GapMind for catabolism of small carbon sources


D-glucuronate catabolism in Burkholderia phytofirmans PsJN

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 BPHYT_RS24120
udh D-glucuronate dehydrogenase BPHYT_RS24165 BPHYT_RS24115
uxuL D-glucaro-1,5-lactonase UxuL or UxuF BPHYT_RS24170 BPHYT_RS16915
gudD D-glucarate dehydratase BPHYT_RS20410 BPHYT_RS31145
garL 5-dehydro-4-deoxy-D-glucarate aldolase BPHYT_RS24135 BPHYT_RS28905
garR tartronate semialdehyde reductase BPHYT_RS24130 BPHYT_RS08825
garK glycerate 2-kinase BPHYT_RS09440
Alternative steps:
dctM D-glucuronate TRAP transporter, large permease component BPHYT_RS24185
dctP D-glucuronate TRAP transporter, solute receptor component BPHYT_RS24175
dctQ D-glucuronate TRAP transporter, small permease component
dopDH 2,5-dioxopentanonate dehydrogenase BPHYT_RS10925 BPHYT_RS28455
eda 2-keto-3-deoxygluconate 6-phosphate aldolase BPHYT_RS16730 BPHYT_RS16945
gci D-glucaro-1,4-lactone cycloisomerase BPHYT_RS16405 BPHYT_RS28240
kdgD 5-dehydro-4-deoxyglucarate dehydratase BPHYT_RS24155 BPHYT_RS20415
kdgK 2-keto-3-deoxygluconate kinase BPHYT_RS09175 BPHYT_RS11300
uxaC D-glucuronate isomerase
uxuA D-mannonate dehydratase BPHYT_RS28515 BPHYT_RS10980
uxuB D-mannonate dehydrogenase BPHYT_RS23425 BPHYT_RS28510

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