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= 038285
         (178 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 = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 33/58 (56%), Gaps = 2/58 (3%)

Query: 24 YKGVRRRN-GKWVCELREPNKK-SRIWLGTFASPDKXXXXXXXXXXXXXGNSASLNFP 79
          Y+GVR+R  GK+  E+R+P K  +R+WLGTF + +              G+ A LNFP
Sbjct: 3  YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFP 60


>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 = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 33/58 (56%), Gaps = 2/58 (3%)

Query: 24 YKGVRRRN-GKWVCELREPNKK-SRIWLGTFASPDKXXXXXXXXXXXXXGNSASLNFP 79
          Y+GVR+R  GK+  E+R+P K  +R+WLGTF + +              G+ A LNFP
Sbjct: 6  YRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFP 63


>pdb|2ZVB|A Chain A, Crystal Structure Of Tt0207 From Thermus Thermophilus Hb8
 pdb|2ZVC|A Chain A, Form 2 Structure (C2221) Of Tt0207 From Thermus
           Thermophilus Hb8
          Length = 295

 Score = 28.5 bits (62), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 15/54 (27%), Positives = 26/54 (48%)

Query: 2   KSSTAQKRKAGRKKFQETRHPVYKGVRRRNGKWVCELREPNKKSRIWLGTFASP 55
           K + A   K+  +K QE      +G+R      +  +   N++SR + GTF +P
Sbjct: 205 KETPAALVKSAYRKRQEVALTTLEGLREAEAGMLTTVVIGNRQSRFYEGTFLTP 258


>pdb|2Q06|A Chain A, Crystal Structure Of Influenza A Virus H5n1 Nucleoprotein
 pdb|2Q06|B Chain B, Crystal Structure Of Influenza A Virus H5n1 Nucleoprotein
          Length = 504

 Score = 26.9 bits (58), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 16/34 (47%), Positives = 22/34 (64%), Gaps = 5/34 (14%)

Query: 17  QETRHPVYKGVRRRNGKWVCELREPNKKS--RIW 48
           ++T  P+Y   RRR+GKWV EL   +K+   RIW
Sbjct: 96  KKTGGPIY---RRRDGKWVRELILYDKEEIRRIW 126


  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
   0.316    0.131    0.398 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,287,381
Number of Sequences: 62578
Number of extensions: 124980
Number of successful extensions: 196
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 193
Number of HSP's gapped (non-prelim): 4
length of query: 178
length of database: 14,973,337
effective HSP length: 92
effective length of query: 86
effective length of database: 9,216,161
effective search space: 792589846
effective search space used: 792589846
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: 48 (23.1 bits)