GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Tistlia consotensis USBA 355

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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase B9O00_RS15090
asd aspartate semi-aldehyde dehydrogenase B9O00_RS08315
dapA 4-hydroxy-tetrahydrodipicolinate synthase B9O00_RS10640 B9O00_RS04005
dapB 4-hydroxy-tetrahydrodipicolinate reductase B9O00_RS07495 B9O00_RS00605
dapD tetrahydrodipicolinate succinylase B9O00_RS07240
dapC N-succinyldiaminopimelate aminotransferase B9O00_RS14565 B9O00_RS06850
dapE succinyl-diaminopimelate desuccinylase B9O00_RS07235 B9O00_RS04430
dapF diaminopimelate epimerase B9O00_RS26990
lysA diaminopimelate decarboxylase B9O00_RS02090 B9O00_RS16780
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase B9O00_RS07240 B9O00_RS09165
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase B9O00_RS11060 B9O00_RS12295
dapX acetyl-diaminopimelate aminotransferase B9O00_RS27325 B9O00_RS12295
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase B9O00_RS01945 B9O00_RS31655
hicdh homo-isocitrate dehydrogenase B9O00_RS11110 B9O00_RS23510
lysJ [LysW]-2-aminoadipate semialdehyde transaminase B9O00_RS06850 B9O00_RS09970
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase B9O00_RS27325 B9O00_RS12295
lysT homoaconitase large subunit B9O00_RS08285
lysU homoaconitase small subunit B9O00_RS08290 B9O00_RS08500
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase B9O00_RS02295

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