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= 040188
         (117 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 = 95.5 bits (236), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 48/63 (76%), Positives = 50/63 (79%)

Query: 20 SKGNHSRGVRQTPSGKFAAEIRDPAKKGARCWLETFATAEQAALANVRAAFKFRGRRALL 79
          +KG H RGVRQ P GKFAAEIRDPAK GAR WL TF TAE AALA  RAAF+ RG RALL
Sbjct: 1  AKGKHYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALL 60

Query: 80 NFP 82
          NFP
Sbjct: 61 NFP 63


>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 = 90.9 bits (224), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 46/59 (77%), Positives = 47/59 (79%)

Query: 24 HSRGVRQTPSGKFAAEIRDPAKKGARCWLETFATAEQAALANVRAAFKFRGRRALLNFP 82
          H RGVRQ P GKFAAEIRDPAK GAR WL TF TAE AALA  RAAF+ RG RALLNFP
Sbjct: 2  HYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFP 60


>pdb|2GAH|A Chain A, Heterotetrameric Sarcosine: Structure Of A Diflavin
           Metaloenzyme At 1.85 A Resolution
          Length = 965

 Score = 29.6 bits (65), Expect = 0.40,   Method: Compositional matrix adjust.
 Identities = 15/41 (36%), Positives = 21/41 (51%)

Query: 20  SKGNHSRGVRQTPSGKFAAEIRDPAKKGARCWLETFATAEQ 60
             G  +R  R + SG+ A EI  PA  G R W + +A  E+
Sbjct: 765 DSGIEARISRISFSGELAFEIAVPAWHGLRVWEDVYAAGEE 805


>pdb|2GAG|A Chain A, Heteroteterameric Sarcosine: Structure Of A Diflavin
           Metaloenzyme At 1.85 A Resolution
          Length = 965

 Score = 28.1 bits (61), Expect = 1.3,   Method: Composition-based stats.
 Identities = 15/39 (38%), Positives = 21/39 (53%)

Query: 22  GNHSRGVRQTPSGKFAAEIRDPAKKGARCWLETFATAEQ 60
           G  +R  R + SG+ A EI  PA  G R W + +A  E+
Sbjct: 767 GIEARISRISFSGELAFEIAVPAWHGLRVWEDVYAAGEE 805


  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    0.130    0.388 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,205,689
Number of Sequences: 62578
Number of extensions: 103440
Number of successful extensions: 129
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 125
Number of HSP's gapped (non-prelim): 4
length of query: 117
length of database: 14,973,337
effective HSP length: 80
effective length of query: 37
effective length of database: 9,967,097
effective search space: 368782589
effective search space used: 368782589
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: 45 (21.9 bits)