should I continue the iteration of psiblast if the blast step produced only below threshold sequences? I used a PSIBLAST (position specific scoring) to detect the similarities between specific proteins and the database of Clostridium. 

The results did not reveal any similarities above the e value threshold of 0.001.

Could I continue iterations of the second and third round of PSIBLAST?
The first round of psiblast is the same as blastp and an evalue of 0.001 is low and below the recommended threshold of (e)-value = 0.005. 

You require significant knowledge of composition bias and globular domains to move into the 2nd and 3rd iterations. I'd recommend reading NCBI's manual here.



From you response you are using psiblast as a tool to look at antibody cross-reactivity, which I presume is pan-Clostridium. 

I  recommend using psi-blast as investigative analysis only and switching to the Immune Epitope Database here. Everything will be explained on the IEDB server. On this server I suggest performing two separate analyses and seeing whether the results correlate,


B-cell epitope prediction on your strongest evalue 
B-cell epitope prediction on your query sequence
Do the epitopes positions match?


If the epitope positions do not match then the hypothesis of a pan-Clostridium cross-reactive antibody can be immediately discarded. If there is a match it provides the basis for further investigation.

Please keep in mind Clostridium will use glycosylation to modulate antibody binding.