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= 029423
         (193 letters)

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

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



>pdb|3IZB|Q Chain Q, Localization Of The Small Subunit Ribosomal Proteins Into
           A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
           Translating 80s Ribosome
 pdb|3O2Z|K Chain K, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
           Of The First 80s In The Asymmetric Unit.
 pdb|3O30|K Chain K, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
           Of The Second 80s In The Asymmetric Unit.
 pdb|3U5C|R Chain R, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 40s
           Subunit, Ribosome A
 pdb|3U5G|R Chain R, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 40s
           Subunit, Ribosome B
          Length = 136

 Score = 30.4 bits (67), Expect = 0.61,   Method: Compositional matrix adjust.
 Identities = 16/51 (31%), Positives = 25/51 (49%)

Query: 128 VASWTKSLCISISQGHMLNHVEDLKSEPVEENDKYLSSWSVLDIGTGNGLL 178
           +A +T  L   I +G +      L+ E  E  D+Y+   S LD+   NG+L
Sbjct: 50  IAGYTTHLMKRIQKGPVRGISFKLQEEERERKDQYVPEVSALDLSRSNGVL 100


>pdb|1NE2|A Chain A, Crystal Structure Of Thermoplasma Acidophilum 1320
           (Apc5513)
 pdb|1NE2|B Chain B, Crystal Structure Of Thermoplasma Acidophilum 1320
           (Apc5513)
          Length = 200

 Score = 26.9 bits (58), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 8/46 (17%)

Query: 141 QGHMLNHVEDLKSEPVEE--------NDKYLSSWSVLDIGTGNGLL 178
           QG+  N++E   ++            ND  +   SV+D GTGNG+L
Sbjct: 20  QGNFKNYLEQYPTDASTAAYFLIEIYNDGNIGGRSVIDAGTGNGIL 65


  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
   0.313    0.131    0.394 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,510,485
Number of Sequences: 62578
Number of extensions: 203926
Number of successful extensions: 322
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: 317
Number of HSP's gapped (non-prelim): 5
length of query: 193
length of database: 14,973,337
effective HSP length: 93
effective length of query: 100
effective length of database: 9,153,583
effective search space: 915358300
effective search space used: 915358300
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 bits)