GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Methanospirillum lacunae Ki8-1

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 DK846_RS15330
asd aspartate semi-aldehyde dehydrogenase DK846_RS02470
dapA 4-hydroxy-tetrahydrodipicolinate synthase DK846_RS02455
dapB 4-hydroxy-tetrahydrodipicolinate reductase DK846_RS02460
DAPtransferase L,L-diaminopimelate aminotransferase DK846_RS09245 DK846_RS09780
dapF diaminopimelate epimerase DK846_RS14525
lysA diaminopimelate decarboxylase DK846_RS09250
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase DK846_RS09700 DK846_RS14130
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase DK846_RS02415
dapH tetrahydrodipicolinate acetyltransferase DK846_RS07905
dapL N-acetyl-diaminopimelate deacetylase
dapX acetyl-diaminopimelate aminotransferase DK846_RS09780 DK846_RS02660
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase DK846_RS11255 DK846_RS15810
hicdh homo-isocitrate dehydrogenase DK846_RS11275 DK846_RS15795
lysJ [LysW]-2-aminoadipate semialdehyde transaminase DK846_RS14130 DK846_RS13185
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase DK846_RS04615 DK846_RS11610
lysT homoaconitase large subunit DK846_RS11260 DK846_RS15805
lysU homoaconitase small subunit DK846_RS15800 DK846_RS11265
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase DK846_RS14040
lysZ [LysW]-2-aminoadipate 6-kinase DK846_RS14055

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