GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Thiomicrorhabdus chilensis DSM 12352

Best path

asp-kinase, asd, dapA, dapB, dapD, dapC, dapE, 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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase B076_RS0104080 B076_RS0103715
asd aspartate semi-aldehyde dehydrogenase B076_RS0108355
dapA 4-hydroxy-tetrahydrodipicolinate synthase B076_RS0105040
dapB 4-hydroxy-tetrahydrodipicolinate reductase B076_RS0107640
dapD tetrahydrodipicolinate succinylase B076_RS0106165
dapC N-succinyldiaminopimelate aminotransferase B076_RS0106705 B076_RS0109690
dapE succinyl-diaminopimelate desuccinylase B076_RS0106155
dapF diaminopimelate epimerase B076_RS0102820
lysA diaminopimelate decarboxylase B076_RS0102145
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase
dapL N-acetyl-diaminopimelate deacetylase B076_RS0101990
DAPtransferase L,L-diaminopimelate aminotransferase B076_RS0106355 B076_RS0103180
dapX acetyl-diaminopimelate aminotransferase B076_RS0103180 B076_RS0101765
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase B076_RS0108940 B076_RS0103090
hicdh homo-isocitrate dehydrogenase B076_RS0108370
lysJ [LysW]-2-aminoadipate semialdehyde transaminase B076_RS0109690 B076_RS0101985
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase B076_RS0103180 B076_RS0103705
lysT homoaconitase large subunit B076_RS0108380
lysU homoaconitase small subunit B076_RS0108375
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase B076_RS0110310
lysZ [LysW]-2-aminoadipate 6-kinase B076_RS0101775

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