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= 037611
         (82 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 = 79.0 bits (193), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 41/71 (57%), Positives = 50/71 (70%)

Query: 5   QGKTSKRVHFERNVIREVSGFAPYEKRIDVLPKVGKDXXXXXXXXXXXCTYERAKMKHGE 64
           +GK +KRVHF RN+IREV+GFAPYEKRI  L KVGKD            T++RAK K  E
Sbjct: 33  KGKGTKRVHFVRNLIREVAGFAPYEKRITELLKVGKDKRALKVAKRKLGTHKRAKKKREE 92

Query: 65  MSNVLCRMRAA 75
           MS+VL +MR+A
Sbjct: 93  MSSVLRKMRSA 103


>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 = 47.8 bits (112), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 30/60 (50%), Positives = 34/60 (56%), Gaps = 3/60 (5%)

Query: 5  QGKTSKRVHFERNVIREVSGFAPYEKRIDVLPKVG--KDXXXXXXXXXXXC-TYERAKMK 61
          +GK  KRV   R VIREV+GFAPYEKRI  L K G  KD             T+ RAK+K
Sbjct: 31 KGKLGKRVALVRQVIREVTGFAPYEKRIIELIKAGSAKDSKKATKIARKRLGTHRRAKVK 90


>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 = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/73 (30%), Positives = 39/73 (53%)

Query: 1  IATAQGKTSKRVHFERNVIREVSGFAPYEKRIDVLPKVGKDXXXXXXXXXXXCTYERAKM 60
          I+  +G  S R  F R+++RE++G +PYE+R+  L +   +            ++ RAK 
Sbjct: 26 ISYKKGAASNRTKFVRSLVREIAGLSPYERRLIDLIRNSGEKRARKVAKKRLGSFTRAKA 85

Query: 61 KHGEMSNVLCRMR 73
          K  EM+N++   R
Sbjct: 86 KVEEMNNIIAASR 98


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

 Score = 29.6 bits (65), Expect = 0.39,   Method: Compositional matrix adjust.
 Identities = 12/32 (37%), Positives = 22/32 (68%)

Query: 10 KRVHFERNVIREVSGFAPYEKRIDVLPKVGKD 41
          K++   + +I ++ GF+P E+R+  L +VGKD
Sbjct: 43 KKLRAVKAIISDLVGFSPMERRVQELLRVGKD 74


  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
   0.321    0.133    0.386 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,671,193
Number of Sequences: 62578
Number of extensions: 39233
Number of successful extensions: 54
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: 49
Number of HSP's gapped (non-prelim): 4
length of query: 82
length of database: 14,973,337
effective HSP length: 51
effective length of query: 31
effective length of database: 11,781,859
effective search space: 365237629
effective search space used: 365237629
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)