GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Haloferax volcanii DS2

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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase C498_RS17705
asd aspartate semi-aldehyde dehydrogenase C498_RS07475
dapA 4-hydroxy-tetrahydrodipicolinate synthase C498_RS12810 C498_RS05640
dapB 4-hydroxy-tetrahydrodipicolinate reductase C498_RS12815
dapD tetrahydrodipicolinate succinylase C498_RS12820
dapC N-succinyldiaminopimelate aminotransferase C498_RS08325 C498_RS17875
dapE succinyl-diaminopimelate desuccinylase C498_RS00930 C498_RS01700
dapF diaminopimelate epimerase C498_RS12830
lysA diaminopimelate decarboxylase C498_RS12825
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase C498_RS09455 C498_RS12820
dapL N-acetyl-diaminopimelate deacetylase C498_RS11365
DAPtransferase L,L-diaminopimelate aminotransferase C498_RS13440 C498_RS03235
dapX acetyl-diaminopimelate aminotransferase C498_RS12000 C498_RS13440
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase C498_RS14985 C498_RS10800
hicdh homo-isocitrate dehydrogenase C498_RS07975 C498_RS10835
lysJ [LysW]-2-aminoadipate semialdehyde transaminase C498_RS17875 C498_RS01375
lysK [LysW]-lysine hydrolase C498_RS17870 C498_RS12835
lysN 2-aminoadipate:2-oxoglutarate aminotransferase C498_RS13440 C498_RS03235
lysT homoaconitase large subunit C498_RS00625 C498_RS04865
lysU homoaconitase small subunit C498_RS00620 C498_RS04865
lysW 2-aminoadipate/glutamate carrier protein C498_RS17895
lysX 2-aminoadipate-LysW ligase C498_RS17890
lysY [LysW]-2-aminoadipate 6-phosphate reductase C498_RS17885
lysZ [LysW]-2-aminoadipate 6-kinase C498_RS17880

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