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.
Or see definitions of steps
Step | Description | Best candidate | 2nd candidate | Known gap? |
---|---|---|---|---|
asp-kinase | aspartate kinase | MA_RS00690 | ||
asd | aspartate semi-aldehyde dehydrogenase | MA_RS02255 | ||
dapA | 4-hydroxy-tetrahydrodipicolinate synthase | MA_RS23345 | ||
dapB | 4-hydroxy-tetrahydrodipicolinate reductase | MA_RS23350 | ||
DAPtransferase | L,L-diaminopimelate aminotransferase | MA_RS08890 | MA_RS04795 | |
dapF? | diaminopimelate epimerase | known gap | ||
lysA | diaminopimelate decarboxylase | MA_RS03800 | MA_RS00690 | |
Alternative steps: | ||||
dapC | N-succinyldiaminopimelate aminotransferase | MA_RS11965 | MA_RS09455 | |
dapD | tetrahydrodipicolinate succinylase | |||
dapE | succinyl-diaminopimelate desuccinylase | MA_RS06200 | ||
dapH | tetrahydrodipicolinate acetyltransferase | MA_RS11280 | MA_RS02155 | |
dapL | N-acetyl-diaminopimelate deacetylase | MA_RS06200 | ||
dapX | acetyl-diaminopimelate aminotransferase | MA_RS04795 | MA_RS07185 | |
ddh | meso-diaminopimelate D-dehydrogenase | |||
hcs | homocitrate synthase | MA_RS17445 | MA_RS24085 | |
hicdh | homo-isocitrate dehydrogenase | MA_RS19530 | MA_RS22270 | |
lysJ | [LysW]-2-aminoadipate semialdehyde transaminase | MA_RS00620 | MA_RS15010 | |
lysK | [LysW]-lysine hydrolase | |||
lysN | 2-aminoadipate:2-oxoglutarate aminotransferase | MA_RS09470 | MA_RS07185 | |
lysT | homoaconitase large subunit | MA_RS16135 | MA_RS07220 | |
lysU | homoaconitase small subunit | MA_RS19545 | MA_RS06360 | |
lysW | 2-aminoadipate/glutamate carrier protein | |||
lysX | 2-aminoadipate-LysW ligase | MA_RS17050 | ||
lysY | [LysW]-2-aminoadipate 6-phosphate reductase | MA_RS18620 | ||
lysZ | [LysW]-2-aminoadipate 6-kinase | MA_RS23550 |
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.
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:
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