Alexa ranks by domain name, so if you have subportal1.mysite.com and subportal2.mysite.com, or www.mysite.com/subportal1 and www.mysite.com/subportal2 then the answer is yes.

If a significant amount of traffic is split between hosts on the same domains then Alexa may split them, but it's not too common.

Here's how Alexa puts it:

What are sites and Web hosts?

Traffic is computed for sites, which are typically defined at the domain level. For example, the Web hosts www.msn.com, carpoint.msn.com and slate.msn.com are all treated as part of the same site, because they all reside on the same domain, msn.com. An exception is blogs or personal home pages, which are treated separately if they can be automatically identified as such from the URLs in question. Also, sites which are found to be serving the "same" content are generally counted together as the same site.

http://www.alexa.com/site/help/traffic_learn_more