M G ++SLR+ SVGEP+N EA W K +G Sbjct: 234 HDEEVTAWYTTPTAIRTMMRYGAALARSYRQNSLRVAASVGEPLNAEAVMWGQKALG--- 290 Query: 407 CPVVDTWWQTETGGFMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGA----TEG 462 P +DTWWQTETG I PG T+ + GS RP GV+ ++ EG + G Sbjct: 291 VPFLDTWWQTETGAITIANGPG-TDRRPGSMGRPLPGVEARIMRCEGGTPKAVDGVDAVG 349 Query: 463 SLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNV 522 L I WP G+ R+ ++ + YF+GD +RD+DG+ W GR DD++ Sbjct: 350 ELAIRTCWPSMFSGALGEETRYGDSFRDGW---YFTGDLVKRDKDGFIWFVGRADDMIKC 406 Query: 523 SGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNW 582 G ++G E+E +L+ HP +AE VVG P + + A+V+LN G E L AE+ ++ Sbjct: 407 GGLQIGPFEVEGSLMDHPAVAEIGVVGKPDMLVREVPVAFVSLNPGFEAGDALRAELLSY 466 Query: 583 VRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRKIAAGD 622 R+E+G P +H+ + LPKT SGKIMRR+L+ A G+ Sbjct: 467 ARQELGAGMAPREIHFVEELPKTNSGKIMRRVLKAKAMGE 506 Lambda K H 0.317 0.135 0.421 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: 1043 Number of extensions: 56 Number of successful extensions: 6 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: 652 Length of database: 526 Length adjustment: 37 Effective length of query: 615 Effective length of database: 489 Effective search space: 300735 Effective search space used: 300735 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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