GapMind for catabolism of small carbon sources

 

Protein WP_076481536.1 in Williamsia sterculiae CPCC 203464

Annotation: NCBI__GCF_900156495.1:WP_076481536.1

Length: 264 amino acids

Source: GCF_900156495.1 in NCBI

Candidate for 27 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-leucine catabolism liuC med methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized) 42% 96% 156.8 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2
4-hydroxybenzoate catabolism paaF lo 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 39% 95% 160.2 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2
L-isoleucine catabolism ech lo 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 39% 95% 160.2 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2
phenylacetate catabolism paaF lo 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 39% 95% 160.2 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2
L-phenylalanine catabolism paaF lo 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) 39% 95% 160.2 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2
4-hydroxybenzoate catabolism badK lo BadK (characterized) 38% 100% 153.3 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2
phenylacetate catabolism badK lo BadK (characterized) 38% 100% 153.3 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2
L-phenylalanine catabolism badK lo BadK (characterized) 38% 100% 153.3 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2
L-isoleucine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 37% 94% 149.8 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2
propionate catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 37% 94% 149.8 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2
L-threonine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 37% 94% 149.8 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2
L-valine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 37% 94% 149.8 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2
4-hydroxybenzoate catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 35% 95% 141 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2
L-arginine catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 35% 95% 141 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2
L-citrulline catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 35% 95% 141 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2
L-lysine catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 35% 95% 141 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2
phenylacetate catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 35% 95% 141 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2
L-phenylalanine catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 35% 95% 141 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2
L-proline catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 35% 95% 141 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2
L-valine catabolism ech lo crotonase (EC 4.2.1.150) (characterized) 35% 95% 141 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2
phenylacetate catabolism paaG lo 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) 33% 95% 127.1 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2
L-phenylalanine catabolism paaG lo 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) 33% 95% 127.1 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2
phenylacetate catabolism paaZ1 lo Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) 34% 95% 124.4 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2
L-phenylalanine catabolism paaZ1 lo Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) 34% 95% 124.4 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2
4-hydroxybenzoate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 31% 98% 107.1 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2
phenylacetate catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 31% 98% 107.1 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2
L-phenylalanine catabolism dch lo cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized) 31% 98% 107.1 crotonobetainyl-CoA hydratase (EC 4.2.1.149) 42% 182.2

Sequence Analysis Tools

View WP_076481536.1 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

MAADSGIPVRYEFADHIAVITLDRPDALNAVNSALAVGLGNALEAAAQDMDVRVVVVTGT
GRAFCAGADLKALAAGDRIDDPDHPERGFAGIVRHWIPKPVIAAVNGFALGGGTELVLAA
DLAVIDETASLGLPEVRRGLIAAAGGLLRVHRQVSPKVANEIALTGQPISAVRAHELGLV
NRVARQGTALDTARELAATIAANAPVSVAQSKWLMHETAKDEQGWDDRAWELNQEALVRV
LSSADAREGPRAFAEKREPRWEGR

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