Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_011385246.1 AMB_RS14445 benzoate-CoA ligase family protein
Query= SwissProt::P39062 (572 letters) >NCBI__GCF_000009985.1:WP_011385246.1 Length = 528 Score = 231 bits (590), Expect = 4e-65 Identities = 172/523 (32%), Positives = 267/523 (51%), Gaps = 28/523 (5%) Query: 43 NAAYEAIDRHAESFRKNKVALYYKDAKRDEKYTFKEMKEESNRAGNVLRRYGNVEKGDRV 102 NAA IDRH + R KVA + DA D +T+ ++ E+ NRAGN L+ G + +R+ Sbjct: 19 NAATWFIDRHIKDGRSAKVA--FIDA--DGSHTYAQLGEKVNRAGNALKSLG-LHMENRI 73 Query: 103 FIFMPRSPELYFIMLGAIKIGAIAGPLFEAFMEGAVKDRLENSEAKVVVTTPELLERIP- 161 + M + + + GAIK G + PL G L +S A+V+V + EL +++ Sbjct: 74 AMIMLDTVDFPSVFWGAIKAGIVPIPLNTLLTTGDYGYMLSDSRARVLVISEELFDKVEP 133 Query: 162 -VDKLPHLQHVFVVGGEAESGTNIINYDEAAKQ-----ESTRLDIE-WMDKKDGFLLHYT 214 + LP L+HV + G A T + + AA+ E+TR D+ W+ Y+ Sbjct: 134 ILPDLPLLEHVVISGKNAHGHTLLSDMMAAAEPKLKTAETTRDDVAFWL---------YS 184 Query: 215 SGSTGTPKGVLHVHEAM-IQQYQTGKWVLDLKEEDIYWCTADPGWVTGTVYGIFAPWLNG 273 SGSTG PKG +H+ + G+ VL + E+D+ + A + G G+ G Sbjct: 185 SGSTGAPKGAVHLQRDLPATAVHYGQQVLGITEDDVTFSAAKLFFAYGLGNGMTFSLHVG 244 Query: 274 ATNVIVGGRFSPESWYGTIEQLGVNVWYSAPTAFRMLMGAGDEMAAKYDLTSLRHVLSVG 333 AT+V++ R +PE+ ++ ++Y PT + ++ A + + T LR +S G Sbjct: 245 ATSVLLKDRPTPEAVMKILKDHQPTIFYGVPTLYGTIL-ADPQYRRETASTRLRACVSAG 303 Query: 334 EPLNPEVIRWGHKVFNKRIHDTWWMTETGSQLICNYPCMDIKPGSMGKPIPGVEAAIVDN 393 E L +V R + F I D TE + N +++ G+ GK +PG + IV + Sbjct: 304 EALPEDVGRRWEERFGAAILDGLGSTEMLHIFLSNRHG-EVRYGTSGKAVPGYDLKIVAD 362 Query: 394 QGNELPPYRMGNLAIKKGWPSMMHTIWNNPEKYESYFMPGGWYVSGDSAYMDEEGYFWFQ 453 G+ELP MG L ++ PS WN EK F G W +GD ++D++GY+ + Sbjct: 363 DGHELPQGEMGELVVRG--PSSATAYWNQREKSLKTFR-GEWTHTGDKYFVDDDGYYRYA 419 Query: 454 GRVDDVIMTSGERVGPFEVESKLVEHPAIAEAGVIGKPDPVRGEIIKAFIALREGFEPSD 513 GR DD++ G V PFEVE+ L+ H + EA V+G+ D KAF+ L G S+ Sbjct: 420 GRGDDMLKVGGIWVSPFEVEAALISHEMVLEAAVVGEADSEGLVKPKAFVVLAPGETGSE 479 Query: 514 KLKEEIRLFVKQGLAAHAAPREIEFKDKLPKTRSGKIMRRVLK 556 LKE+++ +VK LA + PR IEF + LPKT +GKI R L+ Sbjct: 480 VLKEQLQAYVKAKLAPYKYPRWIEFVEALPKTATGKIQRFKLR 522 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: 797 Number of extensions: 52 Number of successful extensions: 7 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: 528 Length adjustment: 36 Effective length of query: 536 Effective length of database: 492 Effective search space: 263712 Effective search space used: 263712 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 17 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