GapMind for catabolism of small carbon sources


D-glucuronate catabolism in Herbaspirillum seropedicae SmR1

Best path

exuT, udh, uxuL, gudD, kdgD, dopDH

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 HSERO_RS23010 HSERO_RS20520
udh D-glucuronate dehydrogenase HSERO_RS23040
uxuL D-glucaro-1,5-lactonase UxuL or UxuF HSERO_RS15795 HSERO_RS19370
gudD D-glucarate dehydratase HSERO_RS05800 HSERO_RS05730
kdgD 5-dehydro-4-deoxyglucarate dehydratase HSERO_RS15785
dopDH 2,5-dioxopentanonate dehydrogenase HSERO_RS00735 HSERO_RS07235
Alternative steps:
dctM D-glucuronate TRAP transporter, large permease component HSERO_RS05555 HSERO_RS04250
dctP D-glucuronate TRAP transporter, solute receptor component
dctQ D-glucuronate TRAP transporter, small permease component
eda 2-keto-3-deoxygluconate 6-phosphate aldolase HSERO_RS05525 HSERO_RS05155
garK glycerate 2-kinase HSERO_RS10055
garL 5-dehydro-4-deoxy-D-glucarate aldolase HSERO_RS01600 HSERO_RS16395
garR tartronate semialdehyde reductase HSERO_RS21160 HSERO_RS15390
gci D-glucaro-1,4-lactone cycloisomerase HSERO_RS05150
kdgK 2-keto-3-deoxygluconate kinase HSERO_RS08715 HSERO_RS07545
uxaC D-glucuronate isomerase
uxuA D-mannonate dehydratase HSERO_RS05150
uxuB D-mannonate dehydrogenase HSERO_RS02215

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