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= 015100
         (413 letters)

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

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



>pdb|3J21|A Chain A, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
           Revealed By Cryo-em: Implications For Evolution Of
           Eukaryotic Ribosomes (50s Ribosomal Proteins)
          Length = 216

 Score = 29.3 bits (64), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 22/95 (23%), Positives = 37/95 (38%)

Query: 138 RKLCDSYDIFLADKRVVXXXXXXXXXXXXXXXXXXXXVDLKHQNWKEQIEKVCGSALLYL 197
           RKL   YD F+A+  ++                    V     +    +EK+  +  + L
Sbjct: 98  RKLAKKYDFFIAEAPLMPKIGRYLGRYLGPRNKMPVVVPPTLTDLTPIVEKLKKTVRIQL 157

Query: 198 RTGTCSVLKVGKVSMGAEDIAENVIAAINGLLESL 232
           +        VG   M  E+IAEN+ A +N ++  L
Sbjct: 158 KNNPVVHAPVGTEKMSDEEIAENIEAVLNAIIGKL 192


>pdb|3ZF7|J Chain J, High-resolution Cryo-electron Microscopy Structure Of The
           Trypanosoma Brucei Ribosome
          Length = 214

 Score = 28.1 bits (61), Expect = 9.0,   Method: Compositional matrix adjust.
 Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 4/36 (11%)

Query: 197 LRTGTCSVLKVGKVSMGAEDIAENVIAAINGLLESL 232
           L  GTC    VG V M  + + +NV+ AIN L+  L
Sbjct: 160 LCLGTC----VGHVDMTEDQVRQNVVMAINFLVSLL 191


  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    0.132    0.371 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,704,466
Number of Sequences: 62578
Number of extensions: 254758
Number of successful extensions: 360
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 359
Number of HSP's gapped (non-prelim): 2
length of query: 413
length of database: 14,973,337
effective HSP length: 101
effective length of query: 312
effective length of database: 8,652,959
effective search space: 2699723208
effective search space used: 2699723208
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: 53 (25.0 bits)