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= psy6889
         (166 letters)

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

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



>pdb|3PTR|B Chain B, Phf2 Jumonji Domain
 pdb|3PU3|A Chain A, Phf2 Jumonji Domain-Nog Complex
 pdb|3PU3|B Chain B, Phf2 Jumonji Domain-Nog Complex
 pdb|3PU8|B Chain B, Phf2 Jumonji-Nog-Fe(Ii) Complex
 pdb|3PU8|A Chain A, Phf2 Jumonji-Nog-Fe(Ii) Complex
 pdb|3PUA|A Chain A, Phf2 Jumonji-Nog-Ni(Ii)
 pdb|3PUS|A Chain A, Phf2 Jumonji-Nog-Ni(Ii)
 pdb|3PUS|B Chain B, Phf2 Jumonji-Nog-Ni(Ii)
          Length = 392

 Score = 26.9 bits (58), Expect = 5.7,   Method: Compositional matrix adjust.
 Identities = 13/50 (26%), Positives = 26/50 (52%), Gaps = 5/50 (10%)

Query: 17  LNGVFHKWSQNEGRSVRPSQISRSVRPSQ----IPRSVRPSQ-IPRSVRP 61
           LNG F  W++ +  +    ++    +PSQ    + + +R S+   ++VRP
Sbjct: 343 LNGAFRSWTKKQALAEHEDELPEHFKPSQLIKDLAKEIRLSENASKAVRP 392


  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
   0.314    0.132    0.383 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,772,867
Number of Sequences: 62578
Number of extensions: 180482
Number of successful extensions: 246
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: 245
Number of HSP's gapped (non-prelim): 3
length of query: 166
length of database: 14,973,337
effective HSP length: 92
effective length of query: 74
effective length of database: 9,216,161
effective search space: 681995914
effective search space used: 681995914
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 47 (22.7 bits)