GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Sulfurimonas denitrificans DSM 1251

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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase SUDEN_RS08595
asd aspartate semi-aldehyde dehydrogenase SUDEN_RS03330
dapA 4-hydroxy-tetrahydrodipicolinate synthase SUDEN_RS06425
dapB 4-hydroxy-tetrahydrodipicolinate reductase SUDEN_RS09710
dapD tetrahydrodipicolinate succinylase SUDEN_RS05740
dapC N-succinyldiaminopimelate aminotransferase SUDEN_RS03970 SUDEN_RS06570
dapE succinyl-diaminopimelate desuccinylase SUDEN_RS07550
dapF diaminopimelate epimerase SUDEN_RS10615
lysA diaminopimelate decarboxylase SUDEN_RS02455
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase SUDEN_RS05970 SUDEN_RS07425
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase SUDEN_RS09890 SUDEN_RS03970
dapX acetyl-diaminopimelate aminotransferase SUDEN_RS05945
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase
hicdh homo-isocitrate dehydrogenase SUDEN_RS05780
lysJ [LysW]-2-aminoadipate semialdehyde transaminase SUDEN_RS05820 SUDEN_RS06570
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase SUDEN_RS05945 SUDEN_RS06570
lysT homoaconitase large subunit SUDEN_RS10470
lysU homoaconitase small subunit SUDEN_RS05785
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase SUDEN_RS08785
lysY [LysW]-2-aminoadipate 6-phosphate reductase SUDEN_RS07995
lysZ [LysW]-2-aminoadipate 6-kinase SUDEN_RS04495

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