Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_016556399.1 RGCCGE502_RS21975 AMP-binding protein
Query= SwissProt::P39062 (572 letters) >NCBI__GCF_000298315.2:WP_016556399.1 Length = 542 Score = 263 bits (671), Expect = 2e-74 Identities = 177/544 (32%), Positives = 265/544 (48%), Gaps = 21/544 (3%) Query: 18 YEETYRHFDWAEAEKHFSWHETGKLNAAYEAIDRHAESFRKNKVALYYKDAKRDEKYTFK 77 YE+ YR F W E N D AE ++ T++ Sbjct: 9 YEDLYRDFAWDLPED---------FNIGRAVSDEWAERAPDRVCLEHFSPDGNHLSMTYR 59 Query: 78 EMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFEAFMEGA 137 ++ + S+ N L G V++GDRV + +P+S E + KIGAIA PL F A Sbjct: 60 QLADRSSSFANALMSLG-VKRGDRVALLLPQSFETVIAHVAIYKIGAIALPLALLFGVEA 118 Query: 138 VKDRLENSEAKVVVTTPELLERIPV--DKLPHLQHVFVVGGEAESGTNIINYDEAAKQES 195 ++ RL + A V+T L+RI ++LP L V V G+ + ++ + Sbjct: 119 LEYRLRTAGASAVITNRFGLDRISHIRERLPDLAEVICVDGDRH---RVRSFAALVESHP 175 Query: 196 TRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGKWVLD--LKEEDIYWCT 253 ++ D L+ +TSG+TG PKG LH H+ + ++ + + D W Sbjct: 176 PVFEVAKTAPHDPALMIFTSGTTGPPKGALHGHQVLAGHIPGMQFAHEGFPQPGDKVWTP 235 Query: 254 ADPGWVTGTVYGIFAPWLNGATNVIVGG-RFSPESWYGTIEQLGVNVWYSAPTAFRMLMG 312 +D W G + + L G V +F + Y + ++ V + PTA R+L Sbjct: 236 SDWAWAGGLLNALLPSLLLGVPVVSSPAQKFDADMAYRIMAEMKVRNGFIPPTALRLLKS 295 Query: 313 AGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQLICNYPCM 372 D + KYDL LR + + GE L E W + +++ + TE L N Sbjct: 296 VPDPRS-KYDLV-LRTIGAAGESLGAETQEWVKRTLGITVNEFYGQTECNFVLSSNAAMG 353 Query: 373 DIKPGSMGKPIPGVEAAIVDNQGNELPPYRMGNLAIKKGWPSMMHTIWNNPEKYESYFMP 432 +PG++G+P+PG AIV G EL G +AI++ P M WN+ E F+ Sbjct: 354 VSRPGAIGRPVPGHSVAIVSEAGEELAVGEAGQIAIRRPDPVMFLGYWNDAAATERKFL- 412 Query: 433 GGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHPAIAEAGVIGKPD 492 G W ++GD D +GY F GR DDVI +SG R+GP E+E L+ HPA+ A +GKPD Sbjct: 413 GDWLLTGDIGRQDADGYVTFFGRDDDVITSSGYRIGPAEIEDCLIGHPAVQLAATVGKPD 472 Query: 493 PVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFKDKLPKTRSGKIMR 552 PVR EI+KA++ L GFE SD+L EI +VK L+ H PRE+EF +LP T +GK++R Sbjct: 473 PVRTEIVKAYVVLAPGFEASDRLASEISDWVKLRLSMHEYPREVEFVTELPLTTTGKVIR 532 Query: 553 RVLK 556 R+L+ Sbjct: 533 RLLR 536 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: 762 Number of extensions: 38 Number of successful extensions: 4 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: 542 Length adjustment: 36 Effective length of query: 536 Effective length of database: 506 Effective search space: 271216 Effective search space used: 271216 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 24 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