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= 038850
         (78 letters)

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

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



>pdb|1JFI|A Chain A, Crystal Structure Of The Nc2-Tbp-Dna Ternary Complex
          Length = 98

 Score = 42.4 bits (98), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 22/54 (40%), Positives = 32/54 (59%), Gaps = 5/54 (9%)

Query: 1  MPQEAEEQNTETTRPEFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFL 54
          MP + ++ N       FP  R+KKI++ DE+I KV +    I+SR+ ELFL  L
Sbjct: 1  MPSKKKKYNAR-----FPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESL 49


>pdb|1N1J|B Chain B, Crystal Structure Of The Nf-YbNF-Yc Histone Pair
          Length = 97

 Score = 39.3 bits (90), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 14/36 (38%), Positives = 28/36 (77%)

Query: 16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFL 51
          E P+ R+KKI+KLDED+  +++EA  + +++ ++F+
Sbjct: 19 ELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFI 54


>pdb|4AWL|C Chain C, The Nf-y Transcription Factor Is Structurally And
          Functionally A Sequence Specific Histone
          Length = 94

 Score = 39.3 bits (90), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 14/36 (38%), Positives = 28/36 (77%)

Query: 16 EFPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFL 51
          E P+ R+KKI+KLDED+  +++EA  + +++ ++F+
Sbjct: 16 ELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFI 51


>pdb|2BYK|A Chain A, Histone Fold Heterodimer Of The Chromatin Accessibility
          Complex
 pdb|2BYK|C Chain C, Histone Fold Heterodimer Of The Chromatin Accessibility
          Complex
 pdb|2BYM|A Chain A, Histone Fold Heterodimer Of The Chromatin Accessibility
          Complex
 pdb|2BYM|C Chain C, Histone Fold Heterodimer Of The Chromatin Accessibility
          Complex
          Length = 140

 Score = 38.1 bits (87), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 16/38 (42%), Positives = 26/38 (68%)

Query: 17 FPVGRVKKIIKLDEDINKVTSEALFIVSRSTELFLRFL 54
           P+ RV+ I+K   D   +T+E LF++++ TELF+R L
Sbjct: 20 LPLSRVRTIMKSSMDTGLITNEVLFLMTKCTELFVRHL 57


  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
   0.318    0.134    0.357 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,429,944
Number of Sequences: 62578
Number of extensions: 33229
Number of successful extensions: 67
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: 63
Number of HSP's gapped (non-prelim): 4
length of query: 78
length of database: 14,973,337
effective HSP length: 47
effective length of query: 31
effective length of database: 12,032,171
effective search space: 372997301
effective search space used: 372997301
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)