GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Methylosarcina fibrata AML-C10

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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase A3OW_RS0110035 A3OW_RS0106475
asd aspartate semi-aldehyde dehydrogenase A3OW_RS0115365
dapA 4-hydroxy-tetrahydrodipicolinate synthase A3OW_RS0107135 A3OW_RS0107170
dapB 4-hydroxy-tetrahydrodipicolinate reductase A3OW_RS0122865 A3OW_RS0111785
dapD tetrahydrodipicolinate succinylase A3OW_RS0117795
dapC N-succinyldiaminopimelate aminotransferase A3OW_RS0117800 A3OW_RS0108115
dapE succinyl-diaminopimelate desuccinylase A3OW_RS0117780
dapF diaminopimelate epimerase A3OW_RS0117480
lysA diaminopimelate decarboxylase A3OW_RS0117165
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase A3OW_RS0117795 A3OW_RS0112825
dapL N-acetyl-diaminopimelate deacetylase A3OW_RS0112425
DAPtransferase L,L-diaminopimelate aminotransferase A3OW_RS0106480 A3OW_RS0120110
dapX acetyl-diaminopimelate aminotransferase A3OW_RS0107000 A3OW_RS0120110
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase A3OW_RS0122190 A3OW_RS0118785
hicdh homo-isocitrate dehydrogenase A3OW_RS0112640 A3OW_RS0118345
lysJ [LysW]-2-aminoadipate semialdehyde transaminase A3OW_RS0104890 A3OW_RS0107650
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase A3OW_RS0107000 A3OW_RS0104890
lysT homoaconitase large subunit A3OW_RS0115375 A3OW_RS0107395
lysU homoaconitase small subunit A3OW_RS0107395 A3OW_RS0115370
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase A3OW_RS0112385
lysZ [LysW]-2-aminoadipate 6-kinase A3OW_RS0105955

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