Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_017600884.1 D471_RS0123490 long-chain fatty acid--CoA ligase
Query= BRENDA::A7KUK6 (562 letters) >NCBI__GCF_000341125.1:WP_017600884.1 Length = 521 Score = 211 bits (538), Expect = 4e-59 Identities = 162/490 (33%), Positives = 244/490 (49%), Gaps = 39/490 (7%) Query: 70 GDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVTQASV-- 127 GD +AL PN PV +G L AG ++ P N T E+A+ L++S A + Sbjct: 52 GDRVALSCPNLPYFPVAYYGVLKAGASVVPLNVLLTESEIAYHLRDSGAGVYLCFEGTPE 111 Query: 128 LPVARE--AAKKVGMPEDRIILIGDQRDPDARVKHFTSVRNIS----GATRYRKQKITPA 181 LP+ AA + +R++LI DP++ V H V +++ G +R R+ T Sbjct: 112 LPLGERGTAAFESVSSCERLVLI--TADPES-VSHRAGVPSLAEFTAGHSRDRRPVATAE 168 Query: 182 KDVAFLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAFLPF 241 D A ++Y+SGTTG PKG ++H N+V N GE D L LP Sbjct: 169 TDTAVVLYTSGTTGRPKGAELTHSNLVHNALVGNRLFGEYAD---------DVHLVALPL 219 Query: 242 YHIYGLTCLITQALYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVD 301 +H + T + L G L++ +FD E+ + ++ +F VP + L + D Sbjct: 220 FHTFAQTVHMNAGLASGATLVLTDRFDPERALSLMEREGVTFFAGVPTMYWGLLRCETAD 279 Query: 302 KYDLS----SLRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWRE 357 ++DL+ ++R+ SG A L E++ R VGI +GYGLSETSP R D Sbjct: 280 RFDLARIATTMRISVSGGAALPMEVLHGFEDRFGVGILEGYGLSETSPLATFNR-PDRPR 338 Query: 358 AMGSVGRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLS 417 GSVG +P + + DG E GE GE+ ++G NV GY + PEAT + Sbjct: 339 RPGSVG--VPVWGVEVGVVGADGGE---AAVGEPGEIRVRGHNVMRGYLDRPEATAEAVD 393 Query: 418 EDGWFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIE 477 DGWF TGD+G +DA G YI DR K++I G+ V P E+E L+ + + AV+G+ Sbjct: 394 ADGWFYTGDIGRRDADGYLYIVDRKKDMIIRGGYNVYPREIEEVLMTHPEVSLAAVVGVP 453 Query: 478 SETHGSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKN 537 +HG E VR+ ++ G++ +E +I W ++A +K R V F D +P Sbjct: 454 HPSHGEE------VRAHVVRAPGSALTEEG--LIAWSRERLAGYKYPR-SVEFADALPMT 504 Query: 538 PSGKILRRIL 547 +GKIL+R L Sbjct: 505 ATGKILKRRL 514 Lambda K H 0.317 0.136 0.410 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: 670 Number of extensions: 32 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: 562 Length of database: 521 Length adjustment: 35 Effective length of query: 527 Effective length of database: 486 Effective search space: 256122 Effective search space used: 256122 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