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= psy5540
         (135 letters)

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

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



>pdb|1R7R|A Chain A, The Crystal Structure Of Murine P97VCP AT 3.6A
          Length = 816

 Score = 26.2 bits (56), Expect = 6.7,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 23/54 (42%)

Query: 71  LFVLGALFRTSFSDPGVIPRATSDEAAFIETQIELKNVNLDSPTFRPPPRTKEI 124
           +F++GA  R    DP ++     D+  +I    E   V +     R  P  K++
Sbjct: 617 VFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDV 670


>pdb|3CF1|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX
 pdb|3CF1|B Chain B, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX
 pdb|3CF1|C Chain C, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX
 pdb|3CF2|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADPAMP-Pnp
 pdb|3CF2|B Chain B, Structure Of P97VCP IN COMPLEX WITH ADPAMP-Pnp
 pdb|3CF2|C Chain C, Structure Of P97VCP IN COMPLEX WITH ADPAMP-Pnp
 pdb|3CF2|D Chain D, Structure Of P97VCP IN COMPLEX WITH ADPAMP-Pnp
 pdb|3CF3|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADP
 pdb|3CF3|B Chain B, Structure Of P97VCP IN COMPLEX WITH ADP
 pdb|3CF3|C Chain C, Structure Of P97VCP IN COMPLEX WITH ADP
          Length = 806

 Score = 25.8 bits (55), Expect = 6.9,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 23/54 (42%)

Query: 71  LFVLGALFRTSFSDPGVIPRATSDEAAFIETQIELKNVNLDSPTFRPPPRTKEI 124
           +F++GA  R    DP ++     D+  +I    E   V +     R  P  K++
Sbjct: 617 VFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDV 670


  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
   0.328    0.142    0.450 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,944,161
Number of Sequences: 62578
Number of extensions: 137853
Number of successful extensions: 197
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: 194
Number of HSP's gapped (non-prelim): 3
length of query: 135
length of database: 14,973,337
effective HSP length: 88
effective length of query: 47
effective length of database: 9,466,473
effective search space: 444924231
effective search space used: 444924231
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 46 (22.3 bits)