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= 035928
         (118 letters)

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

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



>pdb|3R2D|J Chain J, Crystal Structure Of Antitermination Factors Nusb And
          Nuse In Complex With Dsrna
 pdb|3R2D|K Chain K, Crystal Structure Of Antitermination Factors Nusb And
          Nuse In Complex With Dsrna
          Length = 84

 Score = 28.1 bits (61), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 20/57 (35%), Positives = 27/57 (47%), Gaps = 3/57 (5%)

Query: 45 GEEQQKFVIPVIYINHPLFMQLLK---EAEEEYGFDQKGPITLPCHVEEFRTVQGMI 98
          G EQ+K  I +   +H L  Q +K   E  +  G   KGPI LP    EF  +  +I
Sbjct: 1  GMEQEKIRIKLRAYDHRLLDQSVKQIIETVKRTGGVVKGPIPLPTRKSEFSRILDII 57


>pdb|3R2C|J Chain J, Crystal Structure Of Antitermination Factors Nusb And
          Nuse In Complex With Boxa Rna
 pdb|3R2C|K Chain K, Crystal Structure Of Antitermination Factors Nusb And
          Nuse In Complex With Boxa Rna
          Length = 83

 Score = 26.9 bits (58), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 3/55 (5%)

Query: 47 EQQKFVIPVIYINHPLFMQLLK---EAEEEYGFDQKGPITLPCHVEEFRTVQGMI 98
          EQ+K  I +   +H L  Q +K   E  +  G   KGPI LP    EF  +  +I
Sbjct: 2  EQEKIRIKLRAYDHRLLDQSVKQIIETVKRTGGVVKGPIPLPTRKSEFSRILDII 56


  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    0.143    0.444 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,801,622
Number of Sequences: 62578
Number of extensions: 96377
Number of successful extensions: 159
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 158
Number of HSP's gapped (non-prelim): 3
length of query: 118
length of database: 14,973,337
effective HSP length: 81
effective length of query: 37
effective length of database: 9,904,519
effective search space: 366467203
effective search space used: 366467203
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)