GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Calditerrivibrio nitroreducens DSM 19672

Best path

asp-kinase, asd, dapA, dapB, DAPtransferase, 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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase CALNI_RS04345 CALNI_RS04335
asd aspartate semi-aldehyde dehydrogenase CALNI_RS04980
dapA 4-hydroxy-tetrahydrodipicolinate synthase CALNI_RS09140
dapB 4-hydroxy-tetrahydrodipicolinate reductase CALNI_RS09145
DAPtransferase L,L-diaminopimelate aminotransferase CALNI_RS00365
dapF diaminopimelate epimerase CALNI_RS09135
lysA diaminopimelate decarboxylase CALNI_RS02575
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase CALNI_RS01845 CALNI_RS03705
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase CALNI_RS09110 CALNI_RS03095
dapL N-acetyl-diaminopimelate deacetylase CALNI_RS05530
dapX acetyl-diaminopimelate aminotransferase
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase CALNI_RS03360 CALNI_RS02455
hicdh homo-isocitrate dehydrogenase CALNI_RS06250
lysJ [LysW]-2-aminoadipate semialdehyde transaminase CALNI_RS03705 CALNI_RS07435
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase CALNI_RS03705 CALNI_RS07435
lysT homoaconitase large subunit CALNI_RS10295
lysU homoaconitase small subunit CALNI_RS10300 CALNI_RS05335
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase CALNI_RS07965
lysZ [LysW]-2-aminoadipate 6-kinase CALNI_RS01290

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