GapMind for catabolism of small carbon sources

 

D-glucuronate catabolism in Dinoroseobacter shibae DFL-12

Best path

exuT, udh, gci, kdgD, dopDH

Also see fitness data for the top candidates

Rules

Overview: Glucuronate utilization in GapMind is based on MetaCyc pathways D-glucuronate degradation II (oxidation of 5-keto-4-deoxyglucarate, link), a related pathway via 5-keto-4-deoxyglucarate aldolase (link), or degradation via fructuronate (link). GapMind also includes a variation on the oxidative pathway with a glucarolactonase, as in Pseudomonas putida. MetaCyc pathway I (via L-gulonate and xylitol, link) is not reported in prokaryotes and is not described here.

18 steps (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
exuT D-glucuronate:H+ symporter ExuT
udh D-glucuronate dehydrogenase
gci D-glucaro-1,4-lactone cycloisomerase Dshi_0604
kdgD 5-dehydro-4-deoxyglucarate dehydratase Dshi_0149
dopDH 2,5-dioxopentanonate dehydrogenase Dshi_0577 Dshi_2442
Alternative steps:
dctM D-glucuronate TRAP transporter, large permease component Dshi_2753 Dshi_0956
dctP D-glucuronate TRAP transporter, solute receptor component Dshi_0958
dctQ D-glucuronate TRAP transporter, small permease component
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Dshi_1768 Dshi_1241
garK glycerate 2-kinase Dshi_3046
garL 5-dehydro-4-deoxy-D-glucarate aldolase Dshi_1647 Dshi_3145
garR tartronate semialdehyde reductase Dshi_1752 Dshi_3047
gudD D-glucarate dehydratase
kdgK 2-keto-3-deoxygluconate kinase Dshi_1268 Dshi_2797
uxaC D-glucuronate isomerase
uxuA D-mannonate dehydratase
uxuB D-mannonate dehydrogenase Dshi_0969
uxuL D-glucaro-1,5-lactonase UxuL or UxuF Dshi_1240

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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