GapMind for catabolism of small carbon sources

 

Protein WP_011385957.1 in Magnetospirillum magneticum AMB-1

Annotation: AMB_RS18215 acyl-CoA dehydrogenase

Length: 378 amino acids

Source: GCF_000009985.1 in NCBI

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-isoleucine catabolism acdH hi 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized) 71% 99% 545.4
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) 70% 100% 537.3
L-lysine catabolism bcd med butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized) 48% 99% 357.5 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 71% 545.4
4-hydroxybenzoate catabolism Ch1CoA med cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized) 41% 98% 259.6 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 71% 545.4
phenylacetate catabolism Ch1CoA med cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized) 41% 98% 259.6 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 71% 545.4
L-phenylalanine catabolism Ch1CoA med cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized) 41% 98% 259.6 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 71% 545.4
L-leucine catabolism liuA lo acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized) 40% 98% 272.3 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 71% 545.4
4-hydroxybenzoate catabolism gcdH lo glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 33% 93% 207.2 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 71% 545.4
L-arginine catabolism gcdH lo glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 33% 93% 207.2 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 71% 545.4
L-citrulline catabolism gcdH lo glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 33% 93% 207.2 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 71% 545.4
L-lysine catabolism gcdH lo glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 33% 93% 207.2 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 71% 545.4
phenylacetate catabolism gcdH lo glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 33% 93% 207.2 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 71% 545.4
L-phenylalanine catabolism gcdH lo glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 33% 93% 207.2 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 71% 545.4
L-proline catabolism gcdH lo glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized) 33% 93% 207.2 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) 71% 545.4

Sequence Analysis Tools

View WP_011385957.1 at NCBI

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

MIATEEQQLIRDMARSFAREKLAPNAARWDREHLFPTDAIAEMGELGFLGMVVPSEWDGA
GTDYVSYAMAVMEIAAGCGPLSTIMSVHNSVGCMPILTYGTEAQKDEFLRPMARGEKLGC
FCLTEPEAGSDAASIRTRARRDGDHYVLSGAKQFISTAKNGQVAIVFAVTDPQAGKRGIS
AFVVPTDTPGFTVVRVEDKLGQHLSDTCQLAFEDMRVPASRRLGEEGDGLKIALANLEGG
RLGIAAQSVGMARSALDHALAYAKERKQFGKPIFEHQAVAFRLADMATRVEVAEQMVLHA
ASLRDAGLPCLKEASMAKLFASEMAERVCSDAIQIHGGYGYLADFPVERIYRDVRVCQIY
EGTSDIQRLVISRALATQ

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