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= 000736
         (1323 letters)

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

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



>pdb|3J21|Y Chain Y, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
           Revealed By Cryo-em: Implications For Evolution Of
           Eukaryotic Ribosomes (50s Ribosomal Proteins)
          Length = 155

 Score = 32.3 bits (72), Expect = 2.0,   Method: Composition-based stats.
 Identities = 15/35 (42%), Positives = 21/35 (60%), Gaps = 1/35 (2%)

Query: 723 RDALVMVRRHRINFNVIVDHC-GWQAFLQSASEFV 756
           RD L M+R HR+N  VIVD    +   LQ A +++
Sbjct: 20  RDTLAMLRLHRVNHCVIVDDTPSYLGMLQKAKDYI 54


>pdb|1ID3|D Chain D, Crystal Structure Of The Yeast Nucleosome Core Particle
           Reveals Fundamental Differences In Inter-Nucleosome
           Interactions
 pdb|1ID3|H Chain H, Crystal Structure Of The Yeast Nucleosome Core Particle
           Reveals Fundamental Differences In Inter-Nucleosome
           Interactions
          Length = 130

 Score = 30.0 bits (66), Expect = 8.1,   Method: Composition-based stats.
 Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 184 DGKYFATLSEFCNSSKLHKRLKVWERDSGTLQAS-SELKAFMGAVLEWMPSGANIAAVYD 242
           DGK  + + +   SS ++K LK    D+G  Q S S L +F+  + E + + A+  A Y+
Sbjct: 28  DGKKRSKVRKETYSSYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYN 87

Query: 243 RKS 245
           +KS
Sbjct: 88  KKS 90


  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
   0.319    0.134    0.397 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 35,270,055
Number of Sequences: 62578
Number of extensions: 1373358
Number of successful extensions: 2765
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 2765
Number of HSP's gapped (non-prelim): 3
length of query: 1323
length of database: 14,973,337
effective HSP length: 110
effective length of query: 1213
effective length of database: 8,089,757
effective search space: 9812875241
effective search space used: 9812875241
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: 57 (26.6 bits)