GapMind for catabolism of small carbon sources

 

fumarate catabolism

Analysis of pathway fumarate in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 dctA
Azospirillum brasilense Sp245 dctA
Bacteroides thetaiotaomicron VPI-5482 sdcL
Burkholderia phytofirmans PsJN dctA
Caulobacter crescentus NA1000 dctA
Cupriavidus basilensis 4G11 dctA
Dechlorosoma suillum PS dctM, dctP, dctQ
Desulfovibrio vulgaris Hildenborough dauA
Desulfovibrio vulgaris Miyazaki F dauA
Dinoroseobacter shibae DFL-12 Dshi_1194, Dshi_1195
Dyella japonica UNC79MFTsu3.2 dctA
Echinicola vietnamensis KMM 6221, DSM 17526 sdcL
Escherichia coli BW25113 dctA
Herbaspirillum seropedicae SmR1 dctM, dctP, dctQ
Klebsiella michiganensis M5al dctA
Magnetospirillum magneticum AMB-1 dctM, dctP, dctQ
Marinobacter adhaerens HP15 Dshi_1194, Dshi_1195
Paraburkholderia bryophila 376MFSha3.1 dctA
Pedobacter sp. GW460-11-11-14-LB5 dctA
Phaeobacter inhibens BS107 dctM, dctP, dctQ
Pseudomonas fluorescens FW300-N1B4 dctA
Pseudomonas fluorescens FW300-N2C3 dctA
Pseudomonas fluorescens FW300-N2E2 dctA
Pseudomonas fluorescens FW300-N2E3 dctA
Pseudomonas fluorescens GW456-L13 dctA
Pseudomonas putida KT2440 dctA
Pseudomonas simiae WCS417 dctA
Pseudomonas stutzeri RCH2 sdcL
Shewanella amazonensis SB2B dctM, dctP, dctQ
Shewanella loihica PV-4 dctM, dctP, dctQ
Shewanella oneidensis MR-1 dctM, dctP, dctQ
Shewanella sp. ANA-3 dctM, dctP, dctQ
Sinorhizobium meliloti 1021 dctA
Sphingomonas koreensis DSMZ 15582 dctA
Synechococcus elongatus PCC 7942 dctA

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