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= psy16921
(235 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3I5K|A Chain A, Crystal Structure Of The Ns5b Polymerase From Hepatitis C
Virus (Hcv) Strain Jfh1
pdb|3I5K|B Chain B, Crystal Structure Of The Ns5b Polymerase From Hepatitis C
Virus (Hcv) Strain Jfh1
pdb|3I5K|C Chain C, Crystal Structure Of The Ns5b Polymerase From Hepatitis C
Virus (Hcv) Strain Jfh1
pdb|3I5K|D Chain D, Crystal Structure Of The Ns5b Polymerase From Hepatitis C
Virus (Hcv) Strain Jfh1
Length = 566
Score = 28.5 bits (62), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 85 KAGTKVHSFSNLIKGVGSPSFNSESLIKRFRLLKCNILLTIGLG--MVCY 132
+A T +HS + + VG P FNS+ +R + + +LT +G + CY
Sbjct: 248 EARTAIHSLTERLY-VGGPMFNSKGQTCGYRRCRASGVLTTSMGNTITCY 296
>pdb|4AEP|A Chain A, Hcv-Jfh1 Ns5b Polymerase Structure At 1.8 Angstrom
pdb|4AEX|A Chain A, Hcv-Jfh1 Ns5b Polymerase Structure At 2.4 Angstrom In A
Primitive Orthorhombic Space Group
pdb|4AEX|B Chain B, Hcv-Jfh1 Ns5b Polymerase Structure At 2.4 Angstrom In A
Primitive Orthorhombic Space Group
Length = 579
Score = 28.5 bits (62), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 85 KAGTKVHSFSNLIKGVGSPSFNSESLIKRFRLLKCNILLTIGLG--MVCY 132
+A T +HS + + VG P FNS+ +R + + +LT +G + CY
Sbjct: 250 EARTAIHSLTERLY-VGGPMFNSKGQTCGYRRCRASGVLTTSMGNTITCY 298
>pdb|2XXD|A Chain A, Hcv-Jfh1 Ns5b Polymerase Structure At 1.9 Angstrom
Length = 563
Score = 28.5 bits (62), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 85 KAGTKVHSFSNLIKGVGSPSFNSESLIKRFRLLKCNILLTIGLG--MVCY 132
+A T +HS + + VG P FNS+ +R + + +LT +G + CY
Sbjct: 248 EARTAIHSLTERLY-VGGPMFNSKGQTCGYRRCRASGVLTTSMGNTITCY 296
>pdb|2XYM|A Chain A, Hcv-Jfh1 Ns5b T385a Mutant
Length = 563
Score = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 85 KAGTKVHSFSNLIKGVGSPSFNSESLIKRFRLLKCNILLTIGLG--MVCY 132
+A T +HS + + VG P FNS+ +R + + +LT +G + CY
Sbjct: 248 EARTAIHSLTERLY-VGGPMFNSKGQTCGYRRCRASGVLTTSMGNTITCY 296
>pdb|4E76|A Chain A, Apo Crystal Structure Of Hcv Ns5b Genotype 2a Jfh-1
Isolate With Beta Hairpin Loop Deletion
pdb|4E78|A Chain A, Crystal Structure Of A Product State Assembly Of Hcv Ns5b
Genotype 2a Jfh-1 Isolate With Beta Hairpin Loop
Deletion Bound To Primer- Template Rna With 3'-Dg
pdb|4E7A|A Chain A, Crystal Structure Of A Product State Assembly Of Hcv Ns5b
Genotype 2a Jfh-1 Isolate With Beta Hairpin Deletion
Bound To Primer-Template Rna With A 2',3'-Ddc
Length = 572
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 85 KAGTKVHSFSNLIKGVGSPSFNSESLIKRFRLLKCNILLTIGLG--MVCY 132
+A T +HS + + VG P FNS+ +R + + +LT +G + CY
Sbjct: 250 EARTAIHSLTERLY-VGGPMFNSKGQTCGYRRCRASGVLTTSMGNTITCY 298
>pdb|2XWH|A Chain A, Hcv-J6 Ns5b Polymerase Structure At 1.8 Angstrom
Length = 563
Score = 28.5 bits (62), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 85 KAGTKVHSFSNLIKGVGSPSFNSESLIKRFRLLKCNILLTIGLG--MVCY 132
+A T +HS + + VG P FNS+ +R + + +LT +G + CY
Sbjct: 248 EAHTAIHSLTERLY-VGGPMFNSKGQTCGYRRCRASGVLTTSMGNTITCY 296
>pdb|4ADP|A Chain A, Hcv-J6 Ns5b Polymerase V405i Mutant
Length = 579
Score = 28.5 bits (62), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 85 KAGTKVHSFSNLIKGVGSPSFNSESLIKRFRLLKCNILLTIGLG--MVCY 132
+A T +HS + + VG P FNS+ +R + + +LT +G + CY
Sbjct: 250 EAHTAIHSLTERLY-VGGPMFNSKGQTCGYRRCRASGVLTTSMGNTITCY 298
>pdb|1YUY|A Chain A, Hepatitis C Virus Ns5b Rna-Dependent Rna Polymerase
Genotype 2a
pdb|1YV2|A Chain A, Hepatitis C Virus Ns5b Rna-dependent Rna Polymerase
Genotype 2a
pdb|1YVX|A Chain A, Hepatitis C Virus Rna Polymerase Genotype 2a In Complex
With Non- Nucleoside Analogue Inhibitor
pdb|1YVZ|A Chain A, Hepatitis C Virus Rna Polymerase Genotype 2a In Complex
With Non- Nucleoside Analogue Inhibitor
Length = 570
Score = 27.7 bits (60), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 85 KAGTKVHSFSNLIKGVGSPSFNSESLIKRFRLLKCNILLTIGLG--MVCY 132
+A T +HS + + VG P FNS+ +R + + +LT +G + CY
Sbjct: 248 EARTAIHSLTERLY-VGGPMFNSKGQSCGYRRCRASGVLTTSMGNTITCY 296
>pdb|2QEP|A Chain A, Crystal Structure Of The D1 Domain Of Ptprn2 (Ia2beta)
pdb|2QEP|B Chain B, Crystal Structure Of The D1 Domain Of Ptprn2 (Ia2beta)
Length = 304
Score = 27.7 bits (60), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 29/114 (25%), Positives = 52/114 (45%), Gaps = 9/114 (7%)
Query: 8 IVDFF-IFWNHLGICCVYINFIADNFDQACHHFSPDTSLAKIHWELIITVVMIVLNQVKN 66
+ DF+ + W + V + +A+N + C+H+ PD H I V +V +
Sbjct: 114 VADFWQMVWESGCVVIVMLTPLAENGVRQCYHYWPDEGSNLYH----IYEVNLVSEHIWC 169
Query: 67 LHFLSPFSSIESLINQRSKAGTKVHSFSNLIKGVGSPSFNSESLIK-RFRLLKC 119
FL +++L ++ T+ H S +GV S +S SL+ R ++ KC
Sbjct: 170 EDFLVRSFYLKNLQTNETRTVTQFHFLSWYDRGVPS---SSRSLLDFRRKVNKC 220
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
0.328 0.146 0.451
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,073,146
Number of Sequences: 62578
Number of extensions: 289527
Number of successful extensions: 530
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 530
Number of HSP's gapped (non-prelim): 11
length of query: 235
length of database: 14,973,337
effective HSP length: 96
effective length of query: 139
effective length of database: 8,965,849
effective search space: 1246253011
effective search space used: 1246253011
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 50 (23.9 bits)