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| Title: | Annotatingproteins from Endoplasmic Reticulum and Golgi apparatus in eukaryotic proteomes |
| Author: | Kazimierz O Wrzeszczynski, amp; Burkhard Rost, |
| Quote: | quote_xx |
The sub-cellular localization of a native protein constitutes one coarse-grained aspect of its function. Transport between compartments is often regulated through short sequence motifs. Here, we analysed experimentally characterised ER/Golgi retrieval motifs and investigated the accuracy of homology-transfer. Only the C-terminal ER retrieval motifs KDEL, HDEL and AIAKE were sufficiently specific. However, even unspecific motifs may help, provided we know the probability for localization given this motif. We provided such estimates. We also rigorously estimated the accuracy and coverage for inferring ER and Golgi localization through homology-transfer by sequence similarity. In entire proteomes, we could thereby annotate 3304 ER (3182 membrane) and 1853 Golgi proteins (759 membrane). We identified another 5157 globular and 3941 membrane putative ER or Golgi proteins. Each experimental annotation yielded, on average, 1-3 high-accuracy and 5-6 low-accuracy homology-transfers in the six proteomes. These numbers will increase with each new experimental annotation.