Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_110208807.1 DNK54_RS20110 AMP-binding protein
Query= SwissProt::P39062 (572 letters) >NCBI__GCF_003194585.1:WP_110208807.1 Length = 545 Score = 303 bits (777), Expect = 9e-87 Identities = 189/491 (38%), Positives = 272/491 (55%), Gaps = 13/491 (2%) Query: 75 TFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFEAFM 134 ++ ++ E S R VL G V GDRV M +S + +LG + GA+ PLF AF Sbjct: 49 SYGDLGESSRRMAAVLTELG-VRPGDRVATLMGKSADFVTTVLGIWRAGAVHVPLFTAFA 107 Query: 135 EGAVKDRLENSEAKVVVTTPELLERI-PVDKLP-HLQHVFVVGGEAESGTNIINYDEAAK 192 A+ RL S+A+VVV P ++ P + LP VV G+A + ++ + A Sbjct: 108 PPAIGLRLAGSDARVVVVDPGQRSKLDPSEDLPADPSRRIVVAGDAVAEGDLALSELLAA 167 Query: 193 QESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGKWVLDLKEEDIYWC 252 + D + +TSG+TGTPKGV +A+ ++ LD+ ED+YW Sbjct: 168 ADPASAPAVVRAGSDELVRLFTSGTTGTPKGVPIPVKALAAFVIYLEYGLDVTAEDVYWN 227 Query: 253 TADPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNVWYSAPTAFRMLMG 312 ADPGW G YGI AP G N+++ F+PE+ + I+ LGV +APT +R L Sbjct: 228 AADPGWAYGLYYGIAAPLALGRRNILLQAGFTPETTWKVIQDLGVTNLAAAPTVYRSLRS 287 Query: 313 AGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQLICNYP-- 370 A A +LR S GEPLNP+V++WG +V IHDT+ TE G ++ + Sbjct: 288 ATTPAPAGI---ALRRASSAGEPLNPDVVQWGAEVLGSEIHDTYGQTELGMSIVNGWHPE 344 Query: 371 -CMDIKPGSMGKPIPGVEAAIVDNQGNELPPY-RMGNLAIK-KGWPSMMHTIW-NNPEKY 426 +++ GSMG+ +PG A ++ + +E+ +G + I G P M T + + PEK Sbjct: 345 IAAEVRHGSMGRAMPGWAATVLKDDADEVADAGELGRVVIDLAGSPLMWFTGYVDAPEKT 404 Query: 427 -ESYFMPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHPAIAEA 485 E + G WY +GD+ MD++G+ +F R DDVI+ +G R+GPFEVES LV P +AEA Sbjct: 405 AERFSADGRWYYTGDAGQMDDDGFLYFSARDDDVIIMAGYRIGPFEVESVLVGDPRVAEA 464 Query: 486 GVIGKPDPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFKDKLPKT 545 V+G PD +RGE+++AF+ L G EPS +L EE++ VK LAAH PREI F LPKT Sbjct: 465 AVVGVPDALRGEVVEAFVVLAPGTEPSVELAEELKQRVKTKLAAHLYPREIHFVASLPKT 524 Query: 546 RSGKIMRRVLK 556 SGKI R L+ Sbjct: 525 PSGKIQRFELR 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: 801 Number of extensions: 40 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: 545 Length adjustment: 36 Effective length of query: 536 Effective length of database: 509 Effective search space: 272824 Effective search space used: 272824 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