GapMind for catabolism of small carbon sources

 

Protein GFF2642 in Phaeobacter inhibens BS107

Annotation: FitnessBrowser__Phaeo:GFF2642

Length: 261 amino acids

Source: Phaeo in FitnessBrowser

Candidate for 25 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
phenylacetate catabolism paaG hi 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) 56% 100% 272.3 2-cyclohexenylcarbonyl-CoA Δ-isomerase monomer (EC 5.3.3.3) 38% 162.9
L-phenylalanine catabolism paaG hi 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) 56% 100% 272.3 2-cyclohexenylcarbonyl-CoA Δ-isomerase monomer (EC 5.3.3.3) 38% 162.9
L-isoleucine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 35% 99% 153.7 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 56% 272.3
propionate catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 35% 99% 153.7 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 56% 272.3
L-threonine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 35% 99% 153.7 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 56% 272.3
L-valine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 35% 99% 153.7 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 56% 272.3
4-hydroxybenzoate catabolism badK lo BadK (characterized) 36% 99% 150.6 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 56% 272.3
phenylacetate catabolism badK lo BadK (characterized) 36% 99% 150.6 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 56% 272.3
L-phenylalanine catabolism badK lo BadK (characterized) 36% 99% 150.6 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 56% 272.3
4-hydroxybenzoate catabolism ech lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 99% 148.3 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 56% 272.3
4-hydroxybenzoate catabolism paaF lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 99% 148.3 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 56% 272.3
L-arginine catabolism ech lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 99% 148.3 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 56% 272.3
L-citrulline catabolism ech lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 99% 148.3 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 56% 272.3
L-lysine catabolism ech lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 99% 148.3 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 56% 272.3
phenylacetate catabolism ech lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 99% 148.3 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 56% 272.3
phenylacetate catabolism paaF lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 99% 148.3 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 56% 272.3
L-phenylalanine catabolism ech lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 99% 148.3 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 56% 272.3
L-phenylalanine catabolism paaF lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 99% 148.3 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 56% 272.3
L-proline catabolism ech lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 99% 148.3 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 56% 272.3
L-valine catabolism ech lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 35% 99% 148.3 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 56% 272.3
phenylacetate catabolism paaZ1 lo Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) 34% 100% 137.1 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 56% 272.3
L-phenylalanine catabolism paaZ1 lo Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) 34% 100% 137.1 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 56% 272.3
4-hydroxybenzoate catabolism badI lo BadI (characterized) 31% 97% 102.4 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 56% 272.3
phenylacetate catabolism badI lo BadI (characterized) 31% 97% 102.4 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 56% 272.3
L-phenylalanine catabolism badI lo BadI (characterized) 31% 97% 102.4 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) 56% 272.3

Sequence Analysis Tools

View GFF2642 at FitnessBrowser

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

MSETLLVEDHGTWVEITLNRPDRLNSFTEEMHHALRAALEAARDGGARAVLLTGAGRGFC
AGQDLGDRDPRKMDGPPDLGHTVRTFYAPLVNLIRALDFPVICAVNGVAAGAGANLALAC
DVVLAAESAKFIQSFSKVGLIPDTGGSWHLPRLLGEARAKGLALTAEPLPAKKAEDWGLI
WKAVPDEELMAEARAMAEKFANGPTLGLGLTKQTIQAAAVTTLSDQLEIEADAMKTCGES
ADYAEGVASFLEKRVPAFKGK

This GapMind analysis is from Sep 17 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