BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., 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: Altschul, Stephen F.,
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.
Query= psy8719
(33 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|8OHM|A Chain A, Crystal Structure Of Rna Helicase From Genotype 1b
Hepatitis C Virus: Mechanism Of Unwinding Duplex Rna
Length = 435
Score = 27.7 bits (60), Expect = 1.9, Method: Composition-based stats.
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 3 RALIFCRTKLDCDNLERYLNSIDRRLIYYF 32
R LIFC +K CD L L+++ + Y+
Sbjct: 174 RHLIFCHSKKKCDELAAKLSALGLNAVAYY 203
>pdb|2ZJO|A Chain A, Crystal Structure Of Hepatitis C Virus Ns3 Helicase With A
Novel Inhibitor
Length = 482
Score = 27.3 bits (59), Expect = 2.3, Method: Composition-based stats.
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 3 RALIFCRTKLDCDNLERYLNSIDRRLIYYF 32
R LIFC +K CD L L+++ + Y+
Sbjct: 208 RHLIFCHSKKKCDELAAKLSALGIHAVAYY 237
>pdb|3KQL|A Chain A, Three Conformational Snapshots Of The Hepatitis C Virus
Ns3 Helicase Reveal A Ratchet Translocation Mechanism
pdb|3KQL|B Chain B, Three Conformational Snapshots Of The Hepatitis C Virus
Ns3 Helicase Reveal A Ratchet Translocation Mechanism
pdb|3KQN|A Chain A, Three Conformational Snapshots Of The Hepatitis C Virus
Ns3 Helicase Reveal A Ratchet Translocation Mechanism
pdb|3KQU|A Chain A, Three Conformational Snapshots Of The Hepatitis C Virus
Ns3 Helicase Reveal A Ratchet Translocation Mechanism
pdb|3KQU|B Chain B, Three Conformational Snapshots Of The Hepatitis C Virus
Ns3 Helicase Reveal A Ratchet Translocation Mechanism
pdb|3KQU|C Chain C, Three Conformational Snapshots Of The Hepatitis C Virus
Ns3 Helicase Reveal A Ratchet Translocation Mechanism
pdb|3KQU|D Chain D, Three Conformational Snapshots Of The Hepatitis C Virus
Ns3 Helicase Reveal A Ratchet Translocation Mechanism
pdb|3KQU|E Chain E, Three Conformational Snapshots Of The Hepatitis C Virus
Ns3 Helicase Reveal A Ratchet Translocation Mechanism
pdb|3KQU|F Chain F, Three Conformational Snapshots Of The Hepatitis C Virus
Ns3 Helicase Reveal A Ratchet Translocation Mechanism
Length = 437
Score = 26.9 bits (58), Expect = 2.8, Method: Composition-based stats.
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 3 RALIFCRTKLDCDNLERYLNSIDRRLIYYF 32
R LIFC +K CD L L+ + + Y+
Sbjct: 175 RHLIFCHSKKKCDELAAKLSGLGLNAVAYY 204
>pdb|3KQH|A Chain A, Three Conformational Snapshots Of The Hepatitis C Virus
Ns3 Helicase Reveal A Ratchet Translocation Mechanism
pdb|3KQH|B Chain B, Three Conformational Snapshots Of The Hepatitis C Virus
Ns3 Helicase Reveal A Ratchet Translocation Mechanism
pdb|3KQK|A Chain A, Three Conformational Snapshots Of The Hepatitis C Virus
Ns3 Helicase Reveal A Ratchet Translocation Mechanism
pdb|3KQK|B Chain B, Three Conformational Snapshots Of The Hepatitis C Virus
Ns3 Helicase Reveal A Ratchet Translocation Mechanism
Length = 436
Score = 26.9 bits (58), Expect = 2.8, Method: Composition-based stats.
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 3 RALIFCRTKLDCDNLERYLNSIDRRLIYYF 32
R LIFC +K CD L L+ + + Y+
Sbjct: 175 RHLIFCHSKKKCDELAAKLSGLGLNAVAYY 204
>pdb|2F55|A Chain A, Two Hepatitis C Virus Ns3 Helicase Domains Complexed With
The Same Strand Of Dna
pdb|2F55|B Chain B, Two Hepatitis C Virus Ns3 Helicase Domains Complexed With
The Same Strand Of Dna
pdb|2F55|C Chain C, Two Hepatitis C Virus Ns3 Helicase Domains Complexed With
The Same Strand Of Dna
Length = 435
Score = 26.6 bits (57), Expect = 3.4, Method: Composition-based stats.
Identities = 11/30 (36%), Positives = 15/30 (50%)
Query: 3 RALIFCRTKLDCDNLERYLNSIDRRLIYYF 32
R LIFC +K CD L L + + Y+
Sbjct: 174 RHLIFCHSKKKCDELAAKLTGLGLNAVAYY 203
>pdb|4B75|A Chain A, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
pdb|4B75|B Chain B, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
Length = 666
Score = 26.6 bits (57), Expect = 3.6, Method: Composition-based stats.
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 3 RALIFCRTKLDCDNLERYLNSIDRRLIYYF 32
R LIFC +K CD L L+ + + Y+
Sbjct: 398 RHLIFCHSKKKCDELAAKLSGLGINAVAYY 427
>pdb|4B6E|A Chain A, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
pdb|4B6E|B Chain B, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
pdb|4B6F|A Chain A, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
pdb|4B6F|B Chain B, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
Length = 683
Score = 26.6 bits (57), Expect = 3.6, Method: Composition-based stats.
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 3 RALIFCRTKLDCDNLERYLNSIDRRLIYYF 32
R LIFC +K CD L L+ + + Y+
Sbjct: 398 RHLIFCHSKKKCDELAAKLSGLGINAVAYY 427
>pdb|4A92|A Chain A, Full-Length Hcv Ns3-4a Protease-Helicase In Complex With A
Macrocyclic Protease Inhibitor.
pdb|4A92|B Chain B, Full-Length Hcv Ns3-4a Protease-Helicase In Complex With A
Macrocyclic Protease Inhibitor
Length = 666
Score = 26.6 bits (57), Expect = 3.6, Method: Composition-based stats.
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 3 RALIFCRTKLDCDNLERYLNSIDRRLIYYF 32
R LIFC +K CD L L+ + + Y+
Sbjct: 398 RHLIFCHSKKKCDELAAKLSGLGINAVAYY 427
>pdb|3O8B|A Chain A, Visualizing Atp-Dependent Rna Translocation By The Ns3
Helicase From Hcv
pdb|3O8B|B Chain B, Visualizing Atp-Dependent Rna Translocation By The Ns3
Helicase From Hcv
pdb|3O8C|A Chain A, Visualizing Atp-Dependent Rna Translocation By The Ns3
Helicase From Hcv
pdb|3O8C|B Chain B, Visualizing Atp-Dependent Rna Translocation By The Ns3
Helicase From Hcv
pdb|3O8D|A Chain A, Visualizing Atp-Dependent Rna Translocation By The Ns3
Helicase From Hcv
pdb|3O8D|B Chain B, Visualizing Atp-Dependent Rna Translocation By The Ns3
Helicase From Hcv
pdb|3O8R|A Chain A, Visualizing Atp-Dependent Rna Translocation By The Ns3
Helicase From Hcv
pdb|3O8R|B Chain B, Visualizing Atp-Dependent Rna Translocation By The Ns3
Helicase From Hcv
pdb|4B71|A Chain A, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
pdb|4B71|B Chain B, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
pdb|4B73|A Chain A, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
pdb|4B73|B Chain B, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
pdb|4B74|A Chain A, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
pdb|4B74|B Chain B, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
pdb|4B76|A Chain A, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
pdb|4B76|B Chain B, Discovery Of An Allosteric Mechanism For The Regulation Of
Hcv Ns3 Protein Function
Length = 666
Score = 26.6 bits (57), Expect = 3.6, Method: Composition-based stats.
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 3 RALIFCRTKLDCDNLERYLNSIDRRLIYYF 32
R LIFC +K CD L L+ + + Y+
Sbjct: 398 RHLIFCHSKKKCDELAAKLSGLGINAVAYY 427
>pdb|1CU1|A Chain A, Crystal Structure Of An Enzyme Complex From Hepatitis C
Virus
pdb|1CU1|B Chain B, Crystal Structure Of An Enzyme Complex From Hepatitis C
Virus
Length = 645
Score = 26.6 bits (57), Expect = 3.6, Method: Composition-based stats.
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 3 RALIFCRTKLDCDNLERYLNSIDRRLIYYF 32
R LIFC +K CD L L+ + + Y+
Sbjct: 377 RHLIFCHSKKKCDELAAKLSGLGINAVAYY 406
>pdb|1JR6|A Chain A, Solution Structure Of An Engineered Arginine-Rich
Subdomain 2 Of The Hepatitis C Virus Ns3 Rna Helicase
pdb|1ONB|A Chain A, Solution Structure Of An Engineered Arginine-Rich
Subdomain 2 Of The Hepatitis C Virus Ns3 Rna Helicase
Length = 142
Score = 25.8 bits (55), Expect = 6.5, Method: Composition-based stats.
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 3 RALIFCRTKLDCDNLERYLNSIDRRLIYYF 32
R LIFC +K CD L L ++ + Y+
Sbjct: 41 RHLIFCHSKKKCDELAAKLVALGINAVAYY 70
>pdb|1HEI|A Chain A, Structure Of The Hepatitis C Virus Rna Helicase Domain
pdb|1HEI|B Chain B, Structure Of The Hepatitis C Virus Rna Helicase Domain
Length = 451
Score = 25.8 bits (55), Expect = 6.5, Method: Composition-based stats.
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 3 RALIFCRTKLDCDNLERYLNSIDRRLIYYF 32
R LIFC +K CD L L ++ + Y+
Sbjct: 184 RHLIFCHSKKKCDELAAKLVALGINAVAYY 213
>pdb|1A1V|A Chain A, Hepatitis C Virus Ns3 Helicase Domain Complexed With
Single Stranded Sdna
Length = 476
Score = 25.8 bits (55), Expect = 6.5, Method: Composition-based stats.
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 3 RALIFCRTKLDCDNLERYLNSIDRRLIYYF 32
R LIFC +K CD L L ++ + Y+
Sbjct: 198 RHLIFCHSKKKCDELAAKLVALGINAVAYY 227
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.337 0.150 0.473
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 854,783
Number of Sequences: 62578
Number of extensions: 13654
Number of successful extensions: 80
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 67
Number of HSP's gapped (non-prelim): 13
length of query: 33
length of database: 14,973,337
effective HSP length: 7
effective length of query: 26
effective length of database: 14,535,291
effective search space: 377917566
effective search space used: 377917566
T: 11
A: 40
X1: 15 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.7 bits)
S2: 45 (21.9 bits)