Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate 5210425 Shew_2866 acyl-CoA synthetase (RefSeq)
Query= SwissProt::P39062 (572 letters) >FitnessBrowser__PV4:5210425 Length = 569 Score = 191 bits (485), Expect = 7e-53 Identities = 155/522 (29%), Positives = 253/522 (48%), Gaps = 63/522 (12%) Query: 75 TFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFEAFM 134 T+ ++ E S R NVLR G V +GD V +FMP P+ + LG +K GA+ P+ Sbjct: 60 TYAQLDEMSTRFANVLRGLG-VGQGDGVAVFMPNCPQFHIAFLGILKCGAVHMPVSPLSK 118 Query: 135 EGAVKDRLENSEAKVVVTTPELLERI-PVDKLPHLQHVFVVG------------------ 175 E ++ +L +S+ KV + LL + PV + ++H+ Sbjct: 119 EMELRHQLGDSQPKVALCYDALLPTMRPVCQELGIEHIITTSYTDVRPRAITAVLPDLFE 178 Query: 176 -GEAESGTNIINYDEAAKQESTRLDIEWMDKKDGFL-LHYTSGSTGTPKGVLHVHEAMI- 232 + II++ EA S + ++++ D ++YTSG+TG PKGV+H H MI Sbjct: 179 IPKTPLADGIIDFFEAIDNASKEV-LDYIPALDDLAAINYTSGTTGMPKGVMHTHRNMIG 237 Query: 233 ---QQYQTGKWVLDLKEEDIYWCTADPG-WVTGTVYGIFAPWLNGATNVIVGGRFSPESW 288 Y + + D+ + P W+ G G+ P +GAT V++ R+ +++ Sbjct: 238 TMASYYPVTFGEVGPEGTDLVMLSFLPEFWIAGEDTGLLLPLYSGATLVLMA-RWDTKAF 296 Query: 289 YGTIEQLGVNVWYSAPTAFRMLMGAGDEMAA-----KYDLTSLRHV--LSVGEPLNPEVI 341 + VN+ ML+ + DE+ ++DLTSL V +S + LN + Sbjct: 297 MELVHHHKVNMTI-------MLIDSVDEILNHPHLHQFDLTSLTTVPCISFIKKLNRDYR 349 Query: 342 -RWGHKVFNKRIHDTWWMTETGSQLICN-------YPCMDIK--PGSMGKPIPGVEAAIV 391 RW + MTET + C+ MD+ P +G P+PG E I Sbjct: 350 QRWRELTGTTLFEVAYGMTETHT---CDTFTRGFQVDDMDLSFDPAFLGLPVPGTEIKIC 406 Query: 392 DNQGNELPPYRM-GNLAIKKGWPSMMHTIWNNPEKYESYFMPGGWYVSGDSAYMDEEGYF 450 D EL P + G + I+ P+++ WN P+ ++ F GGWY +GD + EEG+F Sbjct: 407 DFVTGELMPLGVEGEIQIRT--PTLLKGYWNKPDLNKNLFEEGGWYRTGDLGMITEEGFF 464 Query: 451 WFQGRVDDVIMTSGERVGPFEVESKLVEHPAIAEAGVIGKPDPVRGEIIKAFIALREGFE 510 + GR +++ +G V P EVES L +HPAIA GV+G+PD +G++ AF+ L+ GF Sbjct: 465 RYLGRRKEMLKVNGMSVFPTEVESMLGQHPAIASCGVVGRPDERKGQVPVAFVTLKPGF- 523 Query: 511 PSDKLKEEIRLFVKQGLAAHAAPREIEFKDKLPKTRSGKIMR 552 D+ +E ++ + +A P EI +++LP T +GKI + Sbjct: 524 --DETQESLQAWCVNAMAIFKVP-EIRIQERLPMTATGKIRK 562 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: 804 Number of extensions: 46 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: 572 Length of database: 569 Length adjustment: 36 Effective length of query: 536 Effective length of database: 533 Effective search space: 285688 Effective search space used: 285688 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