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= 038379
         (93 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 = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 33/91 (36%), Positives = 46/91 (50%), Gaps = 24/91 (26%)

Query: 2   VLFDQGTYDKHFPTLRECLFLVRSCGKVSQEGTKMFVKLCFTSTGNEAGFNCLVHISGSL 61
           VLFD+ TYDK          L+    K  Q    +  +               + I+GSL
Sbjct: 41  VLFDKATYDK----------LLSEVPKYKQITPSVLSER--------------LRINGSL 76

Query: 62  ASRAIKDLVARGSIRMISAYASQQIYTRVIN 92
           A +AIKDL +RG+IR++S ++SQ IYTR  N
Sbjct: 77  ARQAIKDLESRGAIRVVSVHSSQLIYTRATN 107


>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 = 30.8 bits (68), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 16/33 (48%), Positives = 21/33 (63%)

Query: 57  ISGSLASRAIKDLVARGSIRMISAYASQQIYTR 89
           I GSLA  A++ L   G I+ IS ++ Q IYTR
Sbjct: 71  IGGSLARIALRHLEKEGIIKPISKHSKQAIYTR 103


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

 Score = 25.4 bits (54), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 12/36 (33%), Positives = 23/36 (63%)

Query: 55  VHISGSLASRAIKDLVARGSIRMISAYASQQIYTRV 90
           + IS +LA + ++ L  +G IR++S  +  ++YTR 
Sbjct: 75  LKISVALAGKGLQHLCRQGLIRLVSCSSKFRVYTRA 110


  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
   0.326    0.136    0.403 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,407,670
Number of Sequences: 62578
Number of extensions: 72538
Number of successful extensions: 141
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 135
Number of HSP's gapped (non-prelim): 6
length of query: 93
length of database: 14,973,337
effective HSP length: 60
effective length of query: 33
effective length of database: 11,218,657
effective search space: 370215681
effective search space used: 370215681
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 bits)