GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Rhodospirillum centenum SW; ATCC 51521

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 RC1_RS12695 RC1_RS06230
asd aspartate semi-aldehyde dehydrogenase RC1_RS18790
dapA 4-hydroxy-tetrahydrodipicolinate synthase RC1_RS07200
dapB 4-hydroxy-tetrahydrodipicolinate reductase RC1_RS15125
dapD tetrahydrodipicolinate succinylase RC1_RS10995
dapC N-succinyldiaminopimelate aminotransferase RC1_RS08575 RC1_RS11870
dapE succinyl-diaminopimelate desuccinylase RC1_RS11000
dapF diaminopimelate epimerase RC1_RS10540
lysA diaminopimelate decarboxylase RC1_RS19620 RC1_RS04820
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase RC1_RS10995 RC1_RS21665
dapL N-acetyl-diaminopimelate deacetylase RC1_RS04755
DAPtransferase L,L-diaminopimelate aminotransferase RC1_RS06235 RC1_RS14380
dapX acetyl-diaminopimelate aminotransferase RC1_RS09020 RC1_RS14380
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase RC1_RS17665 RC1_RS09455
hicdh homo-isocitrate dehydrogenase RC1_RS04300 RC1_RS18930
lysJ [LysW]-2-aminoadipate semialdehyde transaminase RC1_RS02625 RC1_RS07020
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase RC1_RS09020 RC1_RS02625
lysT homoaconitase large subunit RC1_RS11190
lysU homoaconitase small subunit RC1_RS18925 RC1_RS16110
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase RC1_RS06260
lysZ [LysW]-2-aminoadipate 6-kinase RC1_RS10975

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