The document discusses five secondary structure prediction programs that were used to analyze the query sequence of a pilE protein. While most programs detected one long helix on the N-terminal side, some programs detected two shorter helices separated by a gap. This minor discrepancy can be explained by programs potentially interpreting two close helices as one long helix. When comparing predictions between homologous species, some structures may differ slightly. Additionally, secondary structure prediction is not always 100% accurate and errors can occur.