Prokaryotes	Eukaryotes
	Class 1	Class 2(TATA)	Class 3
Sigma region 1 Enhance specificity binding.		TFIIF
Sigma region 2.1 Binding to core element.	SL1
Sigma region 2.4 Recognizing –10 box.		TFIID	TFIIIC
Sigma region 3 Helix-turn-helix DNA binding domain.
Sigma region 4.2 Recognizing –35 box.			TFIIIC
Alpha Recognizing and binding to promoter UP element. Tighter binding between DNA and RNAP.	UBF UCE binding.	Sp1 GE binding.
Beta Active site DNA binding.
Beta ‘ Zinc finger conformationm.		TFIIE

＊ 以上的類比,不代表之間具有gene上的homology，純粹是功能上的類比。

最大比較：以上的prokaryotes功能,全部都在RNAP中的segments去完成；但eukaryores則必須用許多的transcription factors去輔助RNAP,而有recruitment的機制調控差異。