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
571,282 sequences; 206,678,396 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 resp... 30.0 0.083
sp|P0C6T7|R1A_BCRP3 Replicase polyprotein 1a OS=Bat coronavirus R... 26.9 1.1
sp|P0C6F8|R1A_BCHK3 Replicase polyprotein 1a OS=Bat coronavirus H... 26.9 1.1
sp|P0C6F5|R1A_BC279 Replicase polyprotein 1a OS=Bat coronavirus 2... 26.6 1.2
sp|P0C6U8|R1A_SARS Replicase polyprotein 1a OS=Severe acute respi... 26.6 1.2
>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 = 0.083, 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|P0C6T7|R1A_BCRP3 Replicase polyprotein 1a OS=Bat coronavirus
Rp3/2004 OX=349344 GN=1a PE=3 SV=1
Length=4380
Score = 26.9 bits (58), Expect = 1.1, 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|P0C6F8|R1A_BCHK3 Replicase polyprotein 1a OS=Bat coronavirus
HKU3 OX=442736 GN=1a PE=3 SV=1
Length=4376
Score = 26.9 bits (58), Expect = 1.1, 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|P0C6F5|R1A_BC279 Replicase polyprotein 1a OS=Bat coronavirus
279/2005 OX=389167 GN=1a PE=3 SV=1
Length=4388
Score = 26.6 bits (57), Expect = 1.2, 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
>sp|P0C6U8|R1A_SARS Replicase polyprotein 1a OS=Severe acute respiratory
syndrome coronavirus OX=694009 GN=1a PE=1 SV=1
Length=4382
Score = 26.6 bits (57), Expect = 1.2, 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
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: 2686819148
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 resp... 30.5 0.059
sp|P0C6F5|R1A_BC279 Replicase polyprotein 1a OS=Bat coronavirus 2... 27.0 0.86
sp|P0C6U8|R1A_SARS Replicase polyprotein 1a OS=Severe acute respi... 27.0 0.86
sp|P0C6T7|R1A_BCRP3 Replicase polyprotein 1a OS=Bat coronavirus R... 27.0 0.86
sp|P0C6F8|R1A_BCHK3 Replicase polyprotein 1a OS=Bat coronavirus H... 27.0 0.86
>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 = 0.059, 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|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 = 0.86, 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
>sp|P0C6U8|R1A_SARS Replicase polyprotein 1a OS=Severe acute respiratory
syndrome coronavirus OX=694009 GN=1a PE=1 SV=1
Length=4382
Score = 27.0 bits (58), Expect = 0.86, 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|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 = 0.86, 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|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 = 0.86, 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
Lambda K H a alpha
0.316 0.136 0.392 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: 2686819148
Search has CONVERGED!
Database: uniprot_sprot.fasta
Posted date: Apr 3, 2024 12:05 PM
Number of letters in database: 206,678,396
Number of sequences in database: 571,282
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Neighboring words threshold: 11
Window for multiple hits: 40