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= psy9086
         (115 letters)

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

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



>pdb|3IZR|KK Chain k, Localization Of The Large Subunit Ribosomal Proteins Into
           A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
           Ribosome
          Length = 112

 Score =  102 bits (255), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 59/111 (53%), Positives = 71/111 (63%), Gaps = 12/111 (10%)

Query: 3   PRYELAVGLKKGHRNTKIKWANSLAQKTSKIVKMRPSRLKGIQTKNTKFTRDLVREVCGH 62
           P+  L VG+ KGH  TK            + +  RPS  KG  TK   F R+L+REV G 
Sbjct: 6   PKSGLFVGINKGHVVTK------------RELPPRPSDRKGKGTKRVHFVRNLIREVAGF 53

Query: 63  APYEKRAMELLKVSKDKRALKFLKRRLGTHIRAKRKREELSNILTQMRKAA 113
           APYEKR  ELLKV KDKRALK  KR+LGTH RAK+KREE+S++L +MR A 
Sbjct: 54  APYEKRITELLKVGKDKRALKVAKRKLGTHKRAKKKREEMSSVLRKMRSAG 104


>pdb|3IZS|KK Chain k, Localization Of The Large Subunit Ribosomal Proteins Into
           A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
           Translating 80s Ribosome
 pdb|3U5E|II Chain i, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 60s
           Subunit, Ribosome A
 pdb|3U5I|II Chain i, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 60s
           Subunit, Ribosome B
 pdb|4B6A|II Chain i, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
           With Arx1 And Rei1
          Length = 100

 Score = 75.5 bits (184), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 43/111 (38%), Positives = 65/111 (58%), Gaps = 12/111 (10%)

Query: 1   MAPRYELAVGLKKGHRNTKIKWANSLAQKTSKIVKMRPSRLKGIQTKNTKFTRDLVREVC 60
           M  +  +A+GL KG + T +  A  ++ K            KG  +  TKF R LVRE+ 
Sbjct: 1   MTVKTGIAIGLNKGKKVTSMTPAPKISYK------------KGAASNRTKFVRSLVREIA 48

Query: 61  GHAPYEKRAMELLKVSKDKRALKFLKRRLGTHIRAKRKREELSNILTQMRK 111
           G +PYE+R ++L++ S +KRA K  K+RLG+  RAK K EE++NI+   R+
Sbjct: 49  GLSPYERRLIDLIRNSGEKRARKVAKKRLGSFTRAKAKVEEMNNIIAASRR 99


>pdb|4A18|Q Chain Q, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 1
 pdb|4A1B|Q Chain Q, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 3.
 pdb|4A1D|Q Chain Q, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 4.
 pdb|4A19|Q Chain Q, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 2
          Length = 104

 Score = 56.2 bits (134), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 42/107 (39%), Positives = 58/107 (54%), Gaps = 12/107 (11%)

Query: 8   AVGLKKGHRNTKIKWANSLAQKTSKIVKMRPSRLKGIQTKNTKFTRDLVREVCGHAPYEK 67
           AVG+ KG   T+++          K+ K    + KG   K     R ++REV G APYEK
Sbjct: 6   AVGINKGFITTQLE---------KKLQKHSAVQRKGKLGKRVALVRQVIREVTGFAPYEK 56

Query: 68  RAMELLKV--SKD-KRALKFLKRRLGTHIRAKRKREELSNILTQMRK 111
           R +EL+K   +KD K+A K  ++RLGTH RAK K+  L   +   RK
Sbjct: 57  RIIELIKAGSAKDSKKATKIARKRLGTHRRAKVKKALLEEAVRAQRK 103


>pdb|3ZF7|MM Chain m, High-resolution Cryo-electron Microscopy Structure Of The
           Trypanosoma Brucei Ribosome
          Length = 109

 Score = 53.1 bits (126), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 34/109 (31%), Positives = 56/109 (51%), Gaps = 12/109 (11%)

Query: 3   PRYELAVGLKKGHRNTKIKWANSLAQKTSKIVKMRPSRLKGIQTKNTKFTRDLVREVCGH 62
           PR  +  G  KG++ T+     S   + +            +  K  +  + ++ ++ G 
Sbjct: 11  PRTGIIAGFNKGYKTTRRARRPSSNDRYA------------LPHKKLRAVKAIISDLVGF 58

Query: 63  APYEKRAMELLKVSKDKRALKFLKRRLGTHIRAKRKREELSNILTQMRK 111
           +P E+R  ELL+V KDKRALKF K+RLG+   AK++R ++   L Q  K
Sbjct: 59  SPMERRVQELLRVGKDKRALKFCKKRLGSIKAAKKRRAKVEEALRQQTK 107


  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    0.130    0.366 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,779,470
Number of Sequences: 62578
Number of extensions: 85529
Number of successful extensions: 187
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: 181
Number of HSP's gapped (non-prelim): 4
length of query: 115
length of database: 14,973,337
effective HSP length: 78
effective length of query: 37
effective length of database: 10,092,253
effective search space: 373413361
effective search space used: 373413361
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)