GapMind for catabolism of small carbon sources

 

Protein Pf6N2E2_1146 in Pseudomonas fluorescens FW300-N2E2

Annotation: Butyryl-CoA dehydrogenase (EC 1.3.99.2)

Length: 375 amino acids

Source: pseudo6_N2E2 in FitnessBrowser

Candidate for 18 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism acdH hi 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized) 100% 100% 741.9
L-valine catabolism acdH hi 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized) 94% 100% 700.3
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) 48% 97% 359.4 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 100% 741.9
L-leucine catabolism liuA med Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized) 41% 96% 290.4 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 100% 741.9
4-hydroxybenzoate catabolism Ch1CoA med Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized) 41% 90% 271.2 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 100% 741.9
phenylacetate catabolism Ch1CoA med Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized) 41% 90% 271.2 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 100% 741.9
L-phenylalanine catabolism Ch1CoA med Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized) 41% 90% 271.2 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 100% 741.9
4-hydroxybenzoate catabolism gcdH lo glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized) 35% 93% 214.2 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 100% 741.9
L-arginine catabolism gcdH lo glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized) 35% 93% 214.2 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 100% 741.9
L-citrulline catabolism gcdH lo glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized) 35% 93% 214.2 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 100% 741.9
L-lysine catabolism gcdH lo glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized) 35% 93% 214.2 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 100% 741.9
phenylacetate catabolism gcdH lo glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized) 35% 93% 214.2 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 100% 741.9
L-phenylalanine catabolism gcdH lo glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized) 35% 93% 214.2 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 100% 741.9
L-proline catabolism gcdH lo glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized) 35% 93% 214.2 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 100% 741.9
L-isoleucine catabolism pco lo acyl-CoA oxidase (EC 1.3.3.6) (characterized) 30% 85% 166.8 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 100% 741.9
propionate catabolism pco lo acyl-CoA oxidase (EC 1.3.3.6) (characterized) 30% 85% 166.8 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 100% 741.9
L-threonine catabolism pco lo acyl-CoA oxidase (EC 1.3.3.6) (characterized) 30% 85% 166.8 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 100% 741.9
L-valine catabolism pco lo acyl-CoA oxidase (EC 1.3.3.6) (characterized) 30% 85% 166.8 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 100% 741.9

Sequence Analysis Tools

View Pf6N2E2_1146 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MLATEEQTQIRDMARQFAEERLKPFAAEWDREHRFPREAIDEMAELGFFGMLVPEQWGGC
DTGYLAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGA
FALTEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGIS
AFIVPTDSPGYSVARVEDKLGQHASDTCQILFEDLKVPVGNRLGEEGEGYKIALANLEGG
RVGIAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYA
AALRDSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIY
EGTSDIQRMVISRNL

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, the preprint 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