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= 002516
         (913 letters)

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

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



>pdb|1WID|A Chain A, Solution Structure Of The B3 Dna-Binding Domain Of Rav1
          Length = 130

 Score = 62.0 bits (149), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 36/101 (35%), Positives = 48/101 (47%), Gaps = 2/101 (1%)

Query: 113 FFCKTLTASDTSTHGGFSVPRRAAEKLFPPLDYTMQPPTQELVVRDLHDNTWTFRHIYRG 172
            F K +T SD        +P+  AEK FP     +      L   D++   W FR+ Y  
Sbjct: 13  LFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWN 72

Query: 173 QPKRHLLTTGWSLFVGSKRLRAGDSVLFIRD--EKSQLMVG 211
             + ++LT GWS FV  K LRAGD V F R   +  QL +G
Sbjct: 73  SSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIG 113


>pdb|3HQF|A Chain A, Crystal Structure Of Restriction Endonuclease Ecorii
           N-Terminal Effector-Binding Domain In Complex With
           Cognate Dna
          Length = 181

 Score = 30.0 bits (66), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 15/39 (38%), Positives = 22/39 (56%), Gaps = 4/39 (10%)

Query: 114 FCKTLTASDTSTHGGFSV----PRRAAEKLFPPLDYTMQ 148
           + K L+A+DT   GG  V    P    EKLFP +++T +
Sbjct: 30  YIKRLSANDTGATGGHQVGLYIPSGIVEKLFPSINHTRE 68


>pdb|1NA6|A Chain A, Crystal Structure Of Restriction Endonuclease Ecorii
           Mutant R88a
 pdb|1NA6|B Chain B, Crystal Structure Of Restriction Endonuclease Ecorii
           Mutant R88a
          Length = 404

 Score = 29.6 bits (65), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 14/39 (35%), Positives = 22/39 (56%), Gaps = 4/39 (10%)

Query: 114 FCKTLTASDTSTHGG----FSVPRRAAEKLFPPLDYTMQ 148
           + K L+A+DT   GG      +P    EKLFP +++T +
Sbjct: 21  YIKRLSANDTGATGGHQVGLYIPSGIVEKLFPSINHTRE 59


  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
   0.315    0.131    0.392 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 27,415,349
Number of Sequences: 62578
Number of extensions: 1151717
Number of successful extensions: 2178
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: 2176
Number of HSP's gapped (non-prelim): 3
length of query: 913
length of database: 14,973,337
effective HSP length: 108
effective length of query: 805
effective length of database: 8,214,913
effective search space: 6613004965
effective search space used: 6613004965
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (26.2 bits)