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= 033169
         (125 letters)

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

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



>pdb|3IZR|W Chain W, Localization Of The Large Subunit Ribosomal Proteins Into
           A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
           Ribosome
          Length = 130

 Score =  166 bits (420), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 84/109 (77%), Positives = 90/109 (82%), Gaps = 1/109 (0%)

Query: 18  TFVIDCGKPVEDKIMDIASLEKFLQERIKV-GGKAGALGDSVTVTREKTKITVTSDSNFS 76
           +FVIDC KPVEDKIM+IASLEKFLQERIKV GGKAG LGDSVTVTR+KTK+TVTSD  FS
Sbjct: 22  SFVIDCSKPVEDKIMEIASLEKFLQERIKVAGGKAGNLGDSVTVTRDKTKVTVTSDGAFS 81

Query: 77  XXXXXXXXXXXXXXHNVRDWLRVIASNKDRSVYELRYFNIAENEGEEED 125
                         HNVRDWLRVIA+NKDR+VYELRYFNIAENEGEEED
Sbjct: 82  KRYLKYLTKKYLKKHNVRDWLRVIAANKDRNVYELRYFNIAENEGEEED 130


>pdb|4A18|M Chain M, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 1
 pdb|4A1B|M Chain M, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 3.
 pdb|4A1D|M Chain M, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 4.
 pdb|4A19|M Chain M, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 2
          Length = 118

 Score = 84.3 bits (207), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 41/104 (39%), Positives = 64/104 (61%), Gaps = 2/104 (1%)

Query: 19  FVIDCGKPVEDKIMDIASLEKFLQERIKVGGKAGALGDSVTVTREKTKITVTSDSNFSXX 78
           F IDC +PVEDK++ I    +FL+ +IKVGGK G LG+++T++ +  KI V S   FS  
Sbjct: 17  FKIDCSQPVEDKVILIGEFAEFLKSKIKVGGKLGNLGENITISNDDKKINVQSTIPFSKR 76

Query: 79  XXXXXXXXXXXXHNVRDWLRVIASNKDRSVYELRYFNIAENEGE 122
                        ++R++L V +S  D++ Y+LRYFNI +++ E
Sbjct: 77  YLKYLTKKYLKKQDLRNYLYVTSS--DKNSYQLRYFNIQQDQAE 118


>pdb|3IZS|W Chain W, Localization Of The Large Subunit Ribosomal Proteins Into
           A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
           Translating 80s Ribosome
 pdb|3U5E|U Chain U, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 60s
           Subunit, Ribosome A
 pdb|3U5I|U Chain U, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 60s
           Subunit, Ribosome B
 pdb|4B6A|U Chain U, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
           With Arx1 And Rei1
          Length = 121

 Score = 67.0 bits (162), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 33/99 (33%), Positives = 53/99 (53%), Gaps = 2/99 (2%)

Query: 18  TFVIDCGKPVEDKIMDIASLEKFLQERIKVGGKAGALGDSVTVTREKTKITVTSDSNFSX 77
           TF +D   P E+ + D AS  K+L + IKV G  G LG++VTVT + T +TV S + FS 
Sbjct: 14  TFTVDVSSPTENGVFDPASYAKYLIDHIKVEGAVGNLGNAVTVTEDGTVVTVVSTAKFSG 73

Query: 78  XXXXXXXXXXXXXHNVRDWLRVIASNKDRSVYELRYFNI 116
                        + +RDW+R +++  +   Y L ++ +
Sbjct: 74  KYLKYLTKKYLKKNQLRDWIRFVSTKTNE--YRLAFYQV 110


>pdb|3ZF7|V Chain V, High-resolution Cryo-electron Microscopy Structure Of The
           Trypanosoma Brucei Ribosome
          Length = 130

 Score = 62.0 bits (149), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 29/105 (27%), Positives = 53/105 (50%), Gaps = 5/105 (4%)

Query: 19  FVIDCGKPVEDKIMD---IASLEKFLQERIKVGGKAGALGDSVTVTREKTKITVTSDSNF 75
           F IDC  P  D I     +++ +++ Q+ +K+ G+ G L   V V   +  +++T+   +
Sbjct: 26  FKIDCSIPASDGIFSDDILSNFQQYFQDNVKLNGRKGKLTSKVRVNMRENTLSITTTMAY 85

Query: 76  SXXXXXXXXXXXXXXHNVRDWLRVIASNKDRSVYELRYFNIAENE 120
                           ++RDW+R++A  KD   Y+L+YFNI + E
Sbjct: 86  RKKYFKYLTKKFLKKKDLRDWIRILAKGKD--TYQLKYFNIQDQE 128


  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
   0.314    0.132    0.366 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,596,723
Number of Sequences: 62578
Number of extensions: 71041
Number of successful extensions: 108
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 101
Number of HSP's gapped (non-prelim): 5
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: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 45 (21.9 bits)