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= 028625
         (206 letters)

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

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



>pdb|4G91|C Chain C, Ccaat-Binding Complex From Aspergillus Nidulans
 pdb|4G92|C Chain C, Ccaat-Binding Complex From Aspergillus Nidulans With Dna
          Length = 119

 Score = 89.0 bits (219), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 47/98 (47%), Positives = 63/98 (64%), Gaps = 26/98 (26%)

Query: 43  FWSYQRQEIEQAN-DFKNHQLPLARIKKIMKADEDVRMISAE------------------ 83
           +W +    +E  N D+K HQLPLARIKK+MKAD +V+MISAE                  
Sbjct: 22  YWQHVINHLESDNHDYKIHQLPLARIKKVMKADPEVKMISAEAPILFAKGCDVFITELTM 81

Query: 84  -------ENKRRTLQKNDIAAAITRTDIFDFLVDIVPR 114
                  +NKRRTLQ++DIAAA++++D+FDFL+DIVPR
Sbjct: 82  RAWIHAEDNKRRTLQRSDIAAALSKSDMFDFLIDIVPR 119


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

 Score = 84.0 bits (206), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 46/86 (53%), Positives = 53/86 (61%), Gaps = 25/86 (29%)

Query: 54  ANDFKNHQLPLARIKKIMKADEDVRMISAE-------------------------ENKRR 88
             DF+  +LPLARIKKIMK DEDV+MISAE                         +NKRR
Sbjct: 9   VKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRR 68

Query: 89  TLQKNDIAAAITRTDIFDFLVDIVPR 114
           TLQ+NDIA AIT+ D FDFL+DIVPR
Sbjct: 69  TLQRNDIAMAITKFDQFDFLIDIVPR 94


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

 Score = 84.0 bits (206), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 46/86 (53%), Positives = 53/86 (61%), Gaps = 25/86 (29%)

Query: 54  ANDFKNHQLPLARIKKIMKADEDVRMISAE-------------------------ENKRR 88
             DF+  +LPLARIKKIMK DEDV+MISAE                         +NKRR
Sbjct: 12  VKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRR 71

Query: 89  TLQKNDIAAAITRTDIFDFLVDIVPR 114
           TLQ+NDIA AIT+ D FDFL+DIVPR
Sbjct: 72  TLQRNDIAMAITKFDQFDFLIDIVPR 97


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

 Score = 27.7 bits (60), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 12/24 (50%), Positives = 18/24 (75%)

Query: 59 NHQLPLARIKKIMKADEDVRMISA 82
          N + P ARIKKIM+ DE++  ++A
Sbjct: 9  NARFPPARIKKIMQTDEEIGKVAA 32


  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
   0.317    0.135    0.412 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,355,148
Number of Sequences: 62578
Number of extensions: 214877
Number of successful extensions: 413
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 403
Number of HSP's gapped (non-prelim): 8
length of query: 206
length of database: 14,973,337
effective HSP length: 94
effective length of query: 112
effective length of database: 9,091,005
effective search space: 1018192560
effective search space used: 1018192560
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)