GapMind for catabolism of small carbon sources

 

Protein N515DRAFT_2873 in Dyella japonica UNC79MFTsu3.2

Annotation: N515DRAFT_2873 3-oxoacyl-[acyl-carrier-protein] reductase

Length: 247 amino acids

Source: Dyella79 in FitnessBrowser

Candidate for 18 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-sorbitol (glucitol) catabolism sdh med L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized) 42% 92% 156.4 Acetoacetyl-CoA reductase; EC 1.1.1.36 49% 223.0
4-hydroxybenzoate catabolism badH lo BadH (characterized) 39% 98% 167.9 Acetoacetyl-CoA reductase; EC 1.1.1.36 49% 223.0
phenylacetate catabolism badH lo BadH (characterized) 39% 98% 167.9 Acetoacetyl-CoA reductase; EC 1.1.1.36 49% 223.0
L-phenylalanine catabolism badH lo BadH (characterized) 39% 98% 167.9 Acetoacetyl-CoA reductase; EC 1.1.1.36 49% 223.0
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% 147.5 Acetoacetyl-CoA reductase; EC 1.1.1.36 49% 223.0
L-fucose catabolism fucDH lo 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized) 34% 79% 130.2 Acetoacetyl-CoA reductase; EC 1.1.1.36 49% 223.0
D-mannitol catabolism mt2d lo NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Allergen Alt a 8; EC 1.1.1.138 (characterized) 33% 92% 120.9 Acetoacetyl-CoA reductase; EC 1.1.1.36 49% 223.0
L-isoleucine catabolism ivdG lo 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale) 33% 97% 119.8 Acetoacetyl-CoA reductase; EC 1.1.1.36 49% 223.0
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) 34% 89% 115.9 Acetoacetyl-CoA reductase; EC 1.1.1.36 49% 223.0
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) 34% 89% 115.9 Acetoacetyl-CoA reductase; EC 1.1.1.36 49% 223.0
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) 34% 89% 115.9 Acetoacetyl-CoA reductase; EC 1.1.1.36 49% 223.0
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) 34% 89% 115.9 Acetoacetyl-CoA reductase; EC 1.1.1.36 49% 223.0
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) 34% 89% 115.9 Acetoacetyl-CoA reductase; EC 1.1.1.36 49% 223.0
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) 34% 89% 115.9 Acetoacetyl-CoA reductase; EC 1.1.1.36 49% 223.0
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) 34% 89% 115.9 Acetoacetyl-CoA reductase; EC 1.1.1.36 49% 223.0
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) 34% 89% 115.9 Acetoacetyl-CoA reductase; EC 1.1.1.36 49% 223.0
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) 34% 89% 115.9 Acetoacetyl-CoA reductase; EC 1.1.1.36 49% 223.0
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) 34% 89% 115.9 Acetoacetyl-CoA reductase; EC 1.1.1.36 49% 223.0

Sequence Analysis Tools

View N515DRAFT_2873 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MTRIAIVTGGIGGLGTEICRQLALAGRQVIAADLPARADRVAAFQAELADLDGAVRFEPV
DVSDFASCSELIARVEAAHGRVDVLVNAAGITRDTTLRKMDPQHWQELMRVNLDGVFNMC
RHVVEGMSARGFGRIVNLSSVNGQTGQFGQTNYAAAKAGVHGFGMALARETARKGVTVNT
VSPGYCDTPLVARVPAEIRAQILEDIPVGRLGSPADIARAVCFLAADDAGYITGANLPVN
GGYFMSF

This GapMind analysis is from Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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