Fig. 8.

Homology-based start codon checking for the detection of ORFs, which are too long. 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. The protein sequences are highly homologous. Residues conserved in all sequences are indicated by asterisks (lower alignment block). Spurious N-terminal sequence extensions are possible in three of the four species, but are considered to be incorrect as they are not homologous to each other (upper alignment block). Uppercase letters indicate the protein sequence as obtained from the current database, the first methionine being bold. The position of the probable initiator methionine in the current database sequence is indicated. Lowercase letters indicate gene extensions, which are possible but are considered spurious