GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Novosphingobium aromaticivorans DSM 12444

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 SARO_RS16780
asd aspartate semi-aldehyde dehydrogenase SARO_RS07070
dapA 4-hydroxy-tetrahydrodipicolinate synthase SARO_RS07235 SARO_RS16985
dapB 4-hydroxy-tetrahydrodipicolinate reductase SARO_RS00020
dapD tetrahydrodipicolinate succinylase SARO_RS09185
dapC N-succinyldiaminopimelate aminotransferase SARO_RS13600 SARO_RS15955
dapE succinyl-diaminopimelate desuccinylase SARO_RS02900 SARO_RS16805
dapF diaminopimelate epimerase SARO_RS07030
lysA diaminopimelate decarboxylase SARO_RS13580 SARO_RS11760
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase SARO_RS09185 SARO_RS21665
dapL N-acetyl-diaminopimelate deacetylase SARO_RS11815 SARO_RS14865
DAPtransferase L,L-diaminopimelate aminotransferase SARO_RS02510 SARO_RS02235
dapX acetyl-diaminopimelate aminotransferase SARO_RS02235
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase
hicdh homo-isocitrate dehydrogenase SARO_RS14880 SARO_RS13515
lysJ [LysW]-2-aminoadipate semialdehyde transaminase SARO_RS15955 SARO_RS13120
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase SARO_RS02235 SARO_RS13120
lysT homoaconitase large subunit SARO_RS05835
lysU homoaconitase small subunit SARO_RS05850
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase SARO_RS16740

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