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= 035394
         (51 letters)

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

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



>pdb|3IZR|OO Chain o, Localization Of The Large Subunit Ribosomal Proteins
          Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
          Translating 80s Ribosome
          Length = 51

 Score = 97.4 bits (241), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 47/51 (92%), Positives = 49/51 (96%)

Query: 1  MPSHKTFMIKKKLAKKMRQNRPIPHWIRMRTDNTIRYNAKRRHWRRTKLGF 51
          MPSHKTF IK+KLAKK RQNRPIP+WIRMRTDNTIRYNAKRRHWRRTKLGF
Sbjct: 1  MPSHKTFRIKQKLAKKQRQNRPIPYWIRMRTDNTIRYNAKRRHWRRTKLGF 51


>pdb|2ZKR|3 Chain 3, Structure Of A Mammalian Ribosomal 60s Subunit Within An
          80s Complex Obtained By Docking Homology Models Of The
          Rna And Proteins Into An 8.7 A Cryo-Em Map
          Length = 51

 Score = 81.3 bits (199), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 39/51 (76%), Positives = 43/51 (84%)

Query: 1  MPSHKTFMIKKKLAKKMRQNRPIPHWIRMRTDNTIRYNAKRRHWRRTKLGF 51
          M SHKTF IK+ LAKK +QNRPIP WIRM+T N IRYN+KRRHWRRTKLG 
Sbjct: 1  MSSHKTFRIKRFLAKKQKQNRPIPQWIRMKTGNKIRYNSKRRHWRRTKLGL 51


>pdb|4A18|B Chain B, T.Thermophila 60s Ribosomal Subunit In Complex With
          Initiation Factor 6. This File Contains 26s Rrna And
          Proteins Of Molecule 1
 pdb|4A1B|B Chain B, T.Thermophila 60s Ribosomal Subunit In Complex With
          Initiation Factor 6. This File Contains 26s Rrna And
          Proteins Of Molecule 3.
 pdb|4A1D|B Chain B, T.Thermophila 60s Ribosomal Subunit In Complex With
          Initiation Factor 6. This File Contains 26s Rrna And
          Proteins Of Molecule 4.
 pdb|4A19|B Chain B, T.Thermophila 60s Ribosomal Subunit In Complex With
          Initiation Factor 6. This File Contains 26s Rrna And
          Proteins Of Molecule 2
          Length = 52

 Score = 62.8 bits (151), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 27/49 (55%), Positives = 40/49 (81%)

Query: 1  MPSHKTFMIKKKLAKKMRQNRPIPHWIRMRTDNTIRYNAKRRHWRRTKL 49
          M ++KT  +KK+  +K++QNRP+P+W R ++D  IRYN+KRR+WRRTKL
Sbjct: 1  MGANKTLNMKKRFGRKIKQNRPLPNWYRYKSDTNIRYNSKRRNWRRTKL 49


>pdb|2WW9|O Chain O, Cryo-Em Structure Of The Active Yeast Ssh1 Complex Bound
          To The Yeast 80s Ribosome
 pdb|2WWA|O Chain O, Cryo-Em Structure Of Idle Yeast Ssh1 Complex Bound To
          The Yeast 80s Ribosome
 pdb|2WWB|O Chain O, Cryo-Em Structure Of The Mammalian Sec61 Complex Bound
          To The Actively Translating Wheat Germ 80s Ribosome
 pdb|3IZS|OO Chain o, Localization Of The Large Subunit Ribosomal Proteins
          Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
          Translating 80s Ribosome
 pdb|3O58|EE Chain e, Yeast 80s Ribosome. This Entry Consists Of The 60s
          Subunit Of The First 80s In The Asymmetric Unit.
 pdb|3O5H|EE Chain e, Yeast 80s Ribosome. This Entry Consists Of The 60s
          Subunit Of The Second 80s In The Asymmetric Unit.
 pdb|3U5E|LL Chain l, The Structure Of The Eukaryotic Ribosome At 3.0 A
          Resolution. This Entry Contains Proteins Of The 60s
          Subunit, Ribosome A
 pdb|3U5I|LL Chain l, The Structure Of The Eukaryotic Ribosome At 3.0 A
          Resolution. This Entry Contains Proteins Of The 60s
          Subunit, Ribosome B
 pdb|4B6A|LL Chain l, Cryo-Em Structure Of The 60s Ribosomal Subunit In
          Complex With Arx1 And Rei1
          Length = 51

 Score = 61.6 bits (148), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 33/51 (64%), Positives = 43/51 (84%)

Query: 1  MPSHKTFMIKKKLAKKMRQNRPIPHWIRMRTDNTIRYNAKRRHWRRTKLGF 51
          M + K+F IK+K+AK  +QNRP+P WIR+RT+NTIRYNAKRR+WRRTK+  
Sbjct: 1  MAAQKSFRIKQKMAKAKKQNRPLPQWIRLRTNNTIRYNAKRRNWRRTKMNI 51


>pdb|3JYW|1 Chain 1, Structure Of The 60s Proteins For Eukaryotic Ribosome
          Based On Cryo-Em Map Of Thermomyces Lanuginosus
          Ribosome At 8.9a Resolution
          Length = 48

 Score = 59.7 bits (143), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 32/48 (66%), Positives = 42/48 (87%)

Query: 3  SHKTFMIKKKLAKKMRQNRPIPHWIRMRTDNTIRYNAKRRHWRRTKLG 50
          + K+F IK+K+AK  +QNRP+P WIR+RT+NTIRYNAKRR+WRRTK+ 
Sbjct: 1  AQKSFRIKQKMAKAKKQNRPLPQWIRLRTNNTIRYNAKRRNWRRTKMN 48


>pdb|3ZF7|QQ Chain q, High-resolution Cryo-electron Microscopy Structure Of
          The Trypanosoma Brucei Ribosome
          Length = 51

 Score = 53.1 bits (126), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 23/33 (69%), Positives = 29/33 (87%)

Query: 19 QNRPIPHWIRMRTDNTIRYNAKRRHWRRTKLGF 51
          QNRP+P+WIR+RT N I++N KRRHWRRTKL +
Sbjct: 19 QNRPVPYWIRLRTGNRIKWNEKRRHWRRTKLHY 51


>pdb|1S72|2 Chain 2, Refined Crystal Structure Of The Haloarcula Marismortui
          Large Ribosomal Subunit At 2.4 Angstrom Resolution
 pdb|1YHQ|2 Chain 2, Crystal Structure Of Azithromycin Bound To The G2099a
          Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1YI2|2 Chain 2, Crystal Structure Of Erythromycin Bound To The G2099a
          Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1YIJ|2 Chain 2, Crystal Structure Of Telithromycin Bound To The G2099a
          Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1YIT|2 Chain 2, Crystal Structure Of Virginiamycin M And S Bound To The
          50s Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1YJ9|2 Chain 2, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
          Haloarcula Marismortui Containing A Three Residue
          Deletion In L22
 pdb|1YJN|2 Chain 2, Crystal Structure Of Clindamycin Bound To The G2099a
          Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1YJW|2 Chain 2, Crystal Structure Of Quinupristin Bound To The G2099a
          Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1VQ4|2 Chain 2, The Structure Of The Transition State Analogue "daa"
          Bound To The Large Ribosomal Subunit Of Haloarcula
          Marismortui
 pdb|1VQ5|2 Chain 2, The Structure Of The Transition State Analogue "raa"
          Bound To The Large Ribosomal Subunit Of Haloarcula
          Marismortui
 pdb|1VQ6|2 Chain 2, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
          Large Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1VQ7|2 Chain 2, The Structure Of The Transition State Analogue "dca"
          Bound To The Large Ribosomal Subunit Of Haloarcula
          Marismortui
 pdb|1VQ8|2 Chain 2, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
          Sparsomycin Bound To The Large Ribosomal Subunit Of
          Haloarcula Marismortui
 pdb|1VQ9|2 Chain 2, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
          Sparsomycin Bound To The Large Ribosomal Subunit Of
          Haloarcula Marismortui
 pdb|1VQK|2 Chain 2, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
          The Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1VQL|2 Chain 2, The Structure Of The Transition State Analogue "dcsn"
          Bound To The Large Ribosomal Subunit Of Haloarcula
          Marismortui
 pdb|1VQM|2 Chain 2, The Structure Of The Transition State Analogue "dan"
          Bound To The Large Ribosomal Subunit Of Haloarcula
          Marismortui
 pdb|1VQN|2 Chain 2, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To
          The Large Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1VQO|2 Chain 2, The Structure Of Ccpmn Bound To The Large Ribosomal
          Subunit Haloarcula Marismortui
 pdb|1VQP|2 Chain 2, The Structure Of The Transition State Analogue "rap"
          Bound To The Large Ribosomal Subunit Of Haloarcula
          Marismortui
 pdb|2OTJ|2 Chain 2, 13-Deoxytedanolide Bound To The Large Subunit Of
          Haloarcula Marismortui
 pdb|2OTL|2 Chain 2, Girodazole Bound To The Large Subunit Of Haloarcula
          Marismortui
 pdb|2QA4|2 Chain 2, A More Complete Structure Of The The L7L12 STALK OF THE
          Haloarcula Marismortui 50s Large Ribosomal Subunit
 pdb|3CC2|2 Chain 2, 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|2 Chain 2, Co-Crystal Structure Of Anisomycin Bound To The 50s
          Ribosomal Subunit
 pdb|3CC7|2 Chain 2, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation C2487u
 pdb|3CCE|2 Chain 2, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation U2535a
 pdb|3CCJ|2 Chain 2, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation C2534u
 pdb|3CCL|2 Chain 2, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation U2535c. Density For Anisomycin Is
          Visible But Not Included In Model.
 pdb|3CCM|2 Chain 2, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation G2611u
 pdb|3CCQ|2 Chain 2, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation A2488u
 pdb|3CCR|2 Chain 2, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation A2488c. Density For Anisomycin Is
          Visible But Not Included In The Model.
 pdb|3CCS|2 Chain 2, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation G2482a
 pdb|3CCU|2 Chain 2, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation G2482c
 pdb|3CCV|2 Chain 2, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation G2616a
 pdb|3CD6|2 Chain 2, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
          Cc-puromycin
 pdb|3CPW|1 Chain 1, The Structure Of The Antibiotic Linezolid Bound To The
          Large Ribosomal Subunit Of Haloarcula Marismortui
 pdb|3CMA|2 Chain 2, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
          Large Ribosomal Subunit Of Haloarcula Marismortui
 pdb|3CME|2 Chain 2, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The
          Large Ribosomal Subunit Of Haloarcula Marismortui
 pdb|2QEX|2 Chain 2, Negamycin Binds To The Wall Of The Nascent Chain Exit
          Tunnel Of The 50s Ribosomal Subunit
 pdb|3G4S|2 Chain 2, Co-Crystal Structure Of Tiamulin Bound To The Large
          Ribosomal Subunit
 pdb|3G6E|2 Chain 2, Co-Crystal Structure Of Homoharringtonine Bound To The
          Large Ribosomal Subunit
 pdb|3G71|2 Chain 2, Co-crystal Structure Of Bruceantin Bound To The Large
          Ribosomal Subunit
 pdb|3I55|2 Chain 2, Co-Crystal Structure Of Mycalamide A Bound To The Large
          Ribosomal Subunit
 pdb|3I56|2 Chain 2, Co-Crystal Structure Of Triacetyloleandomcyin Bound To
          The Large Ribosomal Subunit
 pdb|4ADX|2 Chain 2, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
          Subunit In Complex With Initiation Factor 6
          Length = 50

 Score = 42.0 bits (97), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 20/43 (46%), Positives = 28/43 (65%)

Query: 5  KTFMIKKKLAKKMRQNRPIPHWIRMRTDNTIRYNAKRRHWRRT 47
          K+   KK+LAK   QN  +P W+ ++TD  ++ N KRRHWRR 
Sbjct: 4  KSKATKKRLAKLDNQNSRVPAWVMLKTDREVQRNHKRRHWRRN 46


>pdb|3J21|FF Chain f, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
          Revealed By Cryo-em: Implications For Evolution Of
          Eukaryotic Ribosomes (50s Ribosomal Proteins)
          Length = 51

 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 33/49 (67%)

Query: 1  MPSHKTFMIKKKLAKKMRQNRPIPHWIRMRTDNTIRYNAKRRHWRRTKL 49
          M  +K    K +LAK ++QNR +P W+ ++T+  +  + KRR+WRRTKL
Sbjct: 1  MARNKPLAKKLRLAKALKQNRRVPVWVIVKTNRRVLTHPKRRYWRRTKL 49


>pdb|1JJ2|1 Chain 1, Fully Refined Crystal Structure Of The Haloarcula
          Marismortui Large Ribosomal Subunit At 2.4 Angstrom
          Resolution
 pdb|1KQS|1 Chain 1, The Haloarcula Marismortui 50s Complexed With A
          Pretranslocational Intermediate In Protein Synthesis
 pdb|1K8A|3 Chain 3, Co-Crystal Structure Of Carbomycin A Bound To The 50s
          Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1K9M|3 Chain 3, Co-Crystal Structure Of Tylosin Bound To The 50s
          Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1KD1|3 Chain 3, Co-crystal Structure Of Spiramycin Bound To The 50s
          Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1M1K|3 Chain 3, Co-Crystal Structure Of Azithromycin Bound To The 50s
          Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1M90|3 Chain 3, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
          Sparsomycin Bound To The 50s Ribosomal Subunit
 pdb|1K73|3 Chain 3, Co-Crystal Structure Of Anisomycin Bound To The 50s
          Ribosomal Subunit
 pdb|1KC8|3 Chain 3, Co-Crystal Structure Of Blasticidin S Bound To The 50s
          Ribosomal Subunit
 pdb|1N8R|3 Chain 3, Structure Of Large Ribosomal Subunit In Complex With
          Virginiamycin M
 pdb|1NJI|3 Chain 3, Structure Of Chloramphenicol Bound To The 50s Ribosomal
          Subunit
 pdb|1Q7Y|3 Chain 3, Crystal Structure Of Ccdap-puromycin Bound At The
          Peptidyl Transferase Center Of The 50s Ribosomal
          Subunit
 pdb|1Q81|3 Chain 3, Crystal Structure Of Minihelix With 3' Puromycin Bound
          To A- Site Of The 50s Ribosomal Subunit.
 pdb|1Q82|3 Chain 3, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of
          The 50s Ribosomal Subunit
 pdb|1Q86|3 Chain 3, Crystal Structure Of Cca-Phe-Cap-Biotin Bound
          Simultaneously At Half Occupancy To Both The A-Site And
          P- Site Of The The 50s Ribosomal Subunit.
 pdb|1QVF|1 Chain 1, Structure Of A Deacylated Trna Minihelix Bound To The E
          Site Of The Large Ribosomal Subunit Of Haloarcula
          Marismortui
 pdb|1QVG|1 Chain 1, Structure Of Cca Oligonucleotide Bound To The Trna
          Binding Sites Of The Large Ribosomal Subunit Of
          Haloarcula Marismortui
 pdb|1W2B|1 Chain 1, Trigger Factor Ribosome Binding Domain In Complex With
          50s
 pdb|3CXC|1 Chain 1, The Structure Of An Enhanced Oxazolidinone Inhibitor
          Bound To The 50s Ribosomal Subunit Of H. Marismortui
 pdb|3OW2|1 Chain 1, Crystal Structure Of Enhanced Macrolide Bound To 50s
          Ribosomal Subunit
          Length = 48

 Score = 38.5 bits (88), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 20/42 (47%), Positives = 28/42 (66%), Gaps = 1/42 (2%)

Query: 5  KTFMIKKKLAKKMRQNRPIPHWIRMRTDNTIRYNAKRRHWRR 46
          K+   KK+LAK   QN  +P W+ ++TD  ++ N KRRHWRR
Sbjct: 3  KSKATKKRLAKLDNQNSRVPAWVMLKTD-EVQRNHKRRHWRR 43


>pdb|1FFK|Y Chain Y, Crystal Structure Of The Large Ribosomal Subunit From
          Haloarcula Marismortui At 2.4 Angstrom Resolution
          Length = 49

 Score = 32.3 bits (72), Expect = 0.073,   Method: Compositional matrix adjust.
 Identities = 13/30 (43%), Positives = 20/30 (66%)

Query: 19 QNRPIPHWIRMRTDNTIRYNAKRRHWRRTK 48
          QN  +P ++ ++TD  ++ N KRRHWRR  
Sbjct: 17 QNSRVPAYVMLKTDREVQRNHKRRHWRRND 46


  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
   0.329    0.135    0.452 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,358,152
Number of Sequences: 62578
Number of extensions: 31068
Number of successful extensions: 87
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 75
Number of HSP's gapped (non-prelim): 10
length of query: 51
length of database: 14,973,337
effective HSP length: 23
effective length of query: 28
effective length of database: 13,534,043
effective search space: 378953204
effective search space used: 378953204
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)