GapMind for catabolism of small carbon sources


Protein Pf6N2E2_1004 in Pseudomonas fluorescens FW300-N2E2

Annotation: FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1004

Length: 252 amino acids

Source: pseudo6_N2E2 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
L-fucose catabolism fucDH med Short-chain dehydrogenase/reductase SDR (characterized, see rationale) 40% 99% 152.1 cyclohexanol dehydrogenase (EC 48% 223.8
D-xylose catabolism DKDP-dehydrog lo SDR family oxidoreductase (characterized, see rationale) 39% 98% 149.4 cyclohexanol dehydrogenase (EC 48% 223.8
L-arabinose catabolism xacB lo L-arabinose 1-dehydrogenase (EC (characterized) 34% 92% 143.3 cyclohexanol dehydrogenase (EC 48% 223.8
D-galactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC; EC (characterized) 34% 92% 141.7 cyclohexanol dehydrogenase (EC 48% 223.8
lactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC; EC (characterized) 34% 92% 141.7 cyclohexanol dehydrogenase (EC 48% 223.8
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) 35% 97% 133.7 cyclohexanol dehydrogenase (EC 48% 223.8
D-mannitol catabolism mt2d lo Probable NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Short chain dehydrogenase/reductase; YlSDR; EC (characterized) 33% 93% 131.3 cyclohexanol dehydrogenase (EC 48% 223.8
D-xylose catabolism xdh lo D-xylose 1-dehydrogenase (EC (characterized) 33% 94% 127.9 cyclohexanol dehydrogenase (EC 48% 223.8
D-sorbitol (glucitol) catabolism srlD lo Sorbitol-6-phosphate 2-dehydrogenase; EC; Glucitol-6-phosphate dehydrogenase; Ketosephosphate reductase (uncharacterized) 33% 98% 119.4 cyclohexanol dehydrogenase (EC 48% 223.8

Sequence Analysis Tools

View Pf6N2E2_1004 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.



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