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= 028106
         (213 letters)

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

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



>pdb|3PIE|A Chain A, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
           E178q Mutant
 pdb|3PIE|B Chain B, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
           E178q Mutant
 pdb|3PIE|C Chain C, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
           E178q Mutant
 pdb|3PIE|D Chain D, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
           E178q Mutant
 pdb|3PIF|A Chain A, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
           E178q Mutant In Complex With Manganese
 pdb|3PIF|B Chain B, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
           E178q Mutant In Complex With Manganese
 pdb|3PIF|C Chain C, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
           E178q Mutant In Complex With Manganese
 pdb|3PIF|D Chain D, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
           E178q Mutant In Complex With Manganese
          Length = 1155

 Score = 29.3 bits (64), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 19/69 (27%), Positives = 37/69 (53%), Gaps = 2/69 (2%)

Query: 68  LQLARIHLNHIRVNSSPQPTLDLS-FSLVVKVHNRDFFSLNYDSLDVSIGYRGRELGSVR 126
           LQ  +  L H+    + Q  ++L+ FS+ +K +  DF  LN++  D+ + +  ++L ++ 
Sbjct: 310 LQTFKEALQHMDGYINEQGKINLARFSIWLK-YLSDFEYLNFEKKDIDVEWFNQQLENIS 368

Query: 127 SHGGRVRAR 135
             G R R R
Sbjct: 369 LEGERKRTR 377


  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    0.140    0.414 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,631,053
Number of Sequences: 62578
Number of extensions: 204807
Number of successful extensions: 321
Number of sequences better than 100.0: 1
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 321
Number of HSP's gapped (non-prelim): 1
length of query: 213
length of database: 14,973,337
effective HSP length: 95
effective length of query: 118
effective length of database: 9,028,427
effective search space: 1065354386
effective search space used: 1065354386
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: 49 (23.5 bits)