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= 034131
         (103 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 = 76.6 bits (187), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 34/69 (49%), Positives = 46/69 (66%)

Query: 6   SWDEFVGRSVQLYKADPQSTRYCMKYRHCDGKLVLKVTDNKECLKFKTDQAQDAKKMEKL 65
           +W+EF   + +LY ADP   R  +KYRH DG L +KVTD+  CL ++TDQAQD KK+EK 
Sbjct: 152 TWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKKIEKF 211

Query: 66  NNIFFALMA 74
           ++    LM 
Sbjct: 212 HSQLMRLMV 220


>pdb|1E8O|A Chain A, Core Of The Alu Domain Of The Mammalian Srp
 pdb|1E8O|C Chain C, Core Of The Alu Domain Of The Mammalian Srp
 pdb|1E8S|A Chain A, Alu Domain Of The Mammalian Srp (Potential Alu
          Retroposition Intermediate)
 pdb|1RY1|C Chain C, Structure Of The Signal Recognition Particle Interacting
          With The Elongation-Arrested Ribosome
          Length = 85

 Score = 76.3 bits (186), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 35/69 (50%), Positives = 46/69 (66%)

Query: 6  SWDEFVGRSVQLYKADPQSTRYCMKYRHCDGKLVLKVTDNKECLKFKTDQAQDAKKMEKL 65
          +W+EF   + +LY ADP   R  +KYRH DG L +KVTD+  CL +KTDQAQD KK+EK 
Sbjct: 5  TWEEFSRAAEKLYLADPMKARVVLKYRHSDGNLCVKVTDDLVCLVYKTDQAQDVKKIEKF 64

Query: 66 NNIFFALMA 74
          ++    LM 
Sbjct: 65 HSQLMRLMV 73


>pdb|1VFF|A Chain A, Beta-Glycosidase From Pyrococcus Horikoshii
          Length = 423

 Score = 26.6 bits (57), Expect = 3.9,   Method: Composition-based stats.
 Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 2/71 (2%)

Query: 1   MVYVTS-WDEFVGRSVQLYKADPQSTR-YCMKYRHCDGKLVLKVTDNKECLKFKTDQAQD 58
           M Y+T+ W  F+    + +K      + + + Y    GK  + +  N   +   +D+ +D
Sbjct: 162 MGYLTAYWPPFIRSPFKAFKVAANLLKAHAIAYELLHGKFKVGIVKNIPIILPASDKERD 221

Query: 59  AKKMEKLNNIF 69
            K  EK +N+F
Sbjct: 222 RKAAEKADNLF 232


>pdb|3LJS|A Chain A, Crystal Structure Of Fructokinase From Xylella Fastidiosa
 pdb|3LJS|B Chain B, Crystal Structure Of Fructokinase From Xylella Fastidiosa
 pdb|3LKI|A Chain A, Crystal Structure Of Fructokinase With Bound Atp From
           Xylella Fastidiosa
 pdb|3LKI|B Chain B, Crystal Structure Of Fructokinase With Bound Atp From
           Xylella Fastidiosa
          Length = 338

 Score = 25.8 bits (55), Expect = 6.4,   Method: Composition-based stats.
 Identities = 17/47 (36%), Positives = 23/47 (48%), Gaps = 2/47 (4%)

Query: 49  LKFKTDQAQDAKKMEKLNNIFFALMARGPDVDLSEVTGKEQMEAQPA 95
           L F+ +  QDA   + L  IF A      D D++EVT +    AQ A
Sbjct: 115 LLFRVEHFQDASFSDAL--IFHACSNSXTDADIAEVTFEGXRRAQAA 159


  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    0.132    0.389 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,965,440
Number of Sequences: 62578
Number of extensions: 96577
Number of successful extensions: 175
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 171
Number of HSP's gapped (non-prelim): 6
length of query: 103
length of database: 14,973,337
effective HSP length: 68
effective length of query: 35
effective length of database: 10,718,033
effective search space: 375131155
effective search space used: 375131155
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)