Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate PfGW456L13_1911 Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
Query= BRENDA::D3GE78 (556 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1911 Length = 566 Score = 191 bits (485), Expect = 7e-53 Identities = 155/524 (29%), Positives = 245/524 (46%), Gaps = 33/524 (6%) Query: 46 LTTHDLRLWSQRLAAGLRK-SGLQRGDRVLLFSGNDLFFPVVFLGVIMAGGIFTGANPTF 104 LT +L S AA L++ + LQ GDR+ + N L +PV G I AG I NP + Sbjct: 50 LTYGELYELSGAFAAYLQQHTDLQPGDRIAVQLPNVLQYPVAVFGAIRAGLIVVNTNPLY 109 Query: 105 VARELAYQLQDSGATYLLCASNSLETGLEAAKQAKLPQSHIFAYDTSIYDGVTNPQKG-- 162 ARE+ +Q DSGA L+C +N L K H+ T + D + P K Sbjct: 110 TAREMEHQFNDSGAKALVCLANMAH--LAETVVPKTGVKHVIV--TEVAD-LLPPLKRLL 164 Query: 163 ----CAYWSDLLASEEEGAAFTWDELSTPAL----------SSTTLALNYSSGTTGRPKG 208 Y ++ + A ++++ + L S L Y+ GTTG KG Sbjct: 165 INSVIKYVKKMVPAYHLPKAVKFNDVLSKGLGQPVAEANPASGDVAVLQYTGGTTGVAKG 224 Query: 209 VEISHRNYVANMLQYCHTASLHPDYKARLERSRWLCFLPMYHAMAQNIFIAAALYRAT-P 267 ++HRN VANMLQ + + + + LP+YH A A + Sbjct: 225 AMLTHRNLVANMLQCKALMGSNLNEGCEI----LITPLPLYHIYAFTFHCMAMMLAGNHN 280 Query: 268 VYIMSKFDFVKMLEYTQRFRITDFILVPPVVVALAKHPAVGQYDLSSVELVGSGAAPLGR 327 + I + D M++ +++ + F+ + + VAL + + D S++++ SG L Sbjct: 281 ILISNPRDLPAMVKELSKWKFSGFVGLNTLFVALCNNEGFRKLDFSALKVTLSGGMALQL 340 Query: 328 EVCEEVEKLWPPGKINIKQGWGMTEATCSVTGWNPAEISTSASVGELNANCEAKIMFDGV 387 E + + I +G+GMTE T V NP + ++G + KI+ D Sbjct: 341 AAAERWKAV---TGCAICEGYGMTE-TSPVATVNPIQHIQVGTIGIPVPSTLCKIINDAG 396 Query: 388 EVKERNSRGELWVRAPNVMKGYWRNEKATKETKTEDGWLLTGDIAFVDDDGKFHVVDRMK 447 + GEL V+ P VMKGYW+ ++AT E +GWL TGDIA + DG +VDR K Sbjct: 397 VEQPLGEIGELCVKGPQVMKGYWQRQEATDEILDSEGWLKTGDIALIQPDGFMRIVDRKK 456 Query: 448 ELIKVKGNQVAPAELEALLLEHPAISDVAVIGVV-INNDERPRAYVVLRPGQSATANEIA 506 ++I V G V P ELE +L P + A IGV + E + +V +PG + T ++ Sbjct: 457 DMILVSGFNVYPNELEDVLATLPGVLQCAAIGVPDEKSGEAIKILIVAKPGVTLTKEQVM 516 Query: 507 HYLDNKVSAFKRITGGVVFLEAIPKNPSGKILRMKLREQAKEEL 550 ++ V+ +K + V F +A+P GKILR +LR++ +++ Sbjct: 517 EHMRANVTGYK-VPRSVEFRDALPTTNVGKILRRELRDEELKKI 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: 672 Number of extensions: 29 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: 566 Length adjustment: 36 Effective length of query: 520 Effective length of database: 530 Effective search space: 275600 Effective search space used: 275600 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