GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Anaerobutyricum hallii DSM 3353

Best path

asp-kinase, asd, dapA, dapB, DAPtransferase, 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 EUBHAL_RS12075 EUBHAL_RS12910
asd aspartate semi-aldehyde dehydrogenase EUBHAL_RS13320
dapA 4-hydroxy-tetrahydrodipicolinate synthase EUBHAL_RS12465
dapB 4-hydroxy-tetrahydrodipicolinate reductase EUBHAL_RS12470
DAPtransferase L,L-diaminopimelate aminotransferase EUBHAL_RS11975 EUBHAL_RS09815
dapF diaminopimelate epimerase EUBHAL_RS11970
lysA diaminopimelate decarboxylase EUBHAL_RS03150
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase EUBHAL_RS01485 EUBHAL_RS08110
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase EUBHAL_RS07245 EUBHAL_RS07220
dapL N-acetyl-diaminopimelate deacetylase EUBHAL_RS12300
dapX acetyl-diaminopimelate aminotransferase EUBHAL_RS05010
ddh meso-diaminopimelate D-dehydrogenase EUBHAL_RS12550
hcs homocitrate synthase
hicdh homo-isocitrate dehydrogenase EUBHAL_RS13300
lysJ [LysW]-2-aminoadipate semialdehyde transaminase EUBHAL_RS10730 EUBHAL_RS08110
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase EUBHAL_RS05010 EUBHAL_RS10730
lysT homoaconitase large subunit EUBHAL_RS13560 EUBHAL_RS13570
lysU homoaconitase small subunit EUBHAL_RS13555 EUBHAL_RS13565
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase EUBHAL_RS08095
lysZ [LysW]-2-aminoadipate 6-kinase EUBHAL_RS08105

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