Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_076477035.1 BW971_RS04860 AMP-binding protein
Query= SwissProt::P39062 (572 letters) >NCBI__GCF_900156495.1:WP_076477035.1 Length = 510 Score = 263 bits (672), Expect = 1e-74 Identities = 166/489 (33%), Positives = 257/489 (52%), Gaps = 38/489 (7%) Query: 75 TFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFEAFM 134 TF+E+ + S R L R G V +G+ V + M +S +L +LG ++GA+ PLF AF Sbjct: 51 TFRELADRSRRFATGLARCG-VGRGEAVGVLMGKSSDLVVALLGIWRLGAVQVPLFTAFA 109 Query: 135 EGAVKDRLENSEAKVVVTTPELLERI-PVDKLPHLQHVFVVGGEAESGTNIINYDEAAKQ 193 A++ R+ S A+VV+ + ++ P D L ++ GG +G + D + Sbjct: 110 TPAIELRVRASGAQVVIADADQAVKLDPFDDLTVIR-----GGTEFAG---LIADNEPYE 161 Query: 194 ESTRLDIEWMDKKDGFLLH-YTSGSTGTPKGVLHVHEAMIQQYQTGKWVLDLKEEDIYWC 252 S + DG ++ +TSG+TGTPKGV A+ + + LD+ +ED++W Sbjct: 162 ASVAVG------GDGTMVQLFTSGTTGTPKGVPVPVRAIAAFHAYMIYALDVSDEDVFWN 215 Query: 253 TADPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNVWYSAPTAFRMLMG 312 ADPGW G YG+ P G N+++ FSP +++ GV + APT +R L Sbjct: 216 AADPGWAYGLYYGLIGPMAIGRPNLLLRAGFSPHLTLDVMQRFGVTNFAGAPTVYRSL-- 273 Query: 313 AGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQLICNYPC- 371 +LR S GEPL P+V+ W + + D + TE G ++ + Sbjct: 274 ---SKDPAISGVTLRRASSAGEPLTPDVLTWSARALGVEVRDHYGQTELGMLIVNAWHDA 330 Query: 372 --MDIKPGSMGKPIPGVEAAIVDNQGNELPPYRMGNLAIKKGWPSMMHTIW-NNPEKYES 428 + PGSMG P+PG A + D G +AI P + + PEK Sbjct: 331 VRQPVVPGSMGTPLPGFSAELRD-----------GQIAIAADSPLFWFDGYVDAPEKTAE 379 Query: 429 YFMPGG-WYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHPAIAEAGV 487 F WY++GD+A +D+EG F+F R DDVI+ +G R+GPF+VES LV HP + + V Sbjct: 380 RFSEDRTWYLTGDTAKVDDEGRFFFTARDDDVIIMAGYRIGPFDVESVLVTHPQVIDVAV 439 Query: 488 IGKPDPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFKDKLPKTRS 547 +G PD +RGE+++A++ L +G + + +L+ E++ VK AAHA PR + F D LPKT S Sbjct: 440 VGTPDELRGEVLEAYVVLADGVDGTAELEAELQRLVKTQFAAHAYPRRVHFVDGLPKTPS 499 Query: 548 GKIMRRVLK 556 GK+ R +L+ Sbjct: 500 GKVQRFLLR 508 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: 693 Number of extensions: 30 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: 510 Length adjustment: 35 Effective length of query: 537 Effective length of database: 475 Effective search space: 255075 Effective search space used: 255075 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: 52 (24.6 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