GapMind for catabolism of small carbon sources

 

D-glucuronate catabolism in Pseudomonas benzenivorans DSM 8628

Best path

dctP, dctQ, dctM, udh, uxuL, gudD, kdgD, dopDH

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 (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
dctP D-glucuronate TRAP transporter, solute receptor component BLS63_RS03220
dctQ D-glucuronate TRAP transporter, small permease component BLS63_RS03225
dctM D-glucuronate TRAP transporter, large permease component BLS63_RS03230 BLS63_RS10635
udh D-glucuronate dehydrogenase BLS63_RS03210 BLS63_RS13170
uxuL D-glucaro-1,5-lactonase UxuL or UxuF BLS63_RS03215
gudD D-glucarate dehydratase BLS63_RS03165 BLS63_RS03180
kdgD 5-dehydro-4-deoxyglucarate dehydratase BLS63_RS03175 BLS63_RS06945
dopDH 2,5-dioxopentanonate dehydrogenase BLS63_RS03170 BLS63_RS14235
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase BLS63_RS18030
exuT D-glucuronate:H+ symporter ExuT
garK glycerate 2-kinase BLS63_RS21070 BLS63_RS17650
garL 5-dehydro-4-deoxy-D-glucarate aldolase BLS63_RS06945 BLS63_RS07570
garR tartronate semialdehyde reductase BLS63_RS21065 BLS63_RS09690
gci D-glucaro-1,4-lactone cycloisomerase
kdgK 2-keto-3-deoxygluconate kinase
uxaC D-glucuronate isomerase
uxuA D-mannonate dehydratase BLS63_RS03200
uxuB D-mannonate dehydrogenase

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