I'm not sure where the timing comes from in Tomcat but the trace will be most, if not all, of the time the transaction took inside the JVM. Any other time is going to be network time, thinking time on client, basically anything that isn't happening inside Tomcat. Maybe there is some extra instrumentation that could pick out the rest of the time if it is an external call, but most recent agents (10.5.x) should be doing that anyway.
Any further details about what the application does, what the particular call does, could help.. if you can share an example of the trace, ideally as an XML export but a screenshot of trace view, showing as many layers of components as possible, would be a start.