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= 031288
         (162 letters)

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

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



>pdb|3NGQ|A Chain A, Crystal Structure Of The Human Cnot6l Nuclease Domain
          Length = 398

 Score = 28.5 bits (62), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 17/46 (36%), Positives = 22/46 (47%), Gaps = 11/46 (23%)

Query: 117 NHKILKRLSYNDCLVN----------EGKPLVSGGTLKFQYANTFL 152
           NHK  K L YN+CL+N          EG+ +  G  LK  Y N  +
Sbjct: 274 NHKDFKELRYNECLMNFSCNGKNGSSEGR-ITHGFQLKSAYENNLM 318


>pdb|3NGN|A Chain A, Crystal Structure Of The Human Cnot6l Nuclease Domain In
           Complex With Amp
 pdb|3NGO|A Chain A, Crystal Structure Of The Human Cnot6l Nuclease Domain In
           Complex With Poly(A) Dna
          Length = 398

 Score = 28.5 bits (62), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 17/46 (36%), Positives = 22/46 (47%), Gaps = 11/46 (23%)

Query: 117 NHKILKRLSYNDCLVN----------EGKPLVSGGTLKFQYANTFL 152
           NHK  K L YN+CL+N          EG+ +  G  LK  Y N  +
Sbjct: 274 NHKDFKELRYNECLMNFSCNGKNGSSEGR-ITHGFQLKSAYENNLM 318


  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    0.138    0.432 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,582,188
Number of Sequences: 62578
Number of extensions: 178922
Number of successful extensions: 274
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 272
Number of HSP's gapped (non-prelim): 4
length of query: 162
length of database: 14,973,337
effective HSP length: 91
effective length of query: 71
effective length of database: 9,278,739
effective search space: 658790469
effective search space used: 658790469
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: 47 (22.7 bits)