GapMind for catabolism of small carbon sources

 

L-lysine catabolism

Analysis of pathway lysine in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 lysP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
Azospirillum brasilense Sp245 argT, hisM, hisQ, hisP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
Bacteroides thetaiotaomicron VPI-5482 lysP, lat, amaB, lysN, hglS, ydiJ
Burkholderia phytofirmans PsJN argT, hisM, hisQ, hisP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
Caulobacter crescentus NA1000 lysP, lat, amaB, lysN, hglS, ydiJ
Cupriavidus basilensis 4G11 lysP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
Dechlorosoma suillum PS lysP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
Desulfovibrio vulgaris Hildenborough lysP, lat, amaB, lysN, hglS, ydiJ
Desulfovibrio vulgaris Miyazaki F lysP, lat, amaB, lysN, hglS, ydiJ
Dinoroseobacter shibae DFL-12 argT, hisM, hisQ, hisP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
Dyella japonica UNC79MFTsu3.2 lysP, lat, amaB, lysN, hglS, ydiJ
Echinicola vietnamensis KMM 6221, DSM 17526 lysP, lat, amaB, lysN, hglS, ydiJ
Escherichia coli BW25113 argT, hisM, hisQ, hisP, cadA, patA, patD, davT, davD, glaH, lhgD
Herbaspirillum seropedicae SmR1 lysP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
Klebsiella michiganensis M5al argT, hisM, hisQ, hisP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
Magnetospirillum magneticum AMB-1 lysP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
Marinobacter adhaerens HP15 argT, hisM, hisQ, hisP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
Paraburkholderia bryophila 376MFSha3.1 argT, hisM, hisQ, hisP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
Pedobacter sp. GW460-11-11-14-LB5 lysP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
Phaeobacter inhibens BS107 argT, hisM, hisQ, hisP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
Pseudomonas fluorescens FW300-N1B4 argT, hisM, hisQ, hisP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
Pseudomonas fluorescens FW300-N2C3 argT, hisM, hisQ, hisP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
Pseudomonas fluorescens FW300-N2E2 argT, hisM, hisQ, hisP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
Pseudomonas fluorescens FW300-N2E3 argT, hisM, hisQ, hisP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
Pseudomonas fluorescens GW456-L13 argT, hisM, hisQ, hisP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
Pseudomonas putida KT2440 argT, hisM, hisQ, hisP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
Pseudomonas simiae WCS417 argT, hisM, hisQ, hisP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
Pseudomonas stutzeri RCH2 argT, hisM, hisQ, hisP, cadA, patA, patD, davT, davD, gcdG, gcdH, ech, fadB, atoB
Shewanella amazonensis SB2B lysP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
Shewanella loihica PV-4 lysP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
Shewanella oneidensis MR-1 lysP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
Shewanella sp. ANA-3 lysP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
Sinorhizobium meliloti 1021 argT, hisM, hisQ, hisP, lysDH, amaB, lysN, hglS, ydiJ
Sphingomonas koreensis DSMZ 15582 lysP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
Synechococcus elongatus PCC 7942 lysP, lat, amaB, lysN, hglS, ydiJ

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 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