GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Kyrpidia tusciae DSM 2912

Best path

asp-kinase, asd, dapA, dapB, dapH, dapX, dapL, 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 BTUS_RS03195 BTUS_RS07805
asd aspartate semi-aldehyde dehydrogenase BTUS_RS07800
dapA 4-hydroxy-tetrahydrodipicolinate synthase BTUS_RS07810 BTUS_RS07835
dapB 4-hydroxy-tetrahydrodipicolinate reductase BTUS_RS08425
dapH tetrahydrodipicolinate acetyltransferase BTUS_RS16240 BTUS_RS04450
dapX acetyl-diaminopimelate aminotransferase BTUS_RS03510 BTUS_RS16335
dapL N-acetyl-diaminopimelate deacetylase BTUS_RS16235 BTUS_RS15345
dapF diaminopimelate epimerase BTUS_RS07045
lysA diaminopimelate decarboxylase BTUS_RS09135
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase BTUS_RS05070 BTUS_RS11380
dapD tetrahydrodipicolinate succinylase BTUS_RS16240
dapE succinyl-diaminopimelate desuccinylase BTUS_RS15220 BTUS_RS13835
DAPtransferase L,L-diaminopimelate aminotransferase BTUS_RS13735 BTUS_RS03510
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase BTUS_RS04780
hicdh homo-isocitrate dehydrogenase BTUS_RS12190 BTUS_RS04785
lysJ [LysW]-2-aminoadipate semialdehyde transaminase BTUS_RS03025 BTUS_RS11380
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase BTUS_RS01870 BTUS_RS16335
lysT homoaconitase large subunit BTUS_RS11945
lysU homoaconitase small subunit BTUS_RS11950
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase BTUS_RS11400
lysZ [LysW]-2-aminoadipate 6-kinase BTUS_RS11390

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