GapMind for catabolism of small carbon sources

 

D-glucuronate catabolism in Rhizorhabdus wittichii RW1

Best path

exuT, uxaC, uxuB, uxuA, kdgK, eda

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 (10 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
exuT D-glucuronate:H+ symporter ExuT
uxaC D-glucuronate isomerase SWIT_RS09530
uxuB D-mannonate dehydrogenase SWIT_RS09525
uxuA D-mannonate dehydratase SWIT_RS08555 SWIT_RS09540
kdgK 2-keto-3-deoxygluconate kinase SWIT_RS09545 SWIT_RS08585
eda 2-keto-3-deoxygluconate 6-phosphate aldolase SWIT_RS08220 SWIT_RS09510
Alternative steps:
dctM D-glucuronate TRAP transporter, large permease component
dctP D-glucuronate TRAP transporter, solute receptor component
dctQ D-glucuronate TRAP transporter, small permease component
dopDH 2,5-dioxopentanonate dehydrogenase SWIT_RS15260 SWIT_RS15500
garK glycerate 2-kinase
garL 5-dehydro-4-deoxy-D-glucarate aldolase SWIT_RS21815 SWIT_RS21595
garR tartronate semialdehyde reductase SWIT_RS21640 SWIT_RS03295
gci D-glucaro-1,4-lactone cycloisomerase
gudD D-glucarate dehydratase
kdgD 5-dehydro-4-deoxyglucarate dehydratase SWIT_RS02620
udh D-glucuronate dehydrogenase
uxuL D-glucaro-1,5-lactonase UxuL or UxuF SWIT_RS01395 SWIT_RS21370

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 Apr 09 2024. 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