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= psy12385
         (188 letters)

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

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



>pdb|1JEQ|A Chain A, Crystal Structure Of The Ku Heterodimer
 pdb|1JEY|A Chain A, Crystal Structure Of The Ku Heterodimer Bound To Dna
          Length = 609

 Score = 26.9 bits (58), Expect = 6.9,   Method: Composition-based stats.
 Identities = 21/61 (34%), Positives = 29/61 (47%), Gaps = 15/61 (24%)

Query: 95  YISKII----DLLDTIFFVLRKKNSHITFLHVY-------HHAMMVLTTWAFLRYFKGEQ 143
           YISKII    DLL  +F+   K  + + F ++Y         A  +L     L  FKG+Q
Sbjct: 71  YISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILE----LDQFKGQQ 126

Query: 144 G 144
           G
Sbjct: 127 G 127


>pdb|3RFJ|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
           Receptors Of Jawless Vertebrates By Module Engineering
          Length = 279

 Score = 26.9 bits (58), Expect = 7.2,   Method: Compositional matrix adjust.
 Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 4/72 (5%)

Query: 64  NIKYIILAYNLIQTLYNANIVAYFCEASYLYYISKIIDLLDTIFFVLRKKNSHITFLHVY 123
           N+ Y+IL  N +Q+L N            +   +++  L D +F  L    +++T+L++Y
Sbjct: 86  NLTYLILTGNQLQSLPNGVFDKLTNLKELVLVENQLQSLPDGVFDKL----TNLTYLYLY 141

Query: 124 HHAMMVLTTWAF 135
           H+ +  L    F
Sbjct: 142 HNQLQSLPKGVF 153


>pdb|4DI7|A Chain A, Structure Of A2-type Ketoreductase Of Modular Polyketide
          Synthases
          Length = 556

 Score = 26.6 bits (57), Expect = 7.8,   Method: Compositional matrix adjust.
 Identities = 9/20 (45%), Positives = 12/20 (60%)

Query: 22 EHKVVDNWFLMPSWFPVTTI 41
          E   VD+W   P+W PVT +
Sbjct: 77 ERSTVDSWRYRPTWKPVTKL 96


  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
   0.331    0.143    0.460 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,434,742
Number of Sequences: 62578
Number of extensions: 198049
Number of successful extensions: 546
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 545
Number of HSP's gapped (non-prelim): 3
length of query: 188
length of database: 14,973,337
effective HSP length: 93
effective length of query: 95
effective length of database: 9,153,583
effective search space: 869590385
effective search space used: 869590385
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 48 (23.1 bits)