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.
Or see definitions of steps
Step | Description | Best candidate | 2nd candidate |
---|---|---|---|
asp-kinase | aspartate kinase | KVAR_RS21890 | KVAR_RS25005 |
asd | aspartate semi-aldehyde dehydrogenase | KVAR_RS01495 | KVAR_RS12625 |
dapA | 4-hydroxy-tetrahydrodipicolinate synthase | KVAR_RS06260 | KVAR_RS13450 |
dapB | 4-hydroxy-tetrahydrodipicolinate reductase | KVAR_RS21680 | |
dapD | tetrahydrodipicolinate succinylase | KVAR_RS20940 | |
dapC | N-succinyldiaminopimelate aminotransferase | KVAR_RS01765 | KVAR_RS17055 |
dapE | succinyl-diaminopimelate desuccinylase | KVAR_RS06295 | KVAR_RS19155 |
dapF | diaminopimelate epimerase | KVAR_RS24650 | KVAR_RS11945 |
lysA | diaminopimelate decarboxylase | KVAR_RS04100 | KVAR_RS24120 |
Alternative steps: | |||
dapH | tetrahydrodipicolinate acetyltransferase | KVAR_RS20940 | KVAR_RS19605 |
dapL | N-acetyl-diaminopimelate deacetylase | KVAR_RS11965 | KVAR_RS10890 |
DAPtransferase | L,L-diaminopimelate aminotransferase | KVAR_RS06645 | KVAR_RS14595 |
dapX | acetyl-diaminopimelate aminotransferase | KVAR_RS20445 | KVAR_RS08425 |
ddh | meso-diaminopimelate D-dehydrogenase | ||
hcs | homocitrate synthase | KVAR_RS08025 | KVAR_RS21445 |
hicdh | homo-isocitrate dehydrogenase | KVAR_RS16030 | KVAR_RS16670 |
lysJ | [LysW]-2-aminoadipate semialdehyde transaminase | KVAR_RS15350 | KVAR_RS14225 |
lysK | [LysW]-lysine hydrolase | ||
lysN | 2-aminoadipate:2-oxoglutarate aminotransferase | KVAR_RS08425 | KVAR_RS20445 |
lysT | homoaconitase large subunit | KVAR_RS21455 | |
lysU | homoaconitase small subunit | KVAR_RS21460 | |
lysW | 2-aminoadipate/glutamate carrier protein | ||
lysX | 2-aminoadipate-LysW ligase | ||
lysY | [LysW]-2-aminoadipate 6-phosphate reductase | KVAR_RS24955 | |
lysZ | [LysW]-2-aminoadipate 6-kinase | KVAR_RS24950 |
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