GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Thiohalospira halophila HL 3

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 BM272_RS05535
asd aspartate semi-aldehyde dehydrogenase BM272_RS03340 BM272_RS03335
dapA 4-hydroxy-tetrahydrodipicolinate synthase BM272_RS12770
dapB 4-hydroxy-tetrahydrodipicolinate reductase BM272_RS12225
dapD tetrahydrodipicolinate succinylase BM272_RS03545
dapC N-succinyldiaminopimelate aminotransferase BM272_RS03540 BM272_RS03625
dapE succinyl-diaminopimelate desuccinylase BM272_RS03550
dapF diaminopimelate epimerase BM272_RS11100
lysA diaminopimelate decarboxylase BM272_RS09330
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase BM272_RS03545
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase BM272_RS01690 BM272_RS03540
dapX acetyl-diaminopimelate aminotransferase BM272_RS03670
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase BM272_RS05405
hicdh homo-isocitrate dehydrogenase BM272_RS02585 BM272_RS03345
lysJ [LysW]-2-aminoadipate semialdehyde transaminase BM272_RS05075 BM272_RS11010
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase BM272_RS03670 BM272_RS05075
lysT homoaconitase large subunit BM272_RS03355
lysU homoaconitase small subunit BM272_RS03350 BM272_RS02610
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase BM272_RS10940
lysZ [LysW]-2-aminoadipate 6-kinase BM272_RS08520

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