Difference between revisions of "Talk:Protein domains"
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==Codon selection== | ==Codon selection== | ||
| − | {| | + | {| |
|+ | |+ | ||
Inverse table | Inverse table | ||
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! align="center" valign="top" | '''Ala/A''' | ! align="center" valign="top" | '''Ala/A''' | ||
| valign="top" | GCU, GCC, GCA, GCG | | valign="top" | GCU, GCC, GCA, GCG | ||
| + | |----- | ||
! align="center" valign="top" | '''Leu/L''' | ! align="center" valign="top" | '''Leu/L''' | ||
| valign="top" | UUA, UUG, CUU, CUC, CUA, CUG | | valign="top" | UUA, UUG, CUU, CUC, CUA, CUG | ||
| Line 80: | Line 81: | ||
! align="center" valign="top" | '''Arg/R''' | ! align="center" valign="top" | '''Arg/R''' | ||
| valign="top" | CGU, CGC, CGA, CGG, AGA, AGG | | valign="top" | CGU, CGC, CGA, CGG, AGA, AGG | ||
| + | |----- | ||
! width="50" align="center" valign="top" | '''Lys/K''' | ! width="50" align="center" valign="top" | '''Lys/K''' | ||
| width="205" valign="top" | AAA, AAG | | width="205" valign="top" | AAA, AAG | ||
| Line 85: | Line 87: | ||
! align="center" valign="top" | '''Asn/N''' | ! align="center" valign="top" | '''Asn/N''' | ||
| valign="top" | AAU, AAC | | valign="top" | AAU, AAC | ||
| + | |----- | ||
! align="center" valign="top" | '''Met/M''' | ! align="center" valign="top" | '''Met/M''' | ||
| valign="top" | AUG | | valign="top" | AUG | ||
| Line 90: | Line 93: | ||
! align="center" valign="top" | '''Asp/D''' | ! align="center" valign="top" | '''Asp/D''' | ||
| valign="top" | GAU, GAC | | valign="top" | GAU, GAC | ||
| + | |----- | ||
! align="center" valign="top" | '''Phe/F''' | ! align="center" valign="top" | '''Phe/F''' | ||
| valign="top" | UUU, UUC | | valign="top" | UUU, UUC | ||
| Line 95: | Line 99: | ||
! align="center" valign="top" | '''Cys/C''' | ! align="center" valign="top" | '''Cys/C''' | ||
| valign="top" | UGU, UGC | | valign="top" | UGU, UGC | ||
| + | |----- | ||
! align="center" valign="top" | '''Pro/P''' | ! align="center" valign="top" | '''Pro/P''' | ||
| valign="top" | CCU, CCC, CCA, CCG | | valign="top" | CCU, CCC, CCA, CCG | ||
| Line 100: | Line 105: | ||
! align="center" valign="top" | '''Gln/Q''' | ! align="center" valign="top" | '''Gln/Q''' | ||
| valign="top" | CAA, CAG | | valign="top" | CAA, CAG | ||
| + | |----- | ||
! align="center" valign="top" | '''Ser/S''' | ! align="center" valign="top" | '''Ser/S''' | ||
| valign="top" | UCU, UCC, UCA, UCG, AGU, AGC | | valign="top" | UCU, UCC, UCA, UCG, AGU, AGC | ||
| Line 105: | Line 111: | ||
! align="center" valign="top" | '''Glu/E''' | ! align="center" valign="top" | '''Glu/E''' | ||
| valign="top" | GAA, GAG | | valign="top" | GAA, GAG | ||
| + | |----- | ||
! align="center" valign="top" | '''Thr/T''' | ! align="center" valign="top" | '''Thr/T''' | ||
| valign="top" | ACU, ACC, ACA, ACG | | valign="top" | ACU, ACC, ACA, ACG | ||
| Line 110: | Line 117: | ||
! align="center" valign="top" | '''Gly/G''' | ! align="center" valign="top" | '''Gly/G''' | ||
| valign="top" | GGU, GGC, GGA, GGG | | valign="top" | GGU, GGC, GGA, GGG | ||
| + | |----- | ||
! align="center" valign="top" | '''Trp/W''' | ! align="center" valign="top" | '''Trp/W''' | ||
| valign="top" | UGG | | valign="top" | UGG | ||
| Line 115: | Line 123: | ||
! align="center" valign="top" | '''His/H''' | ! align="center" valign="top" | '''His/H''' | ||
| valign="top" | CAU, CAC | | valign="top" | CAU, CAC | ||
| + | |----- | ||
! align="center" valign="top" | '''Tyr/Y''' | ! align="center" valign="top" | '''Tyr/Y''' | ||
| valign="top" | UAU, UAC | | valign="top" | UAU, UAC | ||
| Line 120: | Line 129: | ||
! align="center" valign="top" | '''Ile/I''' | ! align="center" valign="top" | '''Ile/I''' | ||
| valign="top" | AUU, AUC, AUA | | valign="top" | AUU, AUC, AUA | ||
| + | |----- | ||
! align="center" valign="top" | '''Val/V''' | ! align="center" valign="top" | '''Val/V''' | ||
| valign="top" | GUU, GUC, GUA, GUG | | valign="top" | GUU, GUC, GUA, GUG | ||
| Line 125: | Line 135: | ||
! align="center" valign="top" | '''START''' | ! align="center" valign="top" | '''START''' | ||
| valign="top" | AUG | | valign="top" | AUG | ||
| + | |----- | ||
! align="center" valign="top" | '''STOP''' | ! align="center" valign="top" | '''STOP''' | ||
| valign="top" | UAA, UGA, UAG | | valign="top" | UAA, UGA, UAG | ||
|} | |} | ||
Revision as of 21:16, 1 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
| 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 |