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= 039147
         (71 letters)

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

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



>pdb|3IZ6|D Chain D, Localization Of The Small Subunit Ribosomal Proteins
          Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
          Translating 80s Ribosome
          Length = 265

 Score = 40.8 bits (94), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/53 (47%), Positives = 28/53 (52%), Gaps = 6/53 (11%)

Query: 1  MARYLKKHQKRLNAR-----GTCSGTFAPKPLIPQTNSGSECMPFICGPKNRL 48
          MAR LKKH KRLNA          G FAPKP     +   EC+P I   +NRL
Sbjct: 1  MARGLKKHLKRLNAPKHWMLDKLGGAFAPKP-SSGPHKSRECLPLILIIRNRL 52


>pdb|3IZB|D Chain D, Localization Of The Small Subunit Ribosomal Proteins
          Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
          Translating 80s Ribosome
 pdb|3U5C|E Chain E, The Structure Of The Eukaryotic Ribosome At 3.0 A
          Resolution. This Entry Contains Proteins Of The 40s
          Subunit, Ribosome A
 pdb|3U5G|E Chain E, The Structure Of The Eukaryotic Ribosome At 3.0 A
          Resolution. This Entry Contains Proteins Of The 40s
          Subunit, Ribosome B
          Length = 261

 Score = 29.3 bits (64), Expect = 0.57,   Method: Composition-based stats.
 Identities = 21/53 (39%), Positives = 26/53 (49%), Gaps = 6/53 (11%)

Query: 1  MARYLKKHQKRLNAR-----GTCSGTFAPKPLIPQTNSGSECMPFICGPKNRL 48
          MAR  KKH KRL A         SG +AP+P     +   E +P I   +NRL
Sbjct: 1  MARGPKKHLKRLAAPHHWLLDKLSGCYAPRP-SAGPHKLRESLPLIVFLRNRL 52


  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
   0.324    0.138    0.476 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,178,922
Number of Sequences: 62578
Number of extensions: 71127
Number of successful extensions: 132
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 131
Number of HSP's gapped (non-prelim): 2
length of query: 71
length of database: 14,973,337
effective HSP length: 41
effective length of query: 30
effective length of database: 12,407,639
effective search space: 372229170
effective search space used: 372229170
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)