PSIBLAST 2.2.27+


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
           562,253 sequences; 202,348,262 total letters

Results from round 1


Query= YP_009725312.1 nsp11 [Severe acute respiratory syndrome coronavirus
2]

Length=13
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

  sp|P0DTC1|R1A_SARS2 Replicase polyprotein 1a OS=Severe acute re...  30.0    0.44 


> sp|P0DTC1|R1A_SARS2 Replicase polyprotein 1a OS=Severe acute 
respiratory syndrome coronavirus 2 OX=2697049 PE=1 SV=1
Length=4405

 Score = 30.0 bits (66),  Expect = 0.44, Method: Composition-based stats.
 Identities = 13/13 (100%), Positives = 13/13 (100%), Gaps = 0/13 (0%)

Query  1     SADAQSFLNGFAV  13
             SADAQSFLNGFAV
Sbjct  4393  SADAQSFLNGFAV  4405



Lambda      K        H        a         alpha
   0.320    0.128    0.345    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: 2630527406
Results from round 2


Query= YP_009725312.1 nsp11 [Severe acute respiratory syndrome coronavirus
2]

Length=13
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

  sp|P0DTC1|R1A_SARS2 Replicase polyprotein 1a OS=Severe acute re...  30.5    0.32 
  sp|P0C6F8|R1A_BCHK3 Replicase polyprotein 1a OS=Bat coronavirus...  27.0    3.9  
  sp|P0C6T7|R1A_BCRP3 Replicase polyprotein 1a OS=Bat coronavirus...  27.0    3.9  
  sp|P0C6U8|R1A_CVHSA Replicase polyprotein 1a OS=Human SARS coro...  27.0    3.9  
  sp|P0C6F5|R1A_BC279 Replicase polyprotein 1a OS=Bat coronavirus...  27.0    3.9  


> sp|P0DTC1|R1A_SARS2 Replicase polyprotein 1a OS=Severe acute 
respiratory syndrome coronavirus 2 OX=2697049 PE=1 SV=1
Length=4405

 Score = 30.5 bits (67),  Expect = 0.32, Method: Composition-based stats.
 Identities = 13/13 (100%), Positives = 13/13 (100%), Gaps = 0/13 (0%)

Query  1     SADAQSFLNGFAV  13
             SADAQSFLNGFAV
Sbjct  4393  SADAQSFLNGFAV  4405


> sp|P0C6F8|R1A_BCHK3 Replicase polyprotein 1a OS=Bat coronavirus 
HKU3 OX=442736 GN=1a PE=3 SV=1
Length=4376

 Score = 27.0 bits (58),  Expect = 3.9, Method: Composition-based stats.
 Identities = 11/13 (85%), Positives = 12/13 (92%), Gaps = 0/13 (0%)

Query  1     SADAQSFLNGFAV  13
             SADA +FLNGFAV
Sbjct  4364  SADASTFLNGFAV  4376


> sp|P0C6T7|R1A_BCRP3 Replicase polyprotein 1a OS=Bat coronavirus 
Rp3/2004 OX=349344 GN=1a PE=3 SV=1
Length=4380

 Score = 27.0 bits (58),  Expect = 3.9, Method: Composition-based stats.
 Identities = 11/13 (85%), Positives = 12/13 (92%), Gaps = 0/13 (0%)

Query  1     SADAQSFLNGFAV  13
             SADA +FLNGFAV
Sbjct  4368  SADASTFLNGFAV  4380


> sp|P0C6U8|R1A_CVHSA Replicase polyprotein 1a OS=Human SARS coronavirus 
OX=694009 GN=1a PE=1 SV=1
Length=4382

 Score = 27.0 bits (58),  Expect = 3.9, Method: Composition-based stats.
 Identities = 11/13 (85%), Positives = 12/13 (92%), Gaps = 0/13 (0%)

Query  1     SADAQSFLNGFAV  13
             SADA +FLNGFAV
Sbjct  4370  SADASTFLNGFAV  4382


> sp|P0C6F5|R1A_BC279 Replicase polyprotein 1a OS=Bat coronavirus 
279/2005 OX=389167 GN=1a PE=3 SV=1
Length=4388

 Score = 27.0 bits (58),  Expect = 3.9, Method: Composition-based stats.
 Identities = 11/13 (85%), Positives = 12/13 (92%), Gaps = 0/13 (0%)

Query  1     SADAQSFLNGFAV  13
             SADA +FLNGFAV
Sbjct  4376  SADASTFLNGFAV  4388



Lambda      K        H        a         alpha
   0.320    0.128    0.345    0.792     4.96 

Gapped
Lambda      K        H        a         alpha    sigma
   0.267   0.0415    0.140     1.90     42.6     43.6 

Effective search space used: 2630527406

Search has CONVERGED!


  Database: uniprot_sprot.fasta
    Posted date:  Apr 29, 2020  7:48 PM
  Number of letters in database: 202,348,262
  Number of sequences in database:  562,253



Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Neighboring words threshold: 11
Window for multiple hits: 40