Talk:Protein domains

Revision as of 21:14, 1 September 2009 by Rshetty (Talk | contribs)

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

Inverse table
Ala/A GCU, GCC, GCA, GCG Leu/L UUA, UUG, CUU, CUC, CUA, CUG
Arg/R CGU, CGC, CGA, CGG, AGA, AGG 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, CCC, CCA, CCG
Gln/Q CAA, CAG Ser/S UCU, UCC, UCA, UCG, AGU, AGC
Glu/E GAA, GAG Thr/T ACU, ACC, ACA, ACG
Gly/G GGU, GGC, GGA, GGG Trp/W UGG
His/H CAU, CAC Tyr/Y UAU, UAC
Ile/I AUU, AUC, AUA Val/V GUU, GUC, GUA, GUG
START AUG STOP UAA, UGA, UAG