GapMind for catabolism of small carbon sources

 

D-galacturonate catabolism in Caulobacter crescentus NA1000

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 (9 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
exuT D-galacturonate transporter ExuT CCNA_01039 CCNA_01576
uxaC D-galacturonate isomerase CCNA_01557
uxaB tagaturonate reductase
uxaA D-altronate dehydratase CCNA_01555
kdgK 2-keto-3-deoxygluconate kinase CCNA_01110 CCNA_01563
eda 2-keto-3-deoxygluconate 6-phosphate aldolase CCNA_01562 CCNA_00825
Alternative steps:
dopDH 2,5-dioxopentanonate dehydrogenase CCNA_00865 CCNA_02881
garD meso-galactarate dehydratase (L-threo-forming) GarD CCNA_01555
gatA D-galacturonate transporter gatA
gci D-galactarolactone cycloisomerase
gli D-galactarolactone isomerase
kdgD 5-dehydro-4-deoxyglucarate dehydratase CCNA_01253
PS417_04205 D-galacturonate transporter
udh D-galacturonate dehydrogenase
uxuL D-galactaro-1,5-lactonase (UxuL or UxuF) CCNA_01882

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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