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= 029976
         (184 letters)

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

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



>pdb|2ZKR|JJ Chain j, Structure Of A Mammalian Ribosomal 60s Subunit Within An
          80s Complex Obtained By Docking Homology Models Of The
          Rna And Proteins Into An 8.7 A Cryo-Em Map
          Length = 203

 Score = 30.0 bits (66), Expect = 0.68,   Method: Compositional matrix adjust.
 Identities = 15/37 (40%), Positives = 21/37 (56%)

Query: 1  MAASLATQSMLGSSVVAARVTGIRKSGVYQFSSVKYL 37
          +AA +A Q +LG  VV  R  GI  SG +  + + YL
Sbjct: 19 LAAIVAKQVLLGRKVVVVRCEGINISGNFYRNKLNYL 55


>pdb|2LBO|A Chain A, Eimeria Tenella Microneme Protein 3 Mar_b Domain
          Length = 123

 Score = 27.3 bits (59), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 10/19 (52%), Positives = 14/19 (73%)

Query: 51  CMAKNEQQKDQSTQPPKLP 69
           C  K+EQQ  Q+T PP++P
Sbjct: 105 CTDKSEQQPSQATPPPEIP 123


>pdb|2WSC|3 Chain 3, Improved Model Of Plant Photosystem I
 pdb|2WSE|3 Chain 3, Improved Model Of Plant Photosystem I
 pdb|2WSF|3 Chain 3, Improved Model Of Plant Photosystem I
          Length = 276

 Score = 27.3 bits (59), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 12/20 (60%), Positives = 15/20 (75%)

Query: 87  ERINGRLAMIGFVAALAVEL 106
           E INGR AM+G V A+A E+
Sbjct: 103 EIINGRYAMLGAVGAIAPEI 122


>pdb|3LW5|3 Chain 3, Improved Model Of Plant Photosystem I
          Length = 172

 Score = 26.9 bits (58), Expect = 6.4,   Method: Compositional matrix adjust.
 Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 2/38 (5%)

Query: 87  ERINGRLAMIGFVAALAVELSKGQDVFAQLSDGGVAWF 124
           E INGR AM+G V A+A E      +  Q  +  +AWF
Sbjct: 19  EVINGRFAMLGAVGAIAPEYLGKVGLIPQ--ETALAWF 54


  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
   0.318    0.131    0.370 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,272,043
Number of Sequences: 62578
Number of extensions: 141809
Number of successful extensions: 257
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 248
Number of HSP's gapped (non-prelim): 11
length of query: 184
length of database: 14,973,337
effective HSP length: 93
effective length of query: 91
effective length of database: 9,153,583
effective search space: 832976053
effective search space used: 832976053
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)