| Background | The SARS-CoV genome contains five major open reading frames (ORFs) that encode the replicase polyprotein (R), the spike (S), envelope (E), and membrane (M) glycoproteins; and the nucleocapsid protein (N). Other proteins not falling into these categories have been termed PUPs (putative uncharacterized proteins) for their unknown structural or functional features and dissimilarity to those known sequences. However, it has been found that some of the PUPs matched the entries in the NCBI database. PUP1 is equivalent to ORF3 in Isolate Tor2. It receives 11 hits in GenBank through BLAST, two of which are putative transmembrane proteins. One is from Ralstonia solanacearum, cytochrome b-561, with 97 amino acids of PUP1 aligned, and the other is from Sinorhizobium meliloti, with 94 amino acids aligned. Sequence identities are 28% and 25%, respectively. Three putative transmembrane domains are located within PUP1. |
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