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= 042608
         (192 letters)

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

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



>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 = 42.7 bits (99), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 21/57 (36%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 20 FLGVRQRPSGRWVAEIKESSQK-LRLWLGTFDKXXXXXXXXXXXXRLLRGRNAKTNF 75
          + GVRQRP G++ AEI++ ++   R+WLGTF+               +RG  A  NF
Sbjct: 3  YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNF 59


>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 = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 20 FLGVRQRPSGRWVAEIKESSQ-KLRLWLGTFDKXXXXXXXXXXXXRLLRGRNAKTNF 75
          + GVRQRP G++ AEI++ ++   R+WLGTF+               +RG  A  NF
Sbjct: 6  YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNF 62


  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
   0.315    0.128    0.372 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,722,189
Number of Sequences: 62578
Number of extensions: 147285
Number of successful extensions: 213
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: 211
Number of HSP's gapped (non-prelim): 2
length of query: 192
length of database: 14,973,337
effective HSP length: 93
effective length of query: 99
effective length of database: 9,153,583
effective search space: 906204717
effective search space used: 906204717
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: 49 (23.5 bits)