Trypsin is one member of the serine protease family,which is synthesized as proenzyme trypsinogen by pancreas.After being secreted into the intestine,enterokinase removes the N-terminal activation peptide converting it into its active form,trypsin which can specifically cleave at the peptide bond on the carboxyl side of basic L-amino acids such as arginine or lysine residues.Meanwhile,trypsin is one of the most abundant proteases in the digestive system of teleost fish,and plays important roles in the protein absorption from the diet.For further studying the physiological funtions and mechanism of trypsinogen in common carp(Cyprinus carpio),one of the most economically important fish in China,we got three distinct trypsinogen cDNAs(ccTRP1,ccTRP2 and ccTRP3)successfully using in silico cloning technique, and then they were analysed by the method of bioinformatics.The results showed that three of them had an open reading frame of 729 bp in length encoding 242 amino acids,the same sequence of a signal peptide consisted of 15 amino acids and an activation peptide of 5 amino acids,LDDDK.It also showed that they possessed the conserved domains of trypsinlike serine protease superfamily,and had the conversed structural characteristics,such as the catalytic triad(His-57,Asp-102,and Ser-195),12 cysteines forming 6 disulfide bonds,Asp-189 at the bottom of the substratebinding pocket and Gly-216 and Gly-226 lining the sides of the binding pocket,the motif of Gly-Asp-Ser-Gly-Gly-Pro in serine protease family,and so on.But,three of them also had some different characteristics with amino acid composition and phosphorylation sites.These results suggested that common carp trypsinogens we got in the present study may be functional,however,their funtions may be different to a certain degree.The analysis of GRAVY(grand average of hydropathicity)and the instability index indicated that they belonged to the hydrophilic and stable proteins.In the aspect of advanced structure,they mainly contained four secondary structural forms(alpha helix,extended strand,random coil and beta turn)by SOPMA software analysis,and the most abundant was random coil.The alignment and homology analysis based on the amino acid sequences revealed that it had the identity of beyond 90% among the three common carp trypsinogens,and ccTRP1 and ccTRP2 had the highest identity of 93%.Furhermore,compared to other species they had the highest identity with grass carp(Ctenopharyngodon idellus).Although both common carp and topmouth culter(Culter alburnus)blonged to Cyprinidae,they only had the identity of 66%,indicating that they may possess distinct property.The phylogenetic tree,based upon the alignment of amino acid sequences of trypsiongens,showed that three of them clustered with teleost anionic trypsinogen Group I,but the evolutional distances were not the same.These preliminary results from common carp trypsinogens by the method of bioinformatics can provide the foundations for further study of its expression profiles,the molecular characteristics and evolution of fish trypsinogen.