GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bkdC in Pseudomonas fluorescens GW456-L13

Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate PfGW456L13_3542 Dihydrolipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex (EC 2.3.1.168)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_3542
         (425 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3542
           Dihydrolipoamide acyltransferase component of
           branched-chain alpha-keto acid dehydrogenase complex (EC
           2.3.1.168)
          Length = 425

 Score =  814 bits (2102), Expect = 0.0
 Identities = 425/425 (100%), Positives = 425/425 (100%)

Query: 1   MGTHVIKMPDIGEGIAEVELSVWHVKVGDMVVEDQVLADVMTDKAMVDIPSPVHGKVIAL 60
           MGTHVIKMPDIGEGIAEVELSVWHVKVGDMVVEDQVLADVMTDKAMVDIPSPVHGKVIAL
Sbjct: 1   MGTHVIKMPDIGEGIAEVELSVWHVKVGDMVVEDQVLADVMTDKAMVDIPSPVHGKVIAL 60

Query: 61  GGQPGEVMAVGSVLISIEVEGAGNVKESAQPAPVVKEAPVAATKVETVVESKPVAAPAPK 120
           GGQPGEVMAVGSVLISIEVEGAGNVKESAQPAPVVKEAPVAATKVETVVESKPVAAPAPK
Sbjct: 61  GGQPGEVMAVGSVLISIEVEGAGNVKESAQPAPVVKEAPVAATKVETVVESKPVAAPAPK 120

Query: 121 AAVCQGPMVAREADERPLASPAVRKHALDLGIQLRLVRGTGPAGRVLHEDLDAYLAQGQS 180
           AAVCQGPMVAREADERPLASPAVRKHALDLGIQLRLVRGTGPAGRVLHEDLDAYLAQGQS
Sbjct: 121 AAVCQGPMVAREADERPLASPAVRKHALDLGIQLRLVRGTGPAGRVLHEDLDAYLAQGQS 180

Query: 181 NASAPVAAAYAQRTDEQQIPVIGMRRKIAQRMQDATQRAAHFSYVEEIDVTAVEELRAHL 240
           NASAPVAAAYAQRTDEQQIPVIGMRRKIAQRMQDATQRAAHFSYVEEIDVTAVEELRAHL
Sbjct: 181 NASAPVAAAYAQRTDEQQIPVIGMRRKIAQRMQDATQRAAHFSYVEEIDVTAVEELRAHL 240

Query: 241 NEKHGATRGKLTLLPFLVRALVVALRDFPQINARYDDEAQVITRLGAVHVGIATQADIGL 300
           NEKHGATRGKLTLLPFLVRALVVALRDFPQINARYDDEAQVITRLGAVHVGIATQADIGL
Sbjct: 241 NEKHGATRGKLTLLPFLVRALVVALRDFPQINARYDDEAQVITRLGAVHVGIATQADIGL 300

Query: 301 MVPVVRHAEARSLWDSAAEISRLATAARNGKASRDELSGSTITLTSLGALGGIVSTPVLN 360
           MVPVVRHAEARSLWDSAAEISRLATAARNGKASRDELSGSTITLTSLGALGGIVSTPVLN
Sbjct: 301 MVPVVRHAEARSLWDSAAEISRLATAARNGKASRDELSGSTITLTSLGALGGIVSTPVLN 360

Query: 361 LPEVAIVGVNKIVERPMVIKGQIVIRKMMNLSSSFDHRVVDGMDAALFIQAIRGLLEQPA 420
           LPEVAIVGVNKIVERPMVIKGQIVIRKMMNLSSSFDHRVVDGMDAALFIQAIRGLLEQPA
Sbjct: 361 LPEVAIVGVNKIVERPMVIKGQIVIRKMMNLSSSFDHRVVDGMDAALFIQAIRGLLEQPA 420

Query: 421 TLFVE 425
           TLFVE
Sbjct: 421 TLFVE 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: 689
Number of extensions: 11
Number of successful extensions: 1
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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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