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= 022907
         (290 letters)

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

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



>pdb|2VT8|A Chain A, Structure Of A Conserved Dimerisation Domain Within Fbox7
           And Pi31
 pdb|2VT8|B Chain B, Structure Of A Conserved Dimerisation Domain Within Fbox7
           And Pi31
          Length = 153

 Score = 39.7 bits (91), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 23/94 (24%), Positives = 53/94 (56%), Gaps = 2/94 (2%)

Query: 64  WNELDDNYAFVYVKPEKGSKKVLVKCLVMNNKLLVDALADGASEPVHLEINVADFV-AKN 122
           WN   D Y   Y + + GS+K+LVK + + + ++++ L  G+ +   L +N+ D++ A++
Sbjct: 60  WNNNKDLYVLRY-EYKDGSRKLLVKAITVESSMILNVLEYGSQQVADLTLNLDDYIDAEH 118

Query: 123 GSNYSDQFQNLEKLVTDVDKEIILQLYGSSKPAS 156
             ++   ++N E+L + +   II  ++   + A+
Sbjct: 119 LGDFHRTYKNSEELRSRIVSGIITPIHEQWEKAN 152


>pdb|3VNN|A Chain A, Crystal Structure Of A Sub-Domain Of The
           Nucleotidyltransferase (Adenylation) Domain Of Human Dna
           Ligase Iv
          Length = 139

 Score = 28.9 bits (63), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 11/33 (33%), Positives = 20/33 (60%)

Query: 98  VDALADGASEPVHLEINVADFVAKNGSNYSDQF 130
           ++   DG    +H + +V  + ++NG NY+DQF
Sbjct: 3   IETKLDGERMQMHKDGDVYKYFSRNGYNYTDQF 35


  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    0.140    0.435 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,603,630
Number of Sequences: 62578
Number of extensions: 523159
Number of successful extensions: 983
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 981
Number of HSP's gapped (non-prelim): 9
length of query: 290
length of database: 14,973,337
effective HSP length: 98
effective length of query: 192
effective length of database: 8,840,693
effective search space: 1697413056
effective search space used: 1697413056
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: 51 (24.3 bits)