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= 029371
         (194 letters)

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

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



>pdb|3IZS|B Chain B, Localization Of The Large Subunit Ribosomal Proteins Into
           A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
           Translating 80s Ribosome
 pdb|3O58|B Chain B, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
           Of The First 80s In The Asymmetric Unit.
 pdb|3O5H|B Chain B, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
           Of The Second 80s In The Asymmetric Unit.
 pdb|3U5E|A Chain A, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 60s
           Subunit, Ribosome A
 pdb|3U5I|A Chain A, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 60s
           Subunit, Ribosome B
 pdb|4B6A|A Chain A, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
           With Arx1 And Rei1
          Length = 254

 Score = 29.6 bits (65), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 7/77 (9%)

Query: 92  GVEISLMILSGNYIAIALVDQYKLSHSWMEDVIV------PGFYGSDSGYTGHYILICGY 145
           GV     I +G   ++ + +   L  S  E  IV      PG  G+ +  +G+Y++I G+
Sbjct: 81  GVHTGQFIYAGKKASLNVGNVLPLG-SVPEGTIVSNVEEKPGDRGALARASGNYVIIIGH 139

Query: 146 DANSDEFEIRDPASCRK 162
           + + ++  +R P+  +K
Sbjct: 140 NPDENKTRVRLPSGAKK 156


>pdb|1S1I|B Chain B, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From
           Yeast Obtained By Docking Atomic Models For Rna And
           Protein Components Into A 11.7 A Cryo-Em Map. This File,
           1s1i, Contains 60s Subunit. The 40s Ribosomal Subunit Is
           In File 1s1h
          Length = 253

 Score = 29.6 bits (65), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 7/77 (9%)

Query: 92  GVEISLMILSGNYIAIALVDQYKLSHSWMEDVIV------PGFYGSDSGYTGHYILICGY 145
           GV     I +G   ++ + +   L  S  E  IV      PG  G+ +  +G+Y++I G+
Sbjct: 80  GVHTGQFIYAGKKASLNVGNVLPLG-SVPEGTIVSNVEEKPGDRGALARASGNYVIIIGH 138

Query: 146 DANSDEFEIRDPASCRK 162
           + + ++  +R P+  +K
Sbjct: 139 NPDENKTRVRLPSGAKK 155


>pdb|3JYW|B Chain B, Structure Of The 60s Proteins For Eukaryotic Ribosome
           Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
           At 8.9a Resolution
          Length = 243

 Score = 29.6 bits (65), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 7/77 (9%)

Query: 92  GVEISLMILSGNYIAIALVDQYKLSHSWMEDVIV------PGFYGSDSGYTGHYILICGY 145
           GV     I +G   ++ + +   L  S  E  IV      PG  G+ +  +G+Y++I G+
Sbjct: 80  GVHTGQFIYAGKKASLNVGNVLPLG-SVPEGTIVSNVEEKPGDRGALARASGNYVIIIGH 138

Query: 146 DANSDEFEIRDPASCRK 162
           + + ++  +R P+  +K
Sbjct: 139 NPDENKTRVRLPSGAKK 155


  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
   0.321    0.137    0.409 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,810,859
Number of Sequences: 62578
Number of extensions: 233265
Number of successful extensions: 625
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 622
Number of HSP's gapped (non-prelim): 7
length of query: 194
length of database: 14,973,337
effective HSP length: 94
effective length of query: 100
effective length of database: 9,091,005
effective search space: 909100500
effective search space used: 909100500
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: 49 (23.5 bits)