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= psy16238
         (123 letters)

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

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



>pdb|2YPD|A Chain A, Crystal Structure Of The Jumonji Domain Of Human Jumonji
           Domain Containing 1c Protein
 pdb|2YPD|B Chain B, Crystal Structure Of The Jumonji Domain Of Human Jumonji
           Domain Containing 1c Protein
          Length = 392

 Score = 25.8 bits (55), Expect = 7.0,   Method: Composition-based stats.
 Identities = 28/105 (26%), Positives = 42/105 (40%), Gaps = 10/105 (9%)

Query: 7   SLRWNNHQSHLLNAFDSLLQNETLVDV------TLARPRRRSGEACGAQDLSKCPAGSPD 60
           SL + +HQ+ LLN  DS++ N  + +          R + +SGE      L   P+G  D
Sbjct: 57  SLDFGDHQADLLNCKDSIISNANVKEFWDGFEEVSKRQKNKSGETV-VLKLKDWPSGE-D 114

Query: 61  AFIDGPEIPENLSTKKSGP--CTAENNNKTSAHNNNLKLRESLTP 103
                P   E+L      P  C  E     ++H     +R  L P
Sbjct: 115 FKTMMPARYEDLLKSLPLPEYCNPEGKFNLASHLPGFFVRPDLGP 159


  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
   0.309    0.125    0.373 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,860,999
Number of Sequences: 62578
Number of extensions: 146620
Number of successful extensions: 244
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 243
Number of HSP's gapped (non-prelim): 5
length of query: 123
length of database: 14,973,337
effective HSP length: 85
effective length of query: 38
effective length of database: 9,654,207
effective search space: 366859866
effective search space used: 366859866
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)