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= psy7241
         (84 letters)

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

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



>pdb|3IZR|D Chain D, Localization Of The Large Subunit Ribosomal Proteins Into
           A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
           Ribosome
          Length = 405

 Score = 25.8 bits (55), Expect = 6.4,   Method: Composition-based stats.
 Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 2/50 (4%)

Query: 30  RQNVYFQRVLSSKSATQAQMLSYVAAFGCLIMAVP--PVIIGAIAKSTDK 77
           R NV+ +RV  + +     + S V A G  I  VP  P++I   A+S +K
Sbjct: 118 RVNVHLRRVAVASALAATSVPSLVLARGHRIETVPELPLVISDSAESIEK 167


>pdb|2XQ2|A Chain A, Structure Of The K294a Mutant Of Vsglt
          Length = 593

 Score = 25.4 bits (54), Expect = 8.3,   Method: Compositional matrix adjust.
 Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 1/39 (2%)

Query: 23  NVYKLIFRQNVYFQRVLSSKSATQAQMLSYVAAFGCLIM 61
           N+Y   F Q +  QR L++KS ++AQ     AAF  LI+
Sbjct: 260 NLYYWGFNQYI-IQRTLAAKSVSEAQKGIVFAAFLALIV 297


>pdb|2XQ2|B Chain B, Structure Of The K294a Mutant Of Vsglt
          Length = 593

 Score = 25.4 bits (54), Expect = 8.6,   Method: Compositional matrix adjust.
 Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 1/39 (2%)

Query: 23  NVYKLIFRQNVYFQRVLSSKSATQAQMLSYVAAFGCLIM 61
           N+Y   F Q +  QR L++KS ++AQ     AAF  LI+
Sbjct: 260 NLYYWGFNQYI-IQRTLAAKSVSEAQKGIVFAAFLALIV 297


  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
   0.330    0.136    0.388 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,233,962
Number of Sequences: 62578
Number of extensions: 24701
Number of successful extensions: 89
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 89
Number of HSP's gapped (non-prelim): 4
length of query: 84
length of database: 14,973,337
effective HSP length: 52
effective length of query: 32
effective length of database: 11,719,281
effective search space: 375016992
effective search space used: 375016992
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 45 (21.9 bits)