GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Phaeacidiphilus oryzae TH49

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 BS73_RS20470
asd aspartate semi-aldehyde dehydrogenase BS73_RS02665 BS73_RS20475
dapA 4-hydroxy-tetrahydrodipicolinate synthase BS73_RS13970 BS73_RS01230
dapB 4-hydroxy-tetrahydrodipicolinate reductase BS73_RS13985
dapD tetrahydrodipicolinate succinylase BS73_RS12745
dapC N-succinyldiaminopimelate aminotransferase BS73_RS17765 BS73_RS16265
dapE succinyl-diaminopimelate desuccinylase BS73_RS16250 BS73_RS31125
dapF diaminopimelate epimerase BS73_RS13355
lysA diaminopimelate decarboxylase BS73_RS15305 BS73_RS13725
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase BS73_RS30955 BS73_RS13905
dapL N-acetyl-diaminopimelate deacetylase BS73_RS23510 BS73_RS20970
DAPtransferase L,L-diaminopimelate aminotransferase BS73_RS24325 BS73_RS16820
dapX acetyl-diaminopimelate aminotransferase BS73_RS22570 BS73_RS24325
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase BS73_RS14685
hicdh homo-isocitrate dehydrogenase BS73_RS14695
lysJ [LysW]-2-aminoadipate semialdehyde transaminase BS73_RS08925 BS73_RS23310
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase BS73_RS22570 BS73_RS28635
lysT homoaconitase large subunit BS73_RS06160 BS73_RS14595
lysU homoaconitase small subunit BS73_RS06160 BS73_RS14590
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase BS73_RS08940
lysZ [LysW]-2-aminoadipate 6-kinase BS73_RS08930

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