GapMind for catabolism of small carbon sources

 

Protein WP_047006795.1 in Erythrobacter gangjinensis K7-2

Annotation: NCBI__GCF_001010925.1:WP_047006795.1

Length: 240 amino acids

Source: GCF_001010925.1 in NCBI

Candidate for 21 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism badH lo BadH (characterized) 39% 99% 164.5 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 63% 300.8
phenylacetate catabolism badH lo BadH (characterized) 39% 99% 164.5 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 63% 300.8
L-phenylalanine catabolism badH lo BadH (characterized) 39% 99% 164.5 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 63% 300.8
L-isoleucine catabolism ivdG lo 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale) 39% 97% 154.8 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 63% 300.8
D-mannitol catabolism mt2d lo NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Allergen Alt a 8; EC 1.1.1.138 (characterized) 31% 92% 128.3 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 63% 300.8
L-rhamnose catabolism LRA1 lo L-rhamnose 1-dehydrogenase (NADP(+)); RHAD; EC 1.1.1.377 (characterized) 32% 95% 116.7 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 63% 300.8
L-fucose catabolism fucDH lo Short-chain alcohol dehydrogenase protein (characterized, see rationale) 31% 95% 115.2 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 63% 300.8
L-arabinose catabolism xacB lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 35% 92% 112.8 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 63% 300.8
D-galactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 35% 92% 112.8 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 63% 300.8
lactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 35% 92% 112.8 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 63% 300.8
D-xylose catabolism xdh lo D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized) 31% 92% 99 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 63% 300.8
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) 30% 97% 95.5 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 63% 300.8
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) 30% 97% 95.5 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 63% 300.8
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) 30% 97% 95.5 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 63% 300.8
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) 30% 97% 95.5 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 63% 300.8
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) 30% 97% 95.5 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 63% 300.8
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) 30% 97% 95.5 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 63% 300.8
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) 30% 97% 95.5 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 63% 300.8
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) 30% 97% 95.5 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 63% 300.8
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) 30% 97% 95.5 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 63% 300.8
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) 30% 97% 95.5 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 63% 300.8

Sequence Analysis Tools

View WP_047006795.1 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

MARVAVVTGGTRGIGRAICEMLKDDGFTVVATYAGNDEKARAFTDETGIAAYKFDVGDFD
AVQQGCAKIAEEVGPIDVVVNNAGITRDGTLMKMSYDDWNDVMRTNLGGCFNMAKAAFEG
MKERKWGRIVNIGSINGQAGQYGQVNYAAAKSGIHGFTKALAQEGARYGITVNAIAPGYI
DTDMVAAVPENVLEKIVAKIPVGRLGQAHEIARGVSFLASEDGAFVTGSTMSINGGQHMY

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