GapMind for catabolism of small carbon sources

 

Protein WP_009781909.1 in Leeuwenhoekiella blandensis MED217

Annotation: NCBI__GCF_000152985.1:WP_009781909.1

Length: 260 amino acids

Source: GCF_000152985.1 in NCBI

Candidate for 29 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 Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 50% 99% 245.7 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 49% 229.2
L-arginine catabolism ech hi Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 50% 99% 245.7 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 49% 229.2
L-citrulline catabolism ech hi Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 50% 99% 245.7 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 49% 229.2
L-lysine catabolism ech hi Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 50% 99% 245.7 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 49% 229.2
phenylacetate catabolism ech hi Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 50% 99% 245.7 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 49% 229.2
L-phenylalanine catabolism ech hi Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 50% 99% 245.7 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 49% 229.2
L-proline catabolism ech hi Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 50% 99% 245.7 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 49% 229.2
L-valine catabolism ech hi Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) 50% 99% 245.7 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 49% 229.2
L-isoleucine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 49% 100% 229.2 Crotonyl-CoA hydratase; EC 4.2.1.150 50% 245.7
propionate catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 49% 100% 229.2 Crotonyl-CoA hydratase; EC 4.2.1.150 50% 245.7
L-threonine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 49% 100% 229.2 Crotonyl-CoA hydratase; EC 4.2.1.150 50% 245.7
L-valine catabolism hpcD med 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 49% 100% 229.2 Crotonyl-CoA hydratase; EC 4.2.1.150 50% 245.7
L-isoleucine catabolism ech med enoyl-CoA hydratase (EC 4.2.1.17); DELTA3,5-DELTA2,4-dienoyl-CoA isomerase (EC 5.3.3.21) (characterized) 45% 88% 191.8 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) 49% 229.2
4-hydroxybenzoate catabolism paaF med trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 42% 99% 186.4 Crotonyl-CoA hydratase; EC 4.2.1.150 50% 245.7
phenylacetate catabolism paaF med trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 42% 99% 186.4 Crotonyl-CoA hydratase; EC 4.2.1.150 50% 245.7
L-phenylalanine catabolism paaF med trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 42% 99% 186.4 Crotonyl-CoA hydratase; EC 4.2.1.150 50% 245.7
L-leucine catabolism liuC med methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized) 41% 99% 175.6 Crotonyl-CoA hydratase; EC 4.2.1.150 50% 245.7
4-hydroxybenzoate catabolism badK lo BadK (characterized) 38% 99% 161.8 Crotonyl-CoA hydratase; EC 4.2.1.150 50% 245.7
phenylacetate catabolism badK lo BadK (characterized) 38% 99% 161.8 Crotonyl-CoA hydratase; EC 4.2.1.150 50% 245.7
L-phenylalanine catabolism badK lo BadK (characterized) 38% 99% 161.8 Crotonyl-CoA hydratase; EC 4.2.1.150 50% 245.7
phenylacetate catabolism paaG lo 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) 31% 100% 134.4 Crotonyl-CoA hydratase; EC 4.2.1.150 50% 245.7
L-phenylalanine catabolism paaG lo 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) 31% 100% 134.4 Crotonyl-CoA hydratase; EC 4.2.1.150 50% 245.7
4-hydroxybenzoate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 35% 100% 132.1 Crotonyl-CoA hydratase; EC 4.2.1.150 50% 245.7
phenylacetate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 35% 100% 132.1 Crotonyl-CoA hydratase; EC 4.2.1.150 50% 245.7
L-phenylalanine catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 35% 100% 132.1 Crotonyl-CoA hydratase; EC 4.2.1.150 50% 245.7
4-hydroxybenzoate catabolism badI lo BadI (characterized) 34% 98% 129.8 Crotonyl-CoA hydratase; EC 4.2.1.150 50% 245.7
phenylacetate catabolism badI lo BadI (characterized) 34% 98% 129.8 Crotonyl-CoA hydratase; EC 4.2.1.150 50% 245.7
L-phenylalanine catabolism badI lo BadI (characterized) 34% 98% 129.8 Crotonyl-CoA hydratase; EC 4.2.1.150 50% 245.7
L-valine catabolism bch lo 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial; 3-hydroxyisobutyryl-coenzyme A hydrolase; HIB-CoA hydrolase; HIBYL-CoA-H; EC 3.1.2.4 (characterized) 30% 54% 108.6 Crotonyl-CoA hydratase; EC 4.2.1.150 50% 245.7

Sequence Analysis Tools

View WP_009781909.1 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

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Sequence

MNFENLIYEVDDQLAIITINRPKKLNALNKETIQELHDAFAEADADEDIGVIILTGSGEK
AFVAGADISEFANFEEEEGALLARKGQKILFDFIENLSTPVIAAINGFALGGGLELAMAA
HIRIASHNARMGLPETSLGLIPGYGGTQRLPQLVGKGRAFEMIMTAGMIDADRAFQSGLV
NHVTSQEELMALAEKIAGKILNNSGVAIATAIQAVNAGFKPGVNGYDAEIEGFGASFATE
DFKEGTTAFLEKRKPEFPGN

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