GapMind for catabolism of small carbon sources

 

Protein Dsui_2448 in Dechlorosoma suillum PS

Annotation: Dsui_2448 3-oxoacyl-(acyl-carrier-protein) reductase

Length: 246 amino acids

Source: PS in FitnessBrowser

Candidate for 25 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-rhamnose catabolism LRA1 med NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized) 41% 99% 156.8 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 64% 309.3
D-sorbitol (glucitol) catabolism sdh med L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized) 40% 93% 144.8 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 64% 309.3
4-hydroxybenzoate catabolism badH lo BadH (characterized) 38% 98% 165.2 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 64% 309.3
phenylacetate catabolism badH lo BadH (characterized) 38% 98% 165.2 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 64% 309.3
L-phenylalanine catabolism badH lo BadH (characterized) 38% 98% 165.2 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 64% 309.3
L-isoleucine catabolism ivdG lo 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale) 36% 99% 147.9 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 64% 309.3
L-fucose catabolism fucDH lo Short-chain dehydrogenase/reductase SDR (characterized, see rationale) 33% 97% 133.7 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 64% 309.3
ethanol catabolism etoh-dh-nad lo alcohol dehydrogenase (EC 1.1.1.1) (characterized) 35% 97% 129.8 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 64% 309.3
glycerol catabolism dhaD lo NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized) 32% 94% 128.6 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 64% 309.3
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% 125.2 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 64% 309.3
D-xylose catabolism xdh lo D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized) 37% 93% 124 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 64% 309.3
D-sorbitol (glucitol) catabolism srlD lo Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized) 31% 96% 115.9 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 64% 309.3
4-hydroxybenzoate catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 32% 57% 115.2 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 64% 309.3
4-hydroxybenzoate catabolism paaH lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 32% 57% 115.2 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 64% 309.3
L-arginine catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 32% 57% 115.2 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 64% 309.3
L-citrulline catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 32% 57% 115.2 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 64% 309.3
L-lysine catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 32% 57% 115.2 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 64% 309.3
phenylacetate catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 32% 57% 115.2 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 64% 309.3
phenylacetate catabolism paaH lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 32% 57% 115.2 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 64% 309.3
L-phenylalanine catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 32% 57% 115.2 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 64% 309.3
L-phenylalanine catabolism paaH lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 32% 57% 115.2 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 64% 309.3
L-proline catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 32% 57% 115.2 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 64% 309.3
L-arabinose catabolism xacB lo L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 33% 91% 109.8 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 64% 309.3
D-galactose catabolism galdh lo L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 33% 91% 109.8 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 64% 309.3
lactose catabolism galdh lo L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 33% 91% 109.8 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 64% 309.3

Sequence Analysis Tools

View Dsui_2448 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

MLQGQIALVTGASRGIGKAVALELARLGATVVGTATSDDGAGKISAYLAEAGAKGRGALL
EVRDQAQVDALIAALEKEFGAVSILVNNAGITRDNLAMRMKDDEWDAVIDTNLKAVFRLS
KAVMRGMMKARAGRIINITSVVGHAGNPGQANYCAAKAGVSGMTRSLARELGSRNITVNC
VAPGFIDTDMTKALDDKQKEGLLGNIPLGRLGSPEDIAAAVAFLASPAAGYVTGSTIHVN
GGMYMD

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