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= psy7121
         (79 letters)

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

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



>pdb|4GWP|G Chain G, Structure Of The Mediator Head Module From S. Cerevisiae
 pdb|4GWQ|G Chain G, Structure Of The Mediator Head Module From S. Cerevisiae
           In Complex With The Carboxy-Terminal Domain (Ctd) Of Rna
           Polymerase Ii Rpb1 Subunit
          Length = 295

 Score = 58.5 bits (140), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 45/77 (58%), Gaps = 8/77 (10%)

Query: 9   LHVQEPILNMTGLEYIVLHVQEPILYVIRKQHRHSME--------QTTPIADYYIIAGVV 60
           + ++E ++ + G EY++  V+EP  +VIRKQ R +          +  P+ DYYII   +
Sbjct: 101 MQLEEELMKLDGTEYVLSSVREPDFWVIRKQRRTNNSGVGSAKGPEIIPLQDYYIIGANI 160

Query: 61  YQAPDLASVISSRLVGT 77
           YQ+P +  ++ SRL+ T
Sbjct: 161 YQSPTIFKIVQSRLMST 177


>pdb|3RJ1|G Chain G, Architecture Of The Mediator Head Module
 pdb|3RJ1|N Chain N, Architecture Of The Mediator Head Module
 pdb|3RJ1|U Chain U, Architecture Of The Mediator Head Module
          Length = 295

 Score = 54.7 bits (130), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 8/76 (10%)

Query: 10  HVQEPILNMTGLEYIVLHVQEPILYVIRKQHRHSME--------QTTPIADYYIIAGVVY 61
            ++E +  + G EY++  V+EP  +VIRKQ R +          +  P+ DYYII   +Y
Sbjct: 102 QLEEELXKLDGTEYVLSSVREPDFWVIRKQRRTNNSGVGSAKGPEIIPLQDYYIIGANIY 161

Query: 62  QAPDLASVISSRLVGT 77
           Q+P +  ++ SRL  T
Sbjct: 162 QSPTIFKIVQSRLXST 177


>pdb|4H61|A Chain A, Structure Of The Schizosaccharomyces Pombe Mediator
           Subunit Med6
 pdb|4H61|B Chain B, Structure Of The Schizosaccharomyces Pombe Mediator
           Subunit Med6
          Length = 175

 Score = 49.7 bits (117), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 16/59 (27%), Positives = 41/59 (69%)

Query: 18  MTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLVG 76
           +TG++++++H + P L+VI+KQ+R +  +  P+  Y++    +Y AP+  +++++R++ 
Sbjct: 68  LTGIQFVIIHERPPFLWVIQKQNRLNENEVKPLTVYFVCNENIYMAPNAYTLLATRMLN 126


>pdb|4H63|F Chain F, Structure Of The Schizosaccharomyces Pombe Mediator Head
           Module
          Length = 183

 Score = 49.7 bits (117), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 16/59 (27%), Positives = 41/59 (69%)

Query: 18  MTGLEYIVLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLVG 76
           +TG++++++H + P L+VI+KQ+R +  +  P+  Y++    +Y AP+  +++++R++ 
Sbjct: 76  LTGIQFVIIHERPPFLWVIQKQNRLNENEVKPLTVYFVCNENIYMAPNAYTLLATRMLN 134


>pdb|3JSR|A Chain A, X-ray Structure Of All0216 Protein From Nostoc Sp. Pcc
          7120 At The Resolution 1.8a. Northeast Structural
          Genomics Consortium Target Nsr236
          Length = 119

 Score = 27.3 bits (59), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 13/42 (30%), Positives = 26/42 (61%), Gaps = 2/42 (4%)

Query: 29 QEPILYVIRKQHRHSMEQTTPIADYYIIAGVVY-QAPDLASV 69
          +EPI  V++++ RH  EQ   I D++++    + +AP+ A +
Sbjct: 19 EEPIEEVLKERTRHYHEQEKEI-DFWLVPQPAFLEAPEFADI 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
   0.322    0.138    0.393 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,296,312
Number of Sequences: 62578
Number of extensions: 72541
Number of successful extensions: 309
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 300
Number of HSP's gapped (non-prelim): 8
length of query: 79
length of database: 14,973,337
effective HSP length: 48
effective length of query: 31
effective length of database: 11,969,593
effective search space: 371057383
effective search space used: 371057383
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)