GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Methanobacterium lacus AL-21

Best path

asp-kinase, asd, dapA, dapB, DAPtransferase, 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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase METBO_RS09425 METBO_RS01460
asd aspartate semi-aldehyde dehydrogenase METBO_RS09410
dapA 4-hydroxy-tetrahydrodipicolinate synthase METBO_RS09420
dapB 4-hydroxy-tetrahydrodipicolinate reductase METBO_RS09415
DAPtransferase L,L-diaminopimelate aminotransferase METBO_RS04185 METBO_RS03630
dapF diaminopimelate epimerase METBO_RS00590
lysA diaminopimelate decarboxylase METBO_RS00595
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase METBO_RS02880 METBO_RS00600
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase METBO_RS03705 METBO_RS11340
dapL N-acetyl-diaminopimelate deacetylase METBO_RS12525
dapX acetyl-diaminopimelate aminotransferase METBO_RS03630
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase METBO_RS10235 METBO_RS00320
hicdh homo-isocitrate dehydrogenase METBO_RS02965 METBO_RS00860
lysJ [LysW]-2-aminoadipate semialdehyde transaminase METBO_RS00600 METBO_RS10535
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase METBO_RS03620 METBO_RS03630
lysT homoaconitase large subunit METBO_RS10230 METBO_RS00850
lysU homoaconitase small subunit METBO_RS00855 METBO_RS09620
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase METBO_RS04830
lysZ [LysW]-2-aminoadipate 6-kinase METBO_RS04840

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