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= 040945
         (125 letters)

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

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



>pdb|3JYV|K Chain K, Structure Of The 40s Rrna And Proteins And PE TRNA FOR
          EUKARYOTIC Ribosome Based On Cryo-Em Map Of Thermomyces
          Lanuginosus Ribosome At 8.9a Resolution
          Length = 125

 Score = 27.7 bits (60), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 16/33 (48%), Positives = 18/33 (54%), Gaps = 5/33 (15%)

Query: 2  GMGVKQLVVGLVPYAAMVAVQ-----CVQVGIT 29
          GM VK       PYAAM+A Q     C +VGIT
Sbjct: 37 GMKVKADRDESSPYAAMLAAQDVAAKCKEVGIT 69


>pdb|3IZB|K Chain K, Localization Of The Small Subunit Ribosomal Proteins
          Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
          Translating 80s Ribosome
 pdb|3O2Z|H Chain H, Yeast 80s Ribosome. This Entry Consists Of The 40s
          Subunit Of The First 80s In The Asymmetric Unit.
 pdb|3O30|H Chain H, Yeast 80s Ribosome. This Entry Consists Of The 40s
          Subunit Of The Second 80s In The Asymmetric Unit.
 pdb|3U5C|O Chain O, The Structure Of The Eukaryotic Ribosome At 3.0 A
          Resolution. This Entry Contains Proteins Of The 40s
          Subunit, Ribosome A
 pdb|3U5G|O Chain O, The Structure Of The Eukaryotic Ribosome At 3.0 A
          Resolution. This Entry Contains Proteins Of The 40s
          Subunit, Ribosome B
          Length = 137

 Score = 27.7 bits (60), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 16/33 (48%), Positives = 18/33 (54%), Gaps = 5/33 (15%)

Query: 2  GMGVKQLVVGLVPYAAMVAVQ-----CVQVGIT 29
          GM VK       PYAAM+A Q     C +VGIT
Sbjct: 45 GMKVKADRDESSPYAAMLAAQDVAAKCKEVGIT 77


  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
   0.330    0.141    0.403 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,795,335
Number of Sequences: 62578
Number of extensions: 84761
Number of successful extensions: 149
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 148
Number of HSP's gapped (non-prelim): 4
length of query: 125
length of database: 14,973,337
effective HSP length: 86
effective length of query: 39
effective length of database: 9,591,629
effective search space: 374073531
effective search space used: 374073531
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 45 (21.9 bits)