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= psy3261
         (342 letters)

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

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



>pdb|1SXJ|E Chain E, Crystal Structure Of The Eukaryotic Clamp Loader
          (Replication Factor C, Rfc) Bound To The Dna Sliding
          Clamp (Proliferating Cell Nuclear Antigen, Pcna)
          Length = 354

 Score = 33.1 bits (74), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 16/40 (40%), Positives = 25/40 (62%), Gaps = 3/40 (7%)

Query: 52 ELVGYLKSMTNFDRPSPRFVLYGEHGVGK---SMALVYAL 88
          EL  +LKS+++  R  P  +LYG +G GK    MAL+ ++
Sbjct: 21 ELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESI 60


>pdb|2E28|A Chain A, Crystal Structure Analysis Of Pyruvate Kinase From
           Bacillus Stearothermophilus
          Length = 587

 Score = 28.1 bits (61), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 12/30 (40%), Positives = 17/30 (56%)

Query: 103 WVLRWFAYPKEVSHSLTKEGMVDLNIDAAM 132
             L W  Y KE  H  T + M+D+ +DAA+
Sbjct: 412 LALVWGVYTKEAPHVNTTDEMLDVAVDAAV 441


>pdb|3NDY|A Chain A, The Structure Of The Catalytic And Carbohydrate Binding
           Domain Of Endoglucanase D From Clostridium Cellulovorans
 pdb|3NDY|B Chain B, The Structure Of The Catalytic And Carbohydrate Binding
           Domain Of Endoglucanase D From Clostridium Cellulovorans
 pdb|3NDY|C Chain C, The Structure Of The Catalytic And Carbohydrate Binding
           Domain Of Endoglucanase D From Clostridium Cellulovorans
 pdb|3NDY|D Chain D, The Structure Of The Catalytic And Carbohydrate Binding
           Domain Of Endoglucanase D From Clostridium Cellulovorans
 pdb|3NDZ|A Chain A, The Structure Of The Catalytic And Carbohydrate Binding
           Domain Of Endoglucanase D From Clostridium Cellulovorans
           Bound To Cellotriose
 pdb|3NDZ|B Chain B, The Structure Of The Catalytic And Carbohydrate Binding
           Domain Of Endoglucanase D From Clostridium Cellulovorans
           Bound To Cellotriose
 pdb|3NDZ|C Chain C, The Structure Of The Catalytic And Carbohydrate Binding
           Domain Of Endoglucanase D From Clostridium Cellulovorans
           Bound To Cellotriose
 pdb|3NDZ|D Chain D, The Structure Of The Catalytic And Carbohydrate Binding
           Domain Of Endoglucanase D From Clostridium Cellulovorans
           Bound To Cellotriose
          Length = 345

 Score = 27.7 bits (60), Expect = 9.3,   Method: Compositional matrix adjust.
 Identities = 21/99 (21%), Positives = 41/99 (41%), Gaps = 22/99 (22%)

Query: 240 RSVINLVQSDWNNGAIVLALSPRANLPDRRESHLPLYMLKKAGFE--------------- 284
           + ++N ++  WN G  + A+    N  +   +H  +  +K+AGF                
Sbjct: 13  QQIVNEMKVGWNLGNTMDAIGGETNWGNPMTTHAMINKIKEAGFNTLRLPVTWDGHMGAA 72

Query: 285 ---SIDPFVPIHVPELNDEEFHN----LLNLYESKKWLQ 316
              +ID      V E+ +  F N    ++NL+   +WL+
Sbjct: 73  PEYTIDQTWMKRVEEIANYAFDNDMYVIINLHHENEWLK 111


  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
   0.320    0.135    0.410 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,188,899
Number of Sequences: 62578
Number of extensions: 415904
Number of successful extensions: 961
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 954
Number of HSP's gapped (non-prelim): 12
length of query: 342
length of database: 14,973,337
effective HSP length: 100
effective length of query: 242
effective length of database: 8,715,537
effective search space: 2109159954
effective search space used: 2109159954
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)