Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate SMc00741 SMc00741 fatty-acid-CoA ligase
Query= SwissProt::P39062 (572 letters) >FitnessBrowser__Smeli:SMc00741 Length = 548 Score = 249 bits (636), Expect = 2e-70 Identities = 181/551 (32%), Positives = 258/551 (46%), Gaps = 29/551 (5%) Query: 15 LKNYEETYRHFDWAEAEKHFSWHETGKLNAAYEAIDRHAESFRKNKVALYYKDAKRDEKY 74 +++Y+E YR F W E+ N D A + ++ Sbjct: 5 IEDYDELYREFRWRIPER---------FNIGVAVSDAWAARDPERICLQHFSPDGAHLAL 55 Query: 75 TFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFEAFM 134 T+ + S+ L + +V G+RV I +P+ E K+GAIA PL F Sbjct: 56 TYGDFAARSSAFAGGLAAH-DVSPGERVAILLPQGFEAAIAHAAIYKLGAIALPLALLFG 114 Query: 135 EGAVKDRLENSEAKVVVTTPELLERIPV--DKLPHLQHVFVVGGEAESGTNIINYDEAAK 192 A+ RL+++ A VVT ER+ +LP L+ V + + + GT + + + A Sbjct: 115 VEALAYRLKDAGAAAVVTNRFGYERLAAIRGELPELRMVVLAEEDEKPGT--VRFRDIAA 172 Query: 193 QESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQ---YQTGKWVLDLKEEDI 249 + R D D L+ YTSG+TG PKG LH H ++ +Q L + D Sbjct: 173 GQG-RFDPAETKPDDPALMIYTSGTTGPPKGALHGHRVLLGHLPGFQFHHHFLP-QPGDR 230 Query: 250 YWCTADPGWVTGTVYGIFAPWLNGATNVIVGG-RFSPESWYGTIEQLGVNVWYSAPTAFR 308 W AD W G + + G V +F + + IE++ V + PTA R Sbjct: 231 MWTPADWAWAGGLLNALLPSLFFGVPVVSSPAQKFDAHTAFRIIEEMEVRNAFIPPTALR 290 Query: 309 MLMGAG---DEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQL 365 +L D A K LR V S GE L E W + + + TE + Sbjct: 291 LLKSVERPRDRCALK-----LRTVGSAGEALGRETFEWARAALGVEVSEFYGQTECNIVI 345 Query: 366 ICNYPCMDIKPGSMGKPIPGVEAAIVDNQGNELPPYRMGNLAIKKGWPSMMHTIWNNPEK 425 K GSMGK PG + AI+D +G LPP +G +AI++ P M W N E Sbjct: 346 SSATGLGVAKAGSMGKAAPGHQVAIIDGEGRVLPPGTVGQVAIRRPDPVMFLGYWRNEEA 405 Query: 426 YESYFMPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHPAIAEA 485 E+ F+ G W +GD MDEEGYF F GR DDVI +SG R+GP E+E L HP + A Sbjct: 406 TEAKFI-GDWMTTGDQGVMDEEGYFTFFGRDDDVITSSGYRIGPSEIEDCLAGHPDVQLA 464 Query: 486 GVIGKPDPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFKDKLPKT 545 +GKPDP+R EI+KA++ L+ G D+ IR +VK L+ H PREI F D LP T Sbjct: 465 AAVGKPDPLRTEIVKAYVVLKPGVAAGDETAAGIRDWVKNRLSMHEYPREIAFVDSLPLT 524 Query: 546 RSGKIMRRVLK 556 SGK++RR+L+ Sbjct: 525 TSGKVIRRLLR 535 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: 841 Number of extensions: 37 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: 572 Length of database: 548 Length adjustment: 36 Effective length of query: 536 Effective length of database: 512 Effective search space: 274432 Effective search space used: 274432 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