GapMind for catabolism of small carbon sources

 

D-galacturonate catabolism in Bacteroides fluxus YIT 12057

Best path

exuT, uxaC, uxaB, uxaA, kdgK, eda

Rules

Overview: Galacturonate utilization in GapMind is based on MetaCyc pathways D-galacturonate degradation I via tagaturonate (link), pathway II via oxidation to 5-dehydro-4-deoxy-glucarate (link), and another oxidative pathway (PMID:30249705). Pathway III via galactonate (link) is reported only in fungi and is not included in GapMind.

15 steps (8 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
exuT D-galacturonate transporter ExuT HMPREF9446_RS09105
uxaC D-galacturonate isomerase HMPREF9446_RS10250
uxaB tagaturonate reductase HMPREF9446_RS10240
uxaA D-altronate dehydratase HMPREF9446_RS04375
kdgK 2-keto-3-deoxygluconate kinase HMPREF9446_RS04365
eda 2-keto-3-deoxygluconate 6-phosphate aldolase HMPREF9446_RS04360 HMPREF9446_RS00140
Alternative steps:
dopDH 2,5-dioxopentanonate dehydrogenase
garD meso-galactarate dehydratase (L-threo-forming) GarD HMPREF9446_RS04375
gatA D-galacturonate transporter gatA HMPREF9446_RS10365
gci D-galactarolactone cycloisomerase
gli D-galactarolactone isomerase
kdgD 5-dehydro-4-deoxyglucarate dehydratase
PS417_04205 D-galacturonate transporter
udh D-galacturonate dehydrogenase
uxuL D-galactaro-1,5-lactonase (UxuL or UxuF)

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

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