GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Rhodopseudomonas palustris CGA009

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 TX73_RS03125
asd aspartate semi-aldehyde dehydrogenase TX73_RS01185
dapA 4-hydroxy-tetrahydrodipicolinate synthase TX73_RS13720 TX73_RS15305
dapB 4-hydroxy-tetrahydrodipicolinate reductase TX73_RS01755
dapD tetrahydrodipicolinate succinylase TX73_RS03235
dapC N-succinyldiaminopimelate aminotransferase TX73_RS21975 TX73_RS24410
dapE succinyl-diaminopimelate desuccinylase TX73_RS03225 TX73_RS15470
dapF diaminopimelate epimerase TX73_RS01295
lysA diaminopimelate decarboxylase TX73_RS24240 TX73_RS04475
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase TX73_RS22330 TX73_RS03235
dapL N-acetyl-diaminopimelate deacetylase TX73_RS19035 TX73_RS13505
DAPtransferase L,L-diaminopimelate aminotransferase TX73_RS12755 TX73_RS22075
dapX acetyl-diaminopimelate aminotransferase TX73_RS22075 TX73_RS12470
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase TX73_RS23540 TX73_RS10425
hicdh homo-isocitrate dehydrogenase TX73_RS08890 TX73_RS01170
lysJ [LysW]-2-aminoadipate semialdehyde transaminase TX73_RS24410 TX73_RS19050
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase TX73_RS22075 TX73_RS11845
lysT homoaconitase large subunit TX73_RS01240
lysU homoaconitase small subunit TX73_RS01210 TX73_RS01035
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase TX73_RS03250

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