GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Desulfotalea psychrophila LSv54

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate Class of gap
asp-kinase aspartate kinase DP_RS02240  
asd aspartate semi-aldehyde dehydrogenase DP_RS14040  
dapA 4-hydroxy-tetrahydrodipicolinate synthase DP_RS02150  
dapB 4-hydroxy-tetrahydrodipicolinate reductase DP_RS02145  
DAPtransferase? L,L-diaminopimelate aminotransferase spurious
dapF diaminopimelate epimerase DP_RS02155  
lysA diaminopimelate decarboxylase DP_RS14975  
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase DP_RS09895 DP_RS02180  
dapD tetrahydrodipicolinate succinylase  
dapE succinyl-diaminopimelate desuccinylase  
dapH tetrahydrodipicolinate acetyltransferase  
dapL N-acetyl-diaminopimelate deacetylase DP_RS02255  
dapX acetyl-diaminopimelate aminotransferase  
ddh meso-diaminopimelate D-dehydrogenase  
hcs homocitrate synthase DP_RS03295  
hicdh homo-isocitrate dehydrogenase DP_RS06485  
lysJ [LysW]-2-aminoadipate semialdehyde transaminase DP_RS02180 DP_RS04140  
lysK [LysW]-lysine hydrolase  
lysN 2-aminoadipate:2-oxoglutarate aminotransferase DP_RS08170 DP_RS02180  
lysT homoaconitase large subunit DP_RS10015  
lysU homoaconitase small subunit DP_RS10020  
lysW 2-aminoadipate/glutamate carrier protein  
lysX 2-aminoadipate-LysW ligase  
lysY [LysW]-2-aminoadipate 6-phosphate reductase DP_RS06715  
lysZ [LysW]-2-aminoadipate 6-kinase DP_RS02185  

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