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= 042443
         (95 letters)

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

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



>pdb|1QYU|A Chain A, Structure Of The Catalytic Domain Of 23s Rrna
          Pseudouridine Synthase Rlud
          Length = 349

 Score = 30.0 bits (66), Expect = 0.38,   Method: Composition-based stats.
 Identities = 12/24 (50%), Positives = 16/24 (66%)

Query: 71 RRLDEICLERFQQYSRTYIQSWIL 94
          +RLD+   E F  YSR+ I+ WIL
Sbjct: 41 QRLDQALAEXFPDYSRSRIKEWIL 64


>pdb|1V9F|A Chain A, Crystal Structure Of Catalytic Domain Of Pseudouridine
          Synthase Rlud From Escherichia Coli
 pdb|2IST|A Chain A, Crystal Structure Of Rlud From E. Coli
          Length = 325

 Score = 29.6 bits (65), Expect = 0.47,   Method: Composition-based stats.
 Identities = 12/24 (50%), Positives = 16/24 (66%)

Query: 71 RRLDEICLERFQQYSRTYIQSWIL 94
          +RLD+   E F  YSR+ I+ WIL
Sbjct: 17 QRLDQALAEMFPDYSRSRIKEWIL 40


  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
   0.323    0.135    0.396 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,148,657
Number of Sequences: 62578
Number of extensions: 55802
Number of successful extensions: 160
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 158
Number of HSP's gapped (non-prelim): 2
length of query: 95
length of database: 14,973,337
effective HSP length: 62
effective length of query: 33
effective length of database: 11,093,501
effective search space: 366085533
effective search space used: 366085533
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)