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= 042240
         (241 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 = 50.4 bits (119), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 22/31 (70%), Positives = 24/31 (77%)

Query: 109 KTELCRSREEVGMCRFGTKCQFAHGKEELRS 139
           KTELCR  EE G C++G KCQFAHG  ELRS
Sbjct: 5   KTELCRPFEESGTCKYGEKCQFAHGFHELRS 35



 Score = 36.2 bits (82), Expect = 0.015,   Method: Composition-based stats.
 Identities = 13/28 (46%), Positives = 18/28 (64%)

Query: 109 KTELCRSREEVGMCRFGTKCQFAHGKEE 136
           KTELCR+   +G C +G +C F H  +E
Sbjct: 43  KTELCRTFHTIGFCPYGPRCHFIHNADE 70


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

 Score = 49.3 bits (116), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 21/30 (70%), Positives = 23/30 (76%)

Query: 109 KTELCRSREEVGMCRFGTKCQFAHGKEELR 138
           KTELCR+  E G CR+G KCQFAHG  ELR
Sbjct: 11  KTELCRTYSESGRCRYGAKCQFAHGLGELR 40



 Score = 30.4 bits (67), Expect = 0.83,   Method: Composition-based stats.
 Identities = 12/28 (42%), Positives = 16/28 (57%)

Query: 109 KTELCRSREEVGMCRFGTKCQFAHGKEE 136
           KTELC   +  G C +G++C F H   E
Sbjct: 49  KTELCHKFKLQGRCPYGSRCHFIHNPTE 76


  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
   0.314    0.128    0.381 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,381,604
Number of Sequences: 62578
Number of extensions: 149468
Number of successful extensions: 248
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 241
Number of HSP's gapped (non-prelim): 8
length of query: 241
length of database: 14,973,337
effective HSP length: 96
effective length of query: 145
effective length of database: 8,965,849
effective search space: 1300048105
effective search space used: 1300048105
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)