GapMind for catabolism of small carbon sources

 

Protein WP_022389760.1 in Coprobacter fastidiosus NSB1

Annotation: NCBI__GCF_000473955.1:WP_022389760.1

Length: 274 amino acids

Source: GCF_000473955.1 in NCBI

Candidate for 34 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism badI med BadI (characterized) 48% 100% 248.8 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
phenylacetate catabolism badI med BadI (characterized) 48% 100% 248.8 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
L-phenylalanine catabolism badI med BadI (characterized) 48% 100% 248.8 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
L-isoleucine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 35% 99% 142.1 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
propionate catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 35% 99% 142.1 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
L-threonine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 35% 99% 142.1 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
L-valine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 35% 99% 142.1 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
4-hydroxybenzoate catabolism ech lo Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 37% 98% 139.4 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
L-arginine catabolism ech lo Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 37% 98% 139.4 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
L-citrulline catabolism ech lo Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 37% 98% 139.4 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
L-lysine catabolism ech lo Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 37% 98% 139.4 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
phenylacetate catabolism ech lo Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 37% 98% 139.4 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
L-phenylalanine catabolism ech lo Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 37% 98% 139.4 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
L-proline catabolism ech lo Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 37% 98% 139.4 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
L-valine catabolism ech lo Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 37% 98% 139.4 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
L-isoleucine catabolism ech lo Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized) 34% 98% 127.5 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
4-hydroxybenzoate catabolism paaF lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 33% 98% 127.1 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
phenylacetate catabolism paaF lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 33% 98% 127.1 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
L-phenylalanine catabolism paaF lo trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 33% 98% 127.1 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
4-hydroxybenzoate catabolism badK lo BadK (characterized) 34% 94% 119.4 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
phenylacetate catabolism badK lo BadK (characterized) 34% 94% 119.4 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
L-phenylalanine catabolism badK lo BadK (characterized) 34% 94% 119.4 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
4-hydroxybenzoate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 32% 99% 110.9 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
phenylacetate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 32% 99% 110.9 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
L-phenylalanine catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 32% 99% 110.9 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
L-leucine catabolism liuC lo methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized) 33% 86% 107.1 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
phenylacetate catabolism paaZ1 lo Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) 32% 95% 102.4 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
L-phenylalanine catabolism paaZ1 lo Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) 32% 95% 102.4 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
4-hydroxybenzoate catabolism oah lo 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase; 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase; Beta-oxoacyl-CoA hydrolase; Oah; EC 3.7.1.21 (characterized) 31% 52% 98.2 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
phenylacetate catabolism oah lo 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase; 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase; Beta-oxoacyl-CoA hydrolase; Oah; EC 3.7.1.21 (characterized) 31% 52% 98.2 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
phenylacetate catabolism paaG lo 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) 31% 99% 98.2 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
L-phenylalanine catabolism oah lo 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase; 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase; Beta-oxoacyl-CoA hydrolase; Oah; EC 3.7.1.21 (characterized) 31% 52% 98.2 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
L-phenylalanine catabolism paaG lo 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) 31% 99% 98.2 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4
L-valine catabolism bch lo 3-hydroxy-isobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized) 31% 56% 75.5 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 67% 394.4

Sequence Analysis Tools

View WP_022389760.1 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

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Sequence

MATREWKTIKEYEDIKFEFFEGIAKITINRPEVYNAFRPQTNFEMLDAMSICRERSDIGV
VVFTGAGDKAFCSGGDQNVKGIGGYIDKDGVPRLNVLDLHKAIRSIPKPVIAMVNGYAIG
GGHVLHVVCDLTIASENARFGQTGPKVGSFDAGFGSSYLARCVGQKKAREIWFLCRQYTA
REAEEMGMVNKVVPFERLEDETVDWCKTILKRSPMAIRMIKRALNAELDGQRGLMEFAGD
ATLMYYLMEEAQEGKNAFLEKRDPDFQKFPKFPG

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