Matching the names in BioPerl, Biopython has a SeqIO module for sequence file input/output, and AlignIO for multiple sequence alignment input/output. The third member of the BioPerl trio is SearchIO, and a Biopython equivalent is being worked on in summer 2012 by Google Summer of Code student Wibowo Arindrarto (blog).
The final module name in Biopython isn't settled, but Bio.SearchIO is being used initially. This will cover pairwise sequence search file input/output, for example from BLAST, HMMER or Bill Pearson's FASTA suite. See the BioPerl SearchIO HOWTO for background.
This was included in Biopython 1.61 onwards as an experimental module if you want to test it.