GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Rhizobium johnstonii 3841

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 RL_RS22100
asd aspartate semi-aldehyde dehydrogenase RL_RS24260
dapA 4-hydroxy-tetrahydrodipicolinate synthase RL_RS35540 RL_RS07805
dapB 4-hydroxy-tetrahydrodipicolinate reductase RL_RS00950 RL_RS15510
dapD tetrahydrodipicolinate succinylase RL_RS02275
dapC N-succinyldiaminopimelate aminotransferase RL_RS20435 RL_RS02885
dapE succinyl-diaminopimelate desuccinylase RL_RS02270 RL_RS36080
dapF diaminopimelate epimerase RL_RS23415
lysA diaminopimelate decarboxylase RL_RS22305 RL_RS21430
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase RL_RS04265 RL_RS02275
dapL N-acetyl-diaminopimelate deacetylase RL_RS22510 RL_RS28520
DAPtransferase L,L-diaminopimelate aminotransferase RL_RS10875 RL_RS34960
dapX acetyl-diaminopimelate aminotransferase RL_RS17735 RL_RS34960
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase RL_RS07980
hicdh homo-isocitrate dehydrogenase RL_RS30530 RL_RS05175
lysJ [LysW]-2-aminoadipate semialdehyde transaminase RL_RS02885 RL_RS22620
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase RL_RS17735 RL_RS29560
lysT homoaconitase large subunit RL_RS23465
lysU homoaconitase small subunit RL_RS24210 RL_RS23365
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase RL_RS02315

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