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 | Smed_2504 | Smed_1453 |
asd | aspartate semi-aldehyde dehydrogenase | Smed_3182 | |
dapA | 4-hydroxy-tetrahydrodipicolinate synthase | Smed_3989 | Smed_0673 |
dapB | 4-hydroxy-tetrahydrodipicolinate reductase | Smed_3371 | |
dapD | tetrahydrodipicolinate succinylase | Smed_0069 | |
dapC | N-succinyldiaminopimelate aminotransferase | Smed_2619 | Smed_0127 |
dapE | succinyl-diaminopimelate desuccinylase | Smed_0061 | Smed_5605 |
dapF | diaminopimelate epimerase | Smed_3093 | |
lysA | diaminopimelate decarboxylase | Smed_2538 | Smed_2772 |
Alternative steps: | |||
dapH | tetrahydrodipicolinate acetyltransferase | Smed_1810 | Smed_0069 |
dapL | N-acetyl-diaminopimelate deacetylase | Smed_0172 | Smed_2573 |
DAPtransferase | L,L-diaminopimelate aminotransferase | Smed_1454 | Smed_3160 |
dapX | acetyl-diaminopimelate aminotransferase | Smed_2233 | Smed_3160 |
ddh | meso-diaminopimelate D-dehydrogenase | ||
hcs | homocitrate synthase | Smed_0718 | |
hicdh | homo-isocitrate dehydrogenase | Smed_5601 | Smed_3178 |
lysJ | [LysW]-2-aminoadipate semialdehyde transaminase | Smed_0127 | Smed_4677 |
lysK | [LysW]-lysine hydrolase | ||
lysN | 2-aminoadipate:2-oxoglutarate aminotransferase | Smed_3160 | Smed_2233 |
lysT | homoaconitase large subunit | Smed_3059 | |
lysU | homoaconitase small subunit | Smed_3028 | Smed_0365 |
lysW | 2-aminoadipate/glutamate carrier protein | ||
lysX | 2-aminoadipate-LysW ligase | ||
lysY | [LysW]-2-aminoadipate 6-phosphate reductase | ||
lysZ | [LysW]-2-aminoadipate 6-kinase | Smed_0075 |
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