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= psy936
         (344 letters)

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

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



>pdb|3KG2|A Chain A, Ampa Subtype Ionotropic Glutamate Receptor In Complex With
           Competitive Antagonist Zk 200775
 pdb|3KG2|B Chain B, Ampa Subtype Ionotropic Glutamate Receptor In Complex With
           Competitive Antagonist Zk 200775
 pdb|3KG2|C Chain C, Ampa Subtype Ionotropic Glutamate Receptor In Complex With
           Competitive Antagonist Zk 200775
 pdb|3KG2|D Chain D, Ampa Subtype Ionotropic Glutamate Receptor In Complex With
           Competitive Antagonist Zk 200775
          Length = 823

 Score = 85.5 bits (210), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 45/142 (31%), Positives = 72/142 (50%), Gaps = 14/142 (9%)

Query: 185 VMMKRPHESATGS-GLLAPFEIEVWFLILISLVLIGPIMHAIMRV-------------RR 230
           +M+K+P +S  G    L P   E+W  I+ + + +  ++  + R              R 
Sbjct: 493 IMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFEDGRE 552

Query: 231 WLSGTQSELYPISACTWFVYGALMKQGSTLNPRTDSTRIMFASWWIFIMILTAFYTANLT 290
             S   +  + I    WF  GA M+QG+ ++PR+ S RI+   WW F +I+ + YTANL 
Sbjct: 553 TQSSESTNEFGIFNSLWFSLGAFMQQGADISPRSLSGRIVGGVWWFFTLIIISSYTANLA 612

Query: 291 AFLTLSQFTLPIHSVEDIANPT 312
           AFLT+ +   PI S ED++  T
Sbjct: 613 AFLTVERMVSPIESAEDLSKQT 634


>pdb|3IF8|B Chain B, Crystal Structure Of Zwilch, A Member Of The Rzz
           Kinetochore
          Length = 257

 Score = 27.7 bits (60), Expect = 9.5,   Method: Compositional matrix adjust.
 Identities = 16/61 (26%), Positives = 32/61 (52%), Gaps = 4/61 (6%)

Query: 15  VYLIPDEHTRYQVDLTLTGRPDQAYQQSGLPDSWLIIEQLRLPIEPTIPSFLFQDQKPMS 74
           V  +P   +++++  +LT    + Y+Q+ L +  +     +LP+ PT    L+Q +KP  
Sbjct: 141 VSCMPFIKSQHELLFSLTQICIKYYKQNPLDEQHI----FQLPVRPTAVKNLYQSEKPQK 196

Query: 75  W 75
           W
Sbjct: 197 W 197


  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
   0.323    0.136    0.422 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,819,568
Number of Sequences: 62578
Number of extensions: 376339
Number of successful extensions: 645
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: 644
Number of HSP's gapped (non-prelim): 3
length of query: 344
length of database: 14,973,337
effective HSP length: 100
effective length of query: 244
effective length of database: 8,715,537
effective search space: 2126591028
effective search space used: 2126591028
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (24.6 bits)