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, PP_1170, 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, PP_1170, gudD, garL, garR, garK
Caulobacter crescentus NA1000 exuT, uxaC, uxuB, uxuA, kdgK, eda
Cupriavidus basilensis 4G11 exuT, udh, PP_1170, 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, garL, garR, garK
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, PP_1170, 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, PP_1170, 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, PP_1170, gudD, kdgD, dopDH
Pseudomonas fluorescens FW300-N2C3 dctP, dctQ, dctM, udh, PP_1170, gudD, kdgD, dopDH
Pseudomonas fluorescens FW300-N2E2 dctP, dctQ, dctM, udh, PP_1170, gudD, kdgD, dopDH
Pseudomonas fluorescens FW300-N2E3 exuT, udh, PP_1170, gudD, kdgD, dopDH
Pseudomonas fluorescens GW456-L13 exuT, uxaC, uxuB, uxuA, kdgK, eda
Pseudomonas putida KT2440 dctP, dctQ, dctM, udh, PP_1170, gudD, kdgD, dopDH
Pseudomonas simiae WCS417 dctP, dctQ, dctM, udh, PP_1170, gudD, kdgD, dopDH
Pseudomonas stutzeri RCH2 dctP, dctQ, dctM, udh, PP_1170, gudD, kdgD, dopDH
Shewanella amazonensis SB2B exuT, udh, gci, garL, garR, garK
Shewanella loihica PV-4 exuT, udh, gci, garL, garR, garK
Shewanella oneidensis MR-1 exuT, udh, gci, garL, garR, garK
Shewanella sp. ANA-3 exuT, udh, gci, garL, garR, garK
Sinorhizobium meliloti 1021 dctP, dctQ, dctM, udh, PP_1170, 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 May 21 2021. The underlying query database was built on May 21 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, 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