Fig. 7.

Homology-based start codon checking for the detection of ORFs, which are too short. A sequence alignment of four homologous proteins of H. salinarum (strains R1 and NRC-1), N. pharaonis, H. walsbyi and H. marismortui is shown. Codes starting with OE are from H. salinarum strain R1, those with VNG from strain NRC-1, NP from N. pharaonis, HQ from H. walsbyi and those starting with rrnAC from H. marismortui. Uppercase letters indicate the protein sequence as obtained from the current database, the first methionine being bold. Lowercase letters indicate additional residues obtained by our correction of the start codon assignment. Residues conserved in all sequences are indicated by asterisks