Analysis a Functional Gene With Other Software/Websites OR On a Protein analysis Based

Thank you for the reply dear @Nicholas_Bokulich,

Could you please introduce software or a website to do this analyses?
Blast accepts only nucleotide sequences (it has a restricted input number and is time-consuming in process), while without feature table which represents OTUs counts, the analysis would not be ended. I had a look at the FunGene website; it acts like Blast. Similarly, it gets sequences (rep seq) only. I have been making an effort to end this analysis for above three months but I was unsuccessful sadly.
Have you got any solution?

I appreciate you and all members to give me a hand in advance.

Qiimer