From the overview: \"Proteins are large molecules composed of **20 **types of building-blocks known as amino acids\". But some proteins contain 21 letters, including 'U'. What does it mean?
", "messages": [ { "id": "2257464", "postDate": "05/13/2023 11:24:30", "content": "From the overview: \"Proteins are large molecules composed of **20 **types of building-blocks known as amino acids\". But some proteins contain 21 letters, including 'U'. What does it mean?
", "rawMarkdown": "From the overview: \"Proteins are large molecules composed of **20 **types of building-blocks known as amino acids\". But some proteins contain 21 letters, including 'U'. What does it mean?", "votes": null }, { "id": "2257477", "postDate": "05/13/2023 11:35:32", "content": "Selenocysteine. A rare amino acid. It's an analog of cysteine with a selenium atom instead of sulfur.
", "rawMarkdown": "Selenocysteine. A rare amino acid. It's an analog of cysteine with a selenium atom instead of sulfur.", "votes": null }, { "id": "2257482", "postDate": "05/13/2023 11:49:40", "content": "not even U, there is X, Z, B and so on. Just check it :)
", "rawMarkdown": "not even U, there is X, Z, B and so on. Just check it :)", "votes": null }, { "id": "2257506", "postDate": "05/13/2023 12:09:19", "content": "X: some unusual and rare amino acid. The exact aa can be found in the text annotating the protein in swissprot. Those are typically so rare, that a single letter was never assigned to them.
\nZ: either glutamic acid (E) or glutamine (Q)
\nB: either aspartate (D) or asparagine (N)
You can find more information here: https://www.ddbj.nig.ac.jp/ddbj/code-e.html#amino-1
", "rawMarkdown": "X: some unusual and rare amino acid. The exact aa can be found in the text annotating the protein in swissprot. Those are typically so rare, that a single letter was never assigned to them. \nZ: either glutamic acid (E) or glutamine (Q)\nB: either aspartate (D) or asparagine (N)\n\nYou can find more information here: https://www.ddbj.nig.ac.jp/ddbj/code-e.html#amino-1", "votes": null }, { "id": "2261964", "postDate": "05/16/2023 16:36:11", "content": "U stands for unknown. Sometimes during sequencing there are stretches of DNA bases that are not properly resolved, and N is used as a generic replacement for [A,T,C,G]. When such a DNA sequence is translated into a protein, there is no way to assign it a known amino-acid.
Minor correction: U is a special amino acid, X is unknown/any amino acid.
\nThough, for this task, you can probably map all \"special\" amnio acids to X (due to them being so rare in general).
| Letter | \nName | \n
|---|---|
| U | \nSelenocysteine | \n
| O | \nPyrrolysine | \n
| B | \nAspartic acid (D) or Asparagine (N) | \n
| Z | \nGlutamic acid (E) or Glutamine (Q) | \n
| J | \nLeucine (L) or Isoleucine (I) | \n
| X | \nAny amino acid | \n
@iddux1 posted a link to the full table.
", "rawMarkdown": "Minor correction: `U` is a special amino acid, `X` is unknown/any amino acid.\nThough, for this task, you can probably map all \"special\" amnio acids to X (due to them being so rare in general).\n\n\n| Letter | Name |\n| --- | --- |\n| U | Selenocysteine |\n| O | Pyrrolysine |\n| B | Aspartic acid (D) or Asparagine (N) |\n| Z | Glutamic acid (E) or Glutamine (Q) |\n| J | Leucine (L) or Isoleucine (I) |\n| X | Any amino acid |\n\n\n@iddux1 posted a link to the full table.", "votes": null }, { "id": "2264628", "postDate": "05/18/2023 15:34:05", "content": "It is reasonable to replace U by C. It's cysteine, more or less.
", "rawMarkdown": "It is reasonable to replace U by C. It's cysteine, more or less.", "votes": null } ], "comments": [ { "id": 2257477, "author_name": "iddux1", "author_url": "", "post_date": "05/13/2023 11:35:32", "content": "Selenocysteine. A rare amino acid. It's an analog of cysteine with a selenium atom instead of sulfur.
", "votes": null, "replies": [] }, { "id": 2257482, "author_name": "michalinahulak", "author_url": "", "post_date": "05/13/2023 11:49:40", "content": "not even U, there is X, Z, B and so on. Just check it :)
", "votes": null, "replies": [ { "id": 2257506, "author_name": "iddux1", "author_url": "", "post_date": "05/13/2023 12:09:19", "content": "X: some unusual and rare amino acid. The exact aa can be found in the text annotating the protein in swissprot. Those are typically so rare, that a single letter was never assigned to them.
\nZ: either glutamic acid (E) or glutamine (Q)
\nB: either aspartate (D) or asparagine (N)
You can find more information here: https://www.ddbj.nig.ac.jp/ddbj/code-e.html#amino-1
", "votes": null, "replies": [] } ] }, { "id": 2261964, "author_name": "tilii7", "author_url": "", "post_date": "05/16/2023 16:36:11", "content": "U stands for unknown. Sometimes during sequencing there are stretches of DNA bases that are not properly resolved, and N is used as a generic replacement for [A,T,C,G]. When such a DNA sequence is translated into a protein, there is no way to assign it a known amino-acid.
Minor correction: U is a special amino acid, X is unknown/any amino acid.
\nThough, for this task, you can probably map all \"special\" amnio acids to X (due to them being so rare in general).
| Letter | \nName | \n
|---|---|
| U | \nSelenocysteine | \n
| O | \nPyrrolysine | \n
| B | \nAspartic acid (D) or Asparagine (N) | \n
| Z | \nGlutamic acid (E) or Glutamine (Q) | \n
| J | \nLeucine (L) or Isoleucine (I) | \n
| X | \nAny amino acid | \n
@iddux1 posted a link to the full table.
", "votes": null, "replies": [] } ] }, { "id": 2264628, "author_name": "predragradivojac", "author_url": "", "post_date": "05/18/2023 15:34:05", "content": "It is reasonable to replace U by C. It's cysteine, more or less.
", "votes": null, "replies": [] } ], "raw_markdown_by_id": { "2257464": "From the overview: \"Proteins are large molecules composed of **20 **types of building-blocks known as amino acids\". But some proteins contain 21 letters, including 'U'. What does it mean?", "2257477": "Selenocysteine. A rare amino acid. It's an analog of cysteine with a selenium atom instead of sulfur.", "2257482": "not even U, there is X, Z, B and so on. Just check it :)", "2257506": "X: some unusual and rare amino acid. The exact aa can be found in the text annotating the protein in swissprot. Those are typically so rare, that a single letter was never assigned to them. \nZ: either glutamic acid (E) or glutamine (Q)\nB: either aspartate (D) or asparagine (N)\n\nYou can find more information here: https://www.ddbj.nig.ac.jp/ddbj/code-e.html#amino-1", "2261964": "`U` stands for unknown. Sometimes during sequencing there are stretches of DNA bases that are not properly resolved, and `N` is used as a generic replacement for [A,T,C,G]. When such a DNA sequence is translated into a protein, there is no way to assign it a known amino-acid.", "2261995": "Minor correction: `U` is a special amino acid, `X` is unknown/any amino acid.\nThough, for this task, you can probably map all \"special\" amnio acids to X (due to them being so rare in general).\n\n\n| Letter | Name |\n| --- | --- |\n| U | Selenocysteine |\n| O | Pyrrolysine |\n| B | Aspartic acid (D) or Asparagine (N) |\n| Z | Glutamic acid (E) or Glutamine (Q) |\n| J | Leucine (L) or Isoleucine (I) |\n| X | Any amino acid |\n\n\n@iddux1 posted a link to the full table.", "2264628": "It is reasonable to replace U by C. It's cysteine, more or less." }, "source": "meta" }