GnuPG 2.1 no longer uses `~/.gnupg/secring.gpg`; instead, it uses separate files in ~/.gnupg/private-keys-v1.d`, with the help of its agent. There should have been an automatic migration at some point, however there are a number of scenarios where that misses some information (including the case where a private key is added using GnuPG 1 _after_ the 2.1 migration).
To resolve the issue, you should import your secret keyring:
gpg --import ~/.gnupg/secring.gpg
You’ll find more useful information in this handy GnuPG 2.1 migration guide, and in the release notes.
(I think it’s also worth mentioning that your secret keyring should never be exported to a public server, and that GnuPG itself will try to prevent you from doing so; thus you can’t rely on external sources of information as backups of your secret keys.)