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= 034808
         (82 letters)

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

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



>pdb|3IZ6|T Chain T, Localization Of The Small Subunit Ribosomal Proteins
          Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
          Translating 80s Ribosome
          Length = 82

 Score =  144 bits (364), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 63/82 (76%), Positives = 76/82 (92%)

Query: 1  MQNEEGQNMDLYIPRKCSATNRLITSKDHAAVQINIGHVDADGIYTGQFSTFALCGFVRA 60
          MQNEEGQ +DLY+PRKCSATNR+IT+KDHA+VQINIGHVD +G+Y G+F+TFAL GF+RA
Sbjct: 1  MQNEEGQMVDLYVPRKCSATNRIITAKDHASVQINIGHVDENGLYDGRFTTFALSGFIRA 60

Query: 61 QGDGDSAIDRLWQKKKVEVRQQ 82
          QGD DSA+DRLWQK+K EV+QQ
Sbjct: 61 QGDADSALDRLWQKRKAEVKQQ 82


>pdb|3IZB|T Chain T, Localization Of The Small Subunit Ribosomal Proteins
          Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
          Translating 80s Ribosome
 pdb|3U5C|V Chain V, The Structure Of The Eukaryotic Ribosome At 3.0 A
          Resolution. This Entry Contains Proteins Of The 40s
          Subunit, Ribosome A
 pdb|3U5G|V Chain V, The Structure Of The Eukaryotic Ribosome At 3.0 A
          Resolution. This Entry Contains Proteins Of The 40s
          Subunit, Ribosome B
          Length = 87

 Score = 89.4 bits (220), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 38/74 (51%), Positives = 59/74 (79%), Gaps = 1/74 (1%)

Query: 1  MQNEEGQNMDLYIPRKCSATNRLITSKDHAAVQINIGHVDADG-IYTGQFSTFALCGFVR 59
          M+N++GQ ++LY+PRKCSATNR+I + DHA+VQIN+  VD +G    G++ T+AL G+VR
Sbjct: 1  MENDKGQLVELYVPRKCSATNRIIKADDHASVQINVAKVDEEGRAIPGEYVTYALSGYVR 60

Query: 60 AQGDGDSAIDRLWQ 73
          ++G+ D +++RL Q
Sbjct: 61 SRGESDDSLNRLAQ 74


>pdb|3ZEY|R Chain R, High-resolution Cryo-electron Microscopy Structure Of
          The Trypanosoma Brucei Ribosome
          Length = 194

 Score = 88.2 bits (217), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 41/75 (54%), Positives = 53/75 (70%)

Query: 3  NEEGQNMDLYIPRKCSATNRLITSKDHAAVQINIGHVDADGIYTGQFSTFALCGFVRAQG 62
          NEEG N+DLYIPRKC ATN LITS DH+AVQI I +VD +G+  G  +T  + G++R QG
Sbjct: 8  NEEGVNVDLYIPRKCHATNSLITSFDHSAVQIAIANVDPNGVIDGTTTTLCIAGYLRCQG 67

Query: 63 DGDSAIDRLWQKKKV 77
          + D AI+ L   K +
Sbjct: 68 ESDHAINHLAIAKGI 82


>pdb|2XZM|Z Chain Z, Crystal Structure Of The Eukaryotic 40s Ribosomal
          Subunit In Complex With Initiation Factor 1. This File
          Contains The 40s Subunit And Initiation Factor For
          Molecule 1
 pdb|2XZN|Z Chain Z, Crystal Structure Of The Eukaryotic 40s Ribosomal
          Subunit In Complex With Initiation Factor 1. This File
          Contains The 40s Subunit And Initiation Factor For
          Molecule 2
          Length = 97

 Score = 62.4 bits (150), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 47/73 (64%)

Query: 3  NEEGQNMDLYIPRKCSATNRLITSKDHAAVQINIGHVDADGIYTGQFSTFALCGFVRAQG 62
          N++ + +D Y+PRKC  +N+LI S D ++VQI I  V  +G  TG  +   LCG VR++G
Sbjct: 18 NDKKEKIDAYLPRKCDWSNKLIFSNDQSSVQIAIAEVGENGQATGSKTNVVLCGSVRSKG 77

Query: 63 DGDSAIDRLWQKK 75
          +   A++ + +++
Sbjct: 78 EAHIALENILRER 90


  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
   0.319    0.134    0.397 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,433,205
Number of Sequences: 62578
Number of extensions: 80399
Number of successful extensions: 181
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: 176
Number of HSP's gapped (non-prelim): 4
length of query: 82
length of database: 14,973,337
effective HSP length: 51
effective length of query: 31
effective length of database: 11,781,859
effective search space: 365237629
effective search space used: 365237629
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)