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= 035432
         (60 letters)

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

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



>pdb|3IZR|DD Chain d, Localization Of The Large Subunit Ribosomal Proteins
          Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
          Translating 80s Ribosome
          Length = 60

 Score =  105 bits (262), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 51/60 (85%), Positives = 55/60 (91%)

Query: 1  MAKSKNHTAHNQSYKAHKNGIKKPKKHRHTSTKGMDPKFLRNQRYARKHNKSNGGSAEEE 60
          MAKSKNHTAHNQSYKAHKNGIKKPK+HR TSTKGMDPKFLRNQRY+RKHNK +G +  EE
Sbjct: 1  MAKSKNHTAHNQSYKAHKNGIKKPKRHRQTSTKGMDPKFLRNQRYSRKHNKKSGEAESEE 60


>pdb|4A18|T Chain T, T.Thermophila 60s Ribosomal Subunit In Complex With
          Initiation Factor 6. This File Contains 26s Rrna And
          Proteins Of Molecule 1
 pdb|4A1B|T Chain T, T.Thermophila 60s Ribosomal Subunit In Complex With
          Initiation Factor 6. This File Contains 26s Rrna And
          Proteins Of Molecule 3.
 pdb|4A1D|T Chain T, T.Thermophila 60s Ribosomal Subunit In Complex With
          Initiation Factor 6. This File Contains 26s Rrna And
          Proteins Of Molecule 4.
 pdb|4A19|T Chain T, T.Thermophila 60s Ribosomal Subunit In Complex With
          Initiation Factor 6. This File Contains 26s Rrna And
          Proteins Of Molecule 2
          Length = 66

 Score = 68.6 bits (166), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 34/52 (65%), Positives = 42/52 (80%)

Query: 1  MAKSKNHTAHNQSYKAHKNGIKKPKKHRHTSTKGMDPKFLRNQRYARKHNKS 52
          MAKSKN T  NQ  K+H+NGIKKPK HRH STKG++P+FLRN+R A K++ S
Sbjct: 1  MAKSKNSTNKNQISKSHRNGIKKPKDHRHISTKGVNPRFLRNRRRAIKNDPS 52


>pdb|3IZS|DD Chain d, Localization Of The Large Subunit Ribosomal Proteins
          Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
          Translating 80s Ribosome
 pdb|3U5E|BB Chain b, The Structure Of The Eukaryotic Ribosome At 3.0 A
          Resolution. This Entry Contains Proteins Of The 60s
          Subunit, Ribosome A
 pdb|3U5I|BB Chain b, The Structure Of The Eukaryotic Ribosome At 3.0 A
          Resolution. This Entry Contains Proteins Of The 60s
          Subunit, Ribosome B
 pdb|4B6A|BB Chain b, Cryo-Em Structure Of The 60s Ribosomal Subunit In
          Complex With Arx1 And Rei1
          Length = 59

 Score = 66.2 bits (160), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 32/46 (69%), Positives = 40/46 (86%)

Query: 1  MAKSKNHTAHNQSYKAHKNGIKKPKKHRHTSTKGMDPKFLRNQRYA 46
          MAKSKNHTAHNQ+ KAH+NGIKKPK +++ S KG+DPKF RN ++A
Sbjct: 1  MAKSKNHTAHNQTRKAHRNGIKKPKTYKYPSLKGVDPKFRRNHKHA 46


>pdb|3ZF7|DD Chain d, High-resolution Cryo-electron Microscopy Structure Of
          The Trypanosoma Brucei Ribosome
          Length = 71

 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 29/61 (47%), Positives = 35/61 (57%), Gaps = 1/61 (1%)

Query: 1  MAKSKNHTAHNQSYKAHKNGIKKP-KKHRHTSTKGMDPKFLRNQRYARKHNKSNGGSAEE 59
          MAKSKNHT HNQS K H+NGIK P   + + S +G     L N R  RK+N+     A  
Sbjct: 1  MAKSKNHTNHNQSRKNHRNGIKPPLPLYMYNSKRGGWLPALVNTRRVRKNNQKAALKARR 60

Query: 60 E 60
          E
Sbjct: 61 E 61


  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
   0.306    0.119    0.342 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,918,738
Number of Sequences: 62578
Number of extensions: 54620
Number of successful extensions: 60
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 56
Number of HSP's gapped (non-prelim): 4
length of query: 60
length of database: 14,973,337
effective HSP length: 31
effective length of query: 29
effective length of database: 13,033,419
effective search space: 377969151
effective search space used: 377969151
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 45 (21.9 bits)