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= 022209
         (301 letters)

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

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



>pdb|1U6P|A Chain A, Nmr Structure Of The Mlv Encapsidation Signal Bound To The
           Nucleocapsid Protein
 pdb|1WWD|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
           Sequence Aacagu
 pdb|1WWE|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
           Sequence Uuuugcu
 pdb|1WWF|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
           Sequence Ccuccgu
 pdb|1WWG|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
           Sequence Uaucug
          Length = 56

 Score = 30.0 bits (66), Expect = 1.8,   Method: Composition-based stats.
 Identities = 11/20 (55%), Positives = 12/20 (60%)

Query: 273 DAVNCFFCKNKGHMKKACPK 292
           D   C +CK KGH  K CPK
Sbjct: 22  DRDQCAYCKEKGHWAKDCPK 41


>pdb|1A6B|B Chain B, Nmr Structure Of The Complex Between The Zinc Finger
           Protein Ncp10 Of Moloney Murine Leukemia Virus And A
           Sequence Of The Psi-Packaging Domain Of Hiv-1, 20
           Structures
          Length = 40

 Score = 29.6 bits (65), Expect = 2.3,   Method: Composition-based stats.
 Identities = 11/20 (55%), Positives = 12/20 (60%)

Query: 273 DAVNCFFCKNKGHMKKACPK 292
           D   C +CK KGH  K CPK
Sbjct: 9   DRDQCAYCKEKGHWAKDCPK 28


  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    0.134    0.406 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,801,785
Number of Sequences: 62578
Number of extensions: 336427
Number of successful extensions: 662
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 660
Number of HSP's gapped (non-prelim): 3
length of query: 301
length of database: 14,973,337
effective HSP length: 98
effective length of query: 203
effective length of database: 8,840,693
effective search space: 1794660679
effective search space used: 1794660679
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: 51 (24.3 bits)