GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Methylobacterium sp. 4-46 Apr-46

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 M446_RS22805
asd aspartate semi-aldehyde dehydrogenase M446_RS15255
dapA 4-hydroxy-tetrahydrodipicolinate synthase M446_RS03430 M446_RS18420
dapB 4-hydroxy-tetrahydrodipicolinate reductase M446_RS09775
dapD tetrahydrodipicolinate succinylase M446_RS06625
dapC N-succinyldiaminopimelate aminotransferase M446_RS30960 M446_RS31620
dapE succinyl-diaminopimelate desuccinylase M446_RS20265 M446_RS31645
dapF diaminopimelate epimerase M446_RS17525
lysA diaminopimelate decarboxylase M446_RS23310 M446_RS02180
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase M446_RS06625 M446_RS26595
dapL N-acetyl-diaminopimelate deacetylase M446_RS15265 M446_RS22405
DAPtransferase L,L-diaminopimelate aminotransferase M446_RS28030 M446_RS18335
dapX acetyl-diaminopimelate aminotransferase M446_RS18335 M446_RS23585
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase M446_RS17125 M446_RS06860
hicdh homo-isocitrate dehydrogenase M446_RS03775 M446_RS25290
lysJ [LysW]-2-aminoadipate semialdehyde transaminase M446_RS31620 M446_RS03720
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase M446_RS18335 M446_RS23585
lysT homoaconitase large subunit M446_RS09155 M446_RS03955
lysU homoaconitase small subunit M446_RS27530 M446_RS00200
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase M446_RS27910
lysY [LysW]-2-aminoadipate 6-phosphate reductase M446_RS21675
lysZ [LysW]-2-aminoadipate 6-kinase M446_RS04185

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