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= psy15067
         (80 letters)

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

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



>pdb|1RGO|A Chain A, Structural Basis For Recognition Of The Mrna Class Ii
          Au- Rich Element By The Tandem Zinc Finger Domain Of
          Tis11d
          Length = 70

 Score = 67.4 bits (163), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 27/46 (58%), Positives = 38/46 (82%)

Query: 15 DETGVCKFGTGCKFAHGAHELRVIPRHPRYRTKLCQSYHQDGFCPY 60
          +E+G CK+G  C+FAHG HELR + RHP+Y+T+LC+++H  GFCPY
Sbjct: 13 EESGTCKYGEKCQFAHGFHELRSLTRHPKYKTELCRTFHTIGFCPY 58


>pdb|1M9O|A Chain A, Nmr Structure Of The First Zinc Binding Domain Of
          Nup475TTPTIS11
          Length = 77

 Score = 55.5 bits (132), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 23/46 (50%), Positives = 31/46 (67%)

Query: 15 DETGVCKFGTGCKFAHGAHELRVIPRHPRYRTKLCQSYHQDGFCPY 60
           E+G C++G  C+FAHG  ELR   RHP+Y+T+LC  +   G CPY
Sbjct: 19 SESGRCRYGAKCQFAHGLGELRQANRHPKYKTELCHKFKLQGRCPY 64



 Score = 25.4 bits (54), Expect = 9.2,   Method: Compositional matrix adjust.
 Identities = 9/19 (47%), Positives = 14/19 (73%)

Query: 42 PRYRTKLCQSYHQDGFCPY 60
           RY+T+LC++Y + G C Y
Sbjct: 8  SRYKTELCRTYSESGRCRY 26


>pdb|2D9M|A Chain A, Solution Structure Of Ccch Type Zinc-Finger Domain 3 In
          Zinc Finger Ccch-Type Domain Containing 7a
          Length = 69

 Score = 26.2 bits (56), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 11/19 (57%), Positives = 11/19 (57%)

Query: 17 TGVCKFGTGCKFAHGAHEL 35
           G C  G  CKFAHG  EL
Sbjct: 28 NGTCPEGNSCKFAHGNAEL 46


  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
   0.327    0.147    0.510 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,944,464
Number of Sequences: 62578
Number of extensions: 106728
Number of successful extensions: 127
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 117
Number of HSP's gapped (non-prelim): 10
length of query: 80
length of database: 14,973,337
effective HSP length: 49
effective length of query: 31
effective length of database: 11,907,015
effective search space: 369117465
effective search space used: 369117465
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: 45 (21.9 bits)