GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Beijerinckia indica ATCC 9039

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 BIND_RS04530
asd aspartate semi-aldehyde dehydrogenase BIND_RS06020
dapA 4-hydroxy-tetrahydrodipicolinate synthase BIND_RS09460
dapB 4-hydroxy-tetrahydrodipicolinate reductase BIND_RS00670
dapD tetrahydrodipicolinate succinylase BIND_RS16910
dapC N-succinyldiaminopimelate aminotransferase BIND_RS06440 BIND_RS00765
dapE succinyl-diaminopimelate desuccinylase BIND_RS16930
dapF diaminopimelate epimerase BIND_RS17275
lysA diaminopimelate decarboxylase BIND_RS00250 BIND_RS05480
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase BIND_RS16910 BIND_RS01060
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase BIND_RS00395
dapX acetyl-diaminopimelate aminotransferase BIND_RS00395 BIND_RS16265
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase BIND_RS02470 BIND_RS03045
hicdh homo-isocitrate dehydrogenase BIND_RS06000
lysJ [LysW]-2-aminoadipate semialdehyde transaminase BIND_RS00765 BIND_RS14190
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase BIND_RS00395 BIND_RS00765
lysT homoaconitase large subunit BIND_RS04615 BIND_RS17540
lysU homoaconitase small subunit BIND_RS04615 BIND_RS01080
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase BIND_RS16900

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