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There are some things you can do, including using Wireshark to dig a bit further - you've done a good job being able to measure the delay so that's a great start. Get a good understanding the moving parts of the system. I imagine it will be something like this:

client PC ---> Reverse Proxy ---> TomCat ---> Database
                                ------------> Authentication

Using the above as an example (please check your topology though), trace the TCP flows between the Reverse Proxy and TomCat, TomCat to the Database and the Reverse Proxy to the Authentication solution. You can do this using tcpdump on the loopback adapter.

Run the loopback traces at the same time as the traces you were already collecting. Capture some examples of the problem. Start with your external trace to establish a time frame for the problem. So using your trace above as an example, establish the time frame as being from 07:57:30.799403 to 07:57:41.028342 - adjust for time sync difference between your external trace device and the Ubuntu clock. Now look in that time frame for similar delays in the TCP flows you have collected from the loopback adapter.

You can get a blow-by-blow explanation of multi-tier analysis like this in the Network Trace Analysis Guide you'll find here -

Best regards...Paul