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= psy14070
(111 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1ZEJ|A Chain A, Crystal Structure Of The 3-Hydroxyacyl-Coa Dehydrogenase
(Hbd-9, Af2017) From Archaeoglobus Fulgidus Dsm 4304 At
2.00 A Resolution
Length = 293
Score = 26.2 bits (56), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 6/59 (10%)
Query: 53 NDRTRWLNSPNVWKGRKSNDRTRWLNSPNVYQKVEILETGTSDPKKITKVETLITSSSK 111
+D L+SP+ + G W N P+V VEI+ + +D K + VE + K
Sbjct: 113 DDIAERLDSPSRFLG------VHWXNPPHVXPLVEIVISRFTDSKTVAFVEGFLRELGK 165
>pdb|2XYM|A Chain A, Hcv-Jfh1 Ns5b T385a Mutant
Length = 563
Score = 25.8 bits (55), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 30/70 (42%), Gaps = 19/70 (27%)
Query: 15 GDPPRPRNDVEVPPAVSS-----LG------YLLEEE---EMYRNGWKGRKSNDRTRWLN 60
GDPPRP D+E+ + SS LG Y L + + R W+ + + WL
Sbjct: 351 GDPPRPEYDLELITSCSSNVSVALGPRGRRRYYLARDPTTPLARAAWETVRHSPINSWLG 410
Query: 61 -----SPNVW 65
+P +W
Sbjct: 411 NIIQYAPTIW 420
>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 = 25.4 bits (54), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 30/70 (42%), Gaps = 19/70 (27%)
Query: 15 GDPPRPRNDVEVPPAVSS-----LG------YLLEEE---EMYRNGWKGRKSNDRTRWLN 60
GDPPRP D+E+ + SS LG Y L + + R W+ + + WL
Sbjct: 351 GDPPRPEYDLELITSCSSNVSVALGPRGRRRYYLTRDPTTPLARAAWETVRHSPINSWLG 410
Query: 61 -----SPNVW 65
+P +W
Sbjct: 411 NIIQYAPTIW 420
>pdb|2XXD|A Chain A, Hcv-Jfh1 Ns5b Polymerase Structure At 1.9 Angstrom
Length = 563
Score = 25.4 bits (54), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 15 GDPPRPRNDVEVPPAVSS 32
GDPPRP D+E+ + SS
Sbjct: 351 GDPPRPEYDLELITSCSS 368
>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 = 25.4 bits (54), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 15 GDPPRPRNDVEVPPAVSS 32
GDPPRP D+E+ + SS
Sbjct: 353 GDPPRPEYDLELITSCSS 370
>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 = 25.4 bits (54), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 15 GDPPRPRNDVEVPPAVSS 32
GDPPRP D+E+ + SS
Sbjct: 353 GDPPRPEYDLELITSCSS 370
>pdb|2Y3C|A Chain A, Treponema Denticola Variable Protein 1
Length = 294
Score = 25.4 bits (54), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 32/72 (44%), Gaps = 4/72 (5%)
Query: 21 RNDVEV--PPAVSSLGYLLEEEEMYRNGWKGRKSNDRTRWLNSPNVW--KGRKSNDRTRW 76
ND + P VS YL+ E E+ + W+ N+ + + SP V +G++ + W
Sbjct: 44 HNDYSINQPHTVSLSAYLIGETEVTQELWQAVMGNNPSHFNGSPAVGETQGKRPVENVNW 103
Query: 77 LNSPNVYQKVEI 88
+ K+ I
Sbjct: 104 YQAIAFCNKLSI 115
>pdb|3NVN|A Chain A, Molecular Mechanism Of Guidance Cue Recognition
Length = 389
Score = 25.0 bits (53), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 69 KSNDRTRWLNSPNVYQKVEILETGTSDPKKITKV 102
K R +++ Y KV IL T T D K+I K+
Sbjct: 142 KDGVRGAFVDKDGTYDKVYILFTDTIDTKRIVKI 175
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
0.311 0.132 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,820,213
Number of Sequences: 62578
Number of extensions: 153897
Number of successful extensions: 231
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 230
Number of HSP's gapped (non-prelim): 8
length of query: 111
length of database: 14,973,337
effective HSP length: 75
effective length of query: 36
effective length of database: 10,279,987
effective search space: 370079532
effective search space used: 370079532
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 45 (21.9 bits)