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= 033948
         (108 letters)

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

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



>pdb|2O8B|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G T MISPAIR
 pdb|2O8C|B Chain B, Human Mutsalpha (msh2/msh6) Bound To Adp And An
           O6-methyl-guanine T Mispair
 pdb|2O8D|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G DU MISPAIR
 pdb|2O8E|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO A G T MISPAIR, WITH
           ADP BOUND TO Msh2 Only
 pdb|2O8F|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO DNA WITH A SINGLE BASE
           T INSERT
          Length = 1022

 Score = 27.3 bits (59), Expect = 2.1,   Method: Composition-based stats.
 Identities = 9/29 (31%), Positives = 18/29 (62%)

Query: 59  MRFAWMVQPRNYLLLACHASNETVQLYHL 87
           MR  W ++ +N+ L+ C+   +  +LYH+
Sbjct: 72  MRKWWQIKSQNFDLVICYKVGKFYELYHM 100


>pdb|1SEQ|H Chain H, Fab Mnac13
          Length = 225

 Score = 26.6 bits (57), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 14/29 (48%), Positives = 17/29 (58%), Gaps = 1/29 (3%)

Query: 64 MVQPRNYLLLACHASNETVQLYHLSRWAR 92
          +VQP   L L+C AS  T   Y +S WAR
Sbjct: 11 LVQPGGSLKLSCAASGFTFSTYTMS-WAR 38


>pdb|2NOF|A Chain A, Structure Of Q315f Human 8-oxoguanine Glycosylase Proximal
           Crosslink To 8-oxoguanine Dna
          Length = 325

 Score = 25.8 bits (55), Expect = 6.4,   Method: Compositional matrix adjust.
 Identities = 11/30 (36%), Positives = 14/30 (46%)

Query: 9   NSPVGPKTTHFWGPVANWGFVVAGLVDLKK 38
           N  +G      WGP A W F V    DL++
Sbjct: 294 NKELGNFFRSLWGPYAGWAFAVLFSADLRQ 323


>pdb|2NOZ|A Chain A, Structure Of Q315f Human 8-Oxoguanine Glycosylase Distal
           Crosslink To 8-Oxoguanine Dna
          Length = 325

 Score = 25.8 bits (55), Expect = 6.4,   Method: Compositional matrix adjust.
 Identities = 11/30 (36%), Positives = 14/30 (46%)

Query: 9   NSPVGPKTTHFWGPVANWGFVVAGLVDLKK 38
           N  +G      WGP A W F V    DL++
Sbjct: 294 NKELGNFFRSLWGPYAGWAFAVLFSADLRQ 323


  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    0.131    0.435 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,300,408
Number of Sequences: 62578
Number of extensions: 115821
Number of successful extensions: 327
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: 324
Number of HSP's gapped (non-prelim): 5
length of query: 108
length of database: 14,973,337
effective HSP length: 72
effective length of query: 36
effective length of database: 10,467,721
effective search space: 376837956
effective search space used: 376837956
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)