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= 038749
         (934 letters)

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

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



>pdb|3QBU|A Chain A, Crystal Structure Of Putative Peptidoglyacn Deactelyase
           (Hp0310) From Helicobacter Pylori
 pdb|3QBU|B Chain B, Crystal Structure Of Putative Peptidoglyacn Deactelyase
           (Hp0310) From Helicobacter Pylori
 pdb|3QBU|C Chain C, Crystal Structure Of Putative Peptidoglyacn Deactelyase
           (Hp0310) From Helicobacter Pylori
 pdb|3QBU|D Chain D, Crystal Structure Of Putative Peptidoglyacn Deactelyase
           (Hp0310) From Helicobacter Pylori
          Length = 326

 Score = 31.2 bits (69), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 24/86 (27%), Positives = 34/86 (39%), Gaps = 13/86 (15%)

Query: 546 PSDFVRRGSAGKVGSMMLLKSYQSMHAPFTQDAP------------LMTEDMHEERLHAV 593
           P D  R   AG+VG   LLK ++  H P T   P            ++ +  HE   H  
Sbjct: 62  PDDISRGLFAGEVGIPRLLKLFKKYHLPATWFVPGHSIETFPEQMKMIVDAGHEVGAHGY 121

Query: 594 EAFSNSFEFSAQLERDILLSDMSAFK 619
            +  N    S + E D+LL  +   K
Sbjct: 122 -SHENPIAMSTKQEEDVLLKSVELIK 146


>pdb|2O8E|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO A G T MISPAIR, WITH
           ADP BOUND TO Msh2 Only
          Length = 934

 Score = 30.8 bits (68), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 15/33 (45%), Positives = 20/33 (60%)

Query: 579 PLMTEDMHEERLHAVEAFSNSFEFSAQLERDIL 611
           PLM ++  EERL+ VEAF    E    L+ D+L
Sbjct: 349 PLMDKNRIEERLNLVEAFVEDAELRQTLQEDLL 381


>pdb|2O8B|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G T MISPAIR
 pdb|2O8C|A Chain A, Human Mutsalpha (msh2/msh6) Bound To Adp And An
           O6-methyl-guanine T Mispair
 pdb|2O8D|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G DU MISPAIR
 pdb|2O8F|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO DNA WITH A SINGLE BASE
           T INSERT
 pdb|3THW|A Chain A, Human Mutsbeta Complexed With An Idl Of 4 Bases (Loop4)
           And Adp
 pdb|3THX|A Chain A, Human Mutsbeta Complexed With An Idl Of 3 Bases (Loop3)
           And Adp
 pdb|3THY|A Chain A, Human Mutsbeta Complexed With An Idl Of 2 Bases (Loop2)
           And Adp
 pdb|3THZ|A Chain A, Human Mutsbeta Complexed With An Idl Of 6 Bases (Loop6)
           And Adp
          Length = 934

 Score = 30.8 bits (68), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 15/33 (45%), Positives = 20/33 (60%)

Query: 579 PLMTEDMHEERLHAVEAFSNSFEFSAQLERDIL 611
           PLM ++  EERL+ VEAF    E    L+ D+L
Sbjct: 349 PLMDKNRIEERLNLVEAFVEDAELRQTLQEDLL 381


  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
   0.319    0.133    0.404 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 27,690,775
Number of Sequences: 62578
Number of extensions: 1169202
Number of successful extensions: 2325
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 2322
Number of HSP's gapped (non-prelim): 7
length of query: 934
length of database: 14,973,337
effective HSP length: 108
effective length of query: 826
effective length of database: 8,214,913
effective search space: 6785518138
effective search space used: 6785518138
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)