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= 035256
         (69 letters)

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

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



>pdb|3IZR|NN Chain n, Localization Of The Large Subunit Ribosomal Proteins
          Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
          Translating 80s Ribosome
          Length = 69

 Score =  127 bits (318), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 59/69 (85%), Positives = 68/69 (98%)

Query: 1  MPKQIHEIKDFLLTARRKDARSVKIKRSRDVVKFKVRCSKYLYTLCVFDSEKADKLKQSL 60
          MPKQIHEIKDFLLTARRKDARSV+IKR++D VKFKVRCSKYLYTLCVFD++KA+KLKQSL
Sbjct: 1  MPKQIHEIKDFLLTARRKDARSVRIKRTKDAVKFKVRCSKYLYTLCVFDADKANKLKQSL 60

Query: 61 PPGLSVQDL 69
          PPGL+VQ++
Sbjct: 61 PPGLTVQEV 69


>pdb|3ZF7|PP Chain p, High-resolution Cryo-electron Microscopy Structure Of
          The Trypanosoma Brucei Ribosome
          Length = 82

 Score = 71.6 bits (174), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 33/64 (51%), Positives = 48/64 (75%)

Query: 1  MPKQIHEIKDFLLTARRKDARSVKIKRSRDVVKFKVRCSKYLYTLCVFDSEKADKLKQSL 60
          MP++I  +K+FL    RKDAR VK+K +  V KFKVRCS++LYTL + D +KADK+++S+
Sbjct: 1  MPREIKNLKEFLAICSRKDARCVKVKHNPKVTKFKVRCSRHLYTLVMADKKKADKIERSI 60

Query: 61 PPGL 64
           P +
Sbjct: 61 HPSV 64


>pdb|3IZS|NN Chain n, Localization Of The Large Subunit Ribosomal Proteins
          Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
          Translating 80s Ribosome
 pdb|3U5E|KK Chain k, The Structure Of The Eukaryotic Ribosome At 3.0 A
          Resolution. This Entry Contains Proteins Of The 60s
          Subunit, Ribosome A
 pdb|3U5I|KK Chain k, The Structure Of The Eukaryotic Ribosome At 3.0 A
          Resolution. This Entry Contains Proteins Of The 60s
          Subunit, Ribosome B
 pdb|4B6A|KK Chain k, Cryo-Em Structure Of The 60s Ribosomal Subunit In
          Complex With Arx1 And Rei1
          Length = 78

 Score = 56.6 bits (135), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 33/78 (42%), Positives = 44/78 (56%), Gaps = 9/78 (11%)

Query: 1  MPKQIHEIKDFLLTARRKDARSVKIKRSRDV---------VKFKVRCSKYLYTLCVFDSE 51
          M ++I +IK FL   RR D ++  +K ++ +          KFKVR S  LYTL + D+ 
Sbjct: 1  MAREITDIKQFLELTRRADVKTATVKINKKLNKAGKPFRQTKFKVRGSSSLYTLVINDAG 60

Query: 52 KADKLKQSLPPGLSVQDL 69
          KA KL QSLPP L V  L
Sbjct: 61 KAKKLIQSLPPTLKVNRL 78


>pdb|4A18|P Chain P, T.Thermophila 60s Ribosomal Subunit In Complex With
          Initiation Factor 6. This File Contains 26s Rrna And
          Proteins Of Molecule 1
 pdb|4A1B|P Chain P, T.Thermophila 60s Ribosomal Subunit In Complex With
          Initiation Factor 6. This File Contains 26s Rrna And
          Proteins Of Molecule 3.
 pdb|4A1D|P Chain P, T.Thermophila 60s Ribosomal Subunit In Complex With
          Initiation Factor 6. This File Contains 26s Rrna And
          Proteins Of Molecule 4.
 pdb|4A19|P Chain P, T.Thermophila 60s Ribosomal Subunit In Complex With
          Initiation Factor 6. This File Contains 26s Rrna And
          Proteins Of Molecule 2
          Length = 89

 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 39/73 (53%), Gaps = 8/73 (10%)

Query: 1  MPKQIHEIKDFL-LTARRKDA-------RSVKIKRSRDVVKFKVRCSKYLYTLCVFDSEK 52
          MPK+I +IK F+ L    KD        + V +K ++ + KFK+R  KYLYT    D + 
Sbjct: 1  MPKEITDIKKFMKLWQNNKDTPATAGAKKVVYVKTNKRITKFKLRGKKYLYTFKTADPKI 60

Query: 53 ADKLKQSLPPGLS 65
          A  +K ++P   S
Sbjct: 61 AKGIKDAIPATYS 73


  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
   0.323    0.137    0.388 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,765,530
Number of Sequences: 62578
Number of extensions: 47256
Number of successful extensions: 134
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: 130
Number of HSP's gapped (non-prelim): 4
length of query: 69
length of database: 14,973,337
effective HSP length: 39
effective length of query: 30
effective length of database: 12,532,795
effective search space: 375983850
effective search space used: 375983850
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)