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= 047699
         (140 letters)

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

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



>pdb|2LYD|A Chain A, The Solution Structure Of The Dm Dcp1 Evh1 Domain In
          Complex With The Xrn1 Dbm Peptide
          Length = 134

 Score = 68.6 bits (166), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 31/84 (36%), Positives = 51/84 (60%), Gaps = 1/84 (1%)

Query: 5  GKLMPNL-DQQSTKLLSLTVLQRIDPFIEEILITAAHVTFYEFNIDLSQWSRKDVEGSLF 63
          G  M +L   +S   ++L  +++IDP+ +EI+ +++HV FY FN   ++W + DVEG+ F
Sbjct: 1  GPHMADLMADESITRMNLAAIKKIDPYAKEIVDSSSHVAFYTFNSSQNEWEKTDVEGAFF 60

Query: 64 VVKRNTQPRFQFVVMNRRNTGWFV 87
          +  RN +P     + NR NT  FV
Sbjct: 61 IYHRNAEPFHSIFINNRLNTTSFV 84


>pdb|2QKL|A Chain A, The Crystal Structure Of Fission Yeast Mrna Decapping
          Enzyme Dcp1-Dcp2 Complex
 pdb|2QKM|A Chain A, The Crystal Structure Of Fission Yeast Mrna Decapping
          Enzyme Dcp1-Dcp2 Complex
 pdb|2QKM|C Chain C, The Crystal Structure Of Fission Yeast Mrna Decapping
          Enzyme Dcp1-Dcp2 Complex
 pdb|2QKM|E Chain E, The Crystal Structure Of Fission Yeast Mrna Decapping
          Enzyme Dcp1-Dcp2 Complex
 pdb|2QKM|G Chain G, The Crystal Structure Of Fission Yeast Mrna Decapping
          Enzyme Dcp1-Dcp2 Complex
          Length = 127

 Score = 45.8 bits (107), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 22/62 (35%), Positives = 40/62 (64%), Gaps = 1/62 (1%)

Query: 19 LSLTVLQRIDPFIEEILITAAHVTFYEFNIDLSQWSRKDVEGSLFVVKRNTQPRFQFVVM 78
          ++L VL+   P IE I+  A+HV  Y+F++   +W +  +EG+ F+VK + + R  +V++
Sbjct: 11 VNLQVLKFHYPEIESIIDIASHVAVYQFDVGSQKWLKTSIEGTFFLVK-DQRARVGYVIL 69

Query: 79 NR 80
          NR
Sbjct: 70 NR 71


>pdb|1Q67|A Chain A, Crystal Structure Of Dcp1p
 pdb|1Q67|B Chain B, Crystal Structure Of Dcp1p
          Length = 231

 Score = 35.0 bits (79), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 14/52 (26%), Positives = 30/52 (57%)

Query: 17 KLLSLTVLQRIDPFIEEILITAAHVTFYEFNIDLSQWSRKDVEGSLFVVKRN 68
          K L+  V+ R DP I+++L    H + Y+++    +W++ + +G L +  R+
Sbjct: 20 KALNFNVIGRYDPKIKQLLFHTPHASLYKWDFKKDEWNKLEYQGVLAIYLRD 71


  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
   0.323    0.136    0.405 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,821,529
Number of Sequences: 62578
Number of extensions: 139453
Number of successful extensions: 333
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 330
Number of HSP's gapped (non-prelim): 3
length of query: 140
length of database: 14,973,337
effective HSP length: 89
effective length of query: 51
effective length of database: 9,403,895
effective search space: 479598645
effective search space used: 479598645
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 46 (22.3 bits)