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= 002415
         (926 letters)

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

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



>pdb|3HO1|A Chain A, Crystal Structure Of T. Thermophilus Argonaute N546 Mutant
           Protein Complexed With Dna Guide Strand And 12-Nt Rna
           Target Strand
          Length = 685

 Score = 30.0 bits (66), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 26/86 (30%), Positives = 34/86 (39%), Gaps = 14/86 (16%)

Query: 42  AADGDGP----TLPSTELAHLLVSHICWDNHVPITWKFLEKALTLKIVPPSLVLALLSTR 97
           A  GDG     TLP  +    +   + WD      W F  KA  L    PS VL L + R
Sbjct: 493 AVGGDGGHLLWTLPEAQAGERIPQEVVWDLLEETLWAFRRKAGRL----PSRVLLLRNGR 548

Query: 98  VISNRQLHPAAYRLYLEFLTRHAFSF 123
           V  +       + L LE L R   ++
Sbjct: 549 VPQD------EFALALEALAREGIAY 568


  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
   0.319    0.134    0.401 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,005,383
Number of Sequences: 62578
Number of extensions: 954678
Number of successful extensions: 1903
Number of sequences better than 100.0: 1
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1903
Number of HSP's gapped (non-prelim): 1
length of query: 926
length of database: 14,973,337
effective HSP length: 108
effective length of query: 818
effective length of database: 8,214,913
effective search space: 6719798834
effective search space used: 6719798834
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)