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= 033297
         (122 letters)

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

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



>pdb|1914|A Chain A, Signal Recognition Particle Alu Rna Binding Heterodimer,
           Srp914
          Length = 232

 Score = 79.7 bits (195), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 40/94 (42%), Positives = 58/94 (61%), Gaps = 1/94 (1%)

Query: 1   MGLLQPDPFLNELTSMFERNRDKGSVWVTFXXXXXXXXXXXXXMATAG-EPVEYRCLIRA 59
           M LL+ + FL ELT +F++ R  GSV++T               +  G EP E +CL+RA
Sbjct: 20  MVLLESEQFLTELTRLFQKCRSSGSVFITLKKYDGRTKPIPRKSSVEGLEPAENKCLLRA 79

Query: 60  TDGKQKISTTVGAKDHQRFQASYATLLKAHMAAL 93
           TDGK+KIST V +K+  +FQ +Y+ LL+A+M  L
Sbjct: 80  TDGKRKISTVVSSKEVNKFQMAYSNLLRANMDGL 113


>pdb|1E8O|B Chain B, Core Of The Alu Domain Of The Mammalian Srp
 pdb|1E8O|D Chain D, Core Of The Alu Domain Of The Mammalian Srp
 pdb|1E8S|B Chain B, Alu Domain Of The Mammalian Srp (Potential Alu
          Retroposition Intermediate)
 pdb|1RY1|D Chain D, Structure Of The Signal Recognition Particle Interacting
          With The Elongation-Arrested Ribosome
          Length = 106

 Score = 77.0 bits (188), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 38/92 (41%), Positives = 56/92 (60%), Gaps = 1/92 (1%)

Query: 3  LLQPDPFLNELTSMFERNRDKGSVWVTFXXXXXXXXXXXXXMATAG-EPVEYRCLIRATD 61
          LL+ + FL ELT +F++ R  GSV++T                  G EP + +CL+RATD
Sbjct: 2  LLESEQFLTELTRLFQKCRTSGSVYITLKKYDGRTKPIPKKGTVEGFEPADNKCLLRATD 61

Query: 62 GKQKISTTVGAKDHQRFQASYATLLKAHMAAL 93
          GK+KIST V +K+  +FQ +Y+ LL+A+M  L
Sbjct: 62 GKKKISTVVSSKEVNKFQMAYSNLLRANMDGL 93


  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    0.130    0.380 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,459,429
Number of Sequences: 62578
Number of extensions: 60681
Number of successful extensions: 54
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 50
Number of HSP's gapped (non-prelim): 2
length of query: 122
length of database: 14,973,337
effective HSP length: 84
effective length of query: 38
effective length of database: 9,716,785
effective search space: 369237830
effective search space used: 369237830
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: 45 (21.9 bits)