GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Clostridium acetobutylicum ATCC 824

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 Known gap?
asp-kinase aspartate kinase CA_RS01565 CA_RS09395  
asd aspartate semi-aldehyde dehydrogenase CA_RS03110 CA_RS00135  
dapA 4-hydroxy-tetrahydrodipicolinate synthase CA_RS12210 CA_RS18525  
dapB 4-hydroxy-tetrahydrodipicolinate reductase CA_RS12215  
DAPtransferase L,L-diaminopimelate aminotransferase CA_RS08910 CA_RS12220  
dapF diaminopimelate epimerase CA_RS13425  
lysA diaminopimelate decarboxylase CA_RS03310  
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase CA_RS00095 CA_RS01235  
dapD tetrahydrodipicolinate succinylase  
dapE succinyl-diaminopimelate desuccinylase CA_RS14030  
dapH tetrahydrodipicolinate acetyltransferase CA_RS12225 CA_RS20250  
dapL? N-acetyl-diaminopimelate deacetylase CA_RS05395 CA_RS04905 known gap (80% id.)
dapX acetyl-diaminopimelate aminotransferase CA_RS02125 CA_RS12220  
ddh meso-diaminopimelate D-dehydrogenase  
hcs homocitrate synthase CA_RS01455 CA_RS01450  
hicdh homo-isocitrate dehydrogenase CA_RS05180 CA_RS16285  
lysJ [LysW]-2-aminoadipate semialdehyde transaminase CA_RS12260 CA_RS07495  
lysK [LysW]-lysine hydrolase  
lysN 2-aminoadipate:2-oxoglutarate aminotransferase CA_RS09440 CA_RS07495  
lysT homoaconitase large subunit CA_RS16295 CA_RS05175  
lysU homoaconitase small subunit CA_RS16290 CA_RS05175  
lysW 2-aminoadipate/glutamate carrier protein  
lysX 2-aminoadipate-LysW ligase  
lysY [LysW]-2-aminoadipate 6-phosphate reductase CA_RS12270  
lysZ [LysW]-2-aminoadipate 6-kinase CA_RS12265  

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