GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Desulforamulus ruminis DSM 2154

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 DESRU_RS14810 DESRU_RS09750
asd aspartate semi-aldehyde dehydrogenase DESRU_RS09745
dapA 4-hydroxy-tetrahydrodipicolinate synthase DESRU_RS09755
dapB 4-hydroxy-tetrahydrodipicolinate reductase DESRU_RS09730
DAPtransferase L,L-diaminopimelate aminotransferase DESRU_RS11730 DESRU_RS09910
dapF diaminopimelate epimerase DESRU_RS11735
lysA diaminopimelate decarboxylase DESRU_RS15055 DESRU_RS14605
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase DESRU_RS00105 DESRU_RS01825
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase DESRU_RS13225 DESRU_RS00865
dapL N-acetyl-diaminopimelate deacetylase
dapX acetyl-diaminopimelate aminotransferase DESRU_RS18780 DESRU_RS11725
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase DESRU_RS06675 DESRU_RS01880
hicdh homo-isocitrate dehydrogenase DESRU_RS06690 DESRU_RS01895
lysJ [LysW]-2-aminoadipate semialdehyde transaminase DESRU_RS01825 DESRU_RS18845
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase DESRU_RS11725 DESRU_RS02800
lysT homoaconitase large subunit DESRU_RS01885 DESRU_RS06680
lysU homoaconitase small subunit DESRU_RS01890 DESRU_RS06685
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase DESRU_RS01810
lysZ [LysW]-2-aminoadipate 6-kinase DESRU_RS01820

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