GapMind for catabolism of small carbon sources

 

Protein N515DRAFT_0484 in Dyella japonica UNC79MFTsu3.2

Annotation: N515DRAFT_0484 glutaryl-CoA dehydrogenase

Length: 389 amino acids

Source: Dyella79 in FitnessBrowser

Candidate for 15 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism gcdH hi glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 52% 96% 384.4 short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) 37% 243.8
L-arginine catabolism gcdH hi glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 52% 96% 384.4 short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) 37% 243.8
L-citrulline catabolism gcdH hi glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 52% 96% 384.4 short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) 37% 243.8
L-lysine catabolism gcdH hi glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 52% 96% 384.4 short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) 37% 243.8
phenylacetate catabolism gcdH hi glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 52% 96% 384.4 short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) 37% 243.8
L-phenylalanine catabolism gcdH hi glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 52% 96% 384.4 short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) 37% 243.8
L-proline catabolism gcdH hi glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 52% 96% 384.4 short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) 37% 243.8
L-isoleucine catabolism acdH lo short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized) 37% 100% 243.8 glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) 52% 384.4
L-valine catabolism acdH lo 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized) 35% 100% 231.9 glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) 52% 384.4
L-isoleucine catabolism pco lo acyl-CoA oxidase (EC 1.3.3.6) (characterized) 35% 88% 231.1 glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) 52% 384.4
propionate catabolism pco lo acyl-CoA oxidase (EC 1.3.3.6) (characterized) 35% 88% 231.1 glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) 52% 384.4
L-threonine catabolism pco lo acyl-CoA oxidase (EC 1.3.3.6) (characterized) 35% 88% 231.1 glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) 52% 384.4
L-valine catabolism pco lo acyl-CoA oxidase (EC 1.3.3.6) (characterized) 35% 88% 231.1 glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) 52% 384.4
L-lysine catabolism bcd lo butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized) 34% 99% 216.1 glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) 52% 384.4
L-leucine catabolism liuA lo Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized) 34% 96% 213.4 glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) 52% 384.4

Sequence Analysis Tools

View N515DRAFT_0484 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

MSARLNPLDLYDVRSLLTDEERMVQDTVGRFVDERVLPIIGDAFDQGRFPKELIPEIAGL
GLLGATLPEQYGCAGMNGVSYGLICQELERGDSGLRSFASVQSSLCMYPIYAYGTEEQKL
HYLPKMAAGEIIGCFGLTEPHGGSDPANMKTNARKDGGDWIINGAKMWITNGNLAHIAIV
WAQTEDGIQGFIVPTDSQGFTAQEVHKKMSLRASVTSALFFDSVRVPEANRLPNVKGLKG
PLGCLTQARYGITWGPIGAAQACLKEVLDYTQERVLFGRPLASNQAIQLKLAEMARRITM
AQLLSLQLGRLKDAGNMQPTQVSLAKWNNCRIAIDIARECRDILGGAGITTEHVAIRHAL
NLESVITYEGTETVHQLVVGRELTGINAF

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