GapMind for catabolism of small carbon sources

 

D-galacturonate catabolism

Analysis of pathway galacturonate in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 exuT, udh, uxuL, garD, kdgD, dopDH
Azospirillum brasilense Sp245 exuT, uxaC, uxaB, uxaA, kdgK, eda
Bacteroides thetaiotaomicron VPI-5482 exuT, uxaC, uxaB, uxaA, kdgK, eda
Burkholderia phytofirmans PsJN exuT, udh, uxuL, garD, kdgD, dopDH
Caulobacter crescentus NA1000 exuT, uxaC, uxaB, uxaA, kdgK, eda
Cupriavidus basilensis 4G11 exuT, udh, uxuL, garD, kdgD, dopDH
Dechlorosoma suillum PS exuT, udh, gli, gci, kdgD, dopDH
Desulfovibrio vulgaris Hildenborough exuT, uxaC, uxaB, uxaA, kdgK, eda
Desulfovibrio vulgaris Miyazaki F exuT, uxaC, uxaB, uxaA, kdgK, eda
Dinoroseobacter shibae DFL-12 exuT, uxaC, uxaB, uxaA, kdgK, eda
Dyella japonica UNC79MFTsu3.2 exuT, uxaC, uxaB, uxaA, kdgK, eda
Echinicola vietnamensis KMM 6221, DSM 17526 exuT, uxaC, uxaB, uxaA, kdgK, eda
Escherichia coli BW25113 exuT, uxaC, uxaB, uxaA, kdgK, eda
Herbaspirillum seropedicae SmR1 exuT, udh, uxuL, garD, kdgD, dopDH
Klebsiella michiganensis M5al exuT, uxaC, uxaB, uxaA, kdgK, eda
Magnetospirillum magneticum AMB-1 exuT, udh, gli, gci, kdgD, dopDH
Marinobacter adhaerens HP15 exuT, uxaC, uxaB, uxaA, kdgK, eda
Paraburkholderia bryophila 376MFSha3.1 exuT, udh, uxuL, garD, kdgD, dopDH
Pedobacter sp. GW460-11-11-14-LB5 exuT, uxaC, uxaB, uxaA, kdgK, eda
Phaeobacter inhibens BS107 exuT, uxaC, uxaB, uxaA, kdgK, eda
Pseudomonas fluorescens FW300-N1B4 exuT, udh, uxuL, garD, kdgD, dopDH
Pseudomonas fluorescens FW300-N2C3 exuT, udh, uxuL, garD, kdgD, dopDH
Pseudomonas fluorescens FW300-N2E2 PS417_04205, udh, uxuL, garD, kdgD, dopDH
Pseudomonas fluorescens FW300-N2E3 PS417_04205, udh, uxuL, garD, kdgD, dopDH
Pseudomonas fluorescens GW456-L13 PS417_04205, udh, uxuL, garD, kdgD, dopDH
Pseudomonas putida KT2440 PS417_04205, udh, uxuL, garD, kdgD, dopDH
Pseudomonas simiae WCS417 exuT, udh, uxuL, garD, kdgD, dopDH
Pseudomonas stutzeri RCH2 exuT, udh, uxuL, garD, kdgD, dopDH
Shewanella amazonensis SB2B exuT, uxaC, uxaB, uxaA, kdgK, eda
Shewanella loihica PV-4 exuT, uxaC, uxaB, uxaA, kdgK, eda
Shewanella oneidensis MR-1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Shewanella sp. ANA-3 exuT, uxaC, uxaB, uxaA, kdgK, eda
Sinorhizobium meliloti 1021 exuT, udh, uxuL, garD, kdgD, dopDH
Sphingomonas koreensis DSMZ 15582 exuT, uxaC, uxaB, uxaA, kdgK, eda
Synechococcus elongatus PCC 7942 exuT, uxaC, uxaB, uxaA, kdgK, eda

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:

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