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= psy11271
         (78 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 = 93.6 bits (231), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 47/77 (61%), Positives = 57/77 (74%), Gaps = 8/77 (10%)

Query: 1  MPREIKEIKEFLLKARRKDAKSVTIKRNISKNKDKKPDNTKFKVRCSRFLYTLVITDNEK 60
          MP++I EIK+FLL ARRKDA+SV IKR          D  KFKVRCS++LYTL + D +K
Sbjct: 1  MPKQIHEIKDFLLTARRKDARSVRIKRT--------KDAVKFKVRCSKYLYTLCVFDADK 52

Query: 61 AEKLKQSLPPGLQVKEI 77
          A KLKQSLPPGL V+E+
Sbjct: 53 ANKLKQSLPPGLTVQEV 69


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

 Score = 74.3 bits (181), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 38/73 (52%), Positives = 50/73 (68%), Gaps = 8/73 (10%)

Query: 1  MPREIKEIKEFLLKARRKDAKSVTIKRNISKNKDKKPDNTKFKVRCSRFLYTLVITDNEK 60
          MPREIK +KEFL    RKDA+ V +K N        P  TKFKVRCSR LYTLV+ D +K
Sbjct: 1  MPREIKNLKEFLAICSRKDARCVKVKHN--------PKVTKFKVRCSRHLYTLVMADKKK 52

Query: 61 AEKLKQSLPPGLQ 73
          A+K+++S+ P ++
Sbjct: 53 ADKIERSIHPSVK 65


>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 = 73.9 bits (180), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 44/78 (56%), Positives = 51/78 (65%), Gaps = 1/78 (1%)

Query: 1  MPREIKEIKEFLLKARRKDAKSVTIKRNISKNKDKKP-DNTKFKVRCSRFLYTLVITDNE 59
          M REI +IK+FL   RR D K+ T+K N   NK  KP   TKFKVR S  LYTLVI D  
Sbjct: 1  MAREITDIKQFLELTRRADVKTATVKINKKLNKAGKPFRQTKFKVRGSSSLYTLVINDAG 60

Query: 60 KAEKLKQSLPPGLQVKEI 77
          KA+KL QSLPP L+V  +
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 = 37.0 bits (84), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 42/79 (53%), Gaps = 2/79 (2%)

Query: 1  MPREIKEIKEFL-LKARRKDAKSVTIKRNISKNKDKKPDNTKFKVRCSRFLYTLVITDNE 59
          MP+EI +IK+F+ L    KD  +    + +   K  K   TKFK+R  ++LYT    D +
Sbjct: 1  MPKEITDIKKFMKLWQNNKDTPATAGAKKVVYVKTNK-RITKFKLRGKKYLYTFKTADPK 59

Query: 60 KAEKLKQSLPPGLQVKEIK 78
           A+ +K ++P      EIK
Sbjct: 60 IAKGIKDAIPATYSKIEIK 78


  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
   0.314    0.132    0.355 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,064,354
Number of Sequences: 62578
Number of extensions: 62854
Number of successful extensions: 130
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 121
Number of HSP's gapped (non-prelim): 8
length of query: 78
length of database: 14,973,337
effective HSP length: 47
effective length of query: 31
effective length of database: 12,032,171
effective search space: 372997301
effective search space used: 372997301
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 45 (21.9 bits)