Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_057508577.1 ABB28_RS10145 AMP-binding protein
Query= SwissProt::P39062 (572 letters) >NCBI__GCF_001431535.1:WP_057508577.1 Length = 555 Score = 287 bits (735), Expect = 7e-82 Identities = 190/558 (34%), Positives = 292/558 (52%), Gaps = 25/558 (4%) Query: 18 YEETYRHFDWAEAEKHFSWHETGKLNAAYEAIDRHAESFRKNKVALYYKDAKRD-EKYTF 76 Y+ F+ + E +NA E DRH S +++AL + YTF Sbjct: 12 YQRAVDDFNLHDWESRLHGDLQDGINACVECCDRHCGS---DRLALRWISTDGGLHLYTF 68 Query: 77 KEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFEAFMEG 136 ++++ S R +VL G + +GD V +PR+PEL +LG ++GA+ PLF AF Sbjct: 69 EDLRAASTRVAHVLTAQG-IGRGDVVAGMLPRTPELLATILGTWRVGAVYQPLFTAFGAK 127 Query: 137 AVKDRLENSEAKVVVTTPELLERIP-VDKLPHLQHVFVVGGEAESGTNIINYDEAAKQES 195 A++ RL ++VVT ++ V+ P + + G A++ +I A + Sbjct: 128 AIESRLRTGRTRLVVTDHANRHKLDDVEDCPPVATILPAGQPADAA-DIDWRVRIAAAGA 186 Query: 196 TRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGKWVLDLKEEDIYWCTAD 255 + + + +L TSG+TG PKGV A++ + +DL+ D++W AD Sbjct: 187 APFEPVLLRGDELMVLLSTSGTTGAPKGVPVPLRALMSFASYMQLAVDLRPGDVFWNIAD 246 Query: 256 PGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNVWYSAPTAFRMLMGAGD 315 PGW G Y + P + G F+ + + IE+LGV +PTA+R ++ AG+ Sbjct: 247 PGWAYGLYYAVIGPLMLGEATTFNEAPFTVQGLHEVIERLGVTNLAGSPTAYRQIIAAGE 306 Query: 316 EMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQLICNYPCMD-- 373 AA+ LR V S GEPLN E+ RW + + D + TETG ++ N+ + Sbjct: 307 ASAARV-AGQLRAVSSAGEPLNAEIARWFAAHLSTTVLDHYGQTETG-MVVNNHHALHHA 364 Query: 374 IKPGSMGKPIPGVEAAIVDNQGNELPPYRMGNLAIKKGWPSMMHTIWNNPEKYESYF--- 430 ++ GS G +PG A++D+ G+ELP G LAI +M W + Y+ Sbjct: 365 VRTGSSGFAMPGYRVAVLDDDGHELPARTPGILAIDIARSPLM---W-----FTGYYGAD 416 Query: 431 ---MPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHPAIAEAGV 487 + G+Y++GD+ +++G F GR DDVI +SG R+GPF+VES L+EHPA+AEA V Sbjct: 417 TPAIGDGYYLTGDTVECEDDGSISFIGRSDDVITSSGYRIGPFDVESALLEHPAVAEAVV 476 Query: 488 IGKPDPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFKDKLPKTRS 547 IG PDP R EI+KAF+ G E L +++ +VK L+AHA PR +EF ++PKT S Sbjct: 477 IGVPDPQRTEIVKAFVITSTGIEGDAALAAQLQQYVKTRLSAHAYPRLVEFVSEVPKTPS 536 Query: 548 GKIMRRVLKAWELNLPAG 565 GK+ R VL+A E+ AG Sbjct: 537 GKVQRFVLRAAEVARQAG 554 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: 828 Number of extensions: 39 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: 555 Length adjustment: 36 Effective length of query: 536 Effective length of database: 519 Effective search space: 278184 Effective search space used: 278184 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