GapMind for catabolism of small carbon sources


Protein RR42_RS21790 in Cupriavidus basilensis 4G11

Annotation: FitnessBrowser__Cup4G11:RR42_RS21790

Length: 252 amino acids

Source: Cup4G11 in FitnessBrowser

Candidate for 9 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 (characterized) 44% 94% 189.5 D-threitol dehydrogenase; EC 43% 181.4
L-rhamnose catabolism LRA1 med NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC; EC (characterized) 41% 96% 162.2 L-iditol 2-dehydrogenase (EC 44% 189.5
glycerol catabolism dhaD lo NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC (characterized) 38% 95% 167.5 L-iditol 2-dehydrogenase (EC 44% 189.5
L-fucose catabolism fucDH lo Short-chain dehydrogenase/reductase SDR (characterized, see rationale) 37% 98% 156.4 L-iditol 2-dehydrogenase (EC 44% 189.5
D-galactose catabolism galdh lo Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized) 38% 93% 145.2 L-iditol 2-dehydrogenase (EC 44% 189.5
lactose catabolism galdh lo Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized) 38% 93% 145.2 L-iditol 2-dehydrogenase (EC 44% 189.5
L-arabinose catabolism xacB lo L-arabinose 1-dehydrogenase (EC (characterized) 31% 96% 139.4 L-iditol 2-dehydrogenase (EC 44% 189.5
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 (characterized) 33% 96% 139 L-iditol 2-dehydrogenase (EC 44% 189.5
D-xylose catabolism xdh lo D-xylose 1-dehydrogenase (EC (characterized) 36% 96% 134.4 L-iditol 2-dehydrogenase (EC 44% 189.5

Sequence Analysis Tools

View RR42_RS21790 at FitnessBrowser

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

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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:

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