GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Thermomonospora curvata DSM 43183

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 TCUR_RS23935
asd aspartate semi-aldehyde dehydrogenase TCUR_RS23940
dapA 4-hydroxy-tetrahydrodipicolinate synthase TCUR_RS16305
dapB 4-hydroxy-tetrahydrodipicolinate reductase TCUR_RS16355
dapD tetrahydrodipicolinate succinylase TCUR_RS05775
dapC N-succinyldiaminopimelate aminotransferase TCUR_RS04095 TCUR_RS05675
dapE succinyl-diaminopimelate desuccinylase TCUR_RS05780 TCUR_RS22365
dapF diaminopimelate epimerase TCUR_RS16175
lysA diaminopimelate decarboxylase TCUR_RS19375
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase TCUR_RS05775 TCUR_RS02885
dapL N-acetyl-diaminopimelate deacetylase TCUR_RS20615
DAPtransferase L,L-diaminopimelate aminotransferase TCUR_RS14575 TCUR_RS07730
dapX acetyl-diaminopimelate aminotransferase TCUR_RS21415
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase TCUR_RS17460
hicdh homo-isocitrate dehydrogenase TCUR_RS17470
lysJ [LysW]-2-aminoadipate semialdehyde transaminase TCUR_RS10655 TCUR_RS05605
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase TCUR_RS21415 TCUR_RS24380
lysT homoaconitase large subunit TCUR_RS17070
lysU homoaconitase small subunit TCUR_RS17065 TCUR_RS08645
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase TCUR_RS10640
lysZ [LysW]-2-aminoadipate 6-kinase TCUR_RS10650

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