GapMind for catabolism of small carbon sources

 

D-gluconate catabolism

Analysis of pathway gluconate in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 gntA, gntB, gntC, gntK, edd, eda
Azospirillum brasilense Sp245 gntA, gntB, gntC, gntK, gnd
Bacteroides thetaiotaomicron VPI-5482 gntT, gntK, gnd
Burkholderia phytofirmans PsJN gadh1, gadh2, gadh3, kguT, kguK, kguD, edd, eda
Caulobacter crescentus NA1000 gntT, gntK, edd, eda
Cupriavidus basilensis 4G11 gntT, gntK, edd, eda
Dechlorosoma suillum PS gntT, gntK, gnd
Desulfovibrio vulgaris Hildenborough gntA, gntB, gntC, gntK, gnd
Desulfovibrio vulgaris Miyazaki F gntT, gntK, gnd
Dinoroseobacter shibae DFL-12 gntT, gntK, edd, eda
Dyella japonica UNC79MFTsu3.2 gntT, gntK, edd, eda
Echinicola vietnamensis KMM 6221, DSM 17526 gntT, gntK, gnd
Escherichia coli BW25113 gntT, gntK, edd, eda
Herbaspirillum seropedicae SmR1 gntT, gntK, edd, eda
Klebsiella michiganensis M5al gntT, gntK, edd, eda
Magnetospirillum magneticum AMB-1 gntT, gntK, gnd
Marinobacter adhaerens HP15 gntT, gntK, edd, eda
Paraburkholderia bryophila 376MFSha3.1 gntT, gntK, edd, eda
Pedobacter sp. GW460-11-11-14-LB5 gntT, gntK, gnd
Phaeobacter inhibens BS107 gntT, gntK, edd, eda
Pseudomonas fluorescens FW300-N1B4 gntT, gntK, edd, eda
Pseudomonas fluorescens FW300-N2C3 gntT, gntK, edd, eda
Pseudomonas fluorescens FW300-N2E2 gntT, gntK, edd, eda
Pseudomonas fluorescens FW300-N2E3 gadh1, gadh2, gadh3, kguT, kguK, kguD, edd, eda
Pseudomonas fluorescens GW456-L13 gntT, gntK, edd, eda
Pseudomonas putida KT2440 gadh1, gadh2, gadh3, kguT, kguK, kguD, edd, eda
Pseudomonas simiae WCS417 gadh1, gadh2, gadh3, kguT, kguK, kguD, edd, eda
Pseudomonas stutzeri RCH2 gntA, gntB, gntC, gntK, edd, eda
Shewanella amazonensis SB2B gntT, gntK, edd, eda
Shewanella loihica PV-4 gntT, gntK, edd, eda
Shewanella oneidensis MR-1 gntT, gntK, edd, eda
Shewanella sp. ANA-3 gntT, gntK, edd, eda
Sinorhizobium meliloti 1021 gntA, gntB, gntC, gntK, edd, eda
Sphingomonas koreensis DSMZ 15582 gntT, gntK, edd, eda
Synechococcus elongatus PCC 7942 gntT, gntK, gnd

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