D-glucuronate catabolism

GapMind for catabolism of small carbon sources

D-glucuronate catabolism

Analysis of pathway glucuronate in 35 genomes

Genome	Best path
Acidovorax sp. GW101-3H11	dctP, dctQ, dctM, udh, uxuL, gudD, kdgD, dopDH
Azospirillum brasilense Sp245	exuT, uxaC, uxuB, uxuA, kdgK, eda
Bacteroides thetaiotaomicron VPI-5482	exuT, uxaC, uxuB, uxuA, kdgK, eda
Burkholderia phytofirmans PsJN	exuT, udh, uxuL, gudD, garL, garR, garK
Caulobacter crescentus NA1000	exuT, uxaC, uxuB, uxuA, kdgK, eda
Cupriavidus basilensis 4G11	exuT, udh, uxuL, gudD, garL, garR, garK
Dechlorosoma suillum PS	exuT, udh, gci, garL, garR, garK
Desulfovibrio vulgaris Hildenborough	exuT, udh, gci, garL, garR, garK
Desulfovibrio vulgaris Miyazaki F	exuT, udh, gci, garL, garR, garK
Dinoroseobacter shibae DFL-12	exuT, udh, gci, kdgD, dopDH
Dyella japonica UNC79MFTsu3.2	exuT, uxaC, uxuB, uxuA, kdgK, eda
Echinicola vietnamensis KMM 6221, DSM 17526	dctP, dctQ, dctM, uxaC, uxuB, uxuA, kdgK, eda
Escherichia coli BW25113	exuT, uxaC, uxuB, uxuA, kdgK, eda
Herbaspirillum seropedicae SmR1	exuT, udh, uxuL, gudD, kdgD, dopDH
Klebsiella michiganensis M5al	exuT, uxaC, uxuB, uxuA, kdgK, eda
Magnetospirillum magneticum AMB-1	exuT, udh, gci, garL, garR, garK
Marinobacter adhaerens HP15	exuT, udh, gci, kdgD, dopDH
Paraburkholderia bryophila 376MFSha3.1	exuT, udh, uxuL, gudD, garL, garR, garK
Pedobacter sp. GW460-11-11-14-LB5	exuT, uxaC, uxuB, uxuA, kdgK, eda
Phaeobacter inhibens BS107	exuT, udh, gci, garL, garR, garK
Pseudomonas fluorescens FW300-N1B4	exuT, udh, uxuL, gudD, kdgD, dopDH
Pseudomonas fluorescens FW300-N2C3	dctP, dctQ, dctM, udh, uxuL, gudD, kdgD, dopDH
Pseudomonas fluorescens FW300-N2E2	dctP, dctQ, dctM, udh, uxuL, gudD, kdgD, dopDH
Pseudomonas fluorescens FW300-N2E3	exuT, udh, uxuL, gudD, kdgD, dopDH
Pseudomonas fluorescens GW456-L13	exuT, uxaC, uxuB, uxuA, kdgK, eda
Pseudomonas putida KT2440	dctP, dctQ, dctM, udh, uxuL, gudD, kdgD, dopDH
Pseudomonas simiae WCS417	dctP, dctQ, dctM, udh, uxuL, gudD, kdgD, dopDH
Pseudomonas stutzeri RCH2	dctP, dctQ, dctM, udh, uxuL, gudD, kdgD, dopDH
Shewanella amazonensis SB2B	exuT, udh, gci, kdgD, dopDH
Shewanella loihica PV-4	exuT, udh, gci, kdgD, dopDH
Shewanella oneidensis MR-1	exuT, udh, gci, kdgD, dopDH
Shewanella sp. ANA-3	exuT, udh, gci, kdgD, dopDH
Sinorhizobium meliloti 1021	dctP, dctQ, dctM, udh, uxuL, gudD, kdgD, dopDH
Sphingomonas koreensis DSMZ 15582	exuT, uxaC, uxuB, uxuA, kdgK, eda
Synechococcus elongatus PCC 7942	exuT, udh, gci, kdgD, dopDH

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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources