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= 039821
         (555 letters)

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

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



>pdb|3M6A|A Chain A, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
           Domain
 pdb|3M6A|B Chain B, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
           Domain
 pdb|3M6A|C Chain C, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
           Domain
 pdb|3M6A|D Chain D, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
           Domain
 pdb|3M6A|E Chain E, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
           Domain
 pdb|3M6A|F Chain F, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
           Domain
          Length = 543

 Score = 30.4 bits (67), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 18/46 (39%), Positives = 27/46 (58%), Gaps = 4/46 (8%)

Query: 497 HLKEMVVRGCDQLEKLPLDSNSAKERKFVIRGEEDWWNLLQWEDES 542
           H+KE  ++  ++ EK+P  S+SA+    VIR   DW   L W DE+
Sbjct: 25  HVKETALKELNRYEKIP--SSSAESS--VIRNYIDWLVALPWTDET 66


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

 Score = 29.6 bits (65), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 13/44 (29%), Positives = 25/44 (56%)

Query: 155 LIDCWIGEGFLGESDRFGAENQGYDILDTLVRACLLEEVEDDKV 198
           +I+C   +    E  ++  E+QGYDI++   + C LE  + +K+
Sbjct: 840 VIECAKQKALELEEFQYIGESQGYDIMEPAAKKCYLEREQGEKI 883


>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 = 29.6 bits (65), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 13/44 (29%), Positives = 25/44 (56%)

Query: 155 LIDCWIGEGFLGESDRFGAENQGYDILDTLVRACLLEEVEDDKV 198
           +I+C   +    E  ++  E+QGYDI++   + C LE  + +K+
Sbjct: 840 VIECAKQKALELEEFQYIGESQGYDIMEPAAKKCYLEREQGEKI 883


  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
   0.321    0.137    0.422 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,265,192
Number of Sequences: 62578
Number of extensions: 594427
Number of successful extensions: 1265
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1263
Number of HSP's gapped (non-prelim): 3
length of query: 555
length of database: 14,973,337
effective HSP length: 104
effective length of query: 451
effective length of database: 8,465,225
effective search space: 3817816475
effective search space used: 3817816475
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)