GapMind for catabolism of small carbon sources

 

D-glucuronate catabolism in Pseudomonas putida KT2440

Best path

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

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 (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
dctP D-glucuronate TRAP transporter, solute receptor component PP_1169
dctQ D-glucuronate TRAP transporter, small permease component PP_1168
dctM D-glucuronate TRAP transporter, large permease component PP_1167
udh D-glucuronate dehydrogenase PP_1171 PP_0501
uxuL D-glucaro-1,5-lactonase UxuL or UxuF PP_1170 PP_3180
gudD D-glucarate dehydratase PP_4757
kdgD 5-dehydro-4-deoxyglucarate dehydratase PP_3599
dopDH 2,5-dioxopentanonate dehydrogenase PP_3602 PP_1256
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase PP_1024
exuT D-glucuronate:H+ symporter ExuT
garK glycerate 2-kinase PP_4300 PP_3178
garL 5-dehydro-4-deoxy-D-glucarate aldolase
garR tartronate semialdehyde reductase PP_4299 PP_1143
gci D-glucaro-1,4-lactone cycloisomerase
kdgK 2-keto-3-deoxygluconate kinase PP_3378
uxaC D-glucuronate isomerase
uxuA D-mannonate dehydratase
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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