GapMind for catabolism of small carbon sources


D-glucuronate catabolism in Azospirillum brasilense Sp245

Best path

exuT, uxaC, uxuB, uxuA, kdgK, eda

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 (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
exuT D-glucuronate:H+ symporter ExuT AZOBR_RS23835
uxaC D-glucuronate isomerase AZOBR_RS31425
uxuB D-mannonate dehydrogenase AZOBR_RS31375
uxuA D-mannonate dehydratase AZOBR_RS31370 AZOBR_RS25270
kdgK 2-keto-3-deoxygluconate kinase AZOBR_RS29860
eda 2-keto-3-deoxygluconate 6-phosphate aldolase AZOBR_RS29850 AZOBR_RS22730
Alternative steps:
dctM D-glucuronate TRAP transporter, large permease component AZOBR_RS30120 AZOBR_RS27150
dctP D-glucuronate TRAP transporter, solute receptor component AZOBR_RS31400 AZOBR_RS30130
dctQ D-glucuronate TRAP transporter, small permease component
dopDH 2,5-dioxopentanonate dehydrogenase AZOBR_RS18165 AZOBR_RS29750
garK glycerate 2-kinase AZOBR_RS07950
garL 5-dehydro-4-deoxy-D-glucarate aldolase AZOBR_RS08420
garR tartronate semialdehyde reductase AZOBR_RS07955 AZOBR_RS26815
gci D-glucaro-1,4-lactone cycloisomerase AZOBR_RS26635 AZOBR_RS25270
gudD D-glucarate dehydratase
kdgD 5-dehydro-4-deoxyglucarate dehydratase AZOBR_RS08420 AZOBR_RS23300
udh D-glucuronate dehydrogenase
uxuL D-glucaro-1,5-lactonase UxuL or UxuF AZOBR_RS22710 AZOBR_RS31230

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:

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