GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Hippea alviniae EP5-r

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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase G415_RS0108180
asd aspartate semi-aldehyde dehydrogenase G415_RS0105260
dapA 4-hydroxy-tetrahydrodipicolinate synthase G415_RS0102575
dapB 4-hydroxy-tetrahydrodipicolinate reductase G415_RS0102570
DAPtransferase L,L-diaminopimelate aminotransferase G415_RS0101685 G415_RS0104595
dapF diaminopimelate epimerase G415_RS0102580
lysA diaminopimelate decarboxylase G415_RS0102585
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase G415_RS0106790 G415_RS0108335
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase G415_RS10305 G415_RS0105725
dapL N-acetyl-diaminopimelate deacetylase
dapX acetyl-diaminopimelate aminotransferase G415_RS0104595
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase G415_RS0101090
hicdh homo-isocitrate dehydrogenase G415_RS0104080
lysJ [LysW]-2-aminoadipate semialdehyde transaminase G415_RS0106790 G415_RS0101830
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase G415_RS0104595 G415_RS0106790
lysT homoaconitase large subunit G415_RS0104090 G415_RS0106920
lysU homoaconitase small subunit G415_RS0104085 G415_RS0106920
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase G415_RS0107150
lysZ [LysW]-2-aminoadipate 6-kinase G415_RS0100505

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