This chapter explains techniques for recognition of nontrivial remote homology relationships involving proteins of Helicobacter pylori and their implications for function recognition. Using the remote homology detection method, employing multiple-profile representations for every protein domain family, remotely related domain family information has been assigned for the 122, 77, and 95 protein sequences of 26695, and J99, and HPAG1 strains of H. pylori, respectively. Relationships for some of the H. pylori protein sequences with Pfam domain families are reported for the first time. In publicly available domain databases such as Pfam, for some of the H. pylori protein sequences functional domain information is associated only with part(s) of the proteins. In the current study other parts of such proteins have been shown to be remotely related to known domain families, raising the possibility of identifying functions for parts of the proteins that do not yet have domains assigned. Further, homologues of enzymes that potentially catalyze step(s) in various metabolic processes in H. pylori have been identified for the first time.