GapMind for catabolism of small carbon sources

 

Protein WP_058857482.1 in Kocuria flava HO-9041

Annotation: NCBI__GCF_001482365.1:WP_058857482.1

Length: 262 amino acids

Source: GCF_001482365.1 in NCBI

Candidate for 24 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism ech hi crotonase (EC 4.2.1.150) (characterized) 47% 94% 220.3 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 44% 202.6
L-arginine catabolism ech hi crotonase (EC 4.2.1.150) (characterized) 47% 94% 220.3 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 44% 202.6
L-citrulline catabolism ech hi crotonase (EC 4.2.1.150) (characterized) 47% 94% 220.3 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 44% 202.6
L-lysine catabolism ech hi crotonase (EC 4.2.1.150) (characterized) 47% 94% 220.3 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 44% 202.6
phenylacetate catabolism ech hi crotonase (EC 4.2.1.150) (characterized) 47% 94% 220.3 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 44% 202.6
L-phenylalanine catabolism ech hi crotonase (EC 4.2.1.150) (characterized) 47% 94% 220.3 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 44% 202.6
L-proline catabolism ech hi crotonase (EC 4.2.1.150) (characterized) 47% 94% 220.3 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 44% 202.6
L-valine catabolism ech hi crotonase (EC 4.2.1.150) (characterized) 47% 94% 220.3 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 44% 202.6
L-isoleucine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 44% 93% 202.6 crotonase (EC 4.2.1.150) 47% 220.3
propionate catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 44% 93% 202.6 crotonase (EC 4.2.1.150) 47% 220.3
L-threonine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 44% 93% 202.6 crotonase (EC 4.2.1.150) 47% 220.3
L-valine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 44% 93% 202.6 crotonase (EC 4.2.1.150) 47% 220.3
4-hydroxybenzoate catabolism paaF med trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 47% 96% 201.8 crotonase (EC 4.2.1.150) 47% 220.3
L-isoleucine catabolism ech med trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 47% 96% 201.8 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 44% 202.6
phenylacetate catabolism paaF med trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 47% 96% 201.8 crotonase (EC 4.2.1.150) 47% 220.3
L-phenylalanine catabolism paaF med trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 47% 96% 201.8 crotonase (EC 4.2.1.150) 47% 220.3
L-leucine catabolism liuC med methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized) 43% 97% 187.2 crotonase (EC 4.2.1.150) 47% 220.3
phenylacetate catabolism paaG med 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) 42% 97% 157.5 crotonase (EC 4.2.1.150) 47% 220.3
L-phenylalanine catabolism paaG med 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) 42% 97% 157.5 crotonase (EC 4.2.1.150) 47% 220.3
4-hydroxybenzoate catabolism badK lo BadK (characterized) 40% 99% 173.7 crotonase (EC 4.2.1.150) 47% 220.3
phenylacetate catabolism badK lo BadK (characterized) 40% 99% 173.7 crotonase (EC 4.2.1.150) 47% 220.3
L-phenylalanine catabolism badK lo BadK (characterized) 40% 99% 173.7 crotonase (EC 4.2.1.150) 47% 220.3
phenylacetate catabolism paaZ1 lo Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) 32% 96% 106.3 crotonase (EC 4.2.1.150) 47% 220.3
L-phenylalanine catabolism paaZ1 lo Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) 32% 96% 106.3 crotonase (EC 4.2.1.150) 47% 220.3

Sequence Analysis Tools

View WP_058857482.1 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

MTTTPADTRVVDLAVRDQVAVVTVDRPEVRNALNAAVLDGLEAALDECERRTDVRAVVLT
GAGEKAFVAGADISQLVGYTLRDGLRARMQRLWDRIEDLELPTIAAVNGFALGGGTELAM
ACDIRIAAGGARFGLPEANLGIIPGAGGTQRLSRLVGLGRAQELILTGRLVDAEEALRIG
LVTSVVPGPELLDAALGTAATILAKGPLAVRMAKLVVRHGAETDQRTGLLLERLAQSLLY
AADEKAEGAAAFLEKRPARFPG

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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