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= psy7128
         (2056 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 = 64.3 bits (155), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 30/83 (36%), Positives = 48/83 (57%), Gaps = 8/83 (9%)

Query: 241 VQEPILYVIRKQHRHSME--------QTTPIADYYIIAGVVYQAPDLASVISSRLLSTVH 292
           V+EP  +VIRKQ R +          +  P+ DYYII   +YQ+P +  ++ SRL+ST +
Sbjct: 120 VREPDFWVIRKQRRTNNSGVGSAKGPEIIPLQDYYIIGANIYQSPTIFKIVQSRLMSTSY 179

Query: 293 HLQSAFEEVNSLSKYNPNKGYSW 315
           HL S  E +  L ++ P++G  +
Sbjct: 180 HLNSTLESLYDLIEFQPSQGVHY 202


>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 = 62.8 bits (151), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 30/83 (36%), Positives = 47/83 (56%), Gaps = 8/83 (9%)

Query: 241 VQEPILYVIRKQHRHSME--------QTTPIADYYIIAGVVYQAPDLASVISSRLLSTVH 292
           V+EP  +VIRKQ R +          +  P+ DYYII   +YQ+P +  ++ SRL ST +
Sbjct: 120 VREPDFWVIRKQRRTNNSGVGSAKGPEIIPLQDYYIIGANIYQSPTIFKIVQSRLXSTSY 179

Query: 293 HLQSAFEEVNSLSKYNPNKGYSW 315
           HL S  E +  L ++ P++G  +
Sbjct: 180 HLNSTLESLYDLIEFQPSQGVHY 202


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

 Score = 59.7 bits (143), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 22/78 (28%), Positives = 49/78 (62%)

Query: 238 VLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLLSTVHHLQSA 297
           ++H + P L+VI+KQ+R +  +  P+  Y++    +Y AP+  +++++R+L+  +  Q A
Sbjct: 83  IIHERPPFLWVIQKQNRLNENEVKPLTVYFVCNENIYMAPNAYTLLATRMLNATYCFQKA 142

Query: 298 FEEVNSLSKYNPNKGYSW 315
             ++    +YNP +GY++
Sbjct: 143 LTKIEKFPQYNPQEGYTY 160


>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 = 59.7 bits (143), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 22/78 (28%), Positives = 49/78 (62%)

Query: 238 VLHVQEPILYVIRKQHRHSMEQTTPIADYYIIAGVVYQAPDLASVISSRLLSTVHHLQSA 297
           ++H + P L+VI+KQ+R +  +  P+  Y++    +Y AP+  +++++R+L+  +  Q A
Sbjct: 75  IIHERPPFLWVIQKQNRLNENEVKPLTVYFVCNENIYMAPNAYTLLATRMLNATYCFQKA 134

Query: 298 FEEVNSLSKYNPNKGYSW 315
             ++    +YNP +GY++
Sbjct: 135 LTKIEKFPQYNPQEGYTY 152


  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
   0.321    0.135    0.408 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 54,855,289
Number of Sequences: 62578
Number of extensions: 2069550
Number of successful extensions: 4070
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 4064
Number of HSP's gapped (non-prelim): 4
length of query: 2056
length of database: 14,973,337
effective HSP length: 114
effective length of query: 1942
effective length of database: 7,839,445
effective search space: 15224202190
effective search space used: 15224202190
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: 59 (27.3 bits)