<p>I am new to gene ontology and was wondering the best tool to use to test if a gene set is enriched for certain GO terms in a non-model prokaryote?</p>

Not a lot is out there regarding gene set enrichment in Prokaryotes.

A few links that might be helpful and give you a push:

 - https://www.biostars.org/p/85909/
 - https://www.biostars.org/p/50960/

An excerpt from **Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists**

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2615629/

> Several enrichment tools were specifically designed for these less popular species, such as WEGO for rice ([54][1]); easyGO for crops ([66][2]); FINA for prokaryotes ([58][3]); CLENCH for Arabidopsis ([21][4]); JProGo for prokaryotes ([48][5]); BayGo for *Xylella fastidiosa* ([52][6]).

[Protein Localization Analysis of Essential Genes in Prokaryotes][7]

HTH

 [1]: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2615629/#B54
 [2]: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2615629/#B66
 [3]: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2615629/#B58
 [4]: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2615629/#B21
 [5]: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2615629/#B48
 [6]: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2615629/#B52
 [7]: http://www.nature.com/srep/2014/140808/srep06001/full/srep06001.html