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= 034135
         (103 letters)

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

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



>pdb|2WMK|A Chain A, Crystal Structure Of The Catalytic Module Of A Family 98
           Glycoside Hydrolase From Streptococcus Pneumoniae
           Sp3-Bs71 (Sp3gh98) In Complex With The A-Lewisy
           Pentasaccharide Blood Group Antigen.
 pdb|2WMK|B Chain B, Crystal Structure Of The Catalytic Module Of A Family 98
           Glycoside Hydrolase From Streptococcus Pneumoniae
           Sp3-Bs71 (Sp3gh98) In Complex With The A-Lewisy
           Pentasaccharide Blood Group Antigen
          Length = 606

 Score = 27.3 bits (59), Expect = 2.3,   Method: Composition-based stats.
 Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 7/50 (14%)

Query: 33  KQLSFGRDRVK---VRFSKKIVRVHALSSNSNSYLKMNLN----EYMVTL 75
           K   FG  RV    +R   K+  +H+LS  +NSY + +LN     +MVT+
Sbjct: 543 KDTQFGEKRVTKIVLRGIDKLPTIHSLSGTNNSYDQPSLNFDQKNHMVTI 592


>pdb|2WMI|A Chain A, Crystal Structure Of The Catalytic Module Of A Family 98
           Glycoside Hydrolase From Streptococcus Pneumoniae
           Sp3-Bs71 In Complex With The A-Trisaccharide Blood Group
           Antigen.
 pdb|2WMJ|A Chain A, Crystal Structure Of The Catalytic Module Of A Family 98
           Glycoside Hydrolase From Streptococcus Pneumoniae
           Sp3-Bs71 (Sp3gh98) In Complex With The B-Trisaccharide
           Blood Group Antigen.
 pdb|2WMJ|B Chain B, Crystal Structure Of The Catalytic Module Of A Family 98
           Glycoside Hydrolase From Streptococcus Pneumoniae
           Sp3-Bs71 (Sp3gh98) In Complex With The B-Trisaccharide
           Blood Group Antigen
          Length = 606

 Score = 27.3 bits (59), Expect = 2.3,   Method: Composition-based stats.
 Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 7/50 (14%)

Query: 33  KQLSFGRDRVK---VRFSKKIVRVHALSSNSNSYLKMNLN----EYMVTL 75
           K   FG  RV    +R   K+  +H+LS  +NSY + +LN     +MVT+
Sbjct: 543 KDTQFGEKRVTKIVLRGIDKLPTIHSLSGTNNSYDQPSLNFDQKNHMVTI 592


>pdb|2WMI|B Chain B, Crystal Structure Of The Catalytic Module Of A Family 98
           Glycoside Hydrolase From Streptococcus Pneumoniae
           Sp3-Bs71 In Complex With The A-Trisaccharide Blood Group
           Antigen
          Length = 606

 Score = 27.3 bits (59), Expect = 2.4,   Method: Composition-based stats.
 Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 7/50 (14%)

Query: 33  KQLSFGRDRVK---VRFSKKIVRVHALSSNSNSYLKMNLN----EYMVTL 75
           K   FG  RV    +R   K+  +H+LS  +NSY + +LN     +MVT+
Sbjct: 543 KDTQFGEKRVTKIVLRGIDKLPTIHSLSGTNNSYDQPSLNFDQKNHMVTI 592


>pdb|4IFD|I Chain I, Crystal Structure Of An 11-subunit Eukaryotic Exosome
           Complex Bound To Rna
          Length = 301

 Score = 26.6 bits (57), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 22/57 (38%), Positives = 25/57 (43%), Gaps = 9/57 (15%)

Query: 36  SFGRDRVKVRFSKK---IVRVHALSSNSNSYLKMNLNEYMVTLEKPLGIRFALTVDG 89
           S  RDRVKV    K   IVR   LS      L    N Y+ T    LG+ FA   +G
Sbjct: 221 STDRDRVKVIECFKPGDIVRAQVLS------LGDGTNYYLTTARNDLGVVFARAANG 271


  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
   0.323    0.138    0.384 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,332,123
Number of Sequences: 62578
Number of extensions: 72244
Number of successful extensions: 157
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 157
Number of HSP's gapped (non-prelim): 6
length of query: 103
length of database: 14,973,337
effective HSP length: 68
effective length of query: 35
effective length of database: 10,718,033
effective search space: 375131155
effective search space used: 375131155
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)