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= psy1401
         (79 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 = 67.4 bits (163), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/80 (47%), Positives = 47/80 (58%), Gaps = 3/80 (3%)

Query: 3   MEKYLLERIKV-GGKTSNFGNAVSLERQKTKVILTADVAFSXXXXXXXXXXXXXXXXXXD 61
           +EK+L ERIKV GGK  N G++V++ R KTKV +T+D AFS                  D
Sbjct: 41  LEKFLQERIKVAGGKAGNLGDSVTVTRDKTKVTVTSDGAFSKRYLKYLTKKYLKKHNVRD 100

Query: 62  WLRVVANKKDS--YELRYFQ 79
           WLRV+A  KD   YELRYF 
Sbjct: 101 WLRVIAANKDRNVYELRYFN 120


>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 = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 35/75 (46%)

Query: 5   KYLLERIKVGGKTSNFGNAVSLERQKTKVILTADVAFSXXXXXXXXXXXXXXXXXXDWLR 64
           KYL++ IKV G   N GNAV++    T V + +   FS                  DW+R
Sbjct: 35  KYLIDHIKVEGAVGNLGNAVTVTEDGTVVTVVSTAKFSGKYLKYLTKKYLKKNQLRDWIR 94

Query: 65  VVANKKDSYELRYFQ 79
            V+ K + Y L ++Q
Sbjct: 95  FVSTKTNEYRLAFYQ 109


>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 = 42.7 bits (99), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 21/77 (27%), Positives = 38/77 (49%)

Query: 2   DMEKYLLERIKVGGKTSNFGNAVSLERQKTKVILTADVAFSXXXXXXXXXXXXXXXXXXD 61
           +  ++L  +IKVGGK  N G  +++     K+ + + + FS                  +
Sbjct: 34  EFAEFLKSKIKVGGKLGNLGENITISNDDKKINVQSTIPFSKRYLKYLTKKYLKKQDLRN 93

Query: 62  WLRVVANKKDSYELRYF 78
           +L V ++ K+SY+LRYF
Sbjct: 94  YLYVTSSDKNSYQLRYF 110


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

 Score = 37.0 bits (84), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 16/77 (20%), Positives = 37/77 (48%)

Query: 2   DMEKYLLERIKVGGKTSNFGNAVSLERQKTKVILTADVAFSXXXXXXXXXXXXXXXXXXD 61
           + ++Y  + +K+ G+     + V +  ++  + +T  +A+                   D
Sbjct: 46  NFQQYFQDNVKLNGRKGKLTSKVRVNMRENTLSITTTMAYRKKYFKYLTKKFLKKKDLRD 105

Query: 62  WLRVVANKKDSYELRYF 78
           W+R++A  KD+Y+L+YF
Sbjct: 106 WIRILAKGKDTYQLKYF 122


  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
   0.319    0.133    0.371 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,562,535
Number of Sequences: 62578
Number of extensions: 29002
Number of successful extensions: 49
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: 41
Number of HSP's gapped (non-prelim): 4
length of query: 79
length of database: 14,973,337
effective HSP length: 48
effective length of query: 31
effective length of database: 11,969,593
effective search space: 371057383
effective search space used: 371057383
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)