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 |
---|---|---|---|
asp-kinase | aspartate kinase | MMARC5_RS02925 | |
asd | aspartate semi-aldehyde dehydrogenase | MMARC5_RS00960 | |
dapA | 4-hydroxy-tetrahydrodipicolinate synthase | MMARC5_RS05215 | |
dapB | 4-hydroxy-tetrahydrodipicolinate reductase | MMARC5_RS03685 | |
DAPtransferase | L,L-diaminopimelate aminotransferase | MMARC5_RS00255 | MMARC5_RS02615 |
dapF | diaminopimelate epimerase | MMARC5_RS03655 | |
lysA | diaminopimelate decarboxylase | MMARC5_RS01990 | MMARC5_RS02925 |
Alternative steps: | |||
dapC | N-succinyldiaminopimelate aminotransferase | MMARC5_RS06310 | MMARC5_RS02450 |
dapD | tetrahydrodipicolinate succinylase | ||
dapE | succinyl-diaminopimelate desuccinylase | ||
dapH | tetrahydrodipicolinate acetyltransferase | MMARC5_RS08320 | |
dapL | N-acetyl-diaminopimelate deacetylase | ||
dapX | acetyl-diaminopimelate aminotransferase | MMARC5_RS02615 | |
ddh | meso-diaminopimelate D-dehydrogenase | ||
hcs | homocitrate synthase | MMARC5_RS07725 | MMARC5_RS02690 |
hicdh | homo-isocitrate dehydrogenase | MMARC5_RS03475 | MMARC5_RS05395 |
lysJ | [LysW]-2-aminoadipate semialdehyde transaminase | MMARC5_RS02450 | MMARC5_RS07450 |
lysK | [LysW]-lysine hydrolase | ||
lysN | 2-aminoadipate:2-oxoglutarate aminotransferase | MMARC5_RS08060 | MMARC5_RS02450 |
lysT | homoaconitase large subunit | MMARC5_RS00510 | MMARC5_RS02215 |
lysU | homoaconitase small subunit | MMARC5_RS06370 | MMARC5_RS07820 |
lysW | 2-aminoadipate/glutamate carrier protein | ||
lysX | 2-aminoadipate-LysW ligase | MMARC5_RS04415 | |
lysY | [LysW]-2-aminoadipate 6-phosphate reductase | MMARC5_RS07930 | |
lysZ | [LysW]-2-aminoadipate 6-kinase | MMARC5_RS08235 |
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