GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Desulfobacca acetoxidans DSM 11109

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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase DESAC_RS11615 DESAC_RS10105
asd aspartate semi-aldehyde dehydrogenase DESAC_RS14610
dapA 4-hydroxy-tetrahydrodipicolinate synthase DESAC_RS12395
dapB 4-hydroxy-tetrahydrodipicolinate reductase DESAC_RS12400
DAPtransferase L,L-diaminopimelate aminotransferase DESAC_RS12415 DESAC_RS10110
dapF diaminopimelate epimerase DESAC_RS12390
lysA diaminopimelate decarboxylase DESAC_RS12385
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase DESAC_RS06350 DESAC_RS12335
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase DESAC_RS01185 DESAC_RS12255
dapL N-acetyl-diaminopimelate deacetylase
dapX acetyl-diaminopimelate aminotransferase DESAC_RS12075 DESAC_RS10860
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase DESAC_RS12570 DESAC_RS11610
hicdh homo-isocitrate dehydrogenase DESAC_RS06465 DESAC_RS14605
lysJ [LysW]-2-aminoadipate semialdehyde transaminase DESAC_RS12335 DESAC_RS12910
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase DESAC_RS12075 DESAC_RS03760
lysT homoaconitase large subunit DESAC_RS12565 DESAC_RS07630
lysU homoaconitase small subunit DESAC_RS14600 DESAC_RS07630
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase DESAC_RS00695
lysZ [LysW]-2-aminoadipate 6-kinase DESAC_RS12330

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