GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Haloechinothrix alba DSM 45207

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 CHB84_RS13525
asd aspartate semi-aldehyde dehydrogenase CHB84_RS13520
dapA 4-hydroxy-tetrahydrodipicolinate synthase CHB84_RS06975 CHB84_RS11500
dapB 4-hydroxy-tetrahydrodipicolinate reductase CHB84_RS06930
dapD tetrahydrodipicolinate succinylase CHB84_RS04860
dapC N-succinyldiaminopimelate aminotransferase CHB84_RS11310 CHB84_RS04855
dapE succinyl-diaminopimelate desuccinylase CHB84_RS04870 CHB84_RS20220
dapF diaminopimelate epimerase CHB84_RS10265
lysA diaminopimelate decarboxylase CHB84_RS17165
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase CHB84_RS05925 CHB84_RS01395
dapL N-acetyl-diaminopimelate deacetylase CHB84_RS04585 CHB84_RS14885
DAPtransferase L,L-diaminopimelate aminotransferase CHB84_RS05330 CHB84_RS14635
dapX acetyl-diaminopimelate aminotransferase CHB84_RS15310 CHB84_RS14635
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase CHB84_RS03235
hicdh homo-isocitrate dehydrogenase CHB84_RS03230
lysJ [LysW]-2-aminoadipate semialdehyde transaminase CHB84_RS19235 CHB84_RS09600
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase CHB84_RS15310 CHB84_RS16910
lysT homoaconitase large subunit CHB84_RS07295 CHB84_RS03300
lysU homoaconitase small subunit CHB84_RS07295 CHB84_RS03305
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase CHB84_RS19250
lysZ [LysW]-2-aminoadipate 6-kinase CHB84_RS19240

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