Email and digitally submitted queries tend to get read and rejected more quickly than snail mail queries. For that reason, some writers will structure their email queries differently than paper queries; e.g., they will make them shorter or add more paragraph breaks to make it easier to read on a mobile device.
Either way, just for formatting purposes you may want to create two separate versions of your query letter, one for sending online and another that you print and mail.
The subject line for email queries should follow the submission guidelines for the agency. If there are not guidelines, then be clear and professional. Here are a few options for your subject line:
If you have an email address for an editor/agent who doesn’t accept email queries, you can try sending your query on a hope and a prayer, but you probably won’t receive a response. **In fact, I’ve heard many writers complain that they never receive a response from email queries. (Sometimes silence is the new rejection.) This is a phenomenon that must be regrettably accepted. Send one follow-up to inquire, but don’t keep sending emails to figure out if your query was received.