GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Hydrogenovibrio marinus DSM 11271

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 P166_RS0111875 P166_RS0108215
asd aspartate semi-aldehyde dehydrogenase P166_RS0105900
dapA 4-hydroxy-tetrahydrodipicolinate synthase P166_RS0101660
dapB 4-hydroxy-tetrahydrodipicolinate reductase P166_RS0106495
dapD tetrahydrodipicolinate succinylase P166_RS0104355
dapC N-succinyldiaminopimelate aminotransferase P166_RS0103880 P166_RS0100985
dapE succinyl-diaminopimelate desuccinylase P166_RS0104365
dapF diaminopimelate epimerase P166_RS0110925
lysA diaminopimelate decarboxylase P166_RS0106980
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase P166_RS0105490
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase P166_RS0104170 P166_RS0100205
dapX acetyl-diaminopimelate aminotransferase P166_RS0100205 P166_RS0110670
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase P166_RS0101510
hicdh homo-isocitrate dehydrogenase P166_RS0105915
lysJ [LysW]-2-aminoadipate semialdehyde transaminase P166_RS0101110 P166_RS0108225
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase P166_RS0100205 P166_RS0108225
lysT homoaconitase large subunit P166_RS0105925 P166_RS0103590
lysU homoaconitase small subunit P166_RS0105920
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase P166_RS0107170
lysZ [LysW]-2-aminoadipate 6-kinase P166_RS0110685

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