GapMind for catabolism of small carbon sources

 

D-glucuronate catabolism in Klebsiella michiganensis M5al

Best path

exuT, uxaC, uxuB, uxuA, kdgK, eda

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 (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
exuT D-glucuronate:H+ symporter ExuT BWI76_RS24735 BWI76_RS09050
uxaC D-glucuronate isomerase BWI76_RS24730 BWI76_RS23645
uxuB D-mannonate dehydrogenase BWI76_RS05645 BWI76_RS19755
uxuA D-mannonate dehydratase BWI76_RS05650 BWI76_RS23640
kdgK 2-keto-3-deoxygluconate kinase BWI76_RS26750 BWI76_RS26950
eda 2-keto-3-deoxygluconate 6-phosphate aldolase BWI76_RS18095 BWI76_RS27940
Alternative steps:
dctM D-glucuronate TRAP transporter, large permease component BWI76_RS24135
dctP D-glucuronate TRAP transporter, solute receptor component BWI76_RS24125
dctQ D-glucuronate TRAP transporter, small permease component
dopDH 2,5-dioxopentanonate dehydrogenase BWI76_RS05620 BWI76_RS07615
garK glycerate 2-kinase BWI76_RS24820 BWI76_RS07025
garL 5-dehydro-4-deoxy-D-glucarate aldolase BWI76_RS24830 BWI76_RS19980
garR tartronate semialdehyde reductase BWI76_RS24825 BWI76_RS07000
gci D-glucaro-1,4-lactone cycloisomerase BWI76_RS19325 BWI76_RS13570
gudD D-glucarate dehydratase BWI76_RS22825 BWI76_RS22830
kdgD 5-dehydro-4-deoxyglucarate dehydratase
udh D-glucuronate dehydrogenase
uxuL D-glucaro-1,5-lactonase UxuL or UxuF BWI76_RS23720 BWI76_RS08665

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 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, 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