GapMind for catabolism of small carbon sources


D-glucuronate catabolism in Paraburkholderia bryophila 376MFSha3.1

Best path

exuT, udh, uxuL, gudD, garL, garR, garK

Also see fitness data for the top candidates


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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
exuT D-glucuronate:H+ symporter ExuT H281DRAFT_05311 H281DRAFT_03828
udh D-glucuronate dehydrogenase H281DRAFT_05321 H281DRAFT_03826
uxuL D-glucaro-1,5-lactonase UxuL or UxuF H281DRAFT_05322 H281DRAFT_05978
gudD D-glucarate dehydratase H281DRAFT_03815
garL 5-dehydro-4-deoxy-D-glucarate aldolase H281DRAFT_05315 H281DRAFT_03252
garR tartronate semialdehyde reductase H281DRAFT_05314 H281DRAFT_00785
garK glycerate 2-kinase H281DRAFT_00894
Alternative steps:
dctM D-glucuronate TRAP transporter, large permease component H281DRAFT_05326 H281DRAFT_05541
dctP D-glucuronate TRAP transporter, solute receptor component H281DRAFT_05324 H281DRAFT_03359
dctQ D-glucuronate TRAP transporter, small permease component
dopDH 2,5-dioxopentanonate dehydrogenase H281DRAFT_01155 H281DRAFT_05316
eda 2-keto-3-deoxygluconate 6-phosphate aldolase H281DRAFT_04277 H281DRAFT_06295
gci D-glucaro-1,4-lactone cycloisomerase H281DRAFT_04215 H281DRAFT_01747
kdgD 5-dehydro-4-deoxyglucarate dehydratase H281DRAFT_05319 H281DRAFT_03816
kdgK 2-keto-3-deoxygluconate kinase H281DRAFT_00856 H281DRAFT_05211
uxaC D-glucuronate isomerase
uxuA D-mannonate dehydratase H281DRAFT_02953 H281DRAFT_01518
uxuB D-mannonate dehydrogenase H281DRAFT_01519 H281DRAFT_02952

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.



Related tools

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 paper from 2022 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