GapMind for catabolism of small carbon sources


Protein AO356_28740 in Pseudomonas fluorescens FW300-N2C3

Annotation: FitnessBrowser__pseudo5_N2C3_1:AO356_28740

Length: 246 amino acids

Source: pseudo5_N2C3_1 in FitnessBrowser

Candidate for 5 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 hi Short-chain dehydrogenase/reductase SDR (characterized, see rationale) 67% 99% 309.7 3-hydroxybutyrate dehydrogenase type 2; Dehydrogenase/reductase SDR family member 6; Oxidoreductase UCPA; R-beta-hydroxybutyrate dehydrogenase; Short chain dehydrogenase/reductase family 15C member 1; EC 1.1.1.-; EC 56% 251.9
D-xylose catabolism DKDP-dehydrog med SDR family oxidoreductase (characterized, see rationale) 62% 97% 289.7 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- 63% 297.7
2-deoxy-D-ribonate catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate dehydrogenase (characterized) 34% 94% 134.8 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- 63% 297.7
2-deoxy-D-ribose catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate dehydrogenase (characterized) 34% 94% 134.8 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- 63% 297.7
D-xylose catabolism xdh lo D-xylose 1-dehydrogenase (EC (characterized) 33% 94% 118.6 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- 63% 297.7

Sequence Analysis Tools

View AO356_28740 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