GapMind for catabolism of small carbon sources

 

D-glucuronate catabolism in Oceanisphaera arctica V1-41

Best path

dctP, dctQ, dctM, uxaC, uxuB, uxuA, kdgK, eda

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 (11 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
dctP D-glucuronate TRAP transporter, solute receptor component UN63_RS14385 UN63_RS11875
dctQ D-glucuronate TRAP transporter, small permease component
dctM D-glucuronate TRAP transporter, large permease component UN63_RS14395 UN63_RS03410
uxaC D-glucuronate isomerase UN63_RS14365
uxuB D-mannonate dehydrogenase UN63_RS14370
uxuA D-mannonate dehydratase UN63_RS14375
kdgK 2-keto-3-deoxygluconate kinase UN63_RS14360
eda 2-keto-3-deoxygluconate 6-phosphate aldolase UN63_RS14355
Alternative steps:
dopDH 2,5-dioxopentanonate dehydrogenase UN63_RS08875 UN63_RS03450
exuT D-glucuronate:H+ symporter ExuT
garK glycerate 2-kinase UN63_RS09265
garL 5-dehydro-4-deoxy-D-glucarate aldolase UN63_RS00930 UN63_RS15145
garR tartronate semialdehyde reductase UN63_RS09270 UN63_RS11350
gci D-glucaro-1,4-lactone cycloisomerase
gudD D-glucarate dehydratase
kdgD 5-dehydro-4-deoxyglucarate dehydratase
udh D-glucuronate dehydrogenase
uxuL D-glucaro-1,5-lactonase UxuL or UxuF

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 24 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:

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