Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate AO353_19945 AO353_19945 acetyl-CoA synthetase
Query= SwissProt::P39062 (572 letters) >lcl|FitnessBrowser__pseudo3_N2E3:AO353_19945 AO353_19945 acetyl-CoA synthetase Length = 588 Score = 484 bits (1246), Expect = e-141 Identities = 262/568 (46%), Positives = 346/568 (60%), Gaps = 24/568 (4%) Query: 26 DWAEAEKHFSWHET---------GKLNAAYEAIDRHAESFRKNKVALYYKDAKRDE-KYT 75 D +A + FSW G LN AYEA+DRHAE + AL D + Sbjct: 22 DSVQAREGFSWQGEASALAGLPGGGLNLAYEAVDRHAEGKHRRHTALRILDRNGGRCDIS 81 Query: 76 FKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFEAFME 135 + + SNR NVL+ G V G+R+F+ R ELY +LG +K+G + PLF AF Sbjct: 82 YARLSLLSNRFANVLKTLG-VVPGERLFVLCGRGLELYLGVLGGLKLGCVVSPLFCAFGP 140 Query: 136 GAVKDRLENSEAKVVVTTPELLERIPV----DKLPHLQHVFVVGGEAESGTNI---INYD 188 ++ RL E V++T+ E L R V ++LP L+HV + E + T + ++ Sbjct: 141 EPIETRLRLGEGSVLLTS-ETLYRHKVAAIRERLPALKHVLLYDEEGGNTTPVEGTLSLH 199 Query: 189 EAAKQESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGKWVLDLKEED 248 + +I LLH+TSG+TGTPKGVLHVH A++ TGK+ LDL +D Sbjct: 200 RLLANATDHFEIAHTTADSPALLHFTSGTTGTPKGVLHVHGAVLTHRVTGKYALDLHPDD 259 Query: 249 IYWCTADPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNVWYSAPTAFR 308 IYWC+ADPGWVTGT YGI AP L G T+V+ G F E WY T+E+ V VWY+APTA R Sbjct: 260 IYWCSADPGWVTGTSYGIIAPLLLGVTSVVEGREFDAERWYRTLEKQQVTVWYTAPTAIR 319 Query: 309 MLMGAGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQLICN 368 +LM AG E+A + LR + SVGEPLNPE + WG +V IHD WW TETG +I N Sbjct: 320 LLMKAGAELAHSHRFPCLRFIASVGEPLNPEAVWWGQEVLGLPIHDNWWQTETGGIMIAN 379 Query: 369 YPCMDIKPGSMGKPIPGVEAAIV----DNQGNELPPYRMGNLAIKKGWPSMMHTIWNNPE 424 M IKPGSMGKP+PGVEAA+V + + L +G LA+K+ WP+M T E Sbjct: 380 TVAMTIKPGSMGKPLPGVEAAVVVRGAAGELDYLGDNEVGELALKQPWPAMFRTYLGQEE 439 Query: 425 KYESYFMPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHPAIAE 484 +Y F+ GWY+SGD D +GY+WF GR DDVI ++G +GPFEVES L+EHPA+AE Sbjct: 440 RYRQCFV-AGWYLSGDLVRRDADGYYWFIGRSDDVIKSAGHLIGPFEVESSLMEHPAVAE 498 Query: 485 AGVIGKPDPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFKDKLPK 544 A VIGKPDP+ GE +K F++L+ GF S L +E+ ++ L A AP+E+EF + LP Sbjct: 499 AAVIGKPDPLLGETVKVFVSLKSGFTASQALHDELLGHGRKRLGAVVAPKELEFVEALPH 558 Query: 545 TRSGKIMRRVLKAWELNLPAGDLSTMED 572 TRSGK+MRR+LKA EL LP GD S++E+ Sbjct: 559 TRSGKLMRRLLKARELGLPEGDTSSLEN 586 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: 987 Number of extensions: 49 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 572 Length of database: 588 Length adjustment: 36 Effective length of query: 536 Effective length of database: 552 Effective search space: 295872 Effective search space used: 295872 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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