GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Desulfacinum hydrothermale DSM 13146

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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase B9A12_RS03940 B9A12_RS09455
asd aspartate semi-aldehyde dehydrogenase B9A12_RS09570
dapA 4-hydroxy-tetrahydrodipicolinate synthase B9A12_RS04125
dapB 4-hydroxy-tetrahydrodipicolinate reductase B9A12_RS04130
DAPtransferase L,L-diaminopimelate aminotransferase B9A12_RS04135 B9A12_RS09460
dapF diaminopimelate epimerase B9A12_RS04120
lysA diaminopimelate decarboxylase B9A12_RS04115
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase B9A12_RS07725 B9A12_RS04090
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase B9A12_RS00495 B9A12_RS08915
dapL N-acetyl-diaminopimelate deacetylase
dapX acetyl-diaminopimelate aminotransferase B9A12_RS02895 B9A12_RS02325
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase B9A12_RS05830 B9A12_RS09645
hicdh homo-isocitrate dehydrogenase B9A12_RS15255
lysJ [LysW]-2-aminoadipate semialdehyde transaminase B9A12_RS04090 B9A12_RS03895
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase B9A12_RS02895 B9A12_RS03895
lysT homoaconitase large subunit B9A12_RS08400 B9A12_RS09560
lysU homoaconitase small subunit B9A12_RS09565 B9A12_RS07905
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase B9A12_RS02885
lysZ [LysW]-2-aminoadipate 6-kinase B9A12_RS04085

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