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= 036150
         (77 letters)

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

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



>pdb|3IZR|MM Chain m, Localization Of The Large Subunit Ribosomal Proteins
          Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
          Translating 80s Ribosome
          Length = 92

 Score = 39.3 bits (90), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 18/21 (85%), Positives = 19/21 (90%)

Query: 15 KYAVKRKAVGIWSCKYCGKVK 35
          K+AVKRKAVGIW CK CGKVK
Sbjct: 44 KFAVKRKAVGIWGCKDCGKVK 64


>pdb|1YSH|D Chain D, Localization And Dynamic Behavior Of Ribosomal Protein
          L30e
          Length = 73

 Score = 38.9 bits (89), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 18/21 (85%), Positives = 19/21 (90%)

Query: 15 KYAVKRKAVGIWSCKYCGKVK 35
          K+AVKRKAVGIW CK CGKVK
Sbjct: 35 KFAVKRKAVGIWGCKDCGKVK 55


>pdb|4A17|Y Chain Y, T.Thermophila 60s Ribosomal Subunit In Complex With
          Initiation Factor 6. This File Contains 5s Rrna, 5.8s
          Rrna And Proteins Of Molecule 2.
 pdb|4A1A|Y Chain Y, T.Thermophila 60s Ribosomal Subunit In Complex With
          Initiation Factor 6. This File Contains 5s Rrna, 5.8s
          Rrna And Proteins Of Molecule 3.
 pdb|4A1C|Y Chain Y, T.Thermophila 60s Ribosomal Subunit In Complex With
          Initiation Factor 6. This File Contains 5s Rrna, 5.8s
          Rrna And Proteins Of Molecule 4.
 pdb|4A1E|Y Chain Y, T.Thermophila 60s Ribosomal Subunit In Complex With
          Initiation Factor 6. This File Contains 5s Rrna, 5.8s
          Rrna And Proteins Of Molecule 1
          Length = 103

 Score = 29.6 bits (65), Expect = 0.41,   Method: Compositional matrix adjust.
 Identities = 14/20 (70%), Positives = 15/20 (75%)

Query: 15 KYAVKRKAVGIWSCKYCGKV 34
          K AVKR AVGIW CK C K+
Sbjct: 44 KVAVKRAAVGIWKCKPCKKI 63


>pdb|3ZF7|OO Chain o, High-resolution Cryo-electron Microscopy Structure Of
          The Trypanosoma Brucei Ribosome
          Length = 93

 Score = 29.6 bits (65), Expect = 0.50,   Method: Compositional matrix adjust.
 Identities = 12/20 (60%), Positives = 14/20 (70%)

Query: 15 KYAVKRKAVGIWSCKYCGKV 34
          K+A +RKAVGIW C  C K 
Sbjct: 44 KFAFRRKAVGIWRCDGCSKT 63


>pdb|3CC2|Z Chain Z, The Refined Crystal Structure Of The Haloarcula
          Marismortui Large Ribosomal Subunit At 2.4 Angstrom
          Resolution With Rrna Sequence For The 23s Rrna And
          Genome-Derived Sequences For R-Proteins
 pdb|3CC4|Z Chain Z, Co-Crystal Structure Of Anisomycin Bound To The 50s
          Ribosomal Subunit
 pdb|3CC7|Z Chain Z, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation C2487u
 pdb|3CCE|Z Chain Z, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation U2535a
 pdb|3CCJ|Z Chain Z, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation C2534u
 pdb|3CCL|Z Chain Z, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation U2535c. Density For Anisomycin Is
          Visible But Not Included In Model.
 pdb|3CCM|Z Chain Z, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation G2611u
 pdb|3CCQ|Z Chain Z, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation A2488u
 pdb|3CCR|Z Chain Z, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation A2488c. Density For Anisomycin Is
          Visible But Not Included In The Model.
 pdb|3CCS|Z Chain Z, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation G2482a
 pdb|3CCU|Z Chain Z, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation G2482c
 pdb|3CCV|Z Chain Z, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation G2616a
 pdb|3CD6|Z Chain Z, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
          Cc-puromycin
 pdb|3CMA|Z Chain Z, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
          Large Ribosomal Subunit Of Haloarcula Marismortui
 pdb|3CME|Z Chain Z, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The
          Large Ribosomal Subunit Of Haloarcula Marismortui
 pdb|3I55|Z Chain Z, Co-Crystal Structure Of Mycalamide A Bound To The Large
          Ribosomal Subunit
 pdb|3I56|Z Chain Z, Co-Crystal Structure Of Triacetyloleandomcyin Bound To
          The Large Ribosomal Subunit
          Length = 116

 Score = 25.8 bits (55), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 8/14 (57%), Positives = 9/14 (64%)

Query: 18 VKRKAVGIWSCKYC 31
          V R+  GIW C YC
Sbjct: 71 VDRQGTGIWQCSYC 84


>pdb|3CPW|Y Chain Y, The Structure Of The Antibiotic Linezolid Bound To The
          Large Ribosomal Subunit Of Haloarcula Marismortui
 pdb|4ADX|Z Chain Z, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
          Subunit In Complex With Initiation Factor 6
          Length = 92

 Score = 25.8 bits (55), Expect = 7.2,   Method: Compositional matrix adjust.
 Identities = 8/14 (57%), Positives = 9/14 (64%)

Query: 18 VKRKAVGIWSCKYC 31
          V R+  GIW C YC
Sbjct: 47 VDRQGTGIWQCSYC 60


>pdb|2QA4|Z Chain Z, A More Complete Structure Of The The L7L12 STALK OF THE
          Haloarcula Marismortui 50s Large Ribosomal Subunit
          Length = 92

 Score = 25.8 bits (55), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 8/14 (57%), Positives = 9/14 (64%)

Query: 18 VKRKAVGIWSCKYC 31
          V R+  GIW C YC
Sbjct: 47 VDRQGTGIWQCSYC 60


>pdb|1YHQ|Z Chain Z, Crystal Structure Of Azithromycin Bound To The G2099a
          Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1YI2|Z Chain Z, Crystal Structure Of Erythromycin Bound To The G2099a
          Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1YIJ|Z Chain Z, Crystal Structure Of Telithromycin Bound To The G2099a
          Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1YIT|Z Chain Z, Crystal Structure Of Virginiamycin M And S Bound To The
          50s Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1YJ9|Z Chain Z, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
          Haloarcula Marismortui Containing A Three Residue
          Deletion In L22
 pdb|1YJN|Z Chain Z, Crystal Structure Of Clindamycin Bound To The G2099a
          Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1YJW|Z Chain Z, Crystal Structure Of Quinupristin Bound To The G2099a
          Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1VQ4|Z Chain Z, The Structure Of The Transition State Analogue "daa"
          Bound To The Large Ribosomal Subunit Of Haloarcula
          Marismortui
 pdb|1VQ5|Z Chain Z, The Structure Of The Transition State Analogue "raa"
          Bound To The Large Ribosomal Subunit Of Haloarcula
          Marismortui
 pdb|1VQ6|Z Chain Z, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
          Large Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1VQ7|Z Chain Z, The Structure Of The Transition State Analogue "dca"
          Bound To The Large Ribosomal Subunit Of Haloarcula
          Marismortui
 pdb|1VQ8|Z Chain Z, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
          Sparsomycin Bound To The Large Ribosomal Subunit Of
          Haloarcula Marismortui
 pdb|1VQ9|Z Chain Z, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
          Sparsomycin Bound To The Large Ribosomal Subunit Of
          Haloarcula Marismortui
 pdb|1VQK|Z Chain Z, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
          The Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1VQL|Z Chain Z, The Structure Of The Transition State Analogue "dcsn"
          Bound To The Large Ribosomal Subunit Of Haloarcula
          Marismortui
 pdb|1VQM|Z Chain Z, The Structure Of The Transition State Analogue "dan"
          Bound To The Large Ribosomal Subunit Of Haloarcula
          Marismortui
 pdb|1VQN|Z Chain Z, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To
          The Large Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1VQO|Z Chain Z, The Structure Of Ccpmn Bound To The Large Ribosomal
          Subunit Haloarcula Marismortui
 pdb|1VQP|Z Chain Z, The Structure Of The Transition State Analogue "rap"
          Bound To The Large Ribosomal Subunit Of Haloarcula
          Marismortui
          Length = 83

 Score = 25.8 bits (55), Expect = 7.4,   Method: Compositional matrix adjust.
 Identities = 8/14 (57%), Positives = 9/14 (64%)

Query: 18 VKRKAVGIWSCKYC 31
          V R+  GIW C YC
Sbjct: 38 VDRQGTGIWQCSYC 51


>pdb|3J21|II Chain i, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
          Revealed By Cryo-em: Implications For Evolution Of
          Eukaryotic Ribosomes (50s Ribosomal Proteins)
          Length = 83

 Score = 25.4 bits (54), Expect = 7.6,   Method: Compositional matrix adjust.
 Identities = 10/16 (62%), Positives = 12/16 (75%)

Query: 17 AVKRKAVGIWSCKYCG 32
          AVKR + GIW C+ CG
Sbjct: 45 AVKRISTGIWQCQKCG 60


>pdb|3G4S|Z Chain Z, Co-Crystal Structure Of Tiamulin Bound To The Large
          Ribosomal Subunit
 pdb|3G6E|Z Chain Z, Co-Crystal Structure Of Homoharringtonine Bound To The
          Large Ribosomal Subunit
 pdb|3G71|Z Chain Z, Co-crystal Structure Of Bruceantin Bound To The Large
          Ribosomal Subunit
          Length = 73

 Score = 25.4 bits (54), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 8/14 (57%), Positives = 9/14 (64%)

Query: 18 VKRKAVGIWSCKYC 31
          V R+  GIW C YC
Sbjct: 38 VDRQGTGIWQCSYC 51


>pdb|1S72|Z Chain Z, Refined Crystal Structure Of The Haloarcula Marismortui
          Large Ribosomal Subunit At 2.4 Angstrom Resolution
 pdb|2OTJ|Z Chain Z, 13-Deoxytedanolide Bound To The Large Subunit Of
          Haloarcula Marismortui
 pdb|2OTL|Z Chain Z, Girodazole Bound To The Large Subunit Of Haloarcula
          Marismortui
 pdb|2QEX|Z Chain Z, Negamycin Binds To The Wall Of The Nascent Chain Exit
          Tunnel Of The 50s Ribosomal Subunit
          Length = 73

 Score = 25.4 bits (54), Expect = 8.3,   Method: Compositional matrix adjust.
 Identities = 8/14 (57%), Positives = 9/14 (64%)

Query: 18 VKRKAVGIWSCKYC 31
          V R+  GIW C YC
Sbjct: 38 VDRQGTGIWQCSYC 51


  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
   0.330    0.135    0.460 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 988,473
Number of Sequences: 62578
Number of extensions: 14175
Number of successful extensions: 49
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 32
Number of HSP's gapped (non-prelim): 17
length of query: 77
length of database: 14,973,337
effective HSP length: 46
effective length of query: 31
effective length of database: 12,094,749
effective search space: 374937219
effective search space used: 374937219
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 45 (21.9 bits)