GapMind for catabolism of small carbon sources

 

D-glucuronate catabolism in Cupriavidus basilensis 4G11

Best path

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

Also see fitness data for the top candidates

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
exuT D-glucuronate:H+ symporter ExuT RR42_RS11305
udh D-glucuronate dehydrogenase RR42_RS11300
uxuL D-glucaro-1,5-lactonase UxuL or UxuF RR42_RS33665 RR42_RS30140
gudD D-glucarate dehydratase RR42_RS04840 RR42_RS10625
garL 5-dehydro-4-deoxy-D-glucarate aldolase RR42_RS29120 RR42_RS27855
garR tartronate semialdehyde reductase RR42_RS19860 RR42_RS23235
garK glycerate 2-kinase RR42_RS19865 RR42_RS33740
Alternative steps:
dctM D-glucuronate TRAP transporter, large permease component RR42_RS06530 RR42_RS10605
dctP D-glucuronate TRAP transporter, solute receptor component RR42_RS10600 RR42_RS35000
dctQ D-glucuronate TRAP transporter, small permease component
dopDH 2,5-dioxopentanonate dehydrogenase RR42_RS23090 RR42_RS04830
eda 2-keto-3-deoxygluconate 6-phosphate aldolase RR42_RS28865
gci D-glucaro-1,4-lactone cycloisomerase RR42_RS34985
kdgD 5-dehydro-4-deoxyglucarate dehydratase RR42_RS29080 RR42_RS36370
kdgK 2-keto-3-deoxygluconate kinase RR42_RS28860 RR42_RS09470
uxaC D-glucuronate isomerase
uxuA D-mannonate dehydratase RR42_RS34970
uxuB D-mannonate dehydrogenase RR42_RS34965

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.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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