GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Mesorhizobium ciceri WSM1271

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 MESCI_RS08035
asd aspartate semi-aldehyde dehydrogenase MESCI_RS04660
dapA 4-hydroxy-tetrahydrodipicolinate synthase MESCI_RS24210 MESCI_RS06130
dapB 4-hydroxy-tetrahydrodipicolinate reductase MESCI_RS03750 MESCI_RS23520
dapD tetrahydrodipicolinate succinylase MESCI_RS03045
dapC N-succinyldiaminopimelate aminotransferase MESCI_RS06500 MESCI_RS29885
dapE succinyl-diaminopimelate desuccinylase MESCI_RS03020 MESCI_RS17190
dapF diaminopimelate epimerase MESCI_RS04890
lysA diaminopimelate decarboxylase MESCI_RS07765 MESCI_RS09615
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase MESCI_RS03045 MESCI_RS10585
dapL N-acetyl-diaminopimelate deacetylase MESCI_RS07470 MESCI_RS22055
DAPtransferase L,L-diaminopimelate aminotransferase MESCI_RS21155 MESCI_RS09570
dapX acetyl-diaminopimelate aminotransferase MESCI_RS11300 MESCI_RS30990
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase MESCI_RS29140 MESCI_RS24010
hicdh homo-isocitrate dehydrogenase MESCI_RS27015 MESCI_RS04640
lysJ [LysW]-2-aminoadipate semialdehyde transaminase MESCI_RS29885 MESCI_RS00215
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase MESCI_RS30990 MESCI_RS11300
lysT homoaconitase large subunit MESCI_RS05025
lysU homoaconitase small subunit MESCI_RS04620 MESCI_RS04830
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase MESCI_RS28865 MESCI_RS28800
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase MESCI_RS03085

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