Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate AO353_26645 AO353_26645 branched-chain alpha-keto acid dehydrogenase subunit E2
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3542 (425 letters) >FitnessBrowser__pseudo3_N2E3:AO353_26645 Length = 425 Score = 739 bits (1907), Expect = 0.0 Identities = 389/428 (90%), Positives = 402/428 (93%), Gaps = 6/428 (1%) Query: 1 MGTHVIKMPDIGEGIAEVELSVWHVKVGDMVVEDQVLADVMTDKAMVDIPSPVHGKVIAL 60 MGTHVIKMPDIGEGIAEVELSVWHVKVGDMVVEDQVLADVMTDKAMVDIPSPVHGKVI+L Sbjct: 1 MGTHVIKMPDIGEGIAEVELSVWHVKVGDMVVEDQVLADVMTDKAMVDIPSPVHGKVISL 60 Query: 61 GGQPGEVMAVGSVLISIEVEGAGNVKESAQPAPVV---KEAPVAATKVETVVESKPVAAP 117 GG+PGEVMAVGS+LISIEVEG GNVK S+QPAP K APVAA KVE +ESK Sbjct: 61 GGEPGEVMAVGSILISIEVEGEGNVKASSQPAPAAPAPKPAPVAAPKVEAAIESKSAVPA 120 Query: 118 APKAAVCQGPMVAREADERPLASPAVRKHALDLGIQLRLVRGTGPAGRVLHEDLDAYLAQ 177 P A QGPM+AREADERPLASPAVRKHALD GIQLRLVRGTGPAGR+LHEDL+AYLAQ Sbjct: 121 RPVAP--QGPMIAREADERPLASPAVRKHALDAGIQLRLVRGTGPAGRILHEDLEAYLAQ 178 Query: 178 GQSNASAPVAAAYAQRTDEQQIPVIGMRRKIAQRMQDATQRAAHFSYVEEIDVTAVEELR 237 GQSNAS+ VAA YA+R DEQQIPVIGMRRKIAQRMQDATQRAAHFSYVEEIDVTAVEELR Sbjct: 179 GQSNASSTVAA-YAERNDEQQIPVIGMRRKIAQRMQDATQRAAHFSYVEEIDVTAVEELR 237 Query: 238 AHLNEKHGATRGKLTLLPFLVRALVVALRDFPQINARYDDEAQVITRLGAVHVGIATQAD 297 AHLNEKHGATRGKLTLLPFLVRA+VVALRDFPQINARYDDEAQVITRLGAVHVG+ATQ+D Sbjct: 238 AHLNEKHGATRGKLTLLPFLVRAMVVALRDFPQINARYDDEAQVITRLGAVHVGVATQSD 297 Query: 298 IGLMVPVVRHAEARSLWDSAAEISRLATAARNGKASRDELSGSTITLTSLGALGGIVSTP 357 IGLMVPVVRHAEARSLWDSAAEISRLATAARNGKASRDELSGSTITLTSLGALGGIVSTP Sbjct: 298 IGLMVPVVRHAEARSLWDSAAEISRLATAARNGKASRDELSGSTITLTSLGALGGIVSTP 357 Query: 358 VLNLPEVAIVGVNKIVERPMVIKGQIVIRKMMNLSSSFDHRVVDGMDAALFIQAIRGLLE 417 VLNLPEVAIVGVNKIVERPMVIKGQIVIRKMMNLSSSFDHRVVDGMDAA FIQAIRGLLE Sbjct: 358 VLNLPEVAIVGVNKIVERPMVIKGQIVIRKMMNLSSSFDHRVVDGMDAAQFIQAIRGLLE 417 Query: 418 QPATLFVE 425 QPATLFVE Sbjct: 418 QPATLFVE 425 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: 659 Number of extensions: 12 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: 425 Length adjustment: 32 Effective length of query: 393 Effective length of database: 393 Effective search space: 154449 Effective search space used: 154449 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: 51 (24.3 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