Domain search and domain prediction using ProFAT. (A) Results for Dip13α/APPL1 [GenBank:NP_036228] from a ProFAT domain search. RPS-BLAST identified a PH-domain and a PTB-domain in the input query, the N-terminal region does not contain any conserved domains with the chosen E-value cutoff (E <= 1E-04). The upper window gives the user a description of the domain as found in CDD by mousing over the domain box. The image represents the sequence with identified conserved domains. The table at the bottom lists the identified domains with their amino acid boundaries in the input sequence. By either activating the checkboxes or by clicking on the region and/or conserved domain on the image, the user can select conserved domains/regions for further processing by the Annotation Engine and/or Threading Engine (selectable by a check-box and activated by pressing the 'Submit' box). In this case, the N-terminal region from amino acid 1 to 280 was selected for further processing. (B) If no domain was identified, the user can perform Domain Prediction. In this case, a RPS-BLAST search with an E-value cutoff of 100 is used to identify weak domain hits. The consensus sequences of these domains are, in turn, submitted to a regular BLAST-search with subsequent text-mining for keywords occurring in the user-provided keyword list. In the case of the Dip13α/APPL1 N-terminal domain, RPS-BLAST finds SMC-domains, Biopterin_H, as well as a COG-domain. The identified domains can be submitted to the Annotation Engine and Threading Engine for a more detailed analysis (link 'Send to ProFAT').