Difference between revisions of "Talk:Protein domains"
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{| style="border:#c9c9c9 1px solid; margin: 2em 2em 2em 0; border-collapse: collapse;" | {| style="border:#c9c9c9 1px solid; margin: 2em 2em 2em 0; border-collapse: collapse;" | ||
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Ala/A''' | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Ala/A''' | ||
| − | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | GCU, GCC, GCA, GCG | + | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | GCU (rare in Rhodobacter), GCC, GCA (rare in Rhodobacter), GCG |
|----- | |----- | ||
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Leu/L''' | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Leu/L''' | ||
| − | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | UUA (rare in E. coli), UUG, CUU, CUC, CUA (rare in E. coli/Chicken), CUG | + | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | UUA (rare in E. coli/Rhodobacter), UUG (rare in Rhodobacter), CUU, CUC, CUA (rare in E. coli/Chicken/Rhodobacter), CUG |
|----- | |----- | ||
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Arg/R''' | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Arg/R''' | ||
| − | | CGU, CGC, CGA (rare in E. coli), CGG (rare in E. coli/Yeast), AGA (rare in E. coli), AGG (rare in E. coli) | + | | CGU, CGC, CGA (rare in E. coli/Rhodobacter), CGG (rare in E. coli/Yeast), AGA (rare in E. coli/Rhodobacter), AGG (rare in E. coli/Rhodobacter) |
|----- | |----- | ||
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Lys/K''' | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Lys/K''' | ||
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|----- | |----- | ||
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Pro/P''' | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Pro/P''' | ||
| − | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | CCU, CCC (rare in E. coli), CCA, CCG | + | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | CCU (rare in Rhodobacter), CCC (rare in E. coli), CCA (rare in Rhodobacter), CCG |
|----- | |----- | ||
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Gln/Q''' | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Gln/Q''' | ||
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|----- | |----- | ||
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Ser/S''' | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Ser/S''' | ||
| − | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | UCU, UCC, UCA, UCG (rare in Chicken), AGU (rare in E. coli), AGC | + | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | UCU (rare in Rhodobacter), UCC, UCA (rare in Rhodobacter), UCG (rare in Chicken), AGU (rare in E. coli/Rhodobacter), AGC |
|----- | |----- | ||
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Glu/E''' | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Glu/E''' | ||
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|----- | |----- | ||
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Thr/T''' | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Thr/T''' | ||
| − | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | ACU, ACC, ACG, ACA (rare in E. coli) | + | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | ACU (rare in Rhodobacter), ACC, ACG, ACA (rare in E. coli) |
|----- | |----- | ||
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Gly/G''' | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Gly/G''' | ||
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|----- | |----- | ||
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Ile/I''' | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Ile/I''' | ||
| − | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | AUU, AUC, AUA (rare in E. coli) | + | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | AUU, AUC, AUA (rare in E. coli/Rhodobacter) |
|----- | |----- | ||
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Val/V''' | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Val/V''' | ||
| − | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | GUU, GUC, GUA, GUG | + | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | GUU (rare in Rhodobacter), GUC, GUA (rare in Rhodobacter), GUG |
|----- | |----- | ||
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''START''' | | style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''START''' | ||
Revision as of 13:05, 2 September 2009
Contents
Categories
- //proteintags/affinity
- //proteintags/cleavage
- //proteintags/degradation
- //proteintags/localization
Tables
- protein_affinity_tags
- //proteintags/affinity
- protein_cleavage_sites
- //proteintags/cleavage
- protein_degradation_tags
- //proteintags/degradation
- protein_localization_sequences
- //proteintags/localization
Columns for general protein tag tables
- Available/Working
- Part number (left aligned)
- Description (left aligned)
- AA sequence (most of these sequences are very short, courier or other fixed width font, left aligned) <- auto-generated by the computer
- Length (centered) <- auto-generated by the computer
Columns for protein cleavage site tables
- Available/Working
- Part number (left aligned)
- Description (left aligned)
- Protease (centered, ideally should include links to coding sequences of the protease entered in the Registry)
- AA sequence (most of these parts are very short, courier or other fixed width font, left aligned)
- Length (centered)
Columns for protein degradation tag tables
- Available/Working
- Part number (left aligned)
- Description (left aligned)
- Chassis (center)
- Half-life (centered)
- AA sequence (most of these parts are very short, courier or other fixed width font, left aligned)
- Length (centered)
Columns for protein affinity tag tables
- Available/Working
- Part number (left aligned)
- Description (left aligned)
- Column/resin (centered)
- AA sequence (most of these parts are very short, courier or other fixed width font, left aligned)
- Length (centered)
Parts to make
- [http://openwetware.org/wiki/Protein_purification_tags Protein purification tags]
- [http://openwetware.org/wiki/BBRFC14 Protein domains parts]
- [http://openwetware.org/wiki/SynBERC:MIT/Calendar/2007-8-8 Wishlist of wanted parts]
- [http://ca.expasy.org/tools/peptidecutter/peptidecutter_enzymes.html ExPASy PeptideCutter]: The cleavage specificities of selected enzymes and chemicals
- From Ron: KT3, His, VSV-G, S-tag, V5, HSV, T7, DDDK, Glu-Glu, HA, E-tag, Myc
- Of these tags, I think the widely used ones are FLAG, His, Myc, HA, and V5.
Parts that have been designed
The optimal second codon is AAA (Lys) in E. coli. So perhaps make all head domains start with Met-Lys?
- His tag: Part:BBa_T2000 | Part:BBa_T2001 | Part:BBa_T2002 (7xHis)
- FLAG tag: Part:BBa_T2003 | Part:BBa_T2004 | Part:BBa_T2005 (DYKDDDDK)
- C-Myc: Part:BBa_T2006 | Part:BBa_T2007 | Part:BBa_T2008 (EQKLISEEDL)
- HA tag: Part:BBa_T2009 | Part:BBa_T2010 | Part:BBa_T2011 (YPYDVPDYA)
- Strep-tag: Part:BBa_T2012 (WRHPQFGG, originally selected as AWRHPQFGG; can only be a tail domain)
- Strep-tag II: Part:BBa_T2013 | Part:BBa_T2014 (WSHPQFEK)
- S-tag: (KETAAAKFERQHMDS)
Codon selection
Rare is defined as less than 5%.
| Ala/A | GCU (rare in Rhodobacter), GCC, GCA (rare in Rhodobacter), GCG |
| Leu/L | UUA (rare in E. coli/Rhodobacter), UUG (rare in Rhodobacter), CUU, CUC, CUA (rare in E. coli/Chicken/Rhodobacter), CUG |
| Arg/R | CGU, CGC, CGA (rare in E. coli/Rhodobacter), CGG (rare in E. coli/Yeast), AGA (rare in E. coli/Rhodobacter), AGG (rare in E. coli/Rhodobacter) |
| Lys/K | AAA, AAG |
| Asn/N | AAU, AAC |
| Met/M | AUG |
| Asp/D | GAU, GAC |
| Phe/F | UUU, UUC |
| Cys/C | UGU, UGC |
| Pro/P | CCU (rare in Rhodobacter), CCC (rare in E. coli), CCA (rare in Rhodobacter), CCG |
| Gln/Q | CAA, CAG |
| Ser/S | UCU (rare in Rhodobacter), UCC, UCA (rare in Rhodobacter), UCG (rare in Chicken), AGU (rare in E. coli/Rhodobacter), AGC |
| Glu/E | GAA, GAG |
| Thr/T | ACU (rare in Rhodobacter), ACC, ACG, ACA (rare in E. coli) |
| Gly/G | GGU, GGC, GGA (rare in E. coli), GGG (rare in E. coli) |
| Trp/W | UGG |
| His/H | CAU, CAC |
| Tyr/Y | UAU, UAC |
| Ile/I | AUU, AUC, AUA (rare in E. coli/Rhodobacter) |
| Val/V | GUU (rare in Rhodobacter), GUC, GUA (rare in Rhodobacter), GUG |
| START | AUG |
| STOP | UAA, UGA, UAG (rare in Chicken) |