hcs, lysT, lysU, hicdh, lysN, lysW, lysX, lysZ, lysY, lysJ, lysK
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 |
---|---|---|---|
hcs | homocitrate synthase | PYRFU_RS09715 | PYRFU_RS08315 |
lysT | homoaconitase large subunit | PYRFU_RS09265 | PYRFU_RS00315 |
lysU | homoaconitase small subunit | PYRFU_RS07965 | PYRFU_RS03665 |
hicdh | homo-isocitrate dehydrogenase | PYRFU_RS09335 | PYRFU_RS05270 |
lysN | 2-aminoadipate:2-oxoglutarate aminotransferase | PYRFU_RS08035 | PYRFU_RS08855 |
lysW | 2-aminoadipate/glutamate carrier protein | PYRFU_RS03640 | |
lysX | 2-aminoadipate-LysW ligase | PYRFU_RS03645 | PYRFU_RS03725 |
lysZ | [LysW]-2-aminoadipate 6-kinase | PYRFU_RS01990 | |
lysY | [LysW]-2-aminoadipate 6-phosphate reductase | PYRFU_RS03735 | |
lysJ | [LysW]-2-aminoadipate semialdehyde transaminase | PYRFU_RS08855 | PYRFU_RS06770 |
lysK | [LysW]-lysine hydrolase | PYRFU_RS08530 | |
Alternative steps: | |||
asd | aspartate semi-aldehyde dehydrogenase | PYRFU_RS04350 | |
asp-kinase | aspartate kinase | PYRFU_RS06440 | |
dapA | 4-hydroxy-tetrahydrodipicolinate synthase | ||
dapB | 4-hydroxy-tetrahydrodipicolinate reductase | ||
dapC | N-succinyldiaminopimelate aminotransferase | PYRFU_RS03405 | PYRFU_RS08855 |
dapD | tetrahydrodipicolinate succinylase | ||
dapE | succinyl-diaminopimelate desuccinylase | ||
dapF | diaminopimelate epimerase | ||
dapH | tetrahydrodipicolinate acetyltransferase | PYRFU_RS08065 | |
dapL | N-acetyl-diaminopimelate deacetylase | ||
DAPtransferase | L,L-diaminopimelate aminotransferase | ||
dapX | acetyl-diaminopimelate aminotransferase | PYRFU_RS02975 | |
ddh | meso-diaminopimelate D-dehydrogenase | ||
lysA | diaminopimelate decarboxylase |
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 10 2024. The underlying query database was built on Apr 09 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