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= 042480
         (233 letters)

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

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



>pdb|3L2O|B Chain B, Structure-Based Mechanism Of Dimerization-Dependent
          Ubiquitination By The Scffbx4 Ubiquitin Ligase
          Length = 312

 Score = 33.9 bits (76), Expect = 0.082,   Method: Compositional matrix adjust.
 Identities = 13/45 (28%), Positives = 24/45 (53%)

Query: 7  LPVECISHIISLTTPRDACRLAAVSHIFKSAADSDLVWEKFLPSD 51
          LP++   +I+S  +P D C+L + +H +       ++W  FL  D
Sbjct: 8  LPIDVQLYILSFLSPHDLCQLGSTNHYWNETVRDPILWRYFLLRD 52


>pdb|2WMH|A Chain A, Crystal Structure Of The Catalytic Module Of A Family 98
           Glycoside Hydrolase From Streptococcus Pneumoniae Tigr4
           In Complex With The H-Disaccharide Blood Group Antigen
          Length = 581

 Score = 27.7 bits (60), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 9/15 (60%), Positives = 11/15 (73%)

Query: 109 GLCIEWGSTANFWKW 123
           GLC  WGS+ + WKW
Sbjct: 233 GLCDNWGSSTDTWKW 247


>pdb|2WMG|A Chain A, Crystal Structure Of The Catalytic Module Of A Family 98
           Glycoside Hydrolase From Streptococcus Pneumoniae Tigr4
           ( Sp4gh98) In Complex With The Lewisy Pentasaccharide
           Blood Group Antigen
          Length = 581

 Score = 27.7 bits (60), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 9/15 (60%), Positives = 11/15 (73%)

Query: 109 GLCIEWGSTANFWKW 123
           GLC  WGS+ + WKW
Sbjct: 233 GLCDNWGSSTDTWKW 247


>pdb|2WMF|A Chain A, Crystal Structure Of The Catalytic Module Of A Family 98
           Glycoside Hydrolase From Streptococcus Pneumoniae Tigr4
           ( Sp4gh98) In Its Native Form
          Length = 581

 Score = 27.7 bits (60), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 9/15 (60%), Positives = 11/15 (73%)

Query: 109 GLCIEWGSTANFWKW 123
           GLC  WGS+ + WKW
Sbjct: 233 GLCDNWGSSTDTWKW 247


  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
   0.324    0.139    0.445 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,665,461
Number of Sequences: 62578
Number of extensions: 250213
Number of successful extensions: 650
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 645
Number of HSP's gapped (non-prelim): 5
length of query: 233
length of database: 14,973,337
effective HSP length: 96
effective length of query: 137
effective length of database: 8,965,849
effective search space: 1228321313
effective search space used: 1228321313
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 50 (23.9 bits)