protein annotation tools (for machine learning purpose)

protein annotation tools (for machine learning purpose)
http://systers.molgen.mpg.de/cgi-bin/info.pl
http://pir.georgetown.edu/pirwww/search/batch.shtml
http://www.pir.uniprot.org/search/batch.shtml

already tried motif 1D to see if they have anything in common between proteins in fold#1,#2,#8, but there’s nothing in common.