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= psy6223
         (107 letters)

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

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



>pdb|1JE5|A Chain A, Crystal Structure Of Gp2.5, A Single-Stranded Dna Binding
           Protein Encoded By Bacteriophage T7
 pdb|1JE5|B Chain B, Crystal Structure Of Gp2.5, A Single-Stranded Dna Binding
           Protein Encoded By Bacteriophage T7
          Length = 206

 Score = 25.8 bits (55), Expect = 6.9,   Method: Compositional matrix adjust.
 Identities = 17/59 (28%), Positives = 24/59 (40%), Gaps = 8/59 (13%)

Query: 38  PIKPSLPPVAPGNTGPAPLLYKPIPQHQ-------KAANIVVADVLSEKCPPVPAVGGG 89
           P +  +P    G+ G     +K     Q       K  N+VV D   +K   VP +GGG
Sbjct: 89  PYEGDMPFFDNGD-GTTTFKFKCYASFQDKKTKETKHINLVVVDSKGKKMEDVPIIGGG 146


>pdb|1WHA|A Chain A, Solution Structure Of The Second Pdz Domain Of Human
           Scribble (Kiaa0147 Protein)
          Length = 105

 Score = 25.4 bits (54), Expect = 8.6,   Method: Compositional matrix adjust.
 Identities = 12/24 (50%), Positives = 14/24 (58%)

Query: 77  SEKCPPVPAVGGGGSTPHSPGDAG 100
           SE+       GG GSTP+  GDAG
Sbjct: 16  SERGLGFSIAGGKGSTPYRAGDAG 39


  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
   0.310    0.130    0.388 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,456,691
Number of Sequences: 62578
Number of extensions: 128945
Number of successful extensions: 283
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 278
Number of HSP's gapped (non-prelim): 9
length of query: 107
length of database: 14,973,337
effective HSP length: 72
effective length of query: 35
effective length of database: 10,467,721
effective search space: 366370235
effective search space used: 366370235
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 45 (21.9 bits)