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= 034902
         (79 letters)

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

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



>pdb|1GO3|E Chain E, Structure Of An Archeal Homolog Of The Eukaryotic Rna
          Polymerase Ii Rpb4RPB7 COMPLEX
 pdb|1GO3|M Chain M, Structure Of An Archeal Homolog Of The Eukaryotic Rna
          Polymerase Ii Rpb4RPB7 COMPLEX
          Length = 187

 Score = 30.8 bits (68), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 14/33 (42%), Positives = 19/33 (57%)

Query: 14 KDLGCYLAVTTLESTGEGKVRENAGEMLFPVVF 46
          KD+G  L++  ++  GEGKV    G    PVVF
Sbjct: 40 KDVGFVLSIVDVKDIGEGKVVHGDGSAYHPVVF 72


>pdb|2C35|B Chain B, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
 pdb|2C35|D Chain D, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
 pdb|2C35|F Chain F, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
 pdb|2C35|H Chain H, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
          Length = 172

 Score = 29.3 bits (64), Expect = 0.63,   Method: Compositional matrix adjust.
 Identities = 13/40 (32%), Positives = 24/40 (60%)

Query: 13 TKDLGCYLAVTTLESTGEGKVRENAGEMLFPVVFIGKIFQ 52
          T   G  +AVTT+++ G G ++   G +L+PV +   +F+
Sbjct: 39 TGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFR 78


  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
   0.323    0.137    0.414 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,246,588
Number of Sequences: 62578
Number of extensions: 75185
Number of successful extensions: 98
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 94
Number of HSP's gapped (non-prelim): 6
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 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)