Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate GFF4308 PS417_22065 long-chain fatty acid--CoA ligase
Query= BRENDA::D3GE78 (556 letters) >FitnessBrowser__WCS417:GFF4308 Length = 563 Score = 196 bits (499), Expect = 2e-54 Identities = 155/524 (29%), Positives = 249/524 (47%), Gaps = 33/524 (6%) Query: 46 LTTHDLRLWSQRLAAGLRK-SGLQRGDRVLLFSGNDLFFPVVFLGVIMAGGIFTGANPTF 104 +T +L S AA L++ + L+ GDR+ + N L +PV G I AG I NP + Sbjct: 50 ITYGELYELSGAFAAYLQQHTDLKPGDRIAVQLPNVLQYPVAVFGAIRAGLIVVNTNPLY 109 Query: 105 VARELAYQLQDSGATYLLCASNSLETGLEAAKQAKLPQSHIFAYDTSIYDGVTNPQKGCA 164 ARE+ +Q DSGA L+C +N + + + H+ T + D + P K Sbjct: 110 TAREMEHQFNDSGAKALVCLANMAHLAEKVVPKTAV--KHVIV--TEVAD-LLPPLKRLL 164 Query: 165 ------YWSDLLASEEEGAAFTWDEL----------STPALSSTTLALNYSSGTTGRPKG 208 Y ++ + A ++++ SS L Y+ GTTG KG Sbjct: 165 INSVIKYVKKMVPAYHLPNAIKFNDVLAKGHGQPVSDASPTSSDVAVLQYTGGTTGVAKG 224 Query: 209 VEISHRNYVANMLQYCHTASLHPDYKARLERSRWLCFLPMYHAMAQNIF-IAAALYRATP 267 ++HRN VANMLQ + + + + LP+YH A +A L Sbjct: 225 AMLTHRNLVANMLQCKALMGSNLNEGCEI----LITPLPLYHIYAFTFHCMAMMLIGNHN 280 Query: 268 VYIMSKFDFVKMLEYTQRFRITDFILVPPVVVALAKHPAVGQYDLSSVELVGSGAAPLGR 327 + I + D M++ +++ + F+ + + VAL + A + D S++++ SG L Sbjct: 281 ILISNPRDLPAMVKELSKWKFSGFVGLNTLFVALCNNEAFRKLDFSALKVTLSGGMALQL 340 Query: 328 EVCEEVEKLWPPGKINIKQGWGMTEATCSVTGWNPAEISTSASVGELNANCEAKIMFDGV 387 E + + G I +G+GMTE T V NP + ++G + K++ D Sbjct: 341 AAAERWKAVTGCG---ICEGYGMTE-TSPVATVNPIQHIQIGTIGIPVPSTVCKVIADDG 396 Query: 388 EVKERNSRGELWVRAPNVMKGYWRNEKATKETKTEDGWLLTGDIAFVDDDGKFHVVDRMK 447 GEL V+ P VMKGYW+ + AT E +GWL TGDIA + DG +VDR K Sbjct: 397 TELALGETGELCVKGPQVMKGYWQRQDATDEMLDSEGWLKTGDIAIIQPDGYMRIVDRKK 456 Query: 448 ELIKVKGNQVAPAELEALLLEHPAISDVAVIGVV-INNDERPRAYVVLRPGQSATANEIA 506 ++I V G V P ELE +L P + A IGV + E + ++V++PG + T ++ Sbjct: 457 DMILVSGFNVYPNELEDVLAGLPGVLQCAAIGVPDEKSGEHIKLFIVVKPGATLTKEQVM 516 Query: 507 HYLDNKVSAFKRITGGVVFLEAIPKNPSGKILRMKLREQAKEEL 550 ++ V+A+K + V F +A+P GKILR +LR++ ++L Sbjct: 517 EHMRANVTAYK-VPKAVEFRDALPTTNVGKILRRELRDEELKKL 559 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: 645 Number of extensions: 27 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 556 Length of database: 563 Length adjustment: 36 Effective length of query: 520 Effective length of database: 527 Effective search space: 274040 Effective search space used: 274040 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