GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Methanosarcina acetivorans C2A

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 Known gap?
asp-kinase aspartate kinase MA_RS00690  
asd aspartate semi-aldehyde dehydrogenase MA_RS02255  
dapA 4-hydroxy-tetrahydrodipicolinate synthase MA_RS23345  
dapB 4-hydroxy-tetrahydrodipicolinate reductase MA_RS23350  
DAPtransferase L,L-diaminopimelate aminotransferase MA_RS08890 MA_RS04795  
dapF? diaminopimelate epimerase known gap
lysA diaminopimelate decarboxylase MA_RS03800 MA_RS00690  
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase MA_RS11965 MA_RS09455  
dapD tetrahydrodipicolinate succinylase  
dapE succinyl-diaminopimelate desuccinylase  
dapH tetrahydrodipicolinate acetyltransferase MA_RS11280 MA_RS02155  
dapL N-acetyl-diaminopimelate deacetylase MA_RS06200  
dapX acetyl-diaminopimelate aminotransferase MA_RS04795 MA_RS07185  
ddh meso-diaminopimelate D-dehydrogenase  
hcs homocitrate synthase MA_RS17445 MA_RS24085  
hicdh homo-isocitrate dehydrogenase MA_RS19530 MA_RS22270  
lysJ [LysW]-2-aminoadipate semialdehyde transaminase MA_RS00620 MA_RS15010  
lysK [LysW]-lysine hydrolase  
lysN 2-aminoadipate:2-oxoglutarate aminotransferase MA_RS09470 MA_RS07185  
lysT homoaconitase large subunit MA_RS16135 MA_RS07220  
lysU homoaconitase small subunit MA_RS19545 MA_RS06360  
lysW 2-aminoadipate/glutamate carrier protein  
lysX 2-aminoadipate-LysW ligase MA_RS17050  
lysY [LysW]-2-aminoadipate 6-phosphate reductase MA_RS18620  
lysZ [LysW]-2-aminoadipate 6-kinase MA_RS23550  

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