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= 033931
         (108 letters)

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

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



>pdb|3IZ6|V Chain V, Localization Of The Small Subunit Ribosomal Proteins Into
           A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
           Ribosome
          Length = 108

 Score =  119 bits (298), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 55/71 (77%), Positives = 65/71 (91%)

Query: 37  VNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH 96
           VNN VLFD+ATYDKLLSE PK+K ITPS+LS+RLRINGSLAR+AIKDL +RG+IR++S H
Sbjct: 37  VNNSVLFDKATYDKLLSEVPKYKQITPSVLSERLRINGSLARQAIKDLESRGAIRVVSVH 96

Query: 97  ASQQIYTRATN 107
           +SQ IYTRATN
Sbjct: 97  SSQLIYTRATN 107


>pdb|3ZEY|U Chain U, High-resolution Cryo-electron Microscopy Structure Of The
           Trypanosoma Brucei Ribosome
          Length = 113

 Score = 75.5 bits (184), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 33/69 (47%), Positives = 52/69 (75%)

Query: 37  VNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH 96
           + N V+FD+ T DKL+ E PK+K+ITPSI+SDRL+I+ +LA + ++ L  +G IR++S  
Sbjct: 42  LQNAVMFDKETMDKLMKEVPKYKVITPSIISDRLKISVALAGKGLQHLCRQGLIRLVSCS 101

Query: 97  ASQQIYTRA 105
           +  ++YTRA
Sbjct: 102 SKFRVYTRA 110


>pdb|3IZB|V Chain V, Localization Of The Small Subunit Ribosomal Proteins Into
           A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
           Translating 80s Ribosome
 pdb|3O2Z|Q Chain Q, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
           Of The First 80s In The Asymmetric Unit.
 pdb|3O30|Q Chain Q, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
           Of The Second 80s In The Asymmetric Unit.
 pdb|3U5C|Z Chain Z, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 40s
           Subunit, Ribosome A
 pdb|3U5G|Z Chain Z, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 40s
           Subunit, Ribosome B
          Length = 108

 Score = 73.2 bits (178), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 33/71 (46%), Positives = 48/71 (67%)

Query: 38  NNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHA 97
            + V+ DQ  YD++L E P ++ ++ S+L DRL+I GSLAR A++ L   G I+ IS H+
Sbjct: 37  QHAVILDQEKYDRILKEVPTYRYVSVSVLVDRLKIGGSLARIALRHLEKEGIIKPISKHS 96

Query: 98  SQQIYTRATNT 108
            Q IYTRAT +
Sbjct: 97  KQAIYTRATAS 107


>pdb|2XZM|8 Chain 8, 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|8 Chain 8, 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 = 143

 Score = 38.5 bits (88), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 17/68 (25%), Positives = 42/68 (61%), Gaps = 1/68 (1%)

Query: 37  VNNMVLFDQATYDKLLSEAPKF-KLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA 95
           VN+ V  ++   + +++   K  K++T S + ++L++NGSLAR+ ++ +  R  +  ++ 
Sbjct: 39  VNHAVFIEKKNVESIINNPSKVGKVLTVSTVVEKLKVNGSLARQLMRTMADRKLVEKVAK 98

Query: 96  HASQQIYT 103
           + +Q +Y+
Sbjct: 99  NGNQWVYS 106


  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
   0.322    0.131    0.350 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,627,024
Number of Sequences: 62578
Number of extensions: 41494
Number of successful extensions: 92
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: 88
Number of HSP's gapped (non-prelim): 4
length of query: 108
length of database: 14,973,337
effective HSP length: 72
effective length of query: 36
effective length of database: 10,467,721
effective search space: 376837956
effective search space used: 376837956
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)