GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Nostoc punctiforme ATCC 29133; PCC 73102

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 NPUN_RS23210
asd aspartate semi-aldehyde dehydrogenase NPUN_RS04305
dapA 4-hydroxy-tetrahydrodipicolinate synthase NPUN_RS04300
dapB 4-hydroxy-tetrahydrodipicolinate reductase NPUN_RS24855
DAPtransferase L,L-diaminopimelate aminotransferase NPUN_RS18280 NPUN_RS20005
dapF diaminopimelate epimerase NPUN_RS26440
lysA diaminopimelate decarboxylase NPUN_RS30310 NPUN_RS09380
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase NPUN_RS20980 NPUN_RS25070
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase NPUN_RS15480 NPUN_RS25885
dapL N-acetyl-diaminopimelate deacetylase NPUN_RS04930 NPUN_RS11905
dapX acetyl-diaminopimelate aminotransferase NPUN_RS00985 NPUN_RS00030
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase NPUN_RS02205 NPUN_RS04705
hicdh homo-isocitrate dehydrogenase NPUN_RS14260 NPUN_RS12335
lysJ [LysW]-2-aminoadipate semialdehyde transaminase NPUN_RS25070 NPUN_RS09825
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase NPUN_RS00985 NPUN_RS09825
lysT homoaconitase large subunit NPUN_RS12340
lysU homoaconitase small subunit NPUN_RS12340 NPUN_RS00865
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase NPUN_RS17735
lysZ [LysW]-2-aminoadipate 6-kinase NPUN_RS31950

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.



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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 (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