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= 032302
         (143 letters)

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

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



>pdb|3ZF7|KK Chain k, High-resolution Cryo-electron Microscopy Structure Of The
           Trypanosoma Brucei Ribosome
          Length = 127

 Score = 26.9 bits (58), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 22/63 (34%), Positives = 29/63 (46%), Gaps = 4/63 (6%)

Query: 60  KASELRLKSWDDLNKLWYVLLKEKNMLMTQQQMLHAQNLKFPNPERIPKVRKSMCRIKQV 119
           K  +L+ K  DDL K      KE + L   QQM    N+      RI  +RK + RI  V
Sbjct: 6   KIRDLKEKGKDDLLKQLSEFKKELSQLRVSQQM----NVGAARLGRIRTIRKGIARIMTV 61

Query: 120 LTE 122
           L +
Sbjct: 62  LNK 64


>pdb|3IZR|S Chain S, Localization Of The Large Subunit Ribosomal Proteins Into
           A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
           Ribosome
          Length = 178

 Score = 26.9 bits (58), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 20/61 (32%), Positives = 27/61 (44%), Gaps = 7/61 (11%)

Query: 48  PDDQKPVYGRS--WKASELRLKSWDDLNKLWYVLLKEKNMLMTQQQMLHAQNLKFPNPER 105
           P D+ P   R   W  +E+R KS     K WY L K K +  +  Q+L    +   NP  
Sbjct: 19  PTDEHPKIYRMKLWATNEVRAKS-----KFWYFLRKLKKVKKSNGQILAINEIFEKNPTT 73

Query: 106 I 106
           I
Sbjct: 74  I 74


>pdb|3IZS|S Chain S, Localization Of The Large Subunit Ribosomal Proteins Into
           A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
           Translating 80s Ribosome
          Length = 167

 Score = 26.9 bits (58), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 20/61 (32%), Positives = 27/61 (44%), Gaps = 7/61 (11%)

Query: 48  PDDQKPVYGRS--WKASELRLKSWDDLNKLWYVLLKEKNMLMTQQQMLHAQNLKFPNPER 105
           P D+ P   R   W  +E+R KS     K WY L K K +  +  Q+L    +   NP  
Sbjct: 19  PTDEHPKIYRMKLWATNEVRAKS-----KFWYFLRKLKKVKKSNGQILAINEIFEKNPTT 73

Query: 106 I 106
           I
Sbjct: 74  I 74


  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
   0.322    0.136    0.416 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,629,321
Number of Sequences: 62578
Number of extensions: 123670
Number of successful extensions: 265
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 264
Number of HSP's gapped (non-prelim): 5
length of query: 143
length of database: 14,973,337
effective HSP length: 89
effective length of query: 54
effective length of database: 9,403,895
effective search space: 507810330
effective search space used: 507810330
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 46 (22.3 bits)