GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Clostridium kluyveri DSM 555

Best path

asp-kinase, asd, dapA, dapB, dapH, dapX, dapL?, 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 CKL_RS02980 CKL_RS07090  
asd aspartate semi-aldehyde dehydrogenase CKL_RS15615  
dapA 4-hydroxy-tetrahydrodipicolinate synthase CKL_RS15610  
dapB 4-hydroxy-tetrahydrodipicolinate reductase CKL_RS15605 CKL_RS13705  
dapH tetrahydrodipicolinate acetyltransferase CKL_RS15635 CKL_RS14550  
dapX acetyl-diaminopimelate aminotransferase CKL_RS15600 CKL_RS07145  
dapL? N-acetyl-diaminopimelate deacetylase CKL_RS07285 CKL_RS03195 known gap
dapF diaminopimelate epimerase CKL_RS05920  
lysA diaminopimelate decarboxylase CKL_RS02985  
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase CKL_RS18590 CKL_RS18530  
dapD tetrahydrodipicolinate succinylase CKL_RS15635  
dapE succinyl-diaminopimelate desuccinylase  
DAPtransferase L,L-diaminopimelate aminotransferase CKL_RS07145  
ddh meso-diaminopimelate D-dehydrogenase  
hcs homocitrate synthase CKL_RS10580 CKL_RS08630  
hicdh homo-isocitrate dehydrogenase CKL_RS10565  
lysJ [LysW]-2-aminoadipate semialdehyde transaminase CKL_RS07655 CKL_RS10130  
lysK [LysW]-lysine hydrolase  
lysN 2-aminoadipate:2-oxoglutarate aminotransferase CKL_RS07145 CKL_RS02170  
lysT homoaconitase large subunit CKL_RS10575 CKL_RS04790  
lysU homoaconitase small subunit CKL_RS10570 CKL_RS04790  
lysW 2-aminoadipate/glutamate carrier protein  
lysX 2-aminoadipate-LysW ligase  
lysY [LysW]-2-aminoadipate 6-phosphate reductase CKL_RS07640  
lysZ [LysW]-2-aminoadipate 6-kinase CKL_RS07650  

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