GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Prosthecochloris aestuarii DSM 271

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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase PAES_RS01305 PAES_RS10835
asd aspartate semi-aldehyde dehydrogenase PAES_RS09725
dapA 4-hydroxy-tetrahydrodipicolinate synthase PAES_RS02665
dapB 4-hydroxy-tetrahydrodipicolinate reductase PAES_RS09415
DAPtransferase L,L-diaminopimelate aminotransferase PAES_RS04825
dapF diaminopimelate epimerase PAES_RS01355
lysA diaminopimelate decarboxylase PAES_RS07495 PAES_RS10835
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase PAES_RS02955 PAES_RS07515
dapD tetrahydrodipicolinate succinylase PAES_RS00100
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase PAES_RS00100 PAES_RS07740
dapL N-acetyl-diaminopimelate deacetylase PAES_RS05250
dapX acetyl-diaminopimelate aminotransferase PAES_RS06865 PAES_RS07515
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase PAES_RS08115 PAES_RS03705
hicdh homo-isocitrate dehydrogenase PAES_RS03710
lysJ [LysW]-2-aminoadipate semialdehyde transaminase PAES_RS00970 PAES_RS10875
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase PAES_RS06865 PAES_RS02955
lysT homoaconitase large subunit PAES_RS03700
lysU homoaconitase small subunit PAES_RS03695
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase PAES_RS05410
lysZ [LysW]-2-aminoadipate 6-kinase PAES_RS05400

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.



Related tools

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