Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate GFF1013 PGA1_c10300 acetyl-coenzyme A synthetase AcsA
Query= SwissProt::P39062 (572 letters) >FitnessBrowser__Phaeo:GFF1013 Length = 516 Score = 233 bits (593), Expect = 2e-65 Identities = 166/529 (31%), Positives = 264/529 (49%), Gaps = 45/529 (8%) Query: 36 WHETGKLNAAYEAIDRHAESFRKNKVALYYKDAKRDEKYTFKEMKEESNRAGNVLRRYGN 95 W LN A +A+D E + A+RD +Y E+++ + L + Sbjct: 19 WQFPSCLNMAAQALDHPDEQLALIDLTT---GARRDIRYG--ELRQMVDAVARDLMQ--R 71 Query: 96 VEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFEAFMEGAVKDRLENSEAKVVVTTPE 155 V+ GDRV + + +S + L KIGAI+ PLF+ F A+ R+ ++ ++V+T Sbjct: 72 VQPGDRVGVLLSQSVDCAVAHLAIWKIGAISVPLFKLFQHDALASRIGDAGLELVLTDGG 131 Query: 156 LLERIPVDKLPHLQHVFVVGGEAESGTNIINYDEAAKQESTRLDIEWMDKKDGFLLHYTS 215 ++ P L + +S +++ Y E + +L YTS Sbjct: 132 GTAQLGSLAQPLLVADILSASTGQSD-HLLPYAETTPETPA-------------VLIYTS 177 Query: 216 GSTGTPKGVLHVHEAMIQQYQTGKWVLDLKEE--DIYWCTADPGWVTGTVYGIFAPWLNG 273 G+TG+ KG LH H + D + D W AD W+ G ++ + P L Sbjct: 178 GTTGSAKGALHGHRVLSGHLPGVAISHDHLGQPGDCLWTPADWAWIGG-LFDVLMPGLAL 236 Query: 274 ATNVIVG--GRFSPESWYGTIEQLGVNVWYSAPTAFRMLMGAGDEMAAKYDLTSLRHVLS 331 V+ +F+PE+ I Q V + PTA R+L AG L LR V S Sbjct: 237 GVPVVAARLDKFTPEACAEIIRQGDVRNVFFPPTALRLLKAAGQ------GLDGLRSVAS 290 Query: 332 VGEPLNPEVIRWGHKVFNKRIHDTWWMTE---TGSQLICNYPCMDIKPGSMGKPIPGVEA 388 GEPL E++ WG + I++ + TE T S + ++P ++PG +G+P+PG Sbjct: 291 GGEPLGAEMLAWGQRHLGVTINEFYGQTECNMTVSSCVADFP---VRPGCIGRPVPGCTV 347 Query: 389 AIVDNQGNELPPYRMGNLAIKKGWPSMMHTIWNNPEKYESYFMPGGWYVSGDSAYMDEEG 448 ++D+ G P G++A+++G SMM WN P+ F W ++GD + + Sbjct: 348 EVLDDTGT--PTKDEGDVAVRRGAASMMLEYWNRPDATAEKFH-ADWLITGDRGIWEGD- 403 Query: 449 YFWFQGRVDDVIMTSGERVGPFEVESKLVEHPAIAEAGVIGKPDPVRGEIIKAFIALREG 508 Y F GR DDVI ++G R+GP E+E L+ HPA+A GV+GKPD +R EI+KA++ L+ G Sbjct: 404 YLRFVGREDDVITSAGYRIGPAEIEDCLMTHPAVATVGVVGKPDELRTEIVKAYVVLKPG 463 Query: 509 FEPSDKLKEEIRLFVKQGLAAHAAPREIEFKDKLPKTRSGKIMRRVLKA 557 PS+ +++ +VK LA ++ PRE+EF D LP T +GK++R+ LKA Sbjct: 464 HSPSE---SDLQDYVKSRLAKYSYPREVEFLDALPMTVTGKVIRKELKA 509 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: 772 Number of extensions: 46 Number of successful extensions: 7 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: 516 Length adjustment: 35 Effective length of query: 537 Effective length of database: 481 Effective search space: 258297 Effective search space used: 258297 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: 52 (24.6 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