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= psy6945
         (61 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 = 60.1 bits (144), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 29/64 (45%), Positives = 39/64 (60%), Gaps = 4/64 (6%)

Query: 1   VIEFLSTGRVTSDHQDFKDLPYKSVLNKICQNDKSND----FTHSFKLASAYSEDIMPYT 56
           V+E+LS G V  +H+DFK+L Y   L     N K+       TH F+L SAY  ++MPYT
Sbjct: 262 VVEYLSNGGVADNHKDFKELRYNECLMNFSCNGKNGSSEGRITHGFQLKSAYENNLMPYT 321

Query: 57  NYTY 60
           NYT+
Sbjct: 322 NYTF 325


>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 = 60.1 bits (144), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 29/64 (45%), Positives = 39/64 (60%), Gaps = 4/64 (6%)

Query: 1   VIEFLSTGRVTSDHQDFKDLPYKSVLNKICQNDKSND----FTHSFKLASAYSEDIMPYT 56
           V+E+LS G V  +H+DFK+L Y   L     N K+       TH F+L SAY  ++MPYT
Sbjct: 262 VVEYLSNGGVADNHKDFKELRYNECLMNFSCNGKNGSSEGRITHGFQLKSAYENNLMPYT 321

Query: 57  NYTY 60
           NYT+
Sbjct: 322 NYTF 325


>pdb|2E87|A Chain A, Crystal Structure Of Hypothetical Gtp-Binding Protein
           Ph1320 From Pyrococcus Horikoshii Ot3, In Complex With
           Gdp
          Length = 357

 Score = 28.9 bits (63), Expect = 0.80,   Method: Composition-based stats.
 Identities = 12/23 (52%), Positives = 16/23 (69%)

Query: 14  HQDFKDLPYKSVLNKICQNDKSN 36
           H +FKDLP+  V+NKI   D+ N
Sbjct: 275 HGEFKDLPFLVVINKIDVADEEN 297


  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
   0.317    0.132    0.384 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,860,578
Number of Sequences: 62578
Number of extensions: 55244
Number of successful extensions: 113
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 108
Number of HSP's gapped (non-prelim): 3
length of query: 61
length of database: 14,973,337
effective HSP length: 32
effective length of query: 29
effective length of database: 12,970,841
effective search space: 376154389
effective search space used: 376154389
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)