GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Maridesulfovibrio zosterae DSM 11974

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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase H589_RS0114245 H589_RS0113380
asd aspartate semi-aldehyde dehydrogenase H589_RS0110325
dapA 4-hydroxy-tetrahydrodipicolinate synthase H589_RS0112900
dapB 4-hydroxy-tetrahydrodipicolinate reductase H589_RS0115235
DAPtransferase L,L-diaminopimelate aminotransferase H589_RS0114540 H589_RS0113385
dapF diaminopimelate epimerase H589_RS0103290
lysA diaminopimelate decarboxylase H589_RS0114580
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase H589_RS0113085 H589_RS0118185
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase H589_RS0103730 H589_RS0111635
dapL N-acetyl-diaminopimelate deacetylase H589_RS19830
dapX acetyl-diaminopimelate aminotransferase H589_RS0107920 H589_RS0102885
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase H589_RS0111930 H589_RS0116575
hicdh homo-isocitrate dehydrogenase H589_RS0107940 H589_RS0111950
lysJ [LysW]-2-aminoadipate semialdehyde transaminase H589_RS0113085 H589_RS0118050
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase H589_RS0118185 H589_RS0105035
lysT homoaconitase large subunit H589_RS0111935 H589_RS0101690
lysU homoaconitase small subunit H589_RS0111940 H589_RS0101690
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase H589_RS0108510
lysZ [LysW]-2-aminoadipate 6-kinase H589_RS0106305

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