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= psy7112
         (319 letters)

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

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



>pdb|3FBI|B Chain B, Structure Of The Mediator Submodule Med7n31
 pdb|3FBI|D Chain D, Structure Of The Mediator Submodule Med7n31
          Length = 130

 Score = 29.6 bits (65), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 16/33 (48%), Positives = 21/33 (63%), Gaps = 4/33 (12%)

Query: 55 LCNPMYSEC--YIDCLSCLKLL--FRDSKYLDE 83
           CNP YS+C  Y +CL  LKLL  F +S  ++E
Sbjct: 67 WCNPPYSQCIVYPNCLFILKLLNGFXESAIVNE 99


>pdb|3FBN|B Chain B, Structure Of The Mediator Submodule Med7n31
 pdb|3FBN|D Chain D, Structure Of The Mediator Submodule Med7n31
          Length = 130

 Score = 29.3 bits (64), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 16/33 (48%), Positives = 21/33 (63%), Gaps = 4/33 (12%)

Query: 55 LCNPMYSEC--YIDCLSCLKLL--FRDSKYLDE 83
           CNP YS+C  Y +CL  LKLL  F +S  ++E
Sbjct: 67 WCNPPYSQCIVYPNCLFILKLLNGFMESAIVNE 99


  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    0.135    0.392 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,085,917
Number of Sequences: 62578
Number of extensions: 285513
Number of successful extensions: 535
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 535
Number of HSP's gapped (non-prelim): 2
length of query: 319
length of database: 14,973,337
effective HSP length: 99
effective length of query: 220
effective length of database: 8,778,115
effective search space: 1931185300
effective search space used: 1931185300
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: 51 (24.3 bits)