Application Example:
The human translationally controlled tumor protein (TCTP, P13693) was found to be expressed in human mammary carcinoma cells. It shares the translationally controlled tumour protein signature 1 (PROSITE ID TCTP_1) with 61 other proteins. Each of these proteins has a domain with a pattern represented by the regular expression [IFAED]-[GA]-[GASF]-N-[PAK]-S-[GTA]-E-[GDEVCF]-[PAGEQV]-[DEQGAV]. As protein databases grow, searching known patterns quickly and easily is crucial to finding novel candidates. To address this issue, SynaRex offers a simple web-based searching method for rapidly identifying motifs. By using PROSITE regular expressions as the input query, proteins with the TCTP_1 signature can be rapidly identified. By searching UniProtKB/Swiss-Prot Release 52.1, SynaRex identifies all 62 protein sequences that fit the regular expression defined above. These sequences can be further categorized into 37 distinct patterns (Figure 2). The protein sequence for P13693, together with 7 other mammalian and avian protein sequences has the pattern IGGNASAEGPE (Figure 3). Grouping the sequences into patterns assists further refinement of the understanding of protein function because proteins with diverged structures and overall functions may still have strong evolutionary pressure to conserve important domains. When compared to sequential search tools such as Fuzzpro (EMBOSS 4.1.0), under comparable environments, SynaRex reports results 400-fold faster with similar sensitivity.