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= 029213
         (197 letters)

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

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



>pdb|2VRD|A Chain A, The Structure Of The Zinc Finger From The Human
          Spliceosomal Protein U1c
          Length = 61

 Score = 92.4 bits (228), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 43/66 (65%), Positives = 51/66 (77%), Gaps = 7/66 (10%)

Query: 1  MPRYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSYYQQFEEQQTQSLIDQRIKEHLGQ 60
          MP++YCDYCDTYLTHDSPSVRK H +G KHK NV+ YYQ++ E+Q QSLID+        
Sbjct: 1  MPKFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDK-------T 53

Query: 61 TAAFQQ 66
          TAAFQQ
Sbjct: 54 TAAFQQ 59


>pdb|3CW1|L Chain L, Crystal Structure Of Human Spliceosomal U1 Snrnp
 pdb|3CW1|9 Chain 9, Crystal Structure Of Human Spliceosomal U1 Snrnp
 pdb|3CW1|0 Chain 0, Crystal Structure Of Human Spliceosomal U1 Snrnp
 pdb|3CW1|LL Chain l, Crystal Structure Of Human Spliceosomal U1 Snrnp
          Length = 77

 Score = 90.5 bits (223), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 42/66 (63%), Positives = 50/66 (75%), Gaps = 7/66 (10%)

Query: 1  MPRYYCDYCDTYLTHDSPSVRKQHNAGYKHKANVRSYYQQFEEQQTQSLIDQRIKEHLGQ 60
          MP++YCDYCDTYLTHDSPSVRK H +G KHK NV+ YY ++ E+Q QSLID+        
Sbjct: 1  MPKFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYCKWMEEQAQSLIDK-------T 53

Query: 61 TAAFQQ 66
          TAAFQQ
Sbjct: 54 TAAFQQ 59


>pdb|3G4S|R Chain R, Co-Crystal Structure Of Tiamulin Bound To The Large
          Ribosomal Subunit
 pdb|3G6E|R Chain R, Co-Crystal Structure Of Homoharringtonine Bound To The
          Large Ribosomal Subunit
 pdb|3G71|R Chain R, Co-crystal Structure Of Bruceantin Bound To The Large
          Ribosomal Subunit
 pdb|3OW2|Q Chain Q, Crystal Structure Of Enhanced Macrolide Bound To 50s
          Ribosomal Subunit
          Length = 150

 Score = 31.6 bits (70), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 6  CDYCDTYLTHDSPSVRKQHNAGYKHKANVRSY-YQQFEEQQTQSLID 51
           DY +  +  D P   KQHN+G  HK+ V  +   ++ E+ +++ +D
Sbjct: 44 VDYLEAVIEGDQPVPFKQHNSGVGHKSKVDGWDAGRYPEKASKAFLD 90


>pdb|1YJ9|R Chain R, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
          Haloarcula Marismortui Containing A Three Residue
          Deletion In L22
          Length = 152

 Score = 31.6 bits (70), Expect = 0.29,   Method: Compositional matrix adjust.
 Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 6  CDYCDTYLTHDSPSVRKQHNAGYKHKANVRSY-YQQFEEQQTQSLID 51
           DY +  +  D P   KQHN+G  HK+ V  +   ++ E+ +++ +D
Sbjct: 45 VDYLEAVIEGDQPVPFKQHNSGVGHKSKVDGWDAGRYPEKASKAFLD 91


>pdb|1S72|R Chain R, Refined Crystal Structure Of The Haloarcula Marismortui
          Large Ribosomal Subunit At 2.4 Angstrom Resolution
 pdb|1YHQ|R Chain R, Crystal Structure Of Azithromycin Bound To The G2099a
          Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1YI2|R Chain R, Crystal Structure Of Erythromycin Bound To The G2099a
          Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1YIJ|R Chain R, Crystal Structure Of Telithromycin Bound To The G2099a
          Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1YIT|R Chain R, Crystal Structure Of Virginiamycin M And S Bound To The
          50s Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1YJN|R Chain R, Crystal Structure Of Clindamycin Bound To The G2099a
          Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1YJW|R Chain R, Crystal Structure Of Quinupristin Bound To The G2099a
          Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1VQ4|R Chain R, The Structure Of The Transition State Analogue "daa"
          Bound To The Large Ribosomal Subunit Of Haloarcula
          Marismortui
 pdb|1VQ5|R Chain R, The Structure Of The Transition State Analogue "raa"
          Bound To The Large Ribosomal Subunit Of Haloarcula
          Marismortui
 pdb|1VQ6|R Chain R, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
          Large Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1VQ7|R Chain R, The Structure Of The Transition State Analogue "dca"
          Bound To The Large Ribosomal Subunit Of Haloarcula
          Marismortui
 pdb|1VQ8|R Chain R, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
          Sparsomycin Bound To The Large Ribosomal Subunit Of
          Haloarcula Marismortui
 pdb|1VQ9|R Chain R, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
          Sparsomycin Bound To The Large Ribosomal Subunit Of
          Haloarcula Marismortui
 pdb|1VQK|R Chain R, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
          The Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1VQL|R Chain R, The Structure Of The Transition State Analogue "dcsn"
          Bound To The Large Ribosomal Subunit Of Haloarcula
          Marismortui
 pdb|1VQM|R Chain R, The Structure Of The Transition State Analogue "dan"
          Bound To The Large Ribosomal Subunit Of Haloarcula
          Marismortui
 pdb|1VQN|R Chain R, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To
          The Large Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1VQO|R Chain R, The Structure Of Ccpmn Bound To The Large Ribosomal
          Subunit Haloarcula Marismortui
 pdb|1VQP|R Chain R, The Structure Of The Transition State Analogue "rap"
          Bound To The Large Ribosomal Subunit Of Haloarcula
          Marismortui
 pdb|2OTJ|R Chain R, 13-Deoxytedanolide Bound To The Large Subunit Of
          Haloarcula Marismortui
 pdb|2OTL|R Chain R, Girodazole Bound To The Large Subunit Of Haloarcula
          Marismortui
 pdb|2QA4|R Chain R, A More Complete Structure Of The The L7L12 STALK OF THE
          Haloarcula Marismortui 50s Large Ribosomal Subunit
 pdb|3CC2|R Chain R, 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|R Chain R, Co-Crystal Structure Of Anisomycin Bound To The 50s
          Ribosomal Subunit
 pdb|3CC7|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation C2487u
 pdb|3CCE|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation U2535a
 pdb|3CCJ|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation C2534u
 pdb|3CCL|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation U2535c. Density For Anisomycin Is
          Visible But Not Included In Model.
 pdb|3CCM|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation G2611u
 pdb|3CCQ|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation A2488u
 pdb|3CCR|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation A2488c. Density For Anisomycin Is
          Visible But Not Included In The Model.
 pdb|3CCS|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation G2482a
 pdb|3CCU|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation G2482c
 pdb|3CCV|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
          23s Rrna Mutation G2616a
 pdb|3CD6|R Chain R, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
          Cc-puromycin
 pdb|3CPW|Q Chain Q, The Structure Of The Antibiotic Linezolid Bound To The
          Large Ribosomal Subunit Of Haloarcula Marismortui
 pdb|3CMA|R Chain R, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
          Large Ribosomal Subunit Of Haloarcula Marismortui
 pdb|3CME|R Chain R, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The
          Large Ribosomal Subunit Of Haloarcula Marismortui
 pdb|2QEX|R Chain R, Negamycin Binds To The Wall Of The Nascent Chain Exit
          Tunnel Of The 50s Ribosomal Subunit
 pdb|3I55|R Chain R, Co-Crystal Structure Of Mycalamide A Bound To The Large
          Ribosomal Subunit
 pdb|3I56|R Chain R, Co-Crystal Structure Of Triacetyloleandomcyin Bound To
          The Large Ribosomal Subunit
 pdb|4ADX|R Chain R, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
          Subunit In Complex With Initiation Factor 6
          Length = 155

 Score = 31.6 bits (70), Expect = 0.29,   Method: Compositional matrix adjust.
 Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 6  CDYCDTYLTHDSPSVRKQHNAGYKHKANVRSY-YQQFEEQQTQSLID 51
           DY +  +  D P   KQHN+G  HK+ V  +   ++ E+ +++ +D
Sbjct: 45 VDYLEAVIEGDQPVPFKQHNSGVGHKSKVDGWDAGRYPEKASKAFLD 91


>pdb|1FFK|O Chain O, Crystal Structure Of The Large Ribosomal Subunit From
          Haloarcula Marismortui At 2.4 Angstrom Resolution
 pdb|1JJ2|Q Chain Q, Fully Refined Crystal Structure Of The Haloarcula
          Marismortui Large Ribosomal Subunit At 2.4 Angstrom
          Resolution
 pdb|1KQS|Q Chain Q, The Haloarcula Marismortui 50s Complexed With A
          Pretranslocational Intermediate In Protein Synthesis
 pdb|1K8A|S Chain S, Co-Crystal Structure Of Carbomycin A Bound To The 50s
          Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1K9M|S Chain S, Co-Crystal Structure Of Tylosin Bound To The 50s
          Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1KD1|S Chain S, Co-crystal Structure Of Spiramycin Bound To The 50s
          Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1M1K|S Chain S, Co-Crystal Structure Of Azithromycin Bound To The 50s
          Ribosomal Subunit Of Haloarcula Marismortui
 pdb|1M90|S Chain S, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
          Sparsomycin Bound To The 50s Ribosomal Subunit
 pdb|1K73|S Chain S, Co-Crystal Structure Of Anisomycin Bound To The 50s
          Ribosomal Subunit
 pdb|1KC8|S Chain S, Co-Crystal Structure Of Blasticidin S Bound To The 50s
          Ribosomal Subunit
 pdb|1N8R|S Chain S, Structure Of Large Ribosomal Subunit In Complex With
          Virginiamycin M
 pdb|1NJI|S Chain S, Structure Of Chloramphenicol Bound To The 50s Ribosomal
          Subunit
 pdb|1Q7Y|S Chain S, Crystal Structure Of Ccdap-puromycin Bound At The
          Peptidyl Transferase Center Of The 50s Ribosomal
          Subunit
 pdb|1Q81|S Chain S, Crystal Structure Of Minihelix With 3' Puromycin Bound
          To A- Site Of The 50s Ribosomal Subunit.
 pdb|1Q82|S Chain S, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of
          The 50s Ribosomal Subunit
 pdb|1Q86|S Chain S, 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|Q Chain Q, Structure Of A Deacylated Trna Minihelix Bound To The E
          Site Of The Large Ribosomal Subunit Of Haloarcula
          Marismortui
 pdb|1QVG|Q Chain Q, Structure Of Cca Oligonucleotide Bound To The Trna
          Binding Sites Of The Large Ribosomal Subunit Of
          Haloarcula Marismortui
 pdb|1W2B|Q Chain Q, Trigger Factor Ribosome Binding Domain In Complex With
          50s
 pdb|3CXC|Q Chain Q, The Structure Of An Enhanced Oxazolidinone Inhibitor
          Bound To The 50s Ribosomal Subunit Of H. Marismortui
          Length = 154

 Score = 31.6 bits (70), Expect = 0.31,   Method: Compositional matrix adjust.
 Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 6  CDYCDTYLTHDSPSVRKQHNAGYKHKANVRSY-YQQFEEQQTQSLID 51
           DY +  +  D P   KQHN+G  HK+ V  +   ++ E+ +++ +D
Sbjct: 44 VDYLEAVIEGDQPVPFKQHNSGVGHKSKVDGWDAGRYPEKASKAFLD 90


>pdb|2H7O|A Chain A, Crystal Structure Of The Rho-Gtpase Binding Domain Of Ypka
 pdb|2H7V|C Chain C, Co-crystal Structure Of Ypka-rac1
 pdb|2H7V|D Chain D, Co-crystal Structure Of Ypka-rac1
          Length = 303

 Score = 27.3 bits (59), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 10/23 (43%), Positives = 15/23 (65%)

Query: 52  QRIKEHLGQTAAFQQVGAAYNQH 74
           QRI++HL QT +F  +G+    H
Sbjct: 115 QRIQKHLDQTHSFSDIGSLVRAH 137


  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    0.130    0.397 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,129,382
Number of Sequences: 62578
Number of extensions: 110140
Number of successful extensions: 265
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 258
Number of HSP's gapped (non-prelim): 8
length of query: 197
length of database: 14,973,337
effective HSP length: 94
effective length of query: 103
effective length of database: 9,091,005
effective search space: 936373515
effective search space used: 936373515
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)