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= 024373
         (268 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 = 29.3 bits (64), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 7/77 (9%)

Query: 166 GVEISLMILSGNYIAIALVDQYKLSHSWMEDVIV------PGFYGSDSGYTGHYILICGY 219
           GV     I +G   ++ + +   L  S  E  IV      PG  G+ +  +G+Y++I G+
Sbjct: 81  GVHTGQFIYAGKKASLNVGNVLPLG-SVPEGTIVSNVEEKPGDRGALARASGNYVIIIGH 139

Query: 220 DANSDEFEIRDPASCRK 236
           + + ++  +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 = 29.3 bits (64), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 7/77 (9%)

Query: 166 GVEISLMILSGNYIAIALVDQYKLSHSWMEDVIV------PGFYGSDSGYTGHYILICGY 219
           GV     I +G   ++ + +   L  S  E  IV      PG  G+ +  +G+Y++I G+
Sbjct: 80  GVHTGQFIYAGKKASLNVGNVLPLG-SVPEGTIVSNVEEKPGDRGALARASGNYVIIIGH 138

Query: 220 DANSDEFEIRDPASCRK 236
           + + ++  +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 = 29.3 bits (64), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 7/77 (9%)

Query: 166 GVEISLMILSGNYIAIALVDQYKLSHSWMEDVIV------PGFYGSDSGYTGHYILICGY 219
           GV     I +G   ++ + +   L  S  E  IV      PG  G+ +  +G+Y++I G+
Sbjct: 80  GVHTGQFIYAGKKASLNVGNVLPLG-SVPEGTIVSNVEEKPGDRGALARASGNYVIIIGH 138

Query: 220 DANSDEFEIRDPASCRK 236
           + + ++  +R P+  +K
Sbjct: 139 NPDENKTRVRLPSGAKK 155


>pdb|1PMI|A Chain A, Candida Albicans Phosphomannose Isomerase
          Length = 440

 Score = 29.3 bits (64), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 7/78 (8%)

Query: 7   LLNKIL-RTEEEEDQVANVNGANMVECCPSDQSPSGRKCGDSILPSAHFVEVPHINQLFS 65
           LL K+  +    +D V     A ++E   +D+ P   K  DS LP      +  +N+ F 
Sbjct: 200 LLQKVFGKLMNTDDDVIKQQTAKLLER--TDREPQVFKDIDSRLPEL----IQRLNKQFP 253

Query: 66  WDCGLACVLMVLRTIGIN 83
            D GL C  ++L  +G+N
Sbjct: 254 NDIGLFCGCLLLNHVGLN 271


  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    0.422 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,087,026
Number of Sequences: 62578
Number of extensions: 328938
Number of successful extensions: 768
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 765
Number of HSP's gapped (non-prelim): 5
length of query: 268
length of database: 14,973,337
effective HSP length: 97
effective length of query: 171
effective length of database: 8,903,271
effective search space: 1522459341
effective search space used: 1522459341
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: 50 (23.9 bits)