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= 044925
         (103 letters)

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

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



>pdb|3IZR|TT Chain t, Localization Of The Large Subunit Ribosomal Proteins
          Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
          Translating 80s Ribosome
 pdb|3IZR|UU Chain u, Localization Of The Large Subunit Ribosomal Proteins
          Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
          Translating 80s Ribosome
          Length = 110

 Score = 26.6 bits (57), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 12/20 (60%), Positives = 14/20 (70%)

Query: 36 ATLIKLFEKRSADELYLNVG 55
          A   KL EKRS D+L L+VG
Sbjct: 44 ALFAKLLEKRSVDDLILSVG 63


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

 Score = 26.2 bits (56), Expect = 4.6,   Method: Composition-based stats.
 Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 5/47 (10%)

Query: 1  MRVQYMDTVQIFWPHNTIDSGLVEFSFFTSQPEKIATLIKLFEKRSA 47
          M VQ  +T+Q+    +  + G V F  F   PEK  T ++LF++  A
Sbjct: 1  MAVQPKETLQL---ESAAEVGFVRF--FQGMPEKPTTTVRLFDRGDA 42


>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 = 25.4 bits (54), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 5/44 (11%)

Query: 1  MRVQYMDTVQIFWPHNTIDSGLVEFSFFTSQPEKIATLIKLFEK 44
          M VQ  +T+Q+    +  + G V F  F   PEK  T ++LF++
Sbjct: 1  MAVQPKETLQL---ESAAEVGFVRF--FQGMPEKPTTTVRLFDR 39


>pdb|3PPU|A Chain A, Crystal Structure Of The Glutathione-S-Transferase Xi From
           Phanerochaete Chrysosporium
 pdb|3PPU|B Chain B, Crystal Structure Of The Glutathione-S-Transferase Xi From
           Phanerochaete Chrysosporium
          Length = 352

 Score = 25.4 bits (54), Expect = 9.1,   Method: Composition-based stats.
 Identities = 10/31 (32%), Positives = 20/31 (64%)

Query: 13  WPHNTIDSGLVEFSFFTSQPEKIATLIKLFE 43
           W ++T+++G+ +  F ++Q    A +I LFE
Sbjct: 213 WVYDTVNNGVYKSGFASTQKAYEAAVIPLFE 243


  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
   0.322    0.138    0.406 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,711,577
Number of Sequences: 62578
Number of extensions: 38289
Number of successful extensions: 110
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 106
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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)