GapMind for catabolism of small carbon sources

 

Protein WP_095512601.1 in Rubrivirga marina SAORIC-28

Annotation: NCBI__GCF_002283365.1:WP_095512601.1

Length: 249 amino acids

Source: GCF_002283365.1 in NCBI

Candidate for 24 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
ethanol catabolism etoh-dh-nad med alcohol dehydrogenase (EC 1.1.1.1) (characterized) 43% 96% 172.2 cyclohexanol dehydrogenase 58% 275.8
L-rhamnose catabolism LRA1 med NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized) 41% 96% 152.9 cyclohexanol dehydrogenase 58% 275.8
L-rhamnose catabolism LRA5 lo 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; L-KDR 4-dehydrogenase; EC 1.1.1.401 (characterized) 37% 94% 157.9 cyclohexanol dehydrogenase 58% 275.8
L-arabinose catabolism xacB lo L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized) 36% 90% 155.6 cyclohexanol dehydrogenase 58% 275.8
D-galactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 37% 90% 152.5 cyclohexanol dehydrogenase 58% 275.8
lactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 37% 90% 152.5 cyclohexanol dehydrogenase 58% 275.8
D-sorbitol (glucitol) catabolism sdh lo Sorbitol dehydrogenase (EC 1.1.1.14) (characterized) 35% 95% 144.4 cyclohexanol dehydrogenase 58% 275.8
xylitol catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 35% 97% 141.7 cyclohexanol dehydrogenase 58% 275.8
D-xylose catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 35% 97% 141.7 cyclohexanol dehydrogenase 58% 275.8
L-fucose catabolism fucDH lo Short-chain alcohol dehydrogenase protein (characterized, see rationale) 37% 95% 140.2 cyclohexanol dehydrogenase 58% 275.8
D-xylose catabolism xdh lo D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized) 37% 92% 137.1 cyclohexanol dehydrogenase 58% 275.8
4-hydroxybenzoate catabolism fadB lo 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) 32% 98% 118.6 cyclohexanol dehydrogenase 58% 275.8
4-hydroxybenzoate catabolism paaH lo 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) 32% 98% 118.6 cyclohexanol dehydrogenase 58% 275.8
L-arginine catabolism fadB lo 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) 32% 98% 118.6 cyclohexanol dehydrogenase 58% 275.8
L-citrulline catabolism fadB lo 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) 32% 98% 118.6 cyclohexanol dehydrogenase 58% 275.8
L-isoleucine catabolism ivdG lo 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) 32% 98% 118.6 cyclohexanol dehydrogenase 58% 275.8
L-lysine catabolism fadB lo 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) 32% 98% 118.6 cyclohexanol dehydrogenase 58% 275.8
phenylacetate catabolism fadB lo 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) 32% 98% 118.6 cyclohexanol dehydrogenase 58% 275.8
phenylacetate catabolism paaH lo 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) 32% 98% 118.6 cyclohexanol dehydrogenase 58% 275.8
L-phenylalanine catabolism fadB lo 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) 32% 98% 118.6 cyclohexanol dehydrogenase 58% 275.8
L-phenylalanine catabolism paaH lo 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) 32% 98% 118.6 cyclohexanol dehydrogenase 58% 275.8
L-proline catabolism fadB lo 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) 32% 98% 118.6 cyclohexanol dehydrogenase 58% 275.8
L-fucose catabolism fdh lo Short-chain dehydrogenase (characterized, see rationale) 37% 95% 116.7 cyclohexanol dehydrogenase 58% 275.8
D-sorbitol (glucitol) catabolism srlD lo sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized) 30% 95% 95.5 cyclohexanol dehydrogenase 58% 275.8

Sequence Analysis Tools

View WP_095512601.1 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

MTRDSVALVTGAASGIGRAIALRYARDGFRVVVSDVDEAGGRETVQKIEEGGGGALFVSA
DVSDPAACEALVAETVRAFGRLDVACNNAGIGGEQAPTADYPVEAWQRVLAVNLSGVFYG
MKAQIPALREAGGGAIVNVASILGQVGFAGAPAYVAAKHGVVGLTKTAAIELAAEGIRVN
AVGPAFIETPMISALEEDPETLAMLVGLHPAGRLGTPDEVAALVAWLSSAEASFVTGAYY
PVDGGYLAR

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