Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate GFF3431 PS417_17555 branched-chain alpha-keto acid dehydrogenase subunit E2
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3542 (425 letters) >FitnessBrowser__WCS417:GFF3431 Length = 419 Score = 680 bits (1754), Expect = 0.0 Identities = 358/426 (84%), Positives = 383/426 (89%), Gaps = 8/426 (1%) Query: 1 MGTHVIKMPDIGEGIAEVELSVWHVKVGDMVVEDQVLADVMTDKAMVDIPSPVHGKVIAL 60 MGTHVIKMPDIGEGIAEVELSVWHVKVGDMVVEDQVLADVMTDKAMVDIPSPVHGKVI+L Sbjct: 1 MGTHVIKMPDIGEGIAEVELSVWHVKVGDMVVEDQVLADVMTDKAMVDIPSPVHGKVISL 60 Query: 61 GGQPGEVMAVGSVLISIEVEGAGNVKESAQPAPVVKEAPVAATKVETVVESKPVAAPA-P 119 GG+PGEVMAVGS+LISIEVEGAGN KE AP KE P AA VE + PVA + P Sbjct: 61 GGEPGEVMAVGSILISIEVEGAGNAKE----APAAKETPKAAPVVEA--KPAPVAVESKP 114 Query: 120 KAAVCQGPMVAREADERPLASPAVRKHALDLGIQLRLVRGTGPAGRVLHEDLDAYLAQGQ 179 V P VAR ADERPLASPAVRKHALD GIQLRLV+G+GPAGR+LHEDLDAYL QG Sbjct: 115 APVVATQPPVARAADERPLASPAVRKHALDAGIQLRLVQGSGPAGRILHEDLDAYLQQGA 174 Query: 180 SNASAPVAAAYAQRTDEQQIPVIGMRRKIAQRMQDATQRAAHFSYVEEIDVTAVEELRAH 239 S +S YA+R E+QIPVIGMRRKIAQRMQDAT+RAAHFSYVEEIDVTA++ELR H Sbjct: 175 SKSST-ATNPYAERNTEEQIPVIGMRRKIAQRMQDATRRAAHFSYVEEIDVTALDELRVH 233 Query: 240 LNEKHGATRGKLTLLPFLVRALVVALRDFPQINARYDDEAQVITRLGAVHVGIATQADIG 299 LNEKHGATRGKLTLLPF+VRA+VVALRDFPQINARYDDEAQVITRLGAVHVG+ATQ+D+G Sbjct: 234 LNEKHGATRGKLTLLPFIVRAMVVALRDFPQINARYDDEAQVITRLGAVHVGVATQSDVG 293 Query: 300 LMVPVVRHAEARSLWDSAAEISRLATAARNGKASRDELSGSTITLTSLGALGGIVSTPVL 359 LMVPVVRHAEARSLW +A EI+RLATAARNGKASRDELSGSTITLTSLGALGGIVSTPVL Sbjct: 294 LMVPVVRHAEARSLWGNAEEIARLATAARNGKASRDELSGSTITLTSLGALGGIVSTPVL 353 Query: 360 NLPEVAIVGVNKIVERPMVIKGQIVIRKMMNLSSSFDHRVVDGMDAALFIQAIRGLLEQP 419 NLPEVAIVGVN+IVERPMVIKGQIV+RKMMNLSSSFDHRVVDGMDAA FIQAIRGLLEQP Sbjct: 354 NLPEVAIVGVNRIVERPMVIKGQIVVRKMMNLSSSFDHRVVDGMDAAQFIQAIRGLLEQP 413 Query: 420 ATLFVE 425 A+LF+E Sbjct: 414 ASLFLE 419 Lambda K H 0.318 0.133 0.368 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: 650 Number of extensions: 13 Number of successful extensions: 3 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: 425 Length of database: 419 Length adjustment: 32 Effective length of query: 393 Effective length of database: 387 Effective search space: 152091 Effective search space used: 152091 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: 50 (23.9 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