GapMind for catabolism of small carbon sources

 

Protein YP_427243.1 in Rhodospirillum rubrum ATCC 11170

Annotation: NCBI__GCF_000013085.1:YP_427243.1

Length: 261 amino acids

Source: GCF_000013085.1 in NCBI

Candidate for 30 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism ech lo Enoyl-CoA-hydratase; EC 4.2.1.17 (characterized) 39% 96% 150.2 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
L-isoleucine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 36% 94% 149.8 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
propionate catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 36% 94% 149.8 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
L-threonine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 36% 94% 149.8 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
L-valine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 36% 94% 149.8 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
4-hydroxybenzoate catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 36% 95% 147.5 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
L-arginine catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 36% 95% 147.5 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
L-citrulline catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 36% 95% 147.5 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
L-lysine catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 36% 95% 147.5 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
phenylacetate catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 36% 95% 147.5 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
L-phenylalanine catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 36% 95% 147.5 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
L-proline catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 36% 95% 147.5 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
L-valine catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 36% 95% 147.5 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
4-hydroxybenzoate catabolism badK lo BadK (characterized) 38% 98% 146.4 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
phenylacetate catabolism badK lo BadK (characterized) 38% 98% 146.4 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
phenylacetate catabolism paaG lo 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) 39% 97% 146.4 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
L-phenylalanine catabolism badK lo BadK (characterized) 38% 98% 146.4 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
L-phenylalanine catabolism paaG lo 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) 39% 97% 146.4 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
4-hydroxybenzoate catabolism paaF lo enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 37% 96% 139.8 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
phenylacetate catabolism paaF lo enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 37% 96% 139.8 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
L-phenylalanine catabolism paaF lo enoyl-CoA hydratase (EC 4.2.1.17) (characterized) 37% 96% 139.8 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
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) 35% 80% 138.7 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
phenylacetate catabolism paaZ1 lo Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) 35% 97% 114.8 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
L-phenylalanine catabolism paaZ1 lo Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) 35% 97% 114.8 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
4-hydroxybenzoate catabolism badI lo BadI (characterized) 33% 94% 101.7 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
phenylacetate catabolism badI lo BadI (characterized) 33% 94% 101.7 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
L-phenylalanine catabolism badI lo BadI (characterized) 33% 94% 101.7 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
4-hydroxybenzoate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized) 30% 94% 101.3 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
phenylacetate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized) 30% 94% 101.3 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7
L-phenylalanine catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized) 30% 94% 101.3 Enoyl-CoA hydratase domain-containing protein 3, mitochondrial 51% 245.7

Sequence Analysis Tools

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Sequence

MTVPPPLLESLTVDGVRTLTLNRPQARNALSKALMAALQDALDQAAEDPAVRVVVIAASG
PVFCAGHDLRELRGEPNEAAHAALFAQCSRLMTTIVRLPKPVIARVQGLATAAGCQLVAS
CDLAVAARRASFATPGVTIGLFCSTPMVALSRAVGRKTAMEMLLTGRPLDAEEALARGLI
TQVVEEAELAAATDALARILAEKSPLTLAIGKEAFYQQIELPLDEAYAYASAVMTRNMQT
KDAAEGIDAFLEKRPPRWTGQ

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