View source for Talk:Protein domains

==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%.  Also checked Xenopus, human, mouse, B. subtilis, Drosophila, C. elegans, Pichia, Trichoplusia.

{| 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;" | GCU (rare in Rhodobacter/Streptomyces), GCC, GCA (rare in Rhodobacter/Streptomyces), GCG
|-----
| 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/Rhodobacter/Streptomyces/Trichoderma/Sf9 insect cells), UUG (rare in Rhodobacter/Streptomyces), CUU (rare in Streptomyces), CUC (rare in Plasmodium), CUA (rare in E. coli/Chicken/Rhodobacter/Streptomyces/Trichoderma/Sf9 insect cells), CUG (rare in Plasmodium)
|-----
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Arg/R'''
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | CGU (rare in Sf9 insect cells), CGC (rare in Plasmodium), CGA (rare in E. coli/Rhodobacter/Streptomyces/Sf9 insect cells), CGG (rare in E. coli/Yeast/Plasmodium/Sf9 insect cells), AGA (rare in E. coli/Rhodobacter/Streptomyces), AGG (rare in E. coli/Rhodobacter/Streptomyces)
|-----
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Lys/K'''
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | AAA, AAG
|-----
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Asn/N'''
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | AAU (rare in Streptomyces), AAC
|-----
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Met/M'''
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | AUG
|-----
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Asp/D'''
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | GAU, GAC
|-----
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Phe/F'''
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | UUU (rare in Streptomyces), UUC
|-----
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Cys/C'''
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | UGU, UGC
|-----
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Pro/P'''
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | CCU (rare in Rhodobacter/Streptomyces), CCC (rare in E. coli), CCA (rare in Rhodobacter/Streptomyces), CCG
|-----
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Gln/Q'''
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | CAA, CAG
|-----
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Ser/S'''
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | UCU (rare in Rhodobacter/Streptomyces), UCC, UCA (rare in Rhodobacter/Streptomyces), UCG (rare in Chicken/Sf9 insect cells), AGU (rare in E. coli/Rhodobacter/Streptomyces), AGC
|-----
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Glu/E'''
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | GAA, GAG
|-----
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Thr/T'''
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | ACU (rare in Rhodobacter/Streptomyces), ACC, ACG, ACA (rare in E. coli/Streptomyces)
|-----
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Gly/G'''
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | GGU, GGC, GGA (rare in E. coli), GGG (rare in E. coli/Sf9 insect cells)
|-----
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Trp/W'''
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | UGG
|-----
| '''His/H'''
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | CAU, CAC
|-----
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Tyr/Y'''
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" |  UAU, UAC
|-----
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Ile/I'''
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | AUU (rare in Streptomyces), AUC, AUA (rare in E. coli/Rhodobacter/Streptomyces)
|-----
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''Val/V'''
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | GUU (rare in Rhodobacter/Streptomyces), GUC, GUA (rare in Rhodobacter/Streptomyces/Trichoderma), GUG
|-----
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''START'''
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | AUG
|-----
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | '''STOP'''
| style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0;" | UAA, UGA, UAG (rare in Chicken)
|}