Genome sequencing has identified open reading frames which belong to the ATP binding cassette (ABC) transporter family, but which are unlikely to be involved in transport phenomena. These frequently contain a pair of nucleotide binding domains (NBD) with no associated transmembrane domains. The functions of many of these twin-NBD proteins remain unknown. In this manuscript, sequence analysis has been employed to analyse two families of twin-NBD proteins, ABCE and ABCF. The ABCE proteins, postulated to be inhibitors of RNase L, are identified by two potential Fe-S metal-binding domains in addition to two NBDs. Surprisingly, ABCE homologues are identified in numerous species which apparently lack an RNase L, questioning the proposed function of these proteins. The ABCF proteins can be sub-divided into more than a dozen sub-classes. Intriguingly, sequence similarity is shown between eukaryotic ABCF proteins, which are involved in translation initiation and elongation, and prokaryotic ABCF proteins which are implicated in resistance to macrolide inhibitors of protein synthesis.