GapMind for catabolism of small carbon sources

 

D-glucuronate catabolism in Pseudomonas fluorescens FW300-N2C3

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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
dctP D-glucuronate TRAP transporter, solute receptor component AO356_23055 AO356_25645
dctQ D-glucuronate TRAP transporter, small permease component AO356_23050
dctM D-glucuronate TRAP transporter, large permease component AO356_23045 AO356_25640
udh D-glucuronate dehydrogenase AO356_23065 AO356_14875
uxuL D-glucaro-1,5-lactonase UxuL or UxuF AO356_23060 AO356_20235
gudD D-glucarate dehydratase AO356_01240 AO356_25015
kdgD 5-dehydro-4-deoxyglucarate dehydratase AO356_07185 AO356_04530
dopDH 2,5-dioxopentanonate dehydrogenase AO356_24600 AO356_07180
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase AO356_05150 AO356_20285
exuT D-glucuronate:H+ symporter ExuT AO356_14055
garK glycerate 2-kinase AO356_19605 AO356_22870
garL 5-dehydro-4-deoxy-D-glucarate aldolase AO356_26150 AO356_25560
garR tartronate semialdehyde reductase AO356_19610 AO356_30330
gci D-glucaro-1,4-lactone cycloisomerase AO356_20290 AO356_26155
kdgK 2-keto-3-deoxygluconate kinase AO356_28555 AO356_00445
uxaC D-glucuronate isomerase
uxuA D-mannonate dehydratase AO356_28550 AO356_28530
uxuB D-mannonate dehydrogenase AO356_28535 AO356_27690

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