GapMind for catabolism of small carbon sources

 

Protein WP_003466622.1 in Gracilibacillus halophilus YIM-C55.5

Annotation: NCBI__GCF_000359605.1:WP_003466622.1

Length: 232 amino acids

Source: GCF_000359605.1 in NCBI

Candidate for 12 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 31% 76% 92 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 32% 122.9
4-hydroxybenzoate catabolism paaH lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 31% 76% 92 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 32% 122.9
L-arginine catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 31% 76% 92 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 32% 122.9
L-citrulline catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 31% 76% 92 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 32% 122.9
L-isoleucine catabolism ivdG lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 31% 76% 92 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 32% 122.9
L-lysine catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 31% 76% 92 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 32% 122.9
phenylacetate catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 31% 76% 92 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 32% 122.9
phenylacetate catabolism paaH lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 31% 76% 92 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 32% 122.9
L-phenylalanine catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 31% 76% 92 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 32% 122.9
L-phenylalanine catabolism paaH lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 31% 76% 92 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 32% 122.9
L-proline catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 31% 76% 92 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 32% 122.9
D-sorbitol (glucitol) catabolism srlD lo sorbitol-6-phosphate dehydrogenase (characterized) 32% 75% 88.2 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 32% 122.9

Sequence Analysis Tools

View WP_003466622.1 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

MDFSSLRGKVVVIIGASRGIGRATANLLAPYDVKLVLGARNVEHIDIDNALLLPVDVTDE
QSVEMFLSKTRDHYSQIDVLINSAGIGMFDSLLESNTADFDRMIAVNLRGTYLACKHFGK
VMKDQQKGQIINLVSIAGQIALPSNGGYTASKFGVMGLSKVLQAELRSEGVQVTSVLPGA
VDSPFWNDTEMDVDTSNMIPVDSIAEYLLFLIRQPRHSVVDEMTIMPPGGIL

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