GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis

Analysis of pathway lys in 35 genomes

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

Confidence: high confidence medium confidence low confidence
? – known gap: despite the lack of a good candidate for this step, this organism (or a related organism) performs the pathway

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

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 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, or see changes to Amino acid biosynthesis since the publication.

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