GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Methyloferula stellata AR4T

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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase A3OQ_RS0119490
asd aspartate semi-aldehyde dehydrogenase A3OQ_RS0105660
dapA 4-hydroxy-tetrahydrodipicolinate synthase A3OQ_RS0117670
dapB 4-hydroxy-tetrahydrodipicolinate reductase A3OQ_RS0105370
dapD tetrahydrodipicolinate succinylase A3OQ_RS0100125
dapC N-succinyldiaminopimelate aminotransferase A3OQ_RS0106285 A3OQ_RS0105020
dapE succinyl-diaminopimelate desuccinylase A3OQ_RS0100115 A3OQ_RS0111130
dapF diaminopimelate epimerase A3OQ_RS0103175
lysA diaminopimelate decarboxylase A3OQ_RS0103070 A3OQ_RS0106185
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase A3OQ_RS0100125
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase
dapX acetyl-diaminopimelate aminotransferase A3OQ_RS0104145
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase A3OQ_RS0119280 A3OQ_RS0118025
hicdh homo-isocitrate dehydrogenase A3OQ_RS0105685
lysJ [LysW]-2-aminoadipate semialdehyde transaminase A3OQ_RS0105020 A3OQ_RS0105180
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase A3OQ_RS0104145 A3OQ_RS0105020
lysT homoaconitase large subunit
lysU homoaconitase small subunit A3OQ_RS0103450 A3OQ_RS0105720
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase A3OQ_RS0100135

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