GapMind for catabolism of small carbon sources

 

Protein WP_025763018.1 in Dyadobacter tibetensis Y620-1

Annotation: NCBI__GCF_000566685.1:WP_025763018.1

Length: 259 amino acids

Source: GCF_000566685.1 in NCBI

Candidate for 22 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
phenylacetate catabolism paaG med 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) 36% 97% 184.1 2-cyclohexenylcarbonyl-CoA Δ-isomerase monomer (EC 5.3.3.3) 35% 154.8
L-phenylalanine catabolism paaG med 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) 36% 97% 184.1 2-cyclohexenylcarbonyl-CoA Δ-isomerase monomer (EC 5.3.3.3) 35% 154.8
L-isoleucine catabolism ech lo Probable enoyl-CoA hydratase; EC 4.2.1.17 (uncharacterized) 39% 99% 181.4 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 36% 184.1
L-isoleucine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 34% 97% 150.6 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 36% 184.1
propionate catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 34% 97% 150.6 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 36% 184.1
L-threonine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 34% 97% 150.6 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 36% 184.1
L-valine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 34% 97% 150.6 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 36% 184.1
4-hydroxybenzoate catabolism paaF lo enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 34% 100% 147.9 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 36% 184.1
phenylacetate catabolism paaF lo enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 34% 100% 147.9 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 36% 184.1
L-phenylalanine catabolism paaF lo enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 34% 100% 147.9 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 36% 184.1
L-leucine catabolism liuC lo Methylglutaconyl-CoA hydratase, mitochondrial; AU-specific RNA-binding enoyl-CoA hydratase; AU-binding enoyl-CoA hydratase; muAUH; Itaconyl-CoA hydratase; EC 4.2.1.18; EC 4.2.1.56 (characterized) 32% 83% 134 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 36% 184.1
4-hydroxybenzoate catabolism ech lo 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 32% 94% 129 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 36% 184.1
L-arginine catabolism ech lo 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 32% 94% 129 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 36% 184.1
L-citrulline catabolism ech lo 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 32% 94% 129 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 36% 184.1
L-lysine catabolism ech lo 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 32% 94% 129 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 36% 184.1
phenylacetate catabolism ech lo 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 32% 94% 129 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 36% 184.1
L-phenylalanine catabolism ech lo 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 32% 94% 129 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 36% 184.1
L-proline catabolism ech lo 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 32% 94% 129 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 36% 184.1
L-valine catabolism ech lo 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized) 32% 94% 129 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 36% 184.1
4-hydroxybenzoate catabolism badK lo BadK (characterized) 33% 96% 124.8 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 36% 184.1
phenylacetate catabolism badK lo BadK (characterized) 33% 96% 124.8 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 36% 184.1
L-phenylalanine catabolism badK lo BadK (characterized) 33% 96% 124.8 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 36% 184.1

Sequence Analysis Tools

View WP_025763018.1 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

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Sequence

MYQHLNFQNKEGIVRISLNRPHVHHALNKELIKEITLAIEVAASDEEVRAVLLTAEGDTA
FCSGADLKDTLDSKIDVDQTLREYYNPMIMAIRSLPKPVVCRLNGLAVGAGASLALSCDM
VVATESAYLAFMFVQIGLMPDAGATFILPRLVGSARAFALASTGQRVTAREAQHIGMIAH
AVPASELDSTVEKLLLYYRHAPTQAIAAMKQVLNQSQHSSLEQMLDLERIHQHQLSKTTD
AKNGISSFLQKKKPDYQGK

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