I have custom post types where I output the information via custom query to the database. How can I add the pagination block to this custom post type?

It is necessary to add function <?php if ( function_exists( 'pgntn_display_pagination' ) ) pgntn_display_pagination( 'custom', $second_query ); ?> to the necessary place. In this function, specify the name of your custom query to the database instead of $second_query. 

This article related to Pagination by BestWebSoft plugin

Additional resources: Pagination - User Guide

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