Yes, you can include a tax_query, or you can include category parameters in your query if you are using the standard categories taxonomy.
However, if you’re using a custom post type I would suggest that you also use a custom taxonomy. The reason is that WP does not know how to tell the difference between standard posts and a custom post type when showing post categories and your custom posts will probably appear on your category archive pages.
For category parameters: https://codex.wordpress.org/Class_Reference/WP_Query#Category_Parameters
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