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