Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate BPHYT_RS08270 BPHYT_RS08270 long-chain fatty acid--CoA ligase
Query= BRENDA::D3GE78 (556 letters) >FitnessBrowser__BFirm:BPHYT_RS08270 Length = 601 Score = 181 bits (460), Expect = 6e-50 Identities = 149/523 (28%), Positives = 237/523 (45%), Gaps = 36/523 (6%) Query: 46 LTTHDLRLWSQRLAAGLRKSGLQRGDRVLLFSGNDLFFPVVFLGVIMAGGIFTGANPTFV 105 LT +L + AA L+ G++ G+RV + N +PV GV+ AGG+ NP + Sbjct: 84 LTYGELGRKATAFAAYLQSIGVKPGERVAIMLPNTFQYPVSLFGVLKAGGVVVNVNPLYT 143 Query: 106 ARELAYQLQDSGATYLLCASNSLETGLEAAKQAKLPQSHIFAYDTSIYDGVTNPQKG--- 162 RELA+QL+DSGA ++ N +T +A K+ + + DG+ KG Sbjct: 144 VRELAHQLKDSGAQTIIVFENFAKTVEDALPGTKVQNVIVTGLGDLLADGLN--LKGRLL 201 Query: 163 -----------CAYWSDLLASEEEGAAFTWDELSTPA--LSSTTLALNYSSGTTGRPKGV 209 AY E + + TP L Y+ GTTG KG Sbjct: 202 NFMLRHVKKMVPAYNLPKAVPLLEALSTGYSRPLTPVRPTHDDIAFLQYTGGTTGVAKGA 261 Query: 210 EISHRNYVANMLQYCHTASLHPDYKARLERSRWLCFLPMYH--AMAQNIFIAAALYRATP 267 ++H+N +AN+LQ A + + E L LP+YH ++ N I L Sbjct: 262 MLTHKNIIANLLQ----AKAWSEGQLTGEVETVLTPLPLYHIYSLTVNALIFMGL-GGRN 316 Query: 268 VYIMSKFDFVKMLEYTQRFRITDFILVPPVVVALAKHPAVGQYDLSSVELVGSGAAPLGR 327 + I + D +++ + + T V + A + + D S ++L +G + Sbjct: 317 ILIANPRDMKRVMMIIRHEKFTGMTAVNTLYNAFLDNEEFCKRDFSDLKLAMAGGMATQK 376 Query: 328 EVCEEVEKLWPPGKINIKQGWGMTEATCSVTGWNPAEIST----SASVGELNANCEAKIM 383 V E + + GK I +G+G+TE + + NP ++S S+G + + + Sbjct: 377 SVAERFKAV--TGK-PIIEGYGLTECS-PIVSMNPVDLSNMRDFEGSIGLPAPSTQVRFR 432 Query: 384 FDGVEVKERNSRGELWVRAPNVMKGYWRNEKATKETKTEDGWLLTGDIAFVDDDGKFHVV 443 D GEL V+ P VMKGYW T + EDGWL TGDI +D G ++ Sbjct: 433 KDDGSWANIGEAGELCVKGPQVMKGYWNRPDETAKVIDEDGWLATGDIGVMDSRGFIRLI 492 Query: 444 DRMKELIKVKGNQVAPAELEALLLEHPAISDVAVIGVV-INNDERPRAYVVLRPGQSATA 502 DR K++I V G V P E+E ++ HP + +VA IGV ER + ++V R S TA Sbjct: 493 DRKKDMILVSGFNVYPNEVEDVIAAHPDVREVAAIGVPDAAQGERVKVFIVKR-NPSLTA 551 Query: 503 NEIAHYLDNKVSAFKRITGGVVFLEAIPKNPSGKILRMKLREQ 545 ++ + ++ +K + V F + +P+ GKILR LR++ Sbjct: 552 EQVIAHCRKNLTGYK-VPKLVEFRDELPQTNVGKILRRALRDE 593 Lambda K H 0.319 0.134 0.403 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: 709 Number of extensions: 37 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 556 Length of database: 601 Length adjustment: 36 Effective length of query: 520 Effective length of database: 565 Effective search space: 293800 Effective search space used: 293800 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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