-E 1000 HMM pfamseq</search_commands> <cutoffs> <gathering> <sequence>19.9</sequence> <domain>19.9</domain> </gathering> <trusted> <sequence>20.0</sequence> <domain>21.0</domain> </trusted> <noise> <sequence>18.6</sequence> <domain>19.5</domain> </noise> </cutoffs> </hmm_details> </entry> </pfam>% You can see the XML schema for this XML document here . Some Pfam families are removed or merged into others, in which case they become "dead" families. If you try