AGI bibliography Updated 2025-07-16
Alternating group Updated 2025-07-16
Note that odd permutations don't form a subgroup of the symmetric group like the even permutations do, because the composition of two odd permutations is an even permutation.
Bitcoin protocol Updated 2025-07-16
E. Coli K-12 MG1655 gene thrA Updated 2025-07-16
NCBI entry: www.ncbi.nlm.nih.gov/gene/945803.
This protein is an enzyme. The UniProt entry clearly shows the chemical reactions that it catalyses. In this case, there are actually two! It can either transforming the metabolite:Also interestingly, we see that both of those reaction require some extra energy to catalyse, one needing adenosine triphosphate and the other nADP+.
TODO: any mention of how much faster it makes the reaction, numerically?
Since this is an enzyme, it would also be interesting to have a quick search for it in the KEGG entry starting from the organism: www.genome.jp/pathway/eco01100+M00022 We type in the search bar "thrA", it gives a long list, but the last entry is our "thrA". Selecting it highlights two pathways in the large graph, so we understand that it catalyzes two different reactions, as suggested by the protein name itself (fused blah blah). We can now hover over:Note that common cofactor are omitted, since we've learnt from the UniProt entry that this reaction uses ATP.
- the edge: it shows all the enzymes that catalyze the given reaction. Both edges actually have multiple enzymes, e.g. the L-Homoserine path is also catalyzed by another enzyme called metL.
- the node: they are the metabolites, e.g. one of the paths contains "L-homoserine" on one node and "L-aspartate 4-semialdehyde"
If we can now click on the L-Homoserine edge, it takes us to: www.genome.jp/entry/eco:b0002+eco:b3940. Under "Pathway" we see an interesting looking pathway "Glycine, serine and threonine metabolism": www.genome.jp/pathway/eco00260+b0002 which contains a small manually selected and extremely clearly named subset of the larger graph!
But looking at the bottom of this subgraph (the UI is not great, can't Ctrl+F and enzyme names not shown, but the selected enzyme is slightly highlighted in red because it is in the URL www.genome.jp/pathway/eco00260+b0002 vs www.genome.jp/pathway/eco00260) we clearly see that thrA, thrB and thrC for a sequence that directly transforms "L-aspartate 4-semialdehyde" into "Homoserine" to "O-Phospho-L-homoserine" and finally tothreonine. This makes it crystal clear that they are not just located adjacently in the genome by chance: they are actually functionally related, and likely controlled by the same transcription factor: when you want one of them, you basically always want the three, because you must be are lacking threonine. TODO find transcription factor!
The UniProt entry also shows an interactive browser of the tertiary structure of the protein. We note that there are currently two sources available: X-ray crystallography and AlphaFold. To be honest, the AlphaFold one looks quite off!!!
By inspecting the FASTA for the entire genome, or by using the NCBI open reading frame tool, we see that this gene lies entirely in its own open reading frame, so it is quite boring
From the FASTA we see that the very first three Codons at position 337 arewhere
ATG CGA GTGATG is the start codon, and CGA GTG should be the first two that actually go into the protein:ecocyc.org/gene?orgid=ECOLI&id=ASPKINIHOMOSERDEHYDROGI-MONOMER mentions that the enzime is most active as protein complex with four copies of the same protein:TODO image?
Aspartate kinase I / homoserine dehydrogenase I comprises a dimer of ThrA dimers. Although the dimeric form is catalytically active, the binding equilibrium dramatically favors the tetrameric form. The aspartate kinase and homoserine dehydrogenase activities of each ThrA monomer are catalyzed by independent domains connected by a linker region.
FreeBSD Updated 2025-07-16
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Aegisub Updated 2025-07-16
First import video with:They don't have an
aegisub-3.2 ourbigbook-parent.mkvaegisub executable without the version number. Amazing.If you already have a subtitle file that you want to edit, then just pass it on as well:
aegisub-3.2 ourbigbook-parent.mkv ourbigbook-parent.assEnter: finish editing the current entry and start a new one.
Aerobic and anaerobic organisms Updated 2025-07-16
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It is said that you leave Oxford with either
Age of the universe Updated 2025-07-16
Surely You're Joking, Mr. Feynman chapter An Offer You Must Refuse (a play on words on The Godfather (1972)) has an interesting historical mention from the early 1950s while at Caltech:
The next day, I had the greatest luck in making a decision. God must have set it up to help me decide. I was walking to my office, and a guy came running up to me and said, "Hey, Feynman! Did you hear what happened? Baade found that there are two different populations of stars! All the measurements we had been making of the distances to the galaxies had been based on Cephid variables of one type, but there's another type, so the universe is twice, or three, or even four times as old as we thought!"I knew the problem. In those days, the earth appeared to be older than the universe. The earth was four and a half billion, and the universe was only a couple, or three billion years old. It was a great puzzle. And this discovery resolved all that: The universe was now demonstrably older than was previously thought. And I got this information right away - the guy came running up to me to tell me all this.
Aggressively filter your social media follows Updated 2025-07-16
Ciro Santilli very aggressively aggressively people in social media.
There are basically 3 categories:
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