GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Caminibacter mediatlanticus TB-2

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 CMTB2_RS04000
asd aspartate semi-aldehyde dehydrogenase CMTB2_RS00260
dapA 4-hydroxy-tetrahydrodipicolinate synthase CMTB2_RS04585
dapB 4-hydroxy-tetrahydrodipicolinate reductase CMTB2_RS02335
dapD tetrahydrodipicolinate succinylase CMTB2_RS05565
dapC N-succinyldiaminopimelate aminotransferase CMTB2_RS00510 CMTB2_RS01140
dapE succinyl-diaminopimelate desuccinylase CMTB2_RS07950
dapF diaminopimelate epimerase CMTB2_RS05090
lysA diaminopimelate decarboxylase CMTB2_RS03820
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase CMTB2_RS05205
dapL N-acetyl-diaminopimelate deacetylase CMTB2_RS07960
DAPtransferase L,L-diaminopimelate aminotransferase CMTB2_RS07105 CMTB2_RS00510
dapX acetyl-diaminopimelate aminotransferase CMTB2_RS00685 CMTB2_RS04230
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase CMTB2_RS06500
hicdh homo-isocitrate dehydrogenase CMTB2_RS02910
lysJ [LysW]-2-aminoadipate semialdehyde transaminase CMTB2_RS01140 CMTB2_RS01220
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase CMTB2_RS00685 CMTB2_RS01220
lysT homoaconitase large subunit CMTB2_RS06170
lysU homoaconitase small subunit CMTB2_RS02915
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase CMTB2_RS03710
lysZ [LysW]-2-aminoadipate 6-kinase

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