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= 039729
         (179 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 =  102 bits (255), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 50/65 (76%), Positives = 55/65 (84%), Gaps = 1/65 (1%)

Query: 68  YRGVRRRPWGKFAAEIRDPNKKNGARVWLGTYDTPEGAALAYDRAAFNMRGSKAKLNFPH 127
           YRGVR+RPWGKFAAEIRDP  KNGARVWLGT++T E AALAYDRAAF MRGS+A LNFP 
Sbjct: 6   YRGVRQRPWGKFAAEIRDP-AKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFPL 64

Query: 128 LIGSN 132
            + S 
Sbjct: 65  RVNSG 69


>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 =  102 bits (254), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 49/59 (83%), Positives = 53/59 (89%), Gaps = 1/59 (1%)

Query: 68  YRGVRRRPWGKFAAEIRDPNKKNGARVWLGTYDTPEGAALAYDRAAFNMRGSKAKLNFP 126
           YRGVR+RPWGKFAAEIRDP  KNGARVWLGT++T E AALAYDRAAF MRGS+A LNFP
Sbjct: 3   YRGVRQRPWGKFAAEIRDP-AKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFP 60


  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
   0.313    0.129    0.370 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,108,788
Number of Sequences: 62578
Number of extensions: 198474
Number of successful extensions: 335
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 329
Number of HSP's gapped (non-prelim): 5
length of query: 179
length of database: 14,973,337
effective HSP length: 93
effective length of query: 86
effective length of database: 9,153,583
effective search space: 787208138
effective search space used: 787208138
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 bits)