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= 024546
         (266 letters)

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

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



>pdb|2ACT|A Chain A, Crystallographic Refinement Of The Structure Of Actinidin
           At 1.7 Angstroms Resolution By Fast Fourier
           Least-Squares Methods
          Length = 220

 Score = 28.9 bits (63), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 21/64 (32%), Positives = 31/64 (48%), Gaps = 6/64 (9%)

Query: 5   ITYQALTVLKDAVGIAGNIFAFGLFVSPVPTFRR---IIRNHSTEEFSGLPYVYALLNCL 61
           +TYQ ++V  DA G A   +A G+F  P  T      +I  + TE   G+ Y + + N  
Sbjct: 128 VTYQPVSVALDAAGDAFKQYASGIFTGPCGTAVDHAIVIVGYGTE--GGVDY-WIVKNSW 184

Query: 62  ITMW 65
            T W
Sbjct: 185 DTTW 188


>pdb|3BWQ|A Chain A, Structure Of Free Sv40 Vp1 Pentamer
 pdb|3BWQ|B Chain B, Structure Of Free Sv40 Vp1 Pentamer
 pdb|3BWQ|C Chain C, Structure Of Free Sv40 Vp1 Pentamer
 pdb|3BWQ|D Chain D, Structure Of Free Sv40 Vp1 Pentamer
 pdb|3BWQ|E Chain E, Structure Of Free Sv40 Vp1 Pentamer
 pdb|3BWR|A Chain A, Sv40 Vp1 Pentamer In Complex With Gm1 Oligosaccharide
 pdb|3BWR|B Chain B, Sv40 Vp1 Pentamer In Complex With Gm1 Oligosaccharide
 pdb|3BWR|C Chain C, Sv40 Vp1 Pentamer In Complex With Gm1 Oligosaccharide
 pdb|3BWR|D Chain D, Sv40 Vp1 Pentamer In Complex With Gm1 Oligosaccharide
 pdb|3BWR|E Chain E, Sv40 Vp1 Pentamer In Complex With Gm1 Oligosaccharide
          Length = 272

 Score = 27.7 bits (60), Expect = 7.6,   Method: Compositional matrix adjust.
 Identities = 18/56 (32%), Positives = 26/56 (46%)

Query: 2   ILTITYQALTVLKDAVGIAGNIFAFGLFVSPVPTFRRIIRNHSTEEFSGLPYVYAL 57
           +L IT  A TVL D  G+     A  L+VS V           T+++ GLP  + +
Sbjct: 208 VLHITNTATTVLLDEQGVGPLCKADSLYVSAVDICGLFTNTSGTQQWKGLPRYFKI 263


  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
   0.329    0.143    0.430 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,706,619
Number of Sequences: 62578
Number of extensions: 238791
Number of successful extensions: 1070
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: 1067
Number of HSP's gapped (non-prelim): 3
length of query: 266
length of database: 14,973,337
effective HSP length: 97
effective length of query: 169
effective length of database: 8,903,271
effective search space: 1504652799
effective search space used: 1504652799
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 50 (23.9 bits)