Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_086509765.1 BZY95_RS09865 long-chain fatty acid--CoA ligase
Query= BRENDA::A7KUK6 (562 letters) >NCBI__GCF_002151265.1:WP_086509765.1 Length = 533 Score = 176 bits (445), Expect = 3e-48 Identities = 126/373 (33%), Positives = 197/373 (52%), Gaps = 30/373 (8%) Query: 181 AKDVAFLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGPDG--KGDRVLAF 238 A+ VA ++Y+SGTTG PKGVM++HR I+ +IA S +GG +G+RV Sbjct: 177 AEQVAAMIYTSGTTGTPKGVMLTHRGIL------YIA-----SLSGGMRHLREGERVYGV 225 Query: 239 LPFYHIYGLTCLITQALYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHP 298 LP H++GL+ + +LY G L + +FD A + R + VP + + Sbjct: 226 LPMSHVFGLSSVCMGSLYNGACLYSVPRFDAAAMLAALGQERITVLQGVPAMFARTLEFL 285 Query: 299 VVDKYDLSS--LRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWR 356 + L++ LR +++G +PL +L V + + + GYGL+E SPT R ED R Sbjct: 286 RREGRALAAPALRYISAGGSPLDADLKRRVQALFGLTLHNGYGLTEASPTISQTRIED-R 344 Query: 357 EAMGSVGRLMPNMQAKYMTMPEDGS-EPKEVGEGEVGELYLKGPNVFLGYHENPEATKGC 415 +VGR++P ++ + + E G EP+ G GEL+++GPNV GY P AT+ C Sbjct: 345 FDSNTVGRVLPLLEYRLEPLGEGGEDEPEHAG---AGELWVRGPNVMKGYFRQPSATRAC 401 Query: 416 LSEDGWFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIG 475 LSEDGW TGD+ D YI R KELI GF + P ++E + ++ + AV+G Sbjct: 402 LSEDGWLNTGDIARFDEDDQLYIVGRSKELIIRSGFNIYPPDVEAVINEHPDVTLSAVVG 461 Query: 476 IESETHGSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIP 535 + E G+E +A V G +EA R ++L +++A +KR + ++ +P Sbjct: 462 RQVE--GNEEVVAFV-----QCEPGAMLSEEALR--EFLAARLAPYKR-PARLILMESLP 511 Query: 536 KNPSGKILRRILK 548 SGKIL+ L+ Sbjct: 512 ATASGKILKGCLR 524 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: 636 Number of extensions: 32 Number of successful extensions: 4 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: 533 Length adjustment: 36 Effective length of query: 526 Effective length of database: 497 Effective search space: 261422 Effective search space used: 261422 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