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= 047665
         (530 letters)

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

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



>pdb|1D3U|B Chain B, Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BBRE+TATA-
           Box Complex From Pyrococcus Woesei
          Length = 201

 Score = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 40/154 (25%), Positives = 64/154 (41%), Gaps = 8/154 (5%)

Query: 106 GDWFPILIGACSYVVMRLDDKSLPISEVASVLNCDVYELGRMITRVVEFLNLKLPEVDIV 165
           G     ++ AC Y   RL      + E+A +   D  E+GR    +   LNL  P+   V
Sbjct: 49  GRSIESVMAACVYAACRLLKVPRTLDEIADIARVDKKEIGRSYRFIARNLNL-TPKKLFV 107

Query: 166 SMFERVIRNSRLQGFTNLDESMLDRMRKQGVLLLNCAVKWFLTTGRRPMPXXXXXXXXXX 225
              + V + +   G +       +++R++ + +L+ A K  LT+G+ P            
Sbjct: 108 KPTDYVNKFADELGLS-------EKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIAS 160

Query: 226 XXXXXXXKIENVAKEVHCTVVTCRKRYKELLEAL 259
                      VA+    T VT R RYKEL+E L
Sbjct: 161 LLEGEKRTQREVAEVARVTEVTVRNRYKELVEKL 194


>pdb|1AIS|B Chain B, Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BTATA-Box
           Complex From Pyrococcus Woesei
          Length = 200

 Score = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 40/154 (25%), Positives = 64/154 (41%), Gaps = 8/154 (5%)

Query: 106 GDWFPILIGACSYVVMRLDDKSLPISEVASVLNCDVYELGRMITRVVEFLNLKLPEVDIV 165
           G     ++ AC Y   RL      + E+A +   D  E+GR    +   LNL  P+   V
Sbjct: 48  GRSIESVMAACVYAACRLLKVPRTLDEIADIARVDKKEIGRSYRFIARNLNL-TPKKLFV 106

Query: 166 SMFERVIRNSRLQGFTNLDESMLDRMRKQGVLLLNCAVKWFLTTGRRPMPXXXXXXXXXX 225
              + V + +   G +       +++R++ + +L+ A K  LT+G+ P            
Sbjct: 107 KPTDYVNKFADELGLS-------EKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIAS 159

Query: 226 XXXXXXXKIENVAKEVHCTVVTCRKRYKELLEAL 259
                      VA+    T VT R RYKEL+E L
Sbjct: 160 LLEGEKRTQREVAEVARVTEVTVRNRYKELVEKL 193


  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
   0.320    0.139    0.419 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,008,076
Number of Sequences: 62578
Number of extensions: 538797
Number of successful extensions: 1155
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1151
Number of HSP's gapped (non-prelim): 5
length of query: 530
length of database: 14,973,337
effective HSP length: 103
effective length of query: 427
effective length of database: 8,527,803
effective search space: 3641371881
effective search space used: 3641371881
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)