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= 016680
         (384 letters)

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

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



>pdb|1VOL|A Chain A, Tfiib (Human Core Domain)TBP (A.THALIANA)TATA ELEMENT
           Ternary Complex
          Length = 204

 Score = 30.8 bits (68), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 196 SIHELTLTKDEINLLQNKLDEKEKQLEGMAQENKSLKKQLNEASSNISTAQKEKEE 251
           +  E+T   D INL +NK+D +   L   A E KSLK + N+A ++       ++E
Sbjct: 5   AFKEITTMADRINLPRNKVD-RTNNLFRQAYEQKSLKGRANDAIASACLYIACRQE 59


  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
   0.306    0.127    0.347 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,423,717
Number of Sequences: 62578
Number of extensions: 344089
Number of successful extensions: 675
Number of sequences better than 100.0: 36
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 24
Number of HSP's that attempted gapping in prelim test: 654
Number of HSP's gapped (non-prelim): 42
length of query: 384
length of database: 14,973,337
effective HSP length: 101
effective length of query: 283
effective length of database: 8,652,959
effective search space: 2448787397
effective search space used: 2448787397
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (22.0 bits)
S2: 52 (24.6 bits)