GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Azohydromonas australica DSM 1124

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 H537_RS0136235 H537_RS0111835
asd aspartate semi-aldehyde dehydrogenase H537_RS0126795
dapA 4-hydroxy-tetrahydrodipicolinate synthase H537_RS0122440 H537_RS0119980
dapB 4-hydroxy-tetrahydrodipicolinate reductase H537_RS0104665
dapD tetrahydrodipicolinate succinylase H537_RS0117020
dapC N-succinyldiaminopimelate aminotransferase H537_RS0117025 H537_RS0120225
dapE succinyl-diaminopimelate desuccinylase H537_RS0117015
dapF diaminopimelate epimerase H537_RS0122060
lysA diaminopimelate decarboxylase H537_RS0128300 H537_RS0126115
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase H537_RS0117020 H537_RS56675
dapL N-acetyl-diaminopimelate deacetylase H537_RS0128440 H537_RS0124680
DAPtransferase L,L-diaminopimelate aminotransferase H537_RS0117025
dapX acetyl-diaminopimelate aminotransferase H537_RS0108750 H537_RS0111980
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase H537_RS46840 H537_RS0119890
hicdh homo-isocitrate dehydrogenase H537_RS0103110 H537_RS0137465
lysJ [LysW]-2-aminoadipate semialdehyde transaminase H537_RS0120480 H537_RS0137245
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase H537_RS0120050 H537_RS0120045
lysT homoaconitase large subunit H537_RS0126780
lysU homoaconitase small subunit H537_RS0126785 H537_RS0137590
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase H537_RS0109645

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