GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Thiomicrorhabdus arctica DSM 13458

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 F612_RS0105640 F612_RS0100940
asd aspartate semi-aldehyde dehydrogenase F612_RS0101145
dapA 4-hydroxy-tetrahydrodipicolinate synthase F612_RS0103755
dapB 4-hydroxy-tetrahydrodipicolinate reductase F612_RS0101445
DAPtransferase L,L-diaminopimelate aminotransferase F612_RS0102765 F612_RS0106445
dapF diaminopimelate epimerase F612_RS0106660
lysA diaminopimelate decarboxylase F612_RS0109645
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase F612_RS0103100 F612_RS0110440
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase F612_RS0102555
dapH tetrahydrodipicolinate acetyltransferase
dapL N-acetyl-diaminopimelate deacetylase F612_RS0104090
dapX acetyl-diaminopimelate aminotransferase F612_RS0106445 F612_RS0111525
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase F612_RS0100685
hicdh homo-isocitrate dehydrogenase F612_RS0101130
lysJ [LysW]-2-aminoadipate semialdehyde transaminase F612_RS0104085 F612_RS0110440
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase F612_RS0106445 F612_RS0110440
lysT homoaconitase large subunit F612_RS0101120
lysU homoaconitase small subunit F612_RS0101125
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase F612_RS0107000
lysZ [LysW]-2-aminoadipate 6-kinase F612_RS0111535

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