PSIBLAST 2.11.0+ Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Stephen F. Altschul, John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Reference for composition-based statistics starting in round 2: Alejandro A. Schaffer, L. Aravind, Thomas L. Madden, Sergei Shavirin, John L. Spouge, Yuri I. Wolf, Eugene V. Koonin, and Stephen F. Altschul (2001), "Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements", Nucleic Acids Res. 29:2994-3005. Database: uniprot_sprot.fasta 572,214 sequences; 207,235,166 total letters Results from round 1 Query= sp|P0DTF1|ORF3B_SARS2 Putative ORF3b protein OS=Severe acute respiratory syndrome coronavirus 2 OX=2697049 PE=5 SV=1 Length=22 Score E Sequences producing significant alignments: (Bits) Value sp|P0DTF1|ORF3B_SARS2 Putative ORF3b protein OS=Severe acute resp... 41.2 1e-06 sp|Q55C70|TIM50_DICDI Mitochondrial import inner membrane translo... 25.0 8.2 >sp|P0DTF1|ORF3B_SARS2 Putative ORF3b protein OS=Severe acute respiratory syndrome coronavirus 2 OX=2697049 PE=5 SV=1 Length=22 Score = 41.2 bits (95), Expect = 1e-06, Method: Compositional matrix adjust. Identities = 22/22 (100%), Positives = 22/22 (100%), Gaps = 0/22 (0%) Query 1 MMPTIFFAGILIVTTIVYLTIV 22 MMPTIFFAGILIVTTIVYLTIV Sbjct 1 MMPTIFFAGILIVTTIVYLTIV 22 >sp|Q55C70|TIM50_DICDI Mitochondrial import inner membrane translocase subunit tim50 OS=Dictyostelium discoideum OX=44689 GN=timm50 PE=3 SV=1 Length=374 Score = 25.0 bits (53), Expect = 8.2, Method: Composition-based stats. Identities = 9/17 (53%), Positives = 13/17 (76%), Gaps = 0/17 (0%) Query 4 TIFFAGILIVTTIVYLT 20 + FFAG+L+ +T YLT Sbjct 109 STFFAGVLVASTFGYLT 125 Lambda K H a alpha 0.345 0.155 0.442 0.792 4.96 Gapped Lambda K H a alpha sigma 0.267 0.0410 0.140 1.90 42.6 43.6 Effective search space used: 4559173652 Results from round 2 Query= sp|P0DTF1|ORF3B_SARS2 Putative ORF3b protein OS=Severe acute respiratory syndrome coronavirus 2 OX=2697049 PE=5 SV=1 Length=22 Score E Sequences producing significant alignments: (Bits) Value Sequences used in model and found again: sp|P0DTF1|ORF3B_SARS2 Putative ORF3b protein OS=Severe acute resp... 24.4 4.7 Sequences not found previously or not previously below threshold: >sp|P0DTF1|ORF3B_SARS2 Putative ORF3b protein OS=Severe acute respiratory syndrome coronavirus 2 OX=2697049 PE=5 SV=1 Length=22 Score = 24.4 bits (52), Expect = 4.7, Method: Composition-based stats. Identities = 22/22 (100%), Positives = 22/22 (100%), Gaps = 0/22 (0%) Query 1 MMPTIFFAGILIVTTIVYLTIV 22 MMPTIFFAGILIVTTIVYLTIV Sbjct 1 MMPTIFFAGILIVTTIVYLTIV 22 Lambda K H a alpha 0.316 0.158 0.514 0.792 4.96 Gapped Lambda K H a alpha sigma 0.267 0.0485 0.140 1.90 42.6 43.6 Effective search space used: 4559173652 Search has CONVERGED! Database: uniprot_sprot.fasta Posted date: Oct 6, 2024 4:14 PM Number of letters in database: 207,235,166 Number of sequences in database: 572,214 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Neighboring words threshold: 11 Window for multiple hits: 40