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= 040909
         (98 letters)

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

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



>pdb|3IZR|JJ Chain j, Localization Of The Large Subunit Ribosomal Proteins Into
           A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
           Ribosome
          Length = 111

 Score =  147 bits (372), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 74/111 (66%), Positives = 86/111 (77%), Gaps = 14/111 (12%)

Query: 2   VKGRQGERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEE--------------AK 47
           +KGRQG+R++LYVRGTILGYKRSKSNQY NTSL+QI+GVN KEE              AK
Sbjct: 1   MKGRQGQRVRLYVRGTILGYKRSKSNQYENTSLLQIEGVNTKEEVGWYAGKRIAYVYKAK 60

Query: 48  TKKNGTHYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
           TK N +  RCIWGKV R H NSGVVRAKF+SNLPP S+G +VRVFMYP++I
Sbjct: 61  TKSNDSTIRCIWGKVTRPHGNSGVVRAKFRSNLPPTSMGKKVRVFMYPSSI 111


>pdb|3IZS|JJ Chain j, Localization Of The Large Subunit Ribosomal Proteins Into
           A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
           Translating 80s Ribosome
 pdb|3U5E|FF Chain f, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 60s
           Subunit, Ribosome A
 pdb|3U5I|FF Chain f, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 60s
           Subunit, Ribosome B
 pdb|4B6A|FF Chain f, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
           With Arx1 And Rei1
          Length = 107

 Score = 89.7 bits (221), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 47/106 (44%), Positives = 65/106 (61%), Gaps = 14/106 (13%)

Query: 7   GERIKLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAK--------------TKKNG 52
            E  +LYV+G  L Y+RSK    PN SLI+I+GV   ++A+               +  G
Sbjct: 2   AESHRLYVKGKHLSYQRSKRVNNPNVSLIKIEGVATPQDAQFYLGKRIAYVYRASKEVRG 61

Query: 53  THYRCIWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPNNI 98
           +  R +WGKV R+H NSGVVRA F++NLP K+ G  VR+F+YP+NI
Sbjct: 62  SKIRVMWGKVTRTHGNSGVVRATFRNNLPAKTFGASVRIFLYPSNI 107


>pdb|4A18|H Chain H, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 1
 pdb|4A1B|H Chain H, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 3.
 pdb|4A1D|H Chain H, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 4.
 pdb|4A19|H Chain H, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 2
          Length = 113

 Score = 85.9 bits (211), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 38/99 (38%), Positives = 62/99 (62%), Gaps = 13/99 (13%)

Query: 11  KLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAK-------------TKKNGTHYRC 57
           +L+V+    G++RSK  Q  N +L++++ VN KE+                KKNG++YR 
Sbjct: 13  RLWVKAAFTGFRRSKHTQNSNQALLKLQNVNTKEDVAFYQGKRVVYIYKGQKKNGSNYRT 72

Query: 58  IWGKVARSHSNSGVVRAKFKSNLPPKSVGDRVRVFMYPN 96
           IWG++ ++H N+GV  A+F  NLPP+++G  +RV +YPN
Sbjct: 73  IWGRIGKAHGNNGVAVARFAHNLPPQAIGSVLRVMLYPN 111


>pdb|3ZF7|LL Chain l, High-resolution Cryo-electron Microscopy Structure Of The
           Trypanosoma Brucei Ribosome
          Length = 149

 Score = 69.3 bits (168), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 38/113 (33%), Positives = 59/113 (52%), Gaps = 25/113 (22%)

Query: 11  KLYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEA------------------------ 46
           +LY++GT+ GY R    Q  NT+L++I+ VN  E+A                        
Sbjct: 37  RLYMKGTLAGYTRGLHGQNKNTALVRIENVNTTEDAKWYVGKRVCYVYHGYKIKRCVRWS 96

Query: 47  KTKKNGTHYRCIWGKVARSHSNSGVVRAKFK-SNLPPKSVGDRVRVFMYPNNI 98
           K     ++ R IWG++ R H  SG VR KF  S++P  ++G R+RV++YP+ I
Sbjct: 97  KAPARRSNTRAIWGRITRPHGTSGTVRVKFNGSSVPASAIGRRIRVYLYPSRI 149


>pdb|1SQR|A Chain A, Solution Structure Of The 50s Ribosomal Protein L35ae
          From Pyrococcus Furiosus. Northeast Structural Genomics
          Consortium Target Pfr48.
 pdb|2LP6|A Chain A, Refined Solution Nmr Structure Of The 50s Ribosomal
          Protein L35ae From Pyrococcus Furiosus, Northeast
          Structural Genomics Consortium Target (Nesg) Pfr48
          Length = 95

 Score = 56.2 bits (134), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 32/91 (35%), Positives = 51/91 (56%), Gaps = 12/91 (13%)

Query: 12 LYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAKTKKNGTHYRCIW---------GKV 62
          + ++G +L Y+RSK NQ+ N  +I+   VN +EEA +K  G     +W         GK+
Sbjct: 1  MRIKGVVLSYRRSKENQHNNVMIIKPLDVNSREEA-SKLIGR--LVLWKSPSGKILKGKI 57

Query: 63 ARSHSNSGVVRAKFKSNLPPKSVGDRVRVFM 93
           R H   G VRA+F+  LP +++GD V + +
Sbjct: 58 VRVHGTKGAVRARFEKGLPGQALGDYVEIVL 88


>pdb|3J21|CC Chain c, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
          Revealed By Cryo-em: Implications For Evolution Of
          Eukaryotic Ribosomes (50s Ribosomal Proteins)
          Length = 87

 Score = 55.1 bits (131), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 32/89 (35%), Positives = 50/89 (56%), Gaps = 12/89 (13%)

Query: 12 LYVRGTILGYKRSKSNQYPNTSLIQIKGVNIKEEAKTKKNGTHYRCIW---------GKV 62
          + ++G +L Y+RSK NQ+ N  +I+   VN +EEA +K  G     +W         GK+
Sbjct: 1  MRIKGVVLSYRRSKENQHNNVMIIKPLDVNSREEA-SKLIGR--LVLWKSPSGKILKGKI 57

Query: 63 ARSHSNSGVVRAKFKSNLPPKSVGDRVRV 91
           R H   G VRA+F+  LP +++GD V +
Sbjct: 58 VRVHGTKGAVRARFEKGLPGQALGDYVEI 86


>pdb|3TG8|A Chain A, Mutant Ribosomal Protein L1 Lacking Ala158 From Thermus
           Thermophilus
          Length = 228

 Score = 26.6 bits (57), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 1/43 (2%)

Query: 52  GTHYRCIWGKVARSHSNSGVVRAKF-KSNLPPKSVGDRVRVFM 93
           G   R I G++   +  +G + A   K++ PP+ + D +R F+
Sbjct: 151 GEIIREIKGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFI 193


  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
   0.317    0.134    0.391 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,853,649
Number of Sequences: 62578
Number of extensions: 98517
Number of successful extensions: 179
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 166
Number of HSP's gapped (non-prelim): 8
length of query: 98
length of database: 14,973,337
effective HSP length: 64
effective length of query: 34
effective length of database: 10,968,345
effective search space: 372923730
effective search space used: 372923730
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)