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= 035609
         (181 letters)

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

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



>pdb|2KY6|A Chain A, Structure Of Arc92vbdMED25ACID
          Length = 166

 Score = 27.7 bits (60), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 20/74 (27%), Positives = 30/74 (40%), Gaps = 9/74 (12%)

Query: 115 SGVLLSWFPNIPWDRQPLSAIRDL---------CDPYLNLFRNIIPPVFDTLDVSPLLAF 165
           S  LL+W   + W  +P  A  D          C  Y+N   N+    +    +  L+  
Sbjct: 9   SNKLLAWSGVLEWQEKPKPASVDANTKLTRSLPCQVYVNHGENLKTEQWPQKLIMQLIPQ 68

Query: 166 AVLGTLGSILNNSR 179
            +L TLG +  NSR
Sbjct: 69  QLLTTLGPLFRNSR 82


>pdb|2L23|A Chain A, Nmr Structure Of The Acid (Activator Interacting Domain)
           Of The Human Mediator Med25 Protein
          Length = 167

 Score = 27.7 bits (60), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 20/74 (27%), Positives = 30/74 (40%), Gaps = 9/74 (12%)

Query: 115 SGVLLSWFPNIPWDRQPLSAIRDL---------CDPYLNLFRNIIPPVFDTLDVSPLLAF 165
           S  LL+W   + W  +P  A  D          C  Y+N   N+    +    +  L+  
Sbjct: 7   SNKLLAWSGVLEWQEKPKPASVDANTKLTRSLPCQVYVNHGENLKTEQWPQKLIMQLIPQ 66

Query: 166 AVLGTLGSILNNSR 179
            +L TLG +  NSR
Sbjct: 67  QLLTTLGPLFRNSR 80


>pdb|2L6U|A Chain A, Solution Nmr Structure Of Med25(391-543) Comprising The
           Activator- Interacting Domain (Acid) Of Human Mediator
           Subuniti 25. Northeast Structural Genomics Consortium
           Target Hr6188a
          Length = 163

 Score = 27.3 bits (59), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 20/74 (27%), Positives = 30/74 (40%), Gaps = 9/74 (12%)

Query: 115 SGVLLSWFPNIPWDRQPLSAIRDL---------CDPYLNLFRNIIPPVFDTLDVSPLLAF 165
           S  LL+W   + W  +P  A  D          C  Y+N   N+    +    +  L+  
Sbjct: 16  SNKLLAWSGVLEWQEKPKPASVDANTKLTRSLPCQVYVNHGENLKTEQWPQKLIMQLIPQ 75

Query: 166 AVLGTLGSILNNSR 179
            +L TLG +  NSR
Sbjct: 76  QLLTTLGPLFRNSR 89


>pdb|2XNF|A Chain A, The Mediator Med25 Activator Interaction Domain: Structure
           And Cooperative Binding Of Vp16 Subdomains
          Length = 159

 Score = 27.3 bits (59), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 20/74 (27%), Positives = 30/74 (40%), Gaps = 9/74 (12%)

Query: 115 SGVLLSWFPNIPWDRQPLSAIRDL---------CDPYLNLFRNIIPPVFDTLDVSPLLAF 165
           S  LL+W   + W  +P  A  D          C  Y+N   N+    +    +  L+  
Sbjct: 4   SNKLLAWSGVLEWQEKPKPASVDANTKLTRSLPCQVYVNHGENLKTEQWPQKLIMQLIPQ 63

Query: 166 AVLGTLGSILNNSR 179
            +L TLG +  NSR
Sbjct: 64  QLLTTLGPLFRNSR 77


  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
   0.324    0.139    0.437 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,757,515
Number of Sequences: 62578
Number of extensions: 184422
Number of successful extensions: 482
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 482
Number of HSP's gapped (non-prelim): 4
length of query: 181
length of database: 14,973,337
effective HSP length: 93
effective length of query: 88
effective length of database: 9,153,583
effective search space: 805515304
effective search space used: 805515304
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 48 (23.1 bits)