GapMind for catabolism of small carbon sources

 

D-galacturonate catabolism in Pedobacter sp. GW460-11-11-14-LB5

Best path

exuT, uxaC, uxaB, uxaA, kdgK, eda

Also see fitness data for the top candidates

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 (10 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
exuT D-galacturonate transporter ExuT CA265_RS19855
uxaC D-galacturonate isomerase CA265_RS19870
uxaB tagaturonate reductase CA265_RS19880
uxaA D-altronate dehydratase CA265_RS19875 CA265_RS04670
kdgK 2-keto-3-deoxygluconate kinase CA265_RS19865
eda 2-keto-3-deoxygluconate 6-phosphate aldolase CA265_RS19860 CA265_RS02050
Alternative steps:
dopDH 2,5-dioxopentanonate dehydrogenase CA265_RS05705 CA265_RS14635
garD meso-galactarate dehydratase (L-threo-forming) GarD CA265_RS19875 CA265_RS12250
gatA D-galacturonate transporter gatA
gci D-galactarolactone cycloisomerase CA265_RS12250
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) CA265_RS13655

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 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