Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_011426974.1 RHE_RS19290 AMP-binding protein
Query= SwissProt::P39062 (572 letters) >NCBI__GCF_000092045.1:WP_011426974.1 Length = 550 Score = 261 bits (667), Expect = 5e-74 Identities = 175/535 (32%), Positives = 263/535 (49%), Gaps = 13/535 (2%) Query: 27 WAEAEKHFSWHETGKLNAAYEAIDRHAESFRKNKVALYYKDAKRDEKYTFKEMKEESNRA 86 + + + FSW N D A + ++ T+ E+ S+ Sbjct: 9 YGDLYRDFSWRIPEDFNIGRAVSDEWAARDPERVCLEHFSPNGDHLSLTYGELSAASSMF 68 Query: 87 GNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFEAFMEGAVKDRLENSE 146 N L G +++GDRV + +P+S E + KIGAIA PL F A++ RL S Sbjct: 69 ANALASLG-IKRGDRVALLVPQSFETVIAHVAIYKIGAIALPLALLFGVEALEYRLRISG 127 Query: 147 AKVVVTTPELLERIPV--DKLPHLQHVFVVGGEAESGTNIINYDEAAKQESTRLDIEWMD 204 A ++T L+R+ D+LP L+HV V A++ +++ + ++ + E Sbjct: 128 AAAIITNDFGLDRVRQIRDRLPELRHVISVSDAADA----LSFADLIASHASVFEGEKTT 183 Query: 205 KKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGKWVLD--LKEEDIYWCTADPGWVTGT 262 D L+ +TSG+TG PKG LH H + ++ + K D W +D W G Sbjct: 184 PDDAALMIFTSGTTGPPKGALHGHRVLPGHIPGMQFAHEGFPKVGDKVWTPSDWAWAGGL 243 Query: 263 VYGIFAPWLNGATNVIVGG-RFSPESWYGTIEQLGVNVWYSAPTAFRMLMGAGDEMAAKY 321 + + L G V +F ++ Y + ++ V + PTA R++ D + KY Sbjct: 244 LNALLPSLLLGVPVVSSPAQKFDADTAYRIMAEMKVRNAFIPPTALRLMRSVSDPRS-KY 302 Query: 322 DLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQLICNYPCMDIKPGSMGK 381 DL LR V S GE L E W + +++ + TE L + K G++G+ Sbjct: 303 DLV-LRTVGSAGEALGRETYDWARRTLGITVNEFYGQTECNFVLSSSAAFGVTKAGAIGR 361 Query: 382 PIPGVEAAIVDNQGNELPPYRMGNLAIKKGWPSMMHTIWNNPEKYESYFMPGGWYVSGDS 441 +PG AIV G+ELP G +AI P M WN+ E F+ G W ++GD Sbjct: 362 AVPGHRVAIVSEAGDELPAGESGQIAIASPDPVMFLGYWNDAAATERKFLHG-WLLTGDI 420 Query: 442 AYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHPAIAEAGVIGKPDPVRGEIIKA 501 DE+GY F+GR DDVI +SG R+GP E+E L HPA+ A +GKPD VR EI+KA Sbjct: 421 GRQDEDGYVTFEGRDDDVITSSGYRIGPAEIEDCLTGHPAVQLAAAVGKPDVVRTEIVKA 480 Query: 502 FIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFKDKLPKTRSGKIMRRVLK 556 +I L G PS+ L EIR +VK L+ H PRE+EF + LP T +GK++RR+L+ Sbjct: 481 YIVLSPGHSPSEALAAEIREWVKMRLSMHEYPREVEFVESLPLTTTGKVIRRLLR 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: 798 Number of extensions: 40 Number of successful extensions: 5 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: 550 Length adjustment: 36 Effective length of query: 536 Effective length of database: 514 Effective search space: 275504 Effective search space used: 275504 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