GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Nocardiopsis lucentensis DSM 44048

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 D471_RS0113155 D471_RS0121390
asd aspartate semi-aldehyde dehydrogenase D471_RS0113160
dapA 4-hydroxy-tetrahydrodipicolinate synthase D471_RS0111460 D471_RS34485
dapB 4-hydroxy-tetrahydrodipicolinate reductase D471_RS0111485
dapD tetrahydrodipicolinate succinylase D471_RS0101485
dapC N-succinyldiaminopimelate aminotransferase D471_RS0114915 D471_RS0101495
dapE succinyl-diaminopimelate desuccinylase D471_RS0101480 D471_RS0128150
dapF diaminopimelate epimerase D471_RS0111100
lysA diaminopimelate decarboxylase D471_RS0120570 D471_RS34480
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase D471_RS0101485 D471_RS0127185
dapL N-acetyl-diaminopimelate deacetylase D471_RS0113305 D471_RS0101885
DAPtransferase L,L-diaminopimelate aminotransferase D471_RS0110175 D471_RS0101495
dapX acetyl-diaminopimelate aminotransferase D471_RS0110175
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase D471_RS0108165
hicdh homo-isocitrate dehydrogenase D471_RS0108155
lysJ [LysW]-2-aminoadipate semialdehyde transaminase D471_RS0118255 D471_RS0111685
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase D471_RS0110175 D471_RS0113530
lysT homoaconitase large subunit D471_RS0108245
lysU homoaconitase small subunit D471_RS0108250 D471_RS0108975
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase D471_RS0118275
lysZ [LysW]-2-aminoadipate 6-kinase

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