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= psy17506
         (252 letters)

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

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



>pdb|3MMY|B Chain B, Structural And Functional Analysis Of The Interaction
           Between The Nucleoporin Nup98 And The Mrna Export Factor
           Rae1
 pdb|3MMY|D Chain D, Structural And Functional Analysis Of The Interaction
           Between The Nucleoporin Nup98 And The Mrna Export Factor
           Rae1
 pdb|3MMY|F Chain F, Structural And Functional Analysis Of The Interaction
           Between The Nucleoporin Nup98 And The Mrna Export Factor
           Rae1
 pdb|3MMY|H Chain H, Structural And Functional Analysis Of The Interaction
           Between The Nucleoporin Nup98 And The Mrna Export Factor
           Rae1
          Length = 56

 Score = 83.2 bits (204), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 37/52 (71%), Positives = 44/52 (84%)

Query: 160 IKFSPVTGTDTMMRGGSSQTINTRHVCITCMKEYENKSLEELRYEDYKANRK 211
           IKF+P TGTDTM++ G S  I+T+H CIT MKEYE+KSLEELR EDY+ANRK
Sbjct: 5   IKFNPPTGTDTMVKAGVSTNISTKHQCITAMKEYESKSLEELRLEDYQANRK 56


  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    0.124    0.355 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,542,582
Number of Sequences: 62578
Number of extensions: 167837
Number of successful extensions: 170
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 167
Number of HSP's gapped (non-prelim): 3
length of query: 252
length of database: 14,973,337
effective HSP length: 97
effective length of query: 155
effective length of database: 8,903,271
effective search space: 1380007005
effective search space used: 1380007005
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 50 (23.9 bits)