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= 046658
         (413 letters)

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

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



>pdb|1B92|A Chain A, Mobility Of An Hiv-1 Integrase Active Site Loop Is
           Correlated With Catalytic Activity
          Length = 163

 Score = 28.9 bits (63), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 4/67 (5%)

Query: 287 ELTFLEVKLAGSGWRVLPIILHSSPNLERLLVDKECWFEITKEQFGW---IESDCVPQCL 343
           E  +  +KLAG  W V  +   +  N     V   CW+   K++FG     +S  V + +
Sbjct: 47  ETAYFLLKLAGR-WPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQAVIESM 105

Query: 344 LQRVKKI 350
            + +KKI
Sbjct: 106 NKELKKI 112


  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
   0.325    0.138    0.430 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,653,872
Number of Sequences: 62578
Number of extensions: 452837
Number of successful extensions: 1135
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1134
Number of HSP's gapped (non-prelim): 3
length of query: 413
length of database: 14,973,337
effective HSP length: 101
effective length of query: 312
effective length of database: 8,652,959
effective search space: 2699723208
effective search space used: 2699723208
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: 53 (25.0 bits)