Genbank and EMBL often change their file formats. Although often one needs to use sources from cvs, at least the releases would help in some cases. The distribution URL has changed. I'll upload my working ebuild now. Some modules are disabled in this release by default in contrast to 1.41. Maybe you want to re-enable some of them. See biopython mailing list archives for details.
Created attachment 93838 [details] biopython-1.42.ebuild
New version added to Portage. Thanks for reporting and sorry for the delay. I decided to stick with upstream's choices of modules for now. If people have particular needs, I will be happy to add USE flags or enable more modules by default.