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= 029551
         (191 letters)

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

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



>pdb|3BBO|R Chain R, Homology Model For The Spinach Chloroplast 50s Subunit
           Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome
          Length = 233

 Score = 65.9 bits (159), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 30/42 (71%), Positives = 37/42 (88%)

Query: 115 PRKPRVKLGDIMGILNKRAVEASESERPIPDIRTGDVVEIKL 156
           PR+ RVKLGDIMGILNK+AV A+E  RP+P IRTGD+V+I+L
Sbjct: 112 PRQQRVKLGDIMGILNKKAVHAAEELRPVPGIRTGDIVQIRL 153



 Score = 30.0 bits (66), Expect = 0.82,   Method: Compositional matrix adjust.
 Identities = 18/30 (60%), Positives = 21/30 (70%), Gaps = 2/30 (6%)

Query: 1  MGSQVLPQALHWIPRS-STQCIP-SKRLGF 28
          M S+VLPQAL  IP + S QC P  K+LGF
Sbjct: 1  MASKVLPQALLVIPSNHSLQCPPLKKQLGF 30


  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
   0.323    0.141    0.427 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,867,289
Number of Sequences: 62578
Number of extensions: 114382
Number of successful extensions: 217
Number of sequences better than 100.0: 1
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 215
Number of HSP's gapped (non-prelim): 2
length of query: 191
length of database: 14,973,337
effective HSP length: 93
effective length of query: 98
effective length of database: 9,153,583
effective search space: 897051134
effective search space used: 897051134
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 48 (23.1 bits)