Talk:Protein domains

Revision as of 13:13, 2 September 2009 by Rshetty (Talk | contribs) (→‎Codon selection)

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?

Codon selection

Rare is defined as less than 5%.

Ala/A GCU (rare in Rhodobacter/Streptomyces), GCC, GCA (rare in Rhodobacter/Streptomyces), GCG
Leu/L UUA (rare in E. coli/Rhodobacter/Streptomyces), UUG (rare in Rhodobacter/Streptomyces), CUU (rare in Streptomyces), CUC, CUA (rare in E. coli/Chicken/Rhodobacter/Streptomyces), CUG
Arg/R CGU, CGC, CGA (rare in E. coli/Rhodobacter/Streptomyces), CGG (rare in E. coli/Yeast), AGA (rare in E. coli/Rhodobacter/Streptomyces), AGG (rare in E. coli/Rhodobacter/Streptomyces)
Lys/K AAA, AAG
Asn/N AAU (rare in Streptomyces), AAC
Met/M AUG
Asp/D GAU, GAC
Phe/F UUU (rare in Streptomyces), UUC
Cys/C UGU, UGC
Pro/P CCU (rare in Rhodobacter/Streptomyces), CCC (rare in E. coli), CCA (rare in Rhodobacter/Streptomyces), CCG
Gln/Q CAA, CAG
Ser/S UCU (rare in Rhodobacter/Streptomyces), UCC, UCA (rare in Rhodobacter/Streptomyces), UCG (rare in Chicken), AGU (rare in E. coli/Rhodobacter/Streptomyces), AGC
Glu/E GAA, GAG
Thr/T ACU (rare in Rhodobacter/Streptomyces), ACC, ACG, ACA (rare in E. coli/Streptomyces)
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 (rare in Streptomyces), AUC, AUA (rare in E. coli/Rhodobacter/Streptomyces)
Val/V GUU (rare in Rhodobacter/Streptomyces), GUC, GUA (rare in Rhodobacter/Streptomyces), GUG
START AUG
STOP UAA, UGA, UAG (rare in Chicken)