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= 039315
         (77 letters)

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

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



>pdb|3IZB|U Chain U, Localization Of The Small Subunit Ribosomal Proteins Into
           A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
           Translating 80s Ribosome
 pdb|3U5C|Y Chain Y, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 40s
           Subunit, Ribosome A
 pdb|3U5G|Y Chain Y, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 40s
           Subunit, Ribosome B
 pdb|3J16|D Chain D, Models Of Ribosome-Bound Dom34p And Rli1p And Their
           Ribosomal Binding Partners
          Length = 135

 Score = 26.9 bits (58), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 4/41 (9%)

Query: 12  GMAEKTD----YQRKRHREDDRHAHETSKRSADFESRRNSD 48
           G+AEK +     QRK+ +  D+    T KR A   +RRN+D
Sbjct: 95  GLAEKVEKASRQQRKQKKNRDKKIFGTGKRLAKKVARRNAD 135


  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
   0.314    0.125    0.353 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,766,291
Number of Sequences: 62578
Number of extensions: 47473
Number of successful extensions: 59
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 59
Number of HSP's gapped (non-prelim): 4
length of query: 77
length of database: 14,973,337
effective HSP length: 46
effective length of query: 31
effective length of database: 12,094,749
effective search space: 374937219
effective search space used: 374937219
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 45 (21.9 bits)