Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_041100331.1 SUTH_RS14820 acetate--CoA ligase
Query= SwissProt::P39062 (572 letters) >NCBI__GCF_000828635.1:WP_041100331.1 Length = 585 Score = 513 bits (1322), Expect = e-150 Identities = 271/571 (47%), Positives = 361/571 (63%), Gaps = 20/571 (3%) Query: 14 NLKNYEETYRHFDWAEAEKHFSWHETGKLNAAYEAIDRHAESFRKNKVALYYKDAKRDEK 73 N +Y F W F+ ETG N A A++RHA ++KVA + + + Sbjct: 19 NFVDYAGERSTFSWPAVRAQFA--ETG-FNIATHAVERHASGALRDKVAFRFLSRDKPAR 75 Query: 74 -YTFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFEA 132 ++ E+ + ++R NVL G + +G+RVF+ R PELY +LG++K GA+ PLF A Sbjct: 76 DVSYGELSQLTSRFANVLETLG-IGRGERVFVLAGRIPELYVAVLGSLKHGAVVSPLFSA 134 Query: 133 FMEGAVKDRLENSEAKVVVTTPELLERIPV---DKLPHLQHVFVV---GGEAE-SGTNII 185 F + R+ E +V+VTT L ER D++P LQHV +V GG + GT + Sbjct: 135 FGPEPIATRVNLGEGRVLVTTDMLYERKVAKWRDRMPTLQHVLLVAEDGGRTDVPGT--L 192 Query: 186 NYDEAAKQESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGKWVLDLK 245 + + S + + +++ LLH+TSG+TGTPKG +HVH A++ + TG++ LDL Sbjct: 193 DLAVLMAEASDQCTVAATGQEEMSLLHFTSGTTGTPKGAVHVHGAVVTHFATGRYALDLH 252 Query: 246 EEDIYWCTADPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNVWYSAPT 305 +D YWCTADPGWVTGT YGI AP L+G T++I F E WY ++ V VWY+APT Sbjct: 253 ADDTYWCTADPGWVTGTSYGIIAPLLHGVTSIIDREEFDAERWYSILQDEAVTVWYTAPT 312 Query: 306 AFRMLMGAGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQL 365 A RMLM AG E+ KY LR + SVGEPLNPE +RWG +V IHD WW TETG + Sbjct: 313 AIRMLMKAGAEIPHKYRFPQLRFIASVGEPLNPEAVRWGKEVLGLPIHDNWWQTETGGIM 372 Query: 366 ICNYPCMDIKPGSMGKPIPGVEAAIV--DNQGNELP---PYRMGNLAIKKGWPSMMHTIW 420 I N P DIKPGSMG+P+PG++AAI+ G P P G LA+K+GWPSM Sbjct: 373 IANTPAFDIKPGSMGRPLPGIDAAIMRHHEDGTVTPIEEPDVEGELALKRGWPSMFRAYL 432 Query: 421 NNPEKYESYFMPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHP 480 NN E+Y F G WY++GD A D +GYFWF GR DDVI ++G +GPFEVES L+EHP Sbjct: 433 NNEERYRKCF-AGEWYLTGDLAKRDADGYFWFVGRADDVIKSAGHLIGPFEVESALMEHP 491 Query: 481 AIAEAGVIGKPDPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFKD 540 A+AEAGVIGKPDPV GE++KAF++L++GFE S+ L+ E+ ++ L A AP+EI F Sbjct: 492 AVAEAGVIGKPDPVVGEVVKAFVSLKKGFEESEALRMELLGHARKKLGAAVAPKEIAFLP 551 Query: 541 KLPKTRSGKIMRRVLKAWELNLPAGDLSTME 571 LP+TRSGKIMRR+LKA EL LP GD ST+E Sbjct: 552 SLPRTRSGKIMRRLLKARELGLPEGDTSTLE 582 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: 1017 Number of extensions: 58 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: 585 Length adjustment: 36 Effective length of query: 536 Effective length of database: 549 Effective search space: 294264 Effective search space used: 294264 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 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