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= 029363
         (194 letters)

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

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



>pdb|2WAQ|C Chain C, The Complete Structure Of The Archaeal 13-Subunit Dna-
           Directed Rna Polymerase
 pdb|2WB1|C Chain C, The Complete Structure Of The Archaeal 13-Subunit Dna-
           Directed Rna Polymerase
 pdb|2WB1|Y Chain Y, The Complete Structure Of The Archaeal 13-Subunit Dna-
           Directed Rna Polymerase
          Length = 395

 Score = 26.6 bits (57), Expect = 9.9,   Method: Compositional matrix adjust.
 Identities = 13/31 (41%), Positives = 18/31 (58%)

Query: 34  WLLIYRTNSYKTLKSSIDKASKKLETMKIEN 64
            + IY T+ YK  K    + ++KLE  KIEN
Sbjct: 121 MMTIYLTDEYKHDKEKALEVARKLEYTKIEN 151


>pdb|2Y0S|C Chain C, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
           P21 Space Group
 pdb|2Y0S|Y Chain Y, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
           P21 Space Group
 pdb|4AYB|C Chain C, Rnap At 3.2ang
 pdb|4B1O|C Chain C, Archaeal Rnap-Dna Binary Complex At 4.32ang
 pdb|4B1P|Y Chain Y, Archaeal Rnap-Dna Binary Complex At 4.32ang
          Length = 395

 Score = 26.6 bits (57), Expect = 10.0,   Method: Compositional matrix adjust.
 Identities = 13/31 (41%), Positives = 18/31 (58%)

Query: 34  WLLIYRTNSYKTLKSSIDKASKKLETMKIEN 64
            + IY T+ YK  K    + ++KLE  KIEN
Sbjct: 121 MMTIYLTDEYKHDKEKALEVARKLEYTKIEN 151


  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    0.133    0.388 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,390,279
Number of Sequences: 62578
Number of extensions: 128976
Number of successful extensions: 191
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 189
Number of HSP's gapped (non-prelim): 2
length of query: 194
length of database: 14,973,337
effective HSP length: 94
effective length of query: 100
effective length of database: 9,091,005
effective search space: 909100500
effective search space used: 909100500
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: 49 (23.5 bits)