GapMind for catabolism of small carbon sources

 

Protein 353297 in Bacteroides thetaiotaomicron VPI-5482

Annotation: BT3771 3-oxoacyl-[acyl-carrier protein] reductase (NCBI ptt file)

Length: 248 amino acids

Source: Btheta in FitnessBrowser

Candidate for 30 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism ivdG lo 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale) 39% 100% 163.3 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 53% 256.9
ethanol catabolism etoh-dh-nad lo alcohol dehydrogenase (EC 1.1.1.1) (characterized) 38% 98% 161.4 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 53% 256.9
L-rhamnose catabolism LRA1 lo NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized) 39% 98% 160.6 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 53% 256.9
4-hydroxybenzoate catabolism badH lo BadH (characterized) 36% 99% 153.3 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 53% 256.9
phenylacetate catabolism badH lo BadH (characterized) 36% 99% 153.3 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 53% 256.9
L-phenylalanine catabolism badH lo BadH (characterized) 36% 99% 153.3 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 53% 256.9
L-fucose catabolism fucDH lo SDR family oxidoreductase (characterized, see rationale) 37% 98% 152.1 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 53% 256.9
D-xylose catabolism DKDP-dehydrog lo SDR family oxidoreductase (characterized, see rationale) 37% 98% 152.1 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 53% 256.9
D-sorbitol (glucitol) catabolism sdh lo Galactitol 2-dehydrogenase; GDH; Sorbitol dehydrogenase; SorbD; EC 1.1.1.16; EC 1.1.1.- (characterized) 38% 98% 149.4 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 53% 256.9
D-mannitol catabolism mt2d lo NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Allergen Alt a 8; EC 1.1.1.138 (characterized) 36% 92% 141.7 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 53% 256.9
L-arabinose catabolism xacB lo L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized) 33% 96% 139 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 53% 256.9
2-deoxy-D-ribonate catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate dehydrogenase (characterized) 34% 95% 136.3 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 53% 256.9
2-deoxy-D-ribose catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate dehydrogenase (characterized) 34% 95% 136.3 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 53% 256.9
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% 135.2 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 53% 256.9
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% 135.2 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 53% 256.9
glycerol catabolism dhaD lo NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized) 34% 95% 133.3 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 53% 256.9
xylitol catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 32% 98% 131.7 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 53% 256.9
D-xylose catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 32% 98% 131.7 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 53% 256.9
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) 35% 96% 130.2 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 53% 256.9
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) 31% 99% 122.5 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 53% 256.9
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) 31% 99% 122.5 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 53% 256.9
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) 31% 99% 122.5 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 53% 256.9
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) 31% 99% 122.5 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 53% 256.9
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) 31% 99% 122.5 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 53% 256.9
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) 31% 99% 122.5 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 53% 256.9
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) 31% 99% 122.5 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 53% 256.9
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) 31% 99% 122.5 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 53% 256.9
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) 31% 99% 122.5 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 53% 256.9
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) 31% 99% 122.5 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 53% 256.9
D-sorbitol (glucitol) catabolism srlD lo sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized) 32% 96% 118.2 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 53% 256.9

Sequence Analysis Tools

View 353297 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MGLLDGKTAIVTGAARGIGKAIALKFAAEGANIAFTDLVIDENAEKTRVELEAMGVKAKG
YASNAANFEDTAKVVEEIHKDFGRIDILVNNAGITRDGLMMRMSEQQWDMVINVNLKSAF
NFIHACTPVMMRQKAGSIINMASVVGVHGNAGQANYAASKAGMIALAKSIAQELGSRGIR
ANAIAPGFILTDMTAALSDEVRAEWAKKIPLRRGGTPEDVANIATFLASDMSSYVSGQVI
QVDGGMNM

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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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