GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Methanococcus aeolicus Nankai-3

Best path

asp-kinase, asd, dapA, dapB, DAPtransferase, dapF, lysA


Overview: Lysine biosynthesis in GapMind is based on MetaCyc pathways L-lysine biosynthesis I via diaminopimelate (DAP) and succinylated intermediates (link), II with DAP and acetylated intermediates (link), III with DAP and no blocking group (link), V via 2-aminoadipate and LysW carrier protein (link), and VI with DAP aminotransferase (link). Most of these pathways involve tetrahydrodipicolinate and meso-diaminopimelate, with variations in how the amino group is introduced. Pathway V instead involves L-2-aminoadipate and LysW-attached intermediates. Lysine biosynthesis IV (link), via 2-aminoadipate and saccharopine, is only reported to occur in eukaryotes and is not described here.

25 steps (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase MAEO_RS03365
asd aspartate semi-aldehyde dehydrogenase MAEO_RS07025
dapA 4-hydroxy-tetrahydrodipicolinate synthase MAEO_RS04565
dapB 4-hydroxy-tetrahydrodipicolinate reductase MAEO_RS03335
DAPtransferase L,L-diaminopimelate aminotransferase MAEO_RS07650 MAEO_RS06050
dapF diaminopimelate epimerase MAEO_RS01020
lysA diaminopimelate decarboxylase MAEO_RS01035 MAEO_RS03365
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase MAEO_RS06795 MAEO_RS03185
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase MAEO_RS03045 MAEO_RS02125
dapL N-acetyl-diaminopimelate deacetylase
dapX acetyl-diaminopimelate aminotransferase MAEO_RS06050
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase MAEO_RS04995 MAEO_RS04275
hicdh homo-isocitrate dehydrogenase MAEO_RS07600 MAEO_RS07265
lysJ [LysW]-2-aminoadipate semialdehyde transaminase MAEO_RS03185 MAEO_RS06130
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase MAEO_RS06050 MAEO_RS03185
lysT homoaconitase large subunit MAEO_RS01550 MAEO_RS01445
lysU homoaconitase small subunit MAEO_RS03245 MAEO_RS01725
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase MAEO_RS02800
lysY [LysW]-2-aminoadipate 6-phosphate reductase MAEO_RS06695
lysZ [LysW]-2-aminoadipate 6-kinase MAEO_RS00640

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 Apr 09 2024. The underlying query database was built on Apr 09 2024.



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:

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