GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Thiomicrospira microaerophila ASL8-2

Best path

asp-kinase, asd, dapA, dapB, dapD, dapC, dapE, 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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase NA59_RS06170
asd aspartate semi-aldehyde dehydrogenase NA59_RS02600
dapA 4-hydroxy-tetrahydrodipicolinate synthase NA59_RS00560
dapB 4-hydroxy-tetrahydrodipicolinate reductase NA59_RS08240
dapD tetrahydrodipicolinate succinylase NA59_RS07770
dapC N-succinyldiaminopimelate aminotransferase NA59_RS00265 NA59_RS08125
dapE succinyl-diaminopimelate desuccinylase NA59_RS07760
dapF diaminopimelate epimerase NA59_RS03270
lysA diaminopimelate decarboxylase NA59_RS07115
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase NA59_RS07770 NA59_RS06870
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase NA59_RS00225 NA59_RS07410
dapX acetyl-diaminopimelate aminotransferase NA59_RS07410
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase NA59_RS06895
hicdh homo-isocitrate dehydrogenase NA59_RS02615
lysJ [LysW]-2-aminoadipate semialdehyde transaminase NA59_RS08095 NA59_RS08125
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase NA59_RS07410 NA59_RS08125
lysT homoaconitase large subunit NA59_RS02625
lysU homoaconitase small subunit NA59_RS02620
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase NA59_RS10005
lysZ [LysW]-2-aminoadipate 6-kinase NA59_RS07050

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