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= 040877
(281 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1CVR|A Chain A, Crystal Structure Of The Arg Specific Cysteine Proteinase
Gingipain R (Rgpb)
Length = 435
Score = 32.0 bits (71), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 27/53 (50%), Gaps = 12/53 (22%)
Query: 88 DLYSEGVI------YGYRSIGKVHVPL---KDLIDEFNGAVRFVRYQIRTGHG 131
D+ E VI YGY I K + P K++ID FNG + V Y TGHG
Sbjct: 163 DIQHENVIANLLTQYGYTKIIKCYDPGVTPKNIIDAFNGGISLVNY---TGHG 212
>pdb|2G36|A Chain A, Crystal Structure Of Tryptophanyl-Trna Synthetase (Ec
6.1.1.2) (Tryptophan-Trna Ligase)(Trprs) (Tm0492) From
Thermotoga Maritima At 2.50 A Resolution
Length = 340
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 24/48 (50%), Gaps = 6/48 (12%)
Query: 32 SIINGELKKKEQRQTCLQRQKTP--TDREGGGNPE----WNHMMKFDI 73
+IIN E+ +KE QT L+ P R GNPE W + FDI
Sbjct: 212 NIINLEISEKELEQTILRMMTDPARVRRSDPGNPENCPVWKYHQAFDI 259
>pdb|3MC4|A Chain A, Crystal Structure Of WwRSP5WWP DOMAIN: BACTERIAL
TRANSFERASE Hexapeptide Repeat: Serine
O-Acetyltransferase From Brucella Melitensis
pdb|3MC4|B Chain B, Crystal Structure Of WwRSP5WWP DOMAIN: BACTERIAL
TRANSFERASE Hexapeptide Repeat: Serine
O-Acetyltransferase From Brucella Melitensis
Length = 287
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 62 NPEWNHMMKFDIKAFVDN 79
NPEW+H+++ DI+A D
Sbjct: 97 NPEWSHVLRVDIQAVYDR 114
>pdb|3FK4|A Chain A, Crystal Structure Of Rubisco-Like Protein From Bacillus
Cereus Atcc 14579
pdb|3FK4|B Chain B, Crystal Structure Of Rubisco-Like Protein From Bacillus
Cereus Atcc 14579
Length = 414
Score = 28.1 bits (61), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 4/50 (8%)
Query: 197 PLPGFYSPPPNYQYEATRGYGTTLPPLSPVQVSSLMVASGSHYHPCPSPY 246
P+P P + Y A++ YG + SP+ + L+ +G+ + PSPY
Sbjct: 259 PVPIMAHPAVSGAYSASKLYGVS----SPLLLGKLLRYAGADFSLFPSPY 304
>pdb|2DXS|A Chain A, Crystal Structure Of Hcv Ns5b Rna Polymerase Complexed
With A Tetracyclic Inhibitor
pdb|2DXS|B Chain B, Crystal Structure Of Hcv Ns5b Rna Polymerase Complexed
With A Tetracyclic Inhibitor
Length = 552
Score = 27.3 bits (59), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 30/68 (44%), Gaps = 3/68 (4%)
Query: 119 VRFVRYQIRTGHGKPNGVLSFCYKLKGMTIKKGEIPSPEVCLSPGIHSSKEKVNYPCIEV 178
V F R Q+ H + VL K K T+K + E C HS+K K Y +V
Sbjct: 52 VTFDRLQVLDDHYR--DVLKE-MKAKASTVKAKLLSVEEACKLTPPHSAKSKFGYGAKDV 108
Query: 179 DDLSSPGI 186
+LSS +
Sbjct: 109 RNLSSKAV 116
>pdb|2WCX|A Chain A, Crystal Structure Of Hepatitis C Virus Ns5b Polymerase In
Complex With Thienopyrrole-Based Finger-Loop Inhibitors
pdb|2XWY|A Chain A, Structure Of Mk-3281, A Potent Non-Nucleoside Finger-Loop
Inhibitor, In Complex With The Hepatitis C Virus Ns5b
Polymerase
Length = 537
Score = 27.3 bits (59), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 30/68 (44%), Gaps = 3/68 (4%)
Query: 119 VRFVRYQIRTGHGKPNGVLSFCYKLKGMTIKKGEIPSPEVCLSPGIHSSKEKVNYPCIEV 178
V F R Q+ H + VL K K T+K + E C HS+K K Y +V
Sbjct: 53 VTFDRLQVLDDHYR--DVLKE-MKAKASTVKAKLLSVEEACKLTPPHSAKSKFGYGAKDV 109
Query: 179 DDLSSPGI 186
+LSS +
Sbjct: 110 RNLSSKAV 117
>pdb|1NHU|A Chain A, Hepatitis C Virus Rna Polymerase In Complex With Non-
Nucleoside Analogue Inhibitor
pdb|1NHU|B Chain B, Hepatitis C Virus Rna Polymerase In Complex With Non-
Nucleoside Analogue Inhibitor
pdb|1NHV|A Chain A, Hepatitis C Virus Rna Polymerase In Complex With Non-
Nucleoside Analogue Inhibitor
pdb|1NHV|B Chain B, Hepatitis C Virus Rna Polymerase In Complex With Non-
Nucleoside Analogue Inhibitor
Length = 578
Score = 27.3 bits (59), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 30/68 (44%), Gaps = 3/68 (4%)
Query: 119 VRFVRYQIRTGHGKPNGVLSFCYKLKGMTIKKGEIPSPEVCLSPGIHSSKEKVNYPCIEV 178
V F R Q+ H + VL K K T+K + E C HS+K K Y +V
Sbjct: 60 VTFDRLQVLDDHYR--DVLKE-MKAKASTVKAKLLSVEEACKLTPPHSAKSKFGYGAKDV 116
Query: 179 DDLSSPGI 186
+LSS +
Sbjct: 117 RNLSSKAV 124
>pdb|2BRK|A Chain A, Crystal Structure Of Hepatitis C Virus Polymerase In
Complex With An Allosteric Inhibitor (Compound 1)
pdb|2BRL|A Chain A, Crystal Structure Of Hepatitis C Virus Polymerase In
Complex With An Allosteric Inhibitor (Compound 2)
pdb|2WHO|A Chain A, Crystal Structure Of Hepatitis C Virus Ns5b Polymerase
From 1b Genotype In Complex With A Non-Nucleoside
Inhibitor
pdb|2WHO|B Chain B, Crystal Structure Of Hepatitis C Virus Ns5b Polymerase
From 1b Genotype In Complex With A Non-Nucleoside
Inhibitor
pdb|2WRM|A Chain A, Identification Of Novel Allosteric Inhibitors Of Hepatitis
C Virus Ns5b Polymerase Thumb Domain (Site Ii) By
Structure-Based Design
Length = 536
Score = 27.3 bits (59), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 30/68 (44%), Gaps = 3/68 (4%)
Query: 119 VRFVRYQIRTGHGKPNGVLSFCYKLKGMTIKKGEIPSPEVCLSPGIHSSKEKVNYPCIEV 178
V F R Q+ H + VL K K T+K + E C HS+K K Y +V
Sbjct: 52 VTFDRLQVLDDHYR--DVLKE-MKAKASTVKAKLLSVEEACKLTPPHSAKSKFGYGAKDV 108
Query: 179 DDLSSPGI 186
+LSS +
Sbjct: 109 RNLSSKAV 116
>pdb|4EO6|A Chain A, Hcv Ns5b Polymerase Inhibitors: Tri-Substituted
Acylhydrazines As Tertiary Amide Bioisosteres
pdb|4EO6|B Chain B, Hcv Ns5b Polymerase Inhibitors: Tri-Substituted
Acylhydrazines As Tertiary Amide Bioisosteres
pdb|4EO8|A Chain A, Hcv Ns5b Polymerase Inhibitors: Tri-Substituted
Acylhydrazines As Tertiary Amide Bioisosteres
pdb|4EO8|B Chain B, Hcv Ns5b Polymerase Inhibitors: Tri-Substituted
Acylhydrazines As Tertiary Amide Bioisosteres
Length = 577
Score = 27.3 bits (59), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 30/68 (44%), Gaps = 3/68 (4%)
Query: 119 VRFVRYQIRTGHGKPNGVLSFCYKLKGMTIKKGEIPSPEVCLSPGIHSSKEKVNYPCIEV 178
V F R Q+ H + VL K K T+K + E C HS+K K Y +V
Sbjct: 59 VTFDRLQVLDDHYR--DVLKE-MKAKASTVKAKLLSVEEACKLTPPHSAKSKFGYGAKDV 115
Query: 179 DDLSSPGI 186
+LSS +
Sbjct: 116 RNLSSKAV 123
>pdb|3HHK|A Chain A, Hcv Ns5b Polymerase Complex With A Substituted
Benzothiadizine
pdb|3HHK|B Chain B, Hcv Ns5b Polymerase Complex With A Substituted
Benzothiadizine
Length = 563
Score = 27.3 bits (59), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 30/68 (44%), Gaps = 3/68 (4%)
Query: 119 VRFVRYQIRTGHGKPNGVLSFCYKLKGMTIKKGEIPSPEVCLSPGIHSSKEKVNYPCIEV 178
V F R Q+ H + VL K K T+K + E C HS+K K Y +V
Sbjct: 52 VTFDRLQVLDDHYR--DVLKE-MKAKASTVKAKLLSVEEACKLTPPHSAKSKFGYGAKDV 108
Query: 179 DDLSSPGI 186
+LSS +
Sbjct: 109 RNLSSKAV 116
>pdb|2JC0|A Chain A, Crystal Structure Of Hepatitis C Virus Polymerase In
Complex With Inhibitor Sb655264
pdb|2JC0|B Chain B, Crystal Structure Of Hepatitis C Virus Polymerase In
Complex With Inhibitor Sb655264
pdb|2JC1|A Chain A, Crystal Structure Of Hepatitis C Virus Polymerase In
Complex With Inhibitor Sb698223
pdb|2JC1|B Chain B, Crystal Structure Of Hepatitis C Virus Polymerase In
Complex With Inhibitor Sb698223
Length = 570
Score = 27.3 bits (59), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 30/68 (44%), Gaps = 3/68 (4%)
Query: 119 VRFVRYQIRTGHGKPNGVLSFCYKLKGMTIKKGEIPSPEVCLSPGIHSSKEKVNYPCIEV 178
V F R Q+ H + VL K K T+K + E C HS+K K Y +V
Sbjct: 52 VTFDRLQVLDDHYR--DVLKE-MKAKASTVKAKLLSVEEACKLTPPHSAKSKFGYGAKDV 108
Query: 179 DDLSSPGI 186
+LSS +
Sbjct: 109 RNLSSKAV 116
>pdb|3BR9|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3BR9|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3BSA|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3BSA|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3BSC|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3BSC|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3CO9|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3CO9|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3CDE|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3CDE|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3CVK|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3CVK|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3CWJ|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3CWJ|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3D28|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Benzisothiazole Inhibitor
pdb|3D28|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Benzisothiazole Inhibitor
pdb|3D5M|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3D5M|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3E51|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3E51|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Pyridazinone Inhibitor
pdb|3GYN|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Monocyclic Dihydropyridinone Inhibitor
pdb|3GYN|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Monocyclic Dihydropyridinone Inhibitor
pdb|3H2L|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase In Complex With A
Novel Bicyclic Dihydro-Pyridinone Inhibitor
pdb|3H2L|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase In Complex With A
Novel Bicyclic Dihydro-Pyridinone Inhibitor
pdb|3IGV|A Chain A, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Monocyclic Dihydro-Pyridinone Inhibitor
pdb|3IGV|B Chain B, Crystal Structure Of Hcv Ns5b Polymerase With A Novel
Monocyclic Dihydro-Pyridinone Inhibitor
Length = 578
Score = 27.3 bits (59), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 30/68 (44%), Gaps = 3/68 (4%)
Query: 119 VRFVRYQIRTGHGKPNGVLSFCYKLKGMTIKKGEIPSPEVCLSPGIHSSKEKVNYPCIEV 178
V F R Q+ H + VL K K T+K + E C HS+K K Y +V
Sbjct: 52 VTFDRLQVLDDHYR--DVLKE-MKAKASTVKAKLLSVEEACKLTPPHSAKSKFGYGAKDV 108
Query: 179 DDLSSPGI 186
+LSS +
Sbjct: 109 RNLSSKAV 116
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
0.317 0.137 0.434
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,710,575
Number of Sequences: 62578
Number of extensions: 429545
Number of successful extensions: 859
Number of sequences better than 100.0: 39
Number of HSP's better than 100.0 without gapping: 34
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 783
Number of HSP's gapped (non-prelim): 63
length of query: 281
length of database: 14,973,337
effective HSP length: 98
effective length of query: 183
effective length of database: 8,840,693
effective search space: 1617846819
effective search space used: 1617846819
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)