GapMind for catabolism of small carbon sources

 

Protein WP_004130089.1 in Rhizobium freirei PRF 81

Annotation: NCBI__GCF_000359745.1:WP_004130089.1

Length: 255 amino acids

Source: GCF_000359745.1 in NCBI

Candidate for 15 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-fucose catabolism fucDH med Short-chain dehydrogenase/reductase SDR (characterized, see rationale) 42% 98% 176 meso-butanediol dehydrogenase [(R)-acetoin-forming] (EC 1.1.1.304; EC 1.1.1.76) 41% 183.0
L-arabinose catabolism xacB med L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 41% 93% 171 meso-butanediol dehydrogenase [(R)-acetoin-forming] (EC 1.1.1.304; EC 1.1.1.76) 41% 183.0
D-galactose catabolism galdh med L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 41% 93% 171 meso-butanediol dehydrogenase [(R)-acetoin-forming] (EC 1.1.1.304; EC 1.1.1.76) 41% 183.0
lactose catabolism galdh med L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 41% 93% 171 meso-butanediol dehydrogenase [(R)-acetoin-forming] (EC 1.1.1.304; EC 1.1.1.76) 41% 183.0
4-hydroxybenzoate catabolism badH lo BadH (characterized) 37% 99% 178.3 meso-butanediol dehydrogenase [(R)-acetoin-forming] (EC 1.1.1.304; EC 1.1.1.76) 41% 183.0
phenylacetate catabolism badH lo BadH (characterized) 37% 99% 178.3 meso-butanediol dehydrogenase [(R)-acetoin-forming] (EC 1.1.1.304; EC 1.1.1.76) 41% 183.0
L-phenylalanine catabolism badH lo BadH (characterized) 37% 99% 178.3 meso-butanediol dehydrogenase [(R)-acetoin-forming] (EC 1.1.1.304; EC 1.1.1.76) 41% 183.0
D-xylose catabolism DKDP-dehydrog lo SDR family oxidoreductase (characterized, see rationale) 40% 97% 164.9 meso-butanediol dehydrogenase [(R)-acetoin-forming] (EC 1.1.1.304; EC 1.1.1.76) 41% 183.0
glycerol catabolism dhaD lo NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized) 37% 96% 161.4 meso-butanediol dehydrogenase [(R)-acetoin-forming] (EC 1.1.1.304; EC 1.1.1.76) 41% 183.0
xylitol catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 36% 98% 143.7 meso-butanediol dehydrogenase [(R)-acetoin-forming] (EC 1.1.1.304; EC 1.1.1.76) 41% 183.0
D-xylose catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 36% 98% 143.7 meso-butanediol dehydrogenase [(R)-acetoin-forming] (EC 1.1.1.304; EC 1.1.1.76) 41% 183.0
2-deoxy-D-ribonate catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate dehydrogenase (characterized) 33% 93% 142.1 meso-butanediol dehydrogenase [(R)-acetoin-forming] (EC 1.1.1.304; EC 1.1.1.76) 41% 183.0
2-deoxy-D-ribose catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate dehydrogenase (characterized) 33% 93% 142.1 meso-butanediol dehydrogenase [(R)-acetoin-forming] (EC 1.1.1.304; EC 1.1.1.76) 41% 183.0
L-isoleucine catabolism ivdG 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) 33% 98% 127.1 meso-butanediol dehydrogenase [(R)-acetoin-forming] (EC 1.1.1.304; EC 1.1.1.76) 41% 183.0
D-sorbitol (glucitol) catabolism srlD lo sorbitol-6-phosphate dehydrogenase; EC 1.1.1.140 (characterized) 31% 98% 119 meso-butanediol dehydrogenase [(R)-acetoin-forming] (EC 1.1.1.304; EC 1.1.1.76) 41% 183.0

Sequence Analysis Tools

View WP_004130089.1 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

MDLESKVCVVTGAGSGIGRATAELFARQGAKVGVVDVNIDAARDVAREIGTDAIALKADV
SSSAEVEALVRSVKEKWGRIDVLVNNAGFGMTGNVTTIAESDWDRIMAVNVKGIFLCSKY
VVPIMAEQGNGSIINTTSYTAVSAIANRTAYVASKGAISALTRAMALDHAKDGIRVNAVA
PGTIDSPYFTKIFAEAADPQALREDFNARAALHRMGNPEEIAEAMLFLASDRSRFATGSI
LTVDGGSSIGNHLVR

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