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= 026240
         (241 letters)

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

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



>pdb|2GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr,
          Minimized Mean Structure
 pdb|3GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr,
          46 Structures
          Length = 70

 Score = 65.9 bits (159), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/64 (50%), Positives = 40/64 (62%), Gaps = 1/64 (1%)

Query: 21 VKEVHFRGVRKRPWGRYAAEIRDPGKK-SRVWLGTFDTXXXXXXXXXXXXXXXXGAKAKT 79
           K  H+RGVR+RPWG++AAEIRDP K  +RVWLGTF+T                G++A  
Sbjct: 1  AKGKHYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALL 60

Query: 80 NFPL 83
          NFPL
Sbjct: 61 NFPL 64


>pdb|1GCC|A Chain A, Solution Nmr Structure Of The Complex Of Gcc-Box Binding
          Domain Of Aterf1 And Gcc-Box Dna, Minimized Average
          Structure
          Length = 63

 Score = 65.5 bits (158), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/60 (51%), Positives = 39/60 (65%), Gaps = 1/60 (1%)

Query: 25 HFRGVRKRPWGRYAAEIRDPGKK-SRVWLGTFDTXXXXXXXXXXXXXXXXGAKAKTNFPL 83
          H+RGVR+RPWG++AAEIRDP K  +RVWLGTF+T                G++A  NFPL
Sbjct: 2  HYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFPL 61


  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    0.136    0.418 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,569,959
Number of Sequences: 62578
Number of extensions: 154522
Number of successful extensions: 247
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 243
Number of HSP's gapped (non-prelim): 2
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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)