GapMind for catabolism of small carbon sources

 

D-glucuronate catabolism in Pseudomonas stutzeri RCH2

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 Psest_0363 Psest_2125
dctQ D-glucuronate TRAP transporter, small permease component Psest_0362
dctM D-glucuronate TRAP transporter, large permease component Psest_0361 Psest_4270
udh D-glucuronate dehydrogenase Psest_0365 Psest_3572
uxuL D-glucaro-1,5-lactonase UxuL or UxuF Psest_0364
gudD D-glucarate dehydratase Psest_0376 Psest_0373
kdgD 5-dehydro-4-deoxyglucarate dehydratase Psest_0374 Psest_1515
dopDH 2,5-dioxopentanonate dehydrogenase Psest_0375 Psest_4237
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase Psest_0854 Psest_1998
exuT D-glucuronate:H+ symporter ExuT
garK glycerate 2-kinase Psest_1178
garL 5-dehydro-4-deoxy-D-glucarate aldolase Psest_1515
garR tartronate semialdehyde reductase Psest_1179 Psest_1322
gci D-glucaro-1,4-lactone cycloisomerase
kdgK 2-keto-3-deoxygluconate kinase
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.

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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