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= 034868
         (80 letters)

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

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



>pdb|3IZR|VV Chain v, Localization Of The Large Subunit Ribosomal Proteins
          Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
          Translating 80s Ribosome
 pdb|3IZR|WW Chain w, Localization Of The Large Subunit Ribosomal Proteins
          Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
          Translating 80s Ribosome
          Length = 113

 Score = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 22/33 (66%), Positives = 30/33 (90%)

Query: 9  AVGAEADDERIEFLLSEVKGKDITELIASGREK 41
          +VG E D+E++E +LS+VKGKDITEL+A+GREK
Sbjct: 29 SVGCEIDNEKMELMLSQVKGKDITELLAAGREK 61


>pdb|2W1O|A Chain A, Nmr Structure Of Dimerization Domain Of Human Ribosomal
          Protein P2
 pdb|2W1O|B Chain B, Nmr Structure Of Dimerization Domain Of Human Ribosomal
          Protein P2
 pdb|2LBF|B Chain B, Solution Structure Of The Dimerization Domain Of Human
          Ribosomal Protein P1P2 HETERODIMER
          Length = 70

 Score = 36.2 bits (82), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 9  AVGAEADDERIEFLLSEVKGKDITELIASGREKL 42
          +VG EADD+R+  ++SE+ GK+I ++IA G  KL
Sbjct: 30 SVGIEADDDRLNKVISELNGKNIEDVIAQGIGKL 63


>pdb|3IZS|VV Chain v, Localization Of The Large Subunit Ribosomal Proteins Into
           A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
           Translating 80s Ribosome
 pdb|3IZS|WW Chain w, Localization Of The Large Subunit Ribosomal Proteins Into
           A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
           Translating 80s Ribosome
          Length = 106

 Score = 35.8 bits (81), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 34/79 (43%), Gaps = 7/79 (8%)

Query: 9   AVGAEADDERIEFLLSEVKGKDITELIASGREKLXXX-------XXXXXXXXXXXXXXXX 61
           +VG E +DE++  +LS ++GK + ELI  G EKL                          
Sbjct: 28  SVGIEIEDEKVSSVLSALEGKSVDELITEGNEKLAAVPAAGPASAGGAAAASGDAAAEEE 87

Query: 62  XXXXXXXXSDDDMGFSLFD 80
                   SDDDMGF LFD
Sbjct: 88  KEEEAAEESDDDMGFGLFD 106


>pdb|3IZR|TT Chain t, Localization Of The Large Subunit Ribosomal Proteins Into
           A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
           Ribosome
 pdb|3IZR|UU Chain u, Localization Of The Large Subunit Ribosomal Proteins Into
           A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
           Ribosome
          Length = 110

 Score = 26.2 bits (56), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 11/11 (100%), Positives = 11/11 (100%)

Query: 70  SDDDMGFSLFD 80
           SDDDMGFSLFD
Sbjct: 100 SDDDMGFSLFD 110


  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
   0.321    0.140    0.403 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,484,488
Number of Sequences: 62578
Number of extensions: 28149
Number of successful extensions: 105
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 93
Number of HSP's gapped (non-prelim): 12
length of query: 80
length of database: 14,973,337
effective HSP length: 49
effective length of query: 31
effective length of database: 11,907,015
effective search space: 369117465
effective search space used: 369117465
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)