GapMind for catabolism of small carbon sources

 

Protein WP_036259611.1 in Methylocapsa aurea KYG

Annotation: NCBI__GCF_000746085.1:WP_036259611.1

Length: 245 amino acids

Source: GCF_000746085.1 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) 35% 99% 163.7 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 57% 267.7
phenylacetate catabolism badH lo BadH (characterized) 35% 99% 163.7 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 57% 267.7
L-phenylalanine catabolism badH lo BadH (characterized) 35% 99% 163.7 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 57% 267.7
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% 95% 156 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 57% 267.7
D-sorbitol (glucitol) catabolism sdh lo L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized) 39% 95% 145.6 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 57% 267.7
L-fucose catabolism fucDH lo Short-chain dehydrogenase/reductase SDR (characterized, see rationale) 37% 98% 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 57% 267.7
L-isoleucine catabolism ivdG lo 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale) 33% 100% 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 57% 267.7
D-mannitol catabolism mt2d lo NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Allergen Alt a 8; EC 1.1.1.138 (characterized) 32% 95% 124.4 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 57% 267.7
L-rhamnose catabolism LRA1 lo L-rhamnose 1-dehydrogenase (NADP(+)); RHAD; EC 1.1.1.377 (characterized) 30% 99% 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 57% 267.7
4-hydroxybenzoate catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 31% 54% 117.1 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 57% 267.7
4-hydroxybenzoate catabolism paaH lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 31% 54% 117.1 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 57% 267.7
L-arginine catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 31% 54% 117.1 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 57% 267.7
L-citrulline catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 31% 54% 117.1 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 57% 267.7
L-lysine catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 31% 54% 117.1 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 57% 267.7
phenylacetate catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 31% 54% 117.1 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 57% 267.7
phenylacetate catabolism paaH lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 31% 54% 117.1 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 57% 267.7
L-phenylalanine catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 31% 54% 117.1 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 57% 267.7
L-phenylalanine catabolism paaH lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 31% 54% 117.1 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 57% 267.7
L-proline catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 31% 54% 117.1 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 57% 267.7
2-deoxy-D-ribonate catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate 3-dehydrogenase (characterized) 31% 96% 114 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 57% 267.7
2-deoxy-D-ribose catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate 3-dehydrogenase (characterized) 31% 96% 114 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 57% 267.7

Sequence Analysis Tools

View WP_036259611.1 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

MFDLSGKTALVTGASGGLGQAIARGLHRRGAIVGLSGTRRAALDELAAELATNVHILPCD
LADKAAVEALIPAAEAAMGGVDILVNNAGVTKDNLFMRMKDEEWESVLSVNLTAVFRLSR
ACLKGMLRKRYGRIIGISSVVGVTGNAGQGNYAASKAGMIGMFKSLAAEVASRSVTVNCV
APGFIESPMTDVLNEKQKSGILAQVPMGRLGTGAEVAAAVVYLASSEAAYVTGQTLHVNG
GMAMI

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