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= 022511
         (296 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|3N6L|A Chain A, The Crystal Strucutre Of Rna-Dependent Rna Polymerase Of
           Ev71 Virus
 pdb|3N6M|A Chain A, Crystal Structure Of Ev71 Rdrp In Complex With Gtp
 pdb|3N6N|A Chain A, Crystal Structure Of Ev71 Rdrp In Complex With Br-Utp
          Length = 462

 Score = 34.3 bits (77), Expect = 0.093,   Method: Compositional matrix adjust.
 Identities = 16/38 (42%), Positives = 25/38 (65%)

Query: 126 FSFDLSGYSMALTSVFFQTMYLVLVEKSGAEDGLSSVE 163
           F+FD SGY  +L+ V+F+ + LVL E   +E  +S +E
Sbjct: 230 FAFDYSGYDASLSPVWFRALELVLREIGYSEGAISLIE 267


>pdb|2IJD|1 Chain 1, Crystal Structure Of The Poliovirus Precursor Protein 3cd
 pdb|2IJD|2 Chain 2, Crystal Structure Of The Poliovirus Precursor Protein 3cd
          Length = 644

 Score = 30.4 bits (67), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 14/46 (30%), Positives = 28/46 (60%), Gaps = 1/46 (2%)

Query: 126 FSFDLSGYSMALTSVFFQTMYLVLVEKSGAEDGLSSVEIMFYNSFL 171
           F+FD +GY  +L+  +F+ + +VL EK G  D +  ++ + ++  L
Sbjct: 413 FAFDYTGYDASLSPAWFEALKMVL-EKIGFGDRVDYIDYLNHSHHL 457


>pdb|2QMI|A Chain A, Structure Of The Octameric Penicillin-Binding Protein
           Homologue From Pyrococcus Abyssi
 pdb|2QMI|B Chain B, Structure Of The Octameric Penicillin-Binding Protein
           Homologue From Pyrococcus Abyssi
 pdb|2QMI|C Chain C, Structure Of The Octameric Penicillin-Binding Protein
           Homologue From Pyrococcus Abyssi
 pdb|2QMI|D Chain D, Structure Of The Octameric Penicillin-Binding Protein
           Homologue From Pyrococcus Abyssi
 pdb|2QMI|E Chain E, Structure Of The Octameric Penicillin-Binding Protein
           Homologue From Pyrococcus Abyssi
 pdb|2QMI|F Chain F, Structure Of The Octameric Penicillin-Binding Protein
           Homologue From Pyrococcus Abyssi
 pdb|2QMI|G Chain G, Structure Of The Octameric Penicillin-Binding Protein
           Homologue From Pyrococcus Abyssi
 pdb|2QMI|H Chain H, Structure Of The Octameric Penicillin-Binding Protein
           Homologue From Pyrococcus Abyssi
          Length = 447

 Score = 30.0 bits (66), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 29/129 (22%), Positives = 55/129 (42%), Gaps = 9/129 (6%)

Query: 56  PVSLFYNANVAFAL-----ASLKGVNIPMYIAIKRLTPLAVLVAGFFSGKGKPTTQVTLS 110
           P   F+  N  + L       + GV+   YI  K L PL +  + FF  + +    V + 
Sbjct: 154 PGERFFYLNTGYVLLGKIIEKVSGVSYEEYIKKKILEPLGMNRSYFFKEEVEKDKDVAMG 213

Query: 111 VLLTATGCVIAALGDFSFDLSGYSMALTSVFFQTMYLVL-VEKSGAEDGLSSVEIMFYNS 169
            +L   G ++     F + ++     L+SV     YL + +E+  +      +E M   S
Sbjct: 214 YILDKEGRLVPQ--PFPYGITADGGLLSSVLDLAKYLKMYIERDESIVSKEYIEKM-ETS 270

Query: 170 FLSLPFLVF 178
           ++ +P+ +F
Sbjct: 271 YIKVPWEIF 279


>pdb|3OL6|A Chain A, Poliovirus Polymerase Elongation Complex
 pdb|3OL6|E Chain E, Poliovirus Polymerase Elongation Complex
 pdb|3OL6|I Chain I, Poliovirus Polymerase Elongation Complex
 pdb|3OL6|M Chain M, Poliovirus Polymerase Elongation Complex
 pdb|3OL7|A Chain A, Poliovirus Polymerase Elongation Complex With Ctp
 pdb|3OL7|E Chain E, Poliovirus Polymerase Elongation Complex With Ctp
 pdb|3OL7|I Chain I, Poliovirus Polymerase Elongation Complex With Ctp
 pdb|3OL7|M Chain M, Poliovirus Polymerase Elongation Complex With Ctp
 pdb|3OL8|A Chain A, Poliovirus Polymerase Elongation Complex With Ctp-Mn
 pdb|3OL8|E Chain E, Poliovirus Polymerase Elongation Complex With Ctp-Mn
 pdb|3OL8|I Chain I, Poliovirus Polymerase Elongation Complex With Ctp-Mn
 pdb|3OL8|M Chain M, Poliovirus Polymerase Elongation Complex With Ctp-Mn
 pdb|3OL9|A Chain A, Poliovirus Polymerase Elongation Complex With 3'-Deoxy-Ctp
 pdb|3OL9|E Chain E, Poliovirus Polymerase Elongation Complex With 3'-Deoxy-Ctp
 pdb|3OL9|I Chain I, Poliovirus Polymerase Elongation Complex With 3'-Deoxy-Ctp
 pdb|3OL9|M Chain M, Poliovirus Polymerase Elongation Complex With 3'-Deoxy-Ctp
 pdb|3OLA|A Chain A, Poliovirus Polymerase Elongation Complex With 2'-Deoxy-Ctp
 pdb|3OLA|E Chain E, Poliovirus Polymerase Elongation Complex With 2'-Deoxy-Ctp
 pdb|3OLA|I Chain I, Poliovirus Polymerase Elongation Complex With 2'-Deoxy-Ctp
 pdb|3OLA|M Chain M, Poliovirus Polymerase Elongation Complex With 2'-Deoxy-Ctp
 pdb|3OLB|A Chain A, Poliovirus Polymerase Elongation Complex With
           2',3'-Dideoxy-Ctp
 pdb|3OLB|E Chain E, Poliovirus Polymerase Elongation Complex With
           2',3'-Dideoxy-Ctp
 pdb|3OLB|I Chain I, Poliovirus Polymerase Elongation Complex With
           2',3'-Dideoxy-Ctp
 pdb|3OLB|M Chain M, Poliovirus Polymerase Elongation Complex With
           2',3'-Dideoxy-Ctp
          Length = 471

 Score = 30.0 bits (66), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 14/46 (30%), Positives = 28/46 (60%), Gaps = 1/46 (2%)

Query: 126 FSFDLSGYSMALTSVFFQTMYLVLVEKSGAEDGLSSVEIMFYNSFL 171
           F+FD +GY  +L+  +F+ + +VL EK G  D +  ++ + ++  L
Sbjct: 230 FAFDYTGYDASLSPAWFEALKMVL-EKIGFGDRVDYIDYLNHSHHL 274


>pdb|1RDR|A Chain A, Poliovirus 3d Polymerase
          Length = 461

 Score = 30.0 bits (66), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 14/46 (30%), Positives = 28/46 (60%), Gaps = 1/46 (2%)

Query: 126 FSFDLSGYSMALTSVFFQTMYLVLVEKSGAEDGLSSVEIMFYNSFL 171
           F+FD +GY  +L+  +F+ + +VL EK G  D +  ++ + ++  L
Sbjct: 230 FAFDYTGYDASLSPAWFEALKMVL-EKIGFGDRVDYIDYLNHSHHL 274


>pdb|2IJF|A Chain A, Crystal Structure Of The Poliovirus Rna-Dependent Rna
           Polymerase Fidelity Mutant 3dpol G64s
          Length = 461

 Score = 30.0 bits (66), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 14/46 (30%), Positives = 28/46 (60%), Gaps = 1/46 (2%)

Query: 126 FSFDLSGYSMALTSVFFQTMYLVLVEKSGAEDGLSSVEIMFYNSFL 171
           F+FD +GY  +L+  +F+ + +VL EK G  D +  ++ + ++  L
Sbjct: 230 FAFDYTGYDASLSPAWFEALKMVL-EKIGFGDRVDYIDYLNHSHHL 274


>pdb|1RAJ|A Chain A, Poliovirus Polymerase With A 68 Residue N-terminal
           Truncation
          Length = 393

 Score = 30.0 bits (66), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 14/46 (30%), Positives = 28/46 (60%), Gaps = 1/46 (2%)

Query: 126 FSFDLSGYSMALTSVFFQTMYLVLVEKSGAEDGLSSVEIMFYNSFL 171
           F+FD +GY  +L+  +F+ + +VL EK G  D +  ++ + ++  L
Sbjct: 162 FAFDYTGYDASLSPAWFEALKMVL-EKIGFGDRVDYIDYLNHSHHL 206


>pdb|1TQL|A Chain A, Poliovirus Polymerase G1a Mutant
          Length = 461

 Score = 30.0 bits (66), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 14/46 (30%), Positives = 28/46 (60%), Gaps = 1/46 (2%)

Query: 126 FSFDLSGYSMALTSVFFQTMYLVLVEKSGAEDGLSSVEIMFYNSFL 171
           F+FD +GY  +L+  +F+ + +VL EK G  D +  ++ + ++  L
Sbjct: 230 FAFDYTGYDASLSPAWFEALKMVL-EKIGFGDRVDYIDYLNHSHHL 274


>pdb|1RA6|A Chain A, Poliovirus Polymerase Full Length Apo Structure
 pdb|1RA7|A Chain A, Poliovirus Polymerase With Gtp
 pdb|2ILY|A Chain A, Crystal Structure Of Poliovirus Polymerase Complexed With
           Atp And Mg2+
 pdb|2ILZ|A Chain A, Crystal Structure Of Poliovirus Polymerase Complexed With
           Gtp And Mn2+
 pdb|2IM0|A Chain A, Crystal Structure Of Poliovirus Polymerase Complexed With
           Ctp And Mg2+
 pdb|2IM1|A Chain A, Crystal Structure Of Poliovirus Polymerase Complexed With
           Ctp And Mn2+
 pdb|2IM2|A Chain A, Crystal Structure Of Poliovirus Polymerase Complexed With
           Utp And Mg2+
 pdb|2IM3|A Chain A, Crystal Structure Of Poliovirus Polymerase Complexed With
           Utp And Mn2+
          Length = 461

 Score = 29.6 bits (65), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 14/46 (30%), Positives = 28/46 (60%), Gaps = 1/46 (2%)

Query: 126 FSFDLSGYSMALTSVFFQTMYLVLVEKSGAEDGLSSVEIMFYNSFL 171
           F+FD +GY  +L+  +F+ + +VL EK G  D +  ++ + ++  L
Sbjct: 230 FAFDYTGYDASLSPAWFEALKMVL-EKIGFGDRVDYIDYLNHSHHL 274


  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
   0.326    0.139    0.394 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,012,153
Number of Sequences: 62578
Number of extensions: 191739
Number of successful extensions: 486
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 485
Number of HSP's gapped (non-prelim): 9
length of query: 296
length of database: 14,973,337
effective HSP length: 98
effective length of query: 198
effective length of database: 8,840,693
effective search space: 1750457214
effective search space used: 1750457214
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 bits)