Transforming the PhD thesis to a paper to publish and iThenticate
iThenticate might check your paper against your thesis.  Many universities send theses to Proquest, which shares them with iThenticate, as you mentioned.  However, you have no problem.  Most journals allow you to publish parts of your thesis as journal articles. If iThenticate tells the journal your paper is a copy of your thesis, they will ignore this information.  

You should check the policies of the journal before you submit your paper to it.