GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Dechlorosoma suillum PS

Best path

asp-kinase, asd, dapA, dapB, dapD, dapC, dapE, dapF, lysA

Also see fitness data for the top candidates


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
asp-kinase aspartate kinase Dsui_2134 Dsui_2907
asd aspartate semi-aldehyde dehydrogenase Dsui_3197
dapA 4-hydroxy-tetrahydrodipicolinate synthase Dsui_1977
dapB 4-hydroxy-tetrahydrodipicolinate reductase Dsui_3066
dapD tetrahydrodipicolinate succinylase Dsui_2709
dapC N-succinyldiaminopimelate aminotransferase Dsui_2708 Dsui_1939
dapE succinyl-diaminopimelate desuccinylase Dsui_2711
dapF diaminopimelate epimerase Dsui_0649
lysA diaminopimelate decarboxylase Dsui_1182
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase Dsui_2709 Dsui_2368
dapL N-acetyl-diaminopimelate deacetylase Dsui_0989
DAPtransferase L,L-diaminopimelate aminotransferase Dsui_2909 Dsui_0132
dapX acetyl-diaminopimelate aminotransferase Dsui_0132
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase Dsui_0578 Dsui_3519
hicdh homo-isocitrate dehydrogenase Dsui_3296 Dsui_3198
lysJ [LysW]-2-aminoadipate semialdehyde transaminase Dsui_0023 Dsui_3250
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase Dsui_0420 Dsui_0023
lysT homoaconitase large subunit Dsui_3201
lysU homoaconitase small subunit Dsui_3199 Dsui_2347
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase Dsui_1309

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