Sandbox3H04: Difference between revisions

BLAST takes the exact amino acid chain of the protein and runs against a database to view similar sequences which may have similar function. When the chain was inputted into the BLAST software, the results were measured against a “score” showing the significant alignments as well as an E-score which helps show how good of a match it is. The one with the lowest E-score was E. coli MutT with a score of 3 x 10-88, showing that it is a great match. The total score was at the max value with 100% query coverage meaning the sequence was identical. The next several resulting sequences all belonged to Escherichia coli with extremely small E-values and nearly 100% coverage against the 3H04 sequence. The results came from the preliminary search with the MutT line for sequence, however another query was run based upon the PDB sequence which should have more specific results. Again the Escherichia coli appeared with incredible results for Chain A, Nucleoside Triphosphate pyrophosphohydrolase. A third query was used from the RCSB chain for 3H04 “MTEIKYKVITKDAFALPYTIIKAKNQPTKGVIVYIHGGGLMFGKANDLSPQYIDILTEHYDLIQLSYRLLPEVSLDCIIEDVYASFDAIQSQYSNCPIFTFGRSSGAYLSLLIARDRDIDG-VIDFYGYSRINTEPFKTTNSYYAKIAQSINETMIAQLTSPTPVVQDQIAQRFLIYVYARGTGKWINMINIADYTDSKYNIAPDELKTLPPVFIAHC-NGDYDVPVEESEHIMNHVPHSTFERVNKNEHDFDRRPNDEAITIYRKVVDFLNAITMV” which received a top hit of alpha/beta hydrolase [Staphylococcus] with a max score of 570, query coverage of 100%, and E-value of approximately 0.0. The result was incredible because it showed this is exactly where 3H04 arose based on the E-value and gave solid evidence that alpha/beta hydrolase was the function of 3H04.[[Image:INTERPRO.png |300px|center|thumb|]]