Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_086508401.1 BZY95_RS02355 AMP-binding protein
Query= SwissProt::P27550 (652 letters) >NCBI__GCF_002151265.1:WP_086508401.1 Length = 556 Score = 257 bits (657), Expect = 9e-73 Identities = 184/561 (32%), Positives = 266/561 (47%), Gaps = 55/561 (9%) Query: 72 DGTLNLAANCLDRHLQEN-GDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLELGIK 130 DG N +C RHL+ G+ A++ E + ++ +Y EL + R A E G+ Sbjct: 30 DGKFNAFESCCGRHLRAGRGEVLALVHEDTQGNVNRR-TYAELEAESARLAGWFAERGLG 88 Query: 131 KGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGV 190 GD +A +P PE VA+LA RIGAV+ +F F P+AV R+ +++RLVIT Sbjct: 89 VGDRIACMLPRSPELLVAVLATWRIGAVYQPLFTAFGPDAVDYRLGRADTRLVITDHAN- 147 Query: 191 RAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQA 250 + D + P V +V GG + +G DL W + + + Q Sbjct: 148 --------RFKFDGLSQCPPVLAV---------GGPSEGHDG-DLDWDEALAHSPIQANP 189 Query: 251 EEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWV 310 ++ E P ++TSG+ GKPKGV G +A L + D D +W AD GW Sbjct: 190 PRLSPEAPFLQMFTSGTVGKPKGVAVPLSGMPAFA-LYMELAIDLRESDRFWNMADPGWA 248 Query: 311 TGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEG-- 368 G Y + GPL G TT E + + +H++ APTA R + A G Sbjct: 249 YGLYYAIAGPLLLGVTTHFCEA---GFSAEGALDFMRRHRITNFAAAPTAYRLMKASGLF 305 Query: 369 DKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPG 428 D A E + LR+ S GEP+N E W + +G CPV+D + QTETG Sbjct: 306 DSAHESLE---LRVASSAGEPLNTEVVTWVERSLG---CPVMDHYGQTETGMTCCNHHAL 359 Query: 429 ATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQTY 488 G+ P G + A++D E N L PG+ L D ER + Sbjct: 360 GHPKHVGAMGVPMPGYRLAILDAEHNELP-------------PGEPGVLAVDIERSPAHF 406 Query: 489 FSTF---------KNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAH 539 F + Y +GD R+EDG + GR DD++ +G+R+G ++E+ ++ H Sbjct: 407 FQGYTWQEKHPFANGYYLTGDVVIRNEDGTFQFAGRDDDIITTAGYRVGPTDVENTVLTH 466 Query: 540 PKIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWT 599 P +AE+A VG P I+G+ I +YV L G E S EL E+R VR+ + A P V+ + Sbjct: 467 PAVAESAAVGQPDEIRGEIIKSYVVLREGFEASDELAEEIRQRVRERLSTHAFPRVIEFV 526 Query: 600 DSLPKTRSGKIMRRILRKIAA 620 D+LPKT SGKI R LR AA Sbjct: 527 DTLPKTPSGKIQRFKLRADAA 547 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: 921 Number of extensions: 47 Number of successful extensions: 7 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: 556 Length adjustment: 37 Effective length of query: 615 Effective length of database: 519 Effective search space: 319185 Effective search space used: 319185 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