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= psy5407
         (147 letters)

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

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



>pdb|3CAE|A Chain A, Structure Of Nnqqny As An Insert In T7 Endonuclease I
 pdb|3CAE|B Chain B, Structure Of Nnqqny As An Insert In T7 Endonuclease I
 pdb|3CAE|C Chain C, Structure Of Nnqqny As An Insert In T7 Endonuclease I
 pdb|3CAE|D Chain D, Structure Of Nnqqny As An Insert In T7 Endonuclease I
 pdb|3CAE|E Chain E, Structure Of Nnqqny As An Insert In T7 Endonuclease I
 pdb|3CAE|F Chain F, Structure Of Nnqqny As An Insert In T7 Endonuclease I
 pdb|3CAE|G Chain G, Structure Of Nnqqny As An Insert In T7 Endonuclease I
 pdb|3CAE|H Chain H, Structure Of Nnqqny As An Insert In T7 Endonuclease I
 pdb|3CAE|I Chain I, Structure Of Nnqqny As An Insert In T7 Endonuclease I
 pdb|3CAE|J Chain J, Structure Of Nnqqny As An Insert In T7 Endonuclease I
          Length = 132

 Score = 28.1 bits (61), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 37  NAIRTFHMSLSGASVGILCH-HGYRLLDKLYPGRALSTVFKKVLFDQI 83
           ++ RT     S  S G  C  HG +  DKL P   +    K+V FD++
Sbjct: 82  SSSRTKLYKGSPTSYGEFCEKHGIKFADKLIPAEWIKEPKKEVPFDRL 129


>pdb|1M0D|A Chain A, Crystal Structure Of Bacteriophage T7 Endonuclease I With
           A Wild-Type Active Site And Bound Manganese Ions
 pdb|1M0D|B Chain B, Crystal Structure Of Bacteriophage T7 Endonuclease I With
           A Wild-Type Active Site And Bound Manganese Ions
 pdb|1M0D|C Chain C, Crystal Structure Of Bacteriophage T7 Endonuclease I With
           A Wild-Type Active Site And Bound Manganese Ions
 pdb|1M0D|D Chain D, Crystal Structure Of Bacteriophage T7 Endonuclease I With
           A Wild-Type Active Site And Bound Manganese Ions
 pdb|1M0I|A Chain A, Crystal Structure Of Bacteriophage T7 Endonuclease I With
           A Wild-type Active Site
 pdb|1M0I|B Chain B, Crystal Structure Of Bacteriophage T7 Endonuclease I With
           A Wild-type Active Site
 pdb|1M0I|C Chain C, Crystal Structure Of Bacteriophage T7 Endonuclease I With
           A Wild-type Active Site
 pdb|1M0I|D Chain D, Crystal Structure Of Bacteriophage T7 Endonuclease I With
           A Wild-type Active Site
          Length = 138

 Score = 27.3 bits (59), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 37  NAIRTFHMSLSGASVGILCH-HGYRLLDKLYPGRALSTVFKKVLFDQI 83
           ++ RT     S  S G  C  HG +  DKL P   +    K+V FD++
Sbjct: 84  SSSRTKLYKGSPTSYGEFCEKHGIKFADKLIPAEWIKEPKKEVPFDRL 131


>pdb|1FZR|A Chain A, Crystal Structure Of Bacteriophage T7 Endonuclease I
 pdb|1FZR|B Chain B, Crystal Structure Of Bacteriophage T7 Endonuclease I
 pdb|1FZR|C Chain C, Crystal Structure Of Bacteriophage T7 Endonuclease I
 pdb|1FZR|D Chain D, Crystal Structure Of Bacteriophage T7 Endonuclease I
          Length = 138

 Score = 27.3 bits (59), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 37  NAIRTFHMSLSGASVGILCH-HGYRLLDKLYPGRALSTVFKKVLFDQI 83
           ++ RT     S  S G  C  HG +  DKL P   +    K+V FD++
Sbjct: 84  SSSRTKLYKGSPTSYGEFCEKHGIKFADKLIPAEWIKEPKKEVPFDRL 131


>pdb|2PFJ|A Chain A, Crystal Structure Of T7 Endo I Resolvase In Complex With A
           Holliday Junction
 pdb|2PFJ|B Chain B, Crystal Structure Of T7 Endo I Resolvase In Complex With A
           Holliday Junction
          Length = 149

 Score = 26.9 bits (58), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 36  WNAIRTFHMSLSGASVGILCH-HGYRLLDKLYPGRALSTVFKKVLFDQI 83
           +++ RT     S  S G  C  HG +  DKL P   +    K+V FD++
Sbjct: 94  FSSSRTKLYKGSPTSYGEFCEKHGIKFADKLIPAEWIKEPKKEVPFDRL 142


  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
   0.326    0.140    0.434 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,418,515
Number of Sequences: 62578
Number of extensions: 160098
Number of successful extensions: 443
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 442
Number of HSP's gapped (non-prelim): 5
length of query: 147
length of database: 14,973,337
effective HSP length: 90
effective length of query: 57
effective length of database: 9,341,317
effective search space: 532455069
effective search space used: 532455069
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 47 (22.7 bits)