Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_011320678.1 AVA_RS20210 long-chain-fatty-acid--CoA ligase
Query= SwissProt::P39062 (572 letters) >NCBI__GCF_000204075.1:WP_011320678.1 Length = 662 Score = 231 bits (588), Expect = 9e-65 Identities = 160/500 (32%), Positives = 249/500 (49%), Gaps = 23/500 (4%) Query: 59 NKVALYYKDAKRDEKYTFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLG 118 NK AL ++ +T+K++ E +NR N L G +E+GDR+ + +P PE LG Sbjct: 16 NKPALIFEGLY----FTYKQLNEMANRVANALLGLG-IERGDRIALLLPNIPEFVISYLG 70 Query: 119 AIKIGAIAGPLFEAFMEGAVKDRLENSEAKVVVTTPELLERIPVDKLPHLQHVFVVGGEA 178 +KIGAIA + +K L + A V+VTT L E++P LPHL+H+ + G+A Sbjct: 71 ILKIGAIAVSINPNLQSDELKFILNDCGAAVLVTTETLREKLPKVDLPHLKHIIIAEGQA 130 Query: 179 ESGTNIINYDEAAKQESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTG 238 + + A + ++IE + + + YTSG+TG PKG H +I + Sbjct: 131 GEAIALSEFMANASPNARAVEIE---RDEPAAILYTSGTTGFPKGATLSHGNVISNMHSM 187 Query: 239 KWVLDLKEEDIYWCTADPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVN 298 K +++ D G + LN +I+ F PE+ TI + + Sbjct: 188 KHCCEMRPNDQILLFLPMFHCFGQ-NAVLNSGLNTCATIILQRSFDPETVLTTISEYNIT 246 Query: 299 VWYSAPTAFRMLMGAGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWM 358 +++ PT F +L + A+ DL S+R+ S L E+ + F K I+ + + Sbjct: 247 IFFGVPTTFILLC----DKASIRDLDSVRYYFSAAAGLPVEIAKRWQDKFGKVINQGYGL 302 Query: 359 TETGSQLICNYPCMDIKPGSMGKPIPGVEAAIVD-NQGNELPPYRMGNLAIKKGWPSMMH 417 TET N+ + K GS+G PI VE IV + G E+ P +G + I+ ++M Sbjct: 303 TETSPLASYNHE-LRYKLGSIGSPIENVEMKIVSLDDGCEVAPGELGEIVIRG--VNVML 359 Query: 418 TIWNNPEKYESYFMPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLV 477 WN P + + M GW+ +GD +DE GYF+ R+ D+I G +V P EVE+ + Sbjct: 360 GYWNRPAE-TAKAMKNGWFHTGDIGQIDELGYFYIVDRLKDMINNGGLKVYPAEVENVIY 418 Query: 478 EHPAIAEAGVIGKPDPVRGEIIKAFIALREGFEPSDKLKE-EIRLFVKQGLAAHAAPREI 536 +HP IAE V G PD V GE +KA I L+ P + E EI F Q LA + P + Sbjct: 419 QHPGIAEVAVYGVPDSVLGEQVKASIVLK----PDQAVTEAEIIAFCYQKLAQYKVPSAV 474 Query: 537 EFKDKLPKTRSGKIMRRVLK 556 EF +PK +GKI++R+L+ Sbjct: 475 EFVSSIPKNPTGKILKRLLR 494 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: 808 Number of extensions: 37 Number of successful extensions: 8 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: 662 Length adjustment: 37 Effective length of query: 535 Effective length of database: 625 Effective search space: 334375 Effective search space used: 334375 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