GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Sulfuricurvum kujiense DSM 16994

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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase SULKU_RS03040 SULKU_RS11570
asd aspartate semi-aldehyde dehydrogenase SULKU_RS10495
dapA 4-hydroxy-tetrahydrodipicolinate synthase SULKU_RS04720
dapB 4-hydroxy-tetrahydrodipicolinate reductase SULKU_RS01145
dapD tetrahydrodipicolinate succinylase SULKU_RS05035
dapC N-succinyldiaminopimelate aminotransferase SULKU_RS04095 SULKU_RS11860
dapE succinyl-diaminopimelate desuccinylase SULKU_RS03755
dapF diaminopimelate epimerase SULKU_RS00510
lysA diaminopimelate decarboxylase SULKU_RS09640
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase SULKU_RS12000 SULKU_RS12050
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase SULKU_RS11575 SULKU_RS04095
dapX acetyl-diaminopimelate aminotransferase SULKU_RS07470
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase SULKU_RS07600
hicdh homo-isocitrate dehydrogenase SULKU_RS04995
lysJ [LysW]-2-aminoadipate semialdehyde transaminase SULKU_RS13855 SULKU_RS04950
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase SULKU_RS07470 SULKU_RS04655
lysT homoaconitase large subunit SULKU_RS12485
lysU homoaconitase small subunit SULKU_RS04990
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase SULKU_RS02855
lysZ [LysW]-2-aminoadipate 6-kinase SULKU_RS07945

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