GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Methylomonas methanica MC09

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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase METME_RS03820 METME_RS14270
asd aspartate semi-aldehyde dehydrogenase METME_RS20200
dapA 4-hydroxy-tetrahydrodipicolinate synthase METME_RS14240
dapB 4-hydroxy-tetrahydrodipicolinate reductase METME_RS16535
dapD tetrahydrodipicolinate succinylase METME_RS20550
dapC N-succinyldiaminopimelate aminotransferase METME_RS20555 METME_RS09445
dapE succinyl-diaminopimelate desuccinylase METME_RS16650
dapF diaminopimelate epimerase METME_RS01805
lysA diaminopimelate decarboxylase METME_RS01800 METME_RS06135
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase METME_RS20550 METME_RS05995
dapL N-acetyl-diaminopimelate deacetylase METME_RS13475
DAPtransferase L,L-diaminopimelate aminotransferase METME_RS14275 METME_RS20555
dapX acetyl-diaminopimelate aminotransferase METME_RS13060 METME_RS12060
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase METME_RS15615 METME_RS04525
hicdh homo-isocitrate dehydrogenase METME_RS12845 METME_RS20195
lysJ [LysW]-2-aminoadipate semialdehyde transaminase METME_RS12875 METME_RS17430
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase METME_RS13060 METME_RS12875
lysT homoaconitase large subunit METME_RS20185
lysU homoaconitase small subunit METME_RS20190
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase METME_RS06910
lysY [LysW]-2-aminoadipate 6-phosphate reductase METME_RS03960
lysZ [LysW]-2-aminoadipate 6-kinase METME_RS16675

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