GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_4789 in Pseudomonas fluorescens FW300-N1B4

Annotation: Butyryl-CoA dehydrogenase (EC 1.3.99.2)

Length: 383 amino acids

Source: pseudo1_N1B4 in FitnessBrowser

Candidate for 14 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-valine catabolism acdH hi isobutyryl-CoA dehydrogenase (EC 1.3.8.5) (characterized) 97% 100% 742.3
L-isoleucine catabolism acdH hi short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized) 59% 99% 448.4
L-lysine catabolism bcd med butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (subunit 1/2) (EC 1.3.8.1) (characterized) 47% 98% 342.4 isobutyryl-CoA dehydrogenase (EC 1.3.8.5) 97% 742.3
L-leucine catabolism liuA med acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized) 41% 99% 259.6 isobutyryl-CoA dehydrogenase (EC 1.3.8.5) 97% 742.3
4-hydroxybenzoate catabolism Ch1CoA lo cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized) 39% 99% 250.4 isobutyryl-CoA dehydrogenase (EC 1.3.8.5) 97% 742.3
phenylacetate catabolism Ch1CoA lo cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized) 39% 99% 250.4 isobutyryl-CoA dehydrogenase (EC 1.3.8.5) 97% 742.3
L-phenylalanine catabolism Ch1CoA lo cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized) 39% 99% 250.4 isobutyryl-CoA dehydrogenase (EC 1.3.8.5) 97% 742.3
4-hydroxybenzoate catabolism gcdH lo glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 33% 94% 213 isobutyryl-CoA dehydrogenase (EC 1.3.8.5) 97% 742.3
L-arginine catabolism gcdH lo glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 33% 94% 213 isobutyryl-CoA dehydrogenase (EC 1.3.8.5) 97% 742.3
L-citrulline catabolism gcdH lo glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 33% 94% 213 isobutyryl-CoA dehydrogenase (EC 1.3.8.5) 97% 742.3
L-lysine catabolism gcdH lo glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 33% 94% 213 isobutyryl-CoA dehydrogenase (EC 1.3.8.5) 97% 742.3
phenylacetate catabolism gcdH lo glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 33% 94% 213 isobutyryl-CoA dehydrogenase (EC 1.3.8.5) 97% 742.3
L-phenylalanine catabolism gcdH lo glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 33% 94% 213 isobutyryl-CoA dehydrogenase (EC 1.3.8.5) 97% 742.3
L-proline catabolism gcdH lo glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 33% 94% 213 isobutyryl-CoA dehydrogenase (EC 1.3.8.5) 97% 742.3

Sequence Analysis Tools

View Pf1N1B4_4789 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MHDIELSEEQVMIRDMARDFARGEIAPHAQAWEKAGWIDDGLVAKMGELGLLGMVVPEEW
GGTYVDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGTEEQKQQWLPDLASGQA
IGCFCLTEPQAGSEAHNLRTRAELRDGQWVINGAKQFVSNGKRAKLAIVFAVTDPELGKR
GISAFLVPTETAGFIVDRSEHKMGIRASDTCAVTLNNCTVPEANLLGERGKGLAIALSNL
EGGRIGIAAQALGIARAAFEAALAYARDRVQFDKPIIEHQSIANMLADMHTRLNAARLLI
LHAARLRSAGKPCLSEASQAKLFASEMAEKVCSSAIQIHGGYGYLEDYPVERYYRDARIT
QIYEGSSEIQRMVIARELKHYLV

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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