GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Haloglycomyces albus DSM 45210

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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase HALAL_RS0108145
asd aspartate semi-aldehyde dehydrogenase HALAL_RS0108150
dapA 4-hydroxy-tetrahydrodipicolinate synthase HALAL_RS0111045
dapB 4-hydroxy-tetrahydrodipicolinate reductase HALAL_RS0111005
dapD tetrahydrodipicolinate succinylase HALAL_RS0100595
dapC N-succinyldiaminopimelate aminotransferase HALAL_RS0100715 HALAL_RS0106475
dapE succinyl-diaminopimelate desuccinylase HALAL_RS0100600 HALAL_RS0114865
dapF diaminopimelate epimerase HALAL_RS0111255
lysA diaminopimelate decarboxylase HALAL_RS0109850
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase HALAL_RS0100810
dapL N-acetyl-diaminopimelate deacetylase HALAL_RS0106245 HALAL_RS0104400
DAPtransferase L,L-diaminopimelate aminotransferase
dapX acetyl-diaminopimelate aminotransferase
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase HALAL_RS0116090
hicdh homo-isocitrate dehydrogenase HALAL_RS0102630 HALAL_RS0113465
lysJ [LysW]-2-aminoadipate semialdehyde transaminase HALAL_RS0112700 HALAL_RS0109075
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase HALAL_RS0102620 HALAL_RS0106545
lysT homoaconitase large subunit HALAL_RS0101595
lysU homoaconitase small subunit HALAL_RS0101600
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase HALAL_RS0112685
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