GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Methylobacterium nodulans ORS 2060

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 MNOD_RS00510
asd aspartate semi-aldehyde dehydrogenase MNOD_RS01170
dapA 4-hydroxy-tetrahydrodipicolinate synthase MNOD_RS07140 MNOD_RS37360
dapB 4-hydroxy-tetrahydrodipicolinate reductase MNOD_RS02185
dapD tetrahydrodipicolinate succinylase MNOD_RS04885
dapC N-succinyldiaminopimelate aminotransferase MNOD_RS32140 MNOD_RS32865
dapE succinyl-diaminopimelate desuccinylase MNOD_RS22375 MNOD_RS40255
dapF diaminopimelate epimerase MNOD_RS00865
lysA diaminopimelate decarboxylase MNOD_RS08090
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase MNOD_RS04885 MNOD_RS33210
dapL N-acetyl-diaminopimelate deacetylase MNOD_RS01200 MNOD_RS13935
DAPtransferase L,L-diaminopimelate aminotransferase MNOD_RS28520 MNOD_RS09470
dapX acetyl-diaminopimelate aminotransferase MNOD_RS09470 MNOD_RS37310
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase MNOD_RS04585
hicdh homo-isocitrate dehydrogenase MNOD_RS27425 MNOD_RS06955
lysJ [LysW]-2-aminoadipate semialdehyde transaminase MNOD_RS35300 MNOD_RS30030
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase MNOD_RS37310 MNOD_RS09470
lysT homoaconitase large subunit MNOD_RS06830 MNOD_RS10895
lysU homoaconitase small subunit MNOD_RS13205 MNOD_RS00200
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase MNOD_RS28410
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase MNOD_RS06685

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.



Related tools

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