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= psy13065
         (114 letters)

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

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



>pdb|2QKM|B Chain B, The Crystal Structure Of Fission Yeast Mrna Decapping
           Enzyme Dcp1-Dcp2 Complex
 pdb|2QKM|D Chain D, The Crystal Structure Of Fission Yeast Mrna Decapping
           Enzyme Dcp1-Dcp2 Complex
 pdb|2QKM|F Chain F, The Crystal Structure Of Fission Yeast Mrna Decapping
           Enzyme Dcp1-Dcp2 Complex
 pdb|2QKM|H Chain H, The Crystal Structure Of Fission Yeast Mrna Decapping
           Enzyme Dcp1-Dcp2 Complex
          Length = 266

 Score = 71.6 bits (174), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 34/92 (36%), Positives = 53/92 (57%), Gaps = 7/92 (7%)

Query: 14  KQVLEETGFDSSHLIAEDSYLETTYNDQLTRLYLIPGVPIDFKFAPQTRGEIKACQWFPI 73
           ++V EETGFD S  I  + +++ T   Q  RLY+IPG+ +D +F  +TR EI   +W  +
Sbjct: 142 REVYEETGFDCSSRINPNEFIDMTIRGQNVRLYIIPGISLDTRFESRTRKEISKIEWHNL 201

Query: 74  GDLPSSRKEIKTVLINGTPVGTNAFFMIMPFI 105
            DLP+ +K       N      N F+M++PF+
Sbjct: 202 MDLPTFKK-------NKPQTMKNKFYMVIPFL 226


>pdb|2A6T|A Chain A, Crystal Structure Of S.Pombe Mrna Decapping Enzyme Dcp2p
 pdb|2A6T|B Chain B, Crystal Structure Of S.Pombe Mrna Decapping Enzyme Dcp2p
          Length = 271

 Score = 71.2 bits (173), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 34/92 (36%), Positives = 53/92 (57%), Gaps = 7/92 (7%)

Query: 14  KQVLEETGFDSSHLIAEDSYLETTYNDQLTRLYLIPGVPIDFKFAPQTRGEIKACQWFPI 73
           ++V EETGFD S  I  + +++ T   Q  RLY+IPG+ +D +F  +TR EI   +W  +
Sbjct: 147 REVYEETGFDCSSRINPNEFIDMTIRGQNVRLYIIPGISLDTRFESRTRKEISKIEWHNL 206

Query: 74  GDLPSSRKEIKTVLINGTPVGTNAFFMIMPFI 105
            DLP+ +K       N      N F+M++PF+
Sbjct: 207 MDLPTFKK-------NKPQTMKNKFYMVIPFL 231


>pdb|2JVB|A Chain A, Solution Structure Of Catalytic Domain Of Ydcp2
          Length = 146

 Score = 50.8 bits (120), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 2/79 (2%)

Query: 14  KQVLEETGFDSSHLIAEDSYLETTYNDQLTRLYLIPGVPIDFKFAPQTRGEIKACQWFPI 73
           ++V EE GFD +  I ++ ++E     +  +++LI GV   F F PQ R EI   +WF  
Sbjct: 49  REVKEEIGFDLTDYIDDNQFIERNIQGKNYKIFLISGVSEVFNFKPQVRNEIDKIEWFDF 108

Query: 74  GDLPSS--RKEIKTVLING 90
             +  +  +  IK  LIN 
Sbjct: 109 KKISKTMYKSNIKYYLINS 127


>pdb|1LRK|A Chain A, Crystal Structure Of Escherichia Coli Udp-Galactose
           4-Epimerase Mutant Y299c Complexed With
           Udp-N-Acetylglucosamine
 pdb|1LRL|A Chain A, Crystal Structure Of Udp-Galactose 4-Epimerase Mutant
           Y299c Complexed With Udp-Glucose
          Length = 338

 Score = 27.3 bits (59), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 8/19 (42%), Positives = 14/19 (73%)

Query: 50  GVPIDFKFAPQTRGEIKAC 68
           G P+++ FAP+  G++ AC
Sbjct: 281 GKPVNYHFAPRREGDLPAC 299


>pdb|1R8W|A Chain A, Native Structure Of The B12-Independent Glycerol
           Dehydratase From Clostridium Butyricum
 pdb|1R8W|B Chain B, Native Structure Of The B12-Independent Glycerol
           Dehydratase From Clostridium Butyricum
 pdb|1R9D|A Chain A, Glycerol Bound Form Of The B12-Independent Glycerol
           Dehydratase From Clostridium Butyricum
 pdb|1R9D|B Chain B, Glycerol Bound Form Of The B12-Independent Glycerol
           Dehydratase From Clostridium Butyricum
 pdb|1R9E|A Chain A, Structure Of The B12-Independent Glycerol Dehydratase With
           1,2-Propanediol Bound
 pdb|1R9E|B Chain B, Structure Of The B12-Independent Glycerol Dehydratase With
           1,2-Propanediol Bound
          Length = 787

 Score = 26.6 bits (57), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 14/51 (27%), Positives = 20/51 (39%)

Query: 46  YLIPGVPIDFKFAPQTRGEIKACQWFPIGDLPSSRKEIKTVLINGTPVGTN 96
           Y+ P    D     +   E+  C W  + D+   R EI T    G P+  N
Sbjct: 291 YMYPYYENDKNITDKFAQELIDCIWIKLNDINKVRDEISTKHFGGYPMYQN 341


  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
   0.321    0.139    0.414 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,093,765
Number of Sequences: 62578
Number of extensions: 117120
Number of successful extensions: 273
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 264
Number of HSP's gapped (non-prelim): 9
length of query: 114
length of database: 14,973,337
effective HSP length: 77
effective length of query: 37
effective length of database: 10,154,831
effective search space: 375728747
effective search space used: 375728747
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)