GapMind for catabolism of small carbon sources

 

Protein WP_003944701.1 in Rhodococcus qingshengii djl-6-2

Annotation: NCBI__GCF_002893965.1:WP_003944701.1

Length: 259 amino acids

Source: GCF_002893965.1 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 ech hi Probable enoyl-CoA hydratase echA17; EC 4.2.1.17 (characterized) 49% 95% 215.3 AcuK 43% 177.2
4-hydroxybenzoate catabolism ech med crotonase (EC 4.2.1.150) (characterized) 42% 96% 182.2 AcuK 43% 177.2
L-arginine catabolism ech med crotonase (EC 4.2.1.150) (characterized) 42% 96% 182.2 AcuK 43% 177.2
L-citrulline catabolism ech med crotonase (EC 4.2.1.150) (characterized) 42% 96% 182.2 AcuK 43% 177.2
L-lysine catabolism ech med crotonase (EC 4.2.1.150) (characterized) 42% 96% 182.2 AcuK 43% 177.2
phenylacetate catabolism ech med crotonase (EC 4.2.1.150) (characterized) 42% 96% 182.2 AcuK 43% 177.2
L-phenylalanine catabolism ech med crotonase (EC 4.2.1.150) (characterized) 42% 96% 182.2 AcuK 43% 177.2
L-proline catabolism ech med crotonase (EC 4.2.1.150) (characterized) 42% 96% 182.2 AcuK 43% 177.2
L-valine catabolism ech med crotonase (EC 4.2.1.150) (characterized) 42% 96% 182.2 AcuK 43% 177.2
4-hydroxybenzoate catabolism paaF med 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 42% 99% 177.2 Probable enoyl-CoA hydratase echA17; EC 4.2.1.17 49% 215.3
phenylacetate catabolism paaF med 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 42% 99% 177.2 Probable enoyl-CoA hydratase echA17; EC 4.2.1.17 49% 215.3
L-phenylalanine catabolism paaF med 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 42% 99% 177.2 Probable enoyl-CoA hydratase echA17; EC 4.2.1.17 49% 215.3
L-leucine catabolism liuC med methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized) 40% 87% 164.5 Probable enoyl-CoA hydratase echA17; EC 4.2.1.17 49% 215.3
L-valine catabolism bch lo 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized) 31% 51% 79 Probable enoyl-CoA hydratase echA17; EC 4.2.1.17 49% 215.3

Sequence Analysis Tools

View WP_003944701.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MAEFVTLEVSEGIGTIRLARPPMNALNRQVQDELAAAAHAATVDKAVKAVIVYGGEKVFA
AGADVKEMAEMDYGQIRDAIGGMQAGLGAVASIPKPTVAAITGYALGGGLEVALSADRRI
VGDNAKLGVPEILLGIIPGGGGTQRLARLIGPAKAKDLVFTGRFVGADEALAIGLVDEVV
APDDVYTAARTWASQFVGGASRALAAAKAAIDEGLNTDLESGLKIEQHLFAGLFATKDQA
IGMESFIANGPGKAEFTGE

This GapMind analysis is from Sep 24 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:

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