| Sorting Signal Predictions |
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Motifs were those described as being involved in recognition of cargo by accessory proteins of COP and clathrin coated vesicles, as described by McMahon and Mills (2004) (PMID 15261670). The consensus motif sequences were converted to Perl regular expressions, and a Perl script was created to search for motifs in the protein sequences of the cytoplasmic regions of integral membrane proteins (except for KDEL, which was searched for in soluble secreted proteins).
| Motif Name | Regular Expression | Accessory
protein(s) | Region of protein searched |
Protein sorting |
| Lxx[L/M]E | L\w\w[LM]E | Sec24p | all cytoplasmic regions |
signals protein export from ER |
| NPVY | NPVY | ARH1/2 | all cytoplasmic regions |
signals internalization/endocytosis from plasma membrane |
| FxNPxY | F\wNP\wY | Dab2/Doc2 | all cytoplasmic regions |
signals internalization/endocytosis from plasma membrane |
| DxxLL | D\w\wLL\w{0,3}$ | GGA-1 | C-terminus |
signals TGN-endosome/lysosome sorting |
| KKxx | KK\w\w$ | aCOP | C-terminus |
signals retrograde transport from Golgi to ER |
| KxKxx | K\wK\w\w$ | a/b-COP | C-terminus |
signals retrograde transport from Golgi to ER |
| KDEL | [HK]DEL$ | KDEL-R | C-terminus |
ER localization signal |
| yxxΦ | Y\w\w[FIMLV] | AP1, AP2, AP3, AP4 | cytoplasmic tail |
signals TGN-endosome sorting, plasma membrane exocytosis, melanosome
biogenesis, basolateral sorting |
|
| [D/E]xxx[L/I] | [DE]\w\w\w[LI] | AP1, AP3 | cytoplasmic tail |
signals TGN-endosome sorting, melanosome biogenesis |
| [DE]xxxL[LI] | [DE]\w\w\wL[LI] | AP2, AP3 | cytoplasmic tail |
signals plasma membrane exocytosis, melanosome biogenesis |
| DxE | D\wE | Sec24p | cytoplasmic tail |
signals protein export from ER |
| xxRR | ^\w\w[KR][KR] | ER | N-terminus |
ER localization signal |
References:
COP and clathrin-coated vesicle budding: different pathways, common
approaches.
McMahon HT, Mills IG.
Curr Opin Cell Biol. 2004 Aug;16(4):379-91
PMID: 15261670
[Download
article]
Signals for sorting of transmembrane proteins to endosomes and lysosomes.
Bonifacino JS, Traub LM.
Annu Rev Biochem. 2003;72:395-447. Epub 2003 Mar 6
PMID: 12651740
[Download
article]
Signal-mediated sorting of membrane proteins between the endoplasmic reticulum
and the golgi apparatus.
Teasdale RD, Jackson MR.
Annu Rev Cell Dev Biol. 1996;12:27-54
PMID: 8970721
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Copyright 2004, 2005, 2006, 2007
Institute of Molecular Bioscience, The University of Queensland and
the ARC Centre in Bioinformatics
We gratefully acknowledge the support of the Australian Research Council.
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