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= 030875
         (170 letters)

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

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



>pdb|2PUS|A Chain A, Unprecedented Activation Mechanism Of A Non-Canonical
           Rna-Dependent Rna Polymerase
 pdb|2QJ1|A Chain A, Crystal Structure Of Infectious Bursal Disease Virus Vp1
           Polymerase Incubated With An Oligopeptide Mimicking The
           Vp3 C-Terminus
 pdb|2R70|A Chain A, Crystal Structure Of Infectious Bursal Disease Virus Vp1
           Polymerase, Cocrystallized With An Oligopeptide
           Mimicking The Vp3 C-Terminus.
 pdb|2R72|A Chain A, Crystal Structure Of Infectious Bursal Disease Virus Vp1
           Polymerase, Incubated With Mg2+ Ion
          Length = 852

 Score = 28.1 bits (61), Expect = 2.3,   Method: Composition-based stats.
 Identities = 13/43 (30%), Positives = 24/43 (55%), Gaps = 1/43 (2%)

Query: 121 EIDI-GWKDSNLRTLEVMTIIVSATQLFCTGAIHAGVEDAAWK 162
           E+D+ GW  +  + L +   ++   +LFC+ A   GVE+ + K
Sbjct: 574 ELDLLGWSATYSKDLGIYVPVLDKERLFCSAAYPKGVENKSLK 616


>pdb|2PGG|A Chain A, Crystal Structure Of A Birnavirus (Ibdv) Rna-Dependent Rna
           Polymerase Vp1
          Length = 774

 Score = 28.1 bits (61), Expect = 2.3,   Method: Composition-based stats.
 Identities = 13/43 (30%), Positives = 24/43 (55%), Gaps = 1/43 (2%)

Query: 121 EIDI-GWKDSNLRTLEVMTIIVSATQLFCTGAIHAGVEDAAWK 162
           E+D+ GW  +  + L +   ++   +LFC+ A   GVE+ + K
Sbjct: 537 ELDLLGWSATYSKDLGIYVPVLDKERLFCSAAYPKGVENKSLK 579


>pdb|2NY3|A Chain A, Hiv-1 Gp120 Envelope Glycoprotein (K231c, T257s, E267c,
           S334a, S375w) Complexed With Cd4 And Antibody 17b
          Length = 317

 Score = 27.7 bits (60), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 6/55 (10%)

Query: 112 LLAMGLACKEIDIGWKDSNLRTLEVMTIIV---SATQLFCTGAIHAGVEDAAWKR 163
           LL   LAC+E+ I  +  N  T    TIIV   ++ ++ CTGA H  +  A W  
Sbjct: 114 LLNGSLACEEVVI--RSVNF-TDNAKTIIVQLNTSVEINCTGAGHCNIARAKWNN 165


  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    0.137    0.430 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,981,108
Number of Sequences: 62578
Number of extensions: 124089
Number of successful extensions: 238
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 236
Number of HSP's gapped (non-prelim): 3
length of query: 170
length of database: 14,973,337
effective HSP length: 92
effective length of query: 78
effective length of database: 9,216,161
effective search space: 718860558
effective search space used: 718860558
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: 48 (23.1 bits)