GapMind for catabolism of small carbon sources

 

Protein WP_011513566.1 in Psychrobacter cryohalolentis K5

Annotation: NCBI__GCF_000013905.1:WP_011513566.1

Length: 384 amino acids

Source: GCF_000013905.1 in NCBI

Candidate for 15 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 med short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized) 42% 99% 298.9 butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) 42% 293.1
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) 42% 96% 293.1 short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) 42% 298.9
L-valine catabolism acdH med 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized) 42% 98% 289.3 butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) 42% 293.1
L-leucine catabolism liuA lo Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized) 35% 97% 252.7 short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) 42% 298.9
4-hydroxybenzoate catabolism gcdH lo glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized) 35% 92% 207.6 short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) 42% 298.9
L-arginine catabolism gcdH lo glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized) 35% 92% 207.6 short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) 42% 298.9
L-citrulline catabolism gcdH lo glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized) 35% 92% 207.6 short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) 42% 298.9
L-lysine catabolism gcdH lo glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized) 35% 92% 207.6 short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) 42% 298.9
phenylacetate catabolism gcdH lo glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized) 35% 92% 207.6 short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) 42% 298.9
L-phenylalanine catabolism gcdH lo glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized) 35% 92% 207.6 short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) 42% 298.9
L-proline catabolism gcdH lo glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized) 35% 92% 207.6 short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) 42% 298.9
L-isoleucine catabolism pco lo acyl-CoA oxidase (EC 1.3.3.6) (characterized) 30% 83% 171.8 short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) 42% 298.9
propionate catabolism pco lo acyl-CoA oxidase (EC 1.3.3.6) (characterized) 30% 83% 171.8 short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) 42% 298.9
L-threonine catabolism pco lo acyl-CoA oxidase (EC 1.3.3.6) (characterized) 30% 83% 171.8 short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) 42% 298.9
L-valine catabolism pco lo acyl-CoA oxidase (EC 1.3.3.6) (characterized) 30% 83% 171.8 short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) 42% 298.9

Sequence Analysis Tools

View WP_011513566.1 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

MIRDKDVLNQITDTIRQFVNNQLIPMEHWVAENDRLPDDIINQMRELGLFGLTIPEEYGG
LGVTMEEEVTLAFELGRTSPAFRSLIGTNNGIGSSGLVIDGTEAQKQKYLPRLASGEIIG
SFCLTEPDSGSDAASLKTTAIKDGDTYIINGTKRYITNAPEAGVFTVMARTDPQNKRSGG
ISAFIVESDTPGITLGKIDKKMGQKGAHTCDVIFDNCIVPADALIGGVEGVGFKTAMKVL
DKGRLHIAAASTGAATRMLDDALHYAVERKQFGQPIANFQLIQAMLADSKAEIYAAKSMV
LDASRLRDEGKDVVTESSCAKMFATEMCGRVADRAVQIHGGAGYIADYGIERFYRDVRLY
RLYEGTTQIQQIIIARNMIKEVSE

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