GapMind for catabolism of small carbon sources


pyruvate catabolism

Analysis of pathway pyruvate in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 dctM, dctP, dctQ
Azospirillum brasilense Sp245 dctM, dctP, dctQ
Bacteroides thetaiotaomicron VPI-5482 SLC5A8
Burkholderia phytofirmans PsJN mctC
Caulobacter crescentus NA1000 SLC5A8
Cupriavidus basilensis 4G11 dctM, dctP, dctQ
Dechlorosoma suillum PS dctM, dctP, dctQ
Desulfovibrio vulgaris Hildenborough yjcH, actP
Desulfovibrio vulgaris Miyazaki F yjcH, actP
Dinoroseobacter shibae DFL-12 yjcH, actP
Dyella japonica UNC79MFTsu3.2 cstA, ybdD
Echinicola vietnamensis KMM 6221, DSM 17526 yjcH, actP
Escherichia coli BW25113 yjcH, actP
Herbaspirillum seropedicae SmR1 cstA, ybdD
Klebsiella michiganensis M5al yjcH, actP
Magnetospirillum magneticum AMB-1 dctM, dctP, dctQ
Marinobacter adhaerens HP15 yjcH, actP
Paraburkholderia bryophila 376MFSha3.1 mctP
Pedobacter sp. GW460-11-11-14-LB5 SLC5A8
Phaeobacter inhibens BS107 SLC5A8
Pseudomonas fluorescens FW300-N1B4 yjcH, actP
Pseudomonas fluorescens FW300-N2C3 yjcH, actP
Pseudomonas fluorescens FW300-N2E2 yjcH, actP
Pseudomonas fluorescens FW300-N2E3 yjcH, actP
Pseudomonas fluorescens GW456-L13 yjcH, actP
Pseudomonas putida KT2440 yjcH, actP
Pseudomonas simiae WCS417 yjcH, actP
Pseudomonas stutzeri RCH2 yjcH, actP
Shewanella amazonensis SB2B yjcH, actP
Shewanella loihica PV-4 yjcH, actP
Shewanella oneidensis MR-1 yjcH, actP
Shewanella sp. ANA-3 yjcH, actP
Sinorhizobium meliloti 1021 dctM, dctP, dctQ
Sphingomonas koreensis DSMZ 15582 SLC5A8
Synechococcus elongatus PCC 7942 SLC5A8

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 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