GapMind for catabolism of small carbon sources


D-fructose catabolism

Analysis of pathway fructose in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 frcA, frcB, frcC, scrK
Azospirillum brasilense Sp245 fruA, fruI, 1pfk, fba, tpi
Bacteroides thetaiotaomicron VPI-5482 BT1758, scrK
Burkholderia phytofirmans PsJN frcA, frcB, frcC, scrK
Caulobacter crescentus NA1000 glcP, scrK
Cupriavidus basilensis 4G11 frcA, frcB, frcC, scrK
Dechlorosoma suillum PS fruII-ABC, 1pfk, fba, tpi
Desulfovibrio vulgaris Hildenborough fruII-ABC, 1pfk, fba, tpi
Desulfovibrio vulgaris Miyazaki F fruII-ABC, 1pfk, fba, tpi
Dinoroseobacter shibae DFL-12 frcA, frcB, frcC, scrK
Dyella japonica UNC79MFTsu3.2 fruP, scrK
Echinicola vietnamensis KMM 6221, DSM 17526 glcP, scrK
Escherichia coli BW25113 fruA, fruB, 1pfk, fba, tpi
Herbaspirillum seropedicae SmR1 frcA, frcB, frcC, scrK
Klebsiella michiganensis M5al fruA, fruB, 1pfk, fba, tpi
Magnetospirillum magneticum AMB-1 Slc2a5, scrK
Marinobacter adhaerens HP15 fruA, fruI, 1pfk, fba, tpi
Paraburkholderia bryophila 376MFSha3.1 frcA, frcB, frcC, scrK
Pedobacter sp. GW460-11-11-14-LB5 glcP, scrK
Phaeobacter inhibens BS107 frcA, frcB, frcC, scrK
Pseudomonas fluorescens FW300-N1B4 fruA, fruI, 1pfk, fba, tpi
Pseudomonas fluorescens FW300-N2C3 fruA, fruI, 1pfk, fba, tpi
Pseudomonas fluorescens FW300-N2E2 fruA, fruI, 1pfk, fba, tpi
Pseudomonas fluorescens FW300-N2E3 fruA, fruI, 1pfk, fba, tpi
Pseudomonas fluorescens GW456-L13 fruA, fruI, 1pfk, fba, tpi
Pseudomonas putida KT2440 fruA, fruI, 1pfk, fba, tpi
Pseudomonas simiae WCS417 fruA, fruI, 1pfk, fba, tpi
Pseudomonas stutzeri RCH2 fruA, fruI, 1pfk, fba, tpi
Shewanella amazonensis SB2B fruP, scrK
Shewanella loihica PV-4 fruP, scrK
Shewanella oneidensis MR-1 fruII-ABC, 1pfk, fba, tpi
Shewanella sp. ANA-3 fruP, scrK
Sinorhizobium meliloti 1021 frcA, frcB, frcC, scrK
Sphingomonas koreensis DSMZ 15582 glcP, scrK
Synechococcus elongatus PCC 7942 fruII-ABC, 1pfk, fba, tpi

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.



Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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