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= psy12387
         (98 letters)

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

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



>pdb|2JS7|A Chain A, Solution Nmr Structure Of Human Myeloid Differentiation
           Primary Response (Myd88). Northeast Structural Genomics
           Target Hr2869a
          Length = 160

 Score = 26.2 bits (56), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 9/22 (40%), Positives = 15/22 (68%)

Query: 10  NITNYLIETDHTDPRTRDWFWT 31
           +I  ++   D+T+P T+ WFWT
Sbjct: 122 SILRFITVCDYTNPCTKSWFWT 143


>pdb|2Z5V|A Chain A, Solution Structure Of The Tir Domain Of Human Myd88
          Length = 149

 Score = 25.8 bits (55), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 9/22 (40%), Positives = 15/22 (68%)

Query: 10  NITNYLIETDHTDPRTRDWFWT 31
           +I  ++   D+T+P T+ WFWT
Sbjct: 119 SILRFITVCDYTNPCTKSWFWT 140


  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
   0.330    0.145    0.504 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,140,143
Number of Sequences: 62578
Number of extensions: 110542
Number of successful extensions: 299
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 297
Number of HSP's gapped (non-prelim): 2
length of query: 98
length of database: 14,973,337
effective HSP length: 64
effective length of query: 34
effective length of database: 10,968,345
effective search space: 372923730
effective search space used: 372923730
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 45 (21.9 bits)