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= psy12139
         (65 letters)

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

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



>pdb|3NTW|A Chain A, Structure Of The Mlle Domain Of Edd In Complex With A
          Pam2 Peptide From Paip1
 pdb|3NTW|C Chain C, Structure Of The Mlle Domain Of Edd In Complex With A
          Pam2 Peptide From Paip1
          Length = 65

 Score = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 22/32 (68%), Positives = 31/32 (96%)

Query: 1  MLLELSPAQLLMLLASDEALRQKVEEAMDIVM 32
          MLLELSPAQLL+LLAS+++LR +VEEAM++++
Sbjct: 32 MLLELSPAQLLLLLASEDSLRARVEEAMELIV 63


>pdb|1I2T|A Chain A, X-Ray Structure Of The Human Hyperplastic Discs Protein:
          An Ortholog Of The C-Terminal Domain Of Poly(A)-Binding
          Protein
          Length = 61

 Score = 37.4 bits (85), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 21/32 (65%), Positives = 31/32 (96%)

Query: 1  MLLELSPAQLLMLLASDEALRQKVEEAMDIVM 32
          MLLELSPAQLL+LLAS+++LR +V+EAM++++
Sbjct: 27 MLLELSPAQLLLLLASEDSLRARVDEAMELII 58


>pdb|2DYD|A Chain A, Solution Structure Of The Pabc Domain From Triticum
          Aevestium Poly(A)-Binding Protein
          Length = 85

 Score = 30.4 bits (67), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 16/37 (43%), Positives = 25/37 (67%)

Query: 1  MLLELSPAQLLMLLASDEALRQKVEEAMDIVMNLSGH 37
          MLLE+   ++L LL S +AL+ KV EAM+++ +   H
Sbjct: 48 MLLEMDQTEVLHLLESPDALKAKVAEAMEVLRSAQQH 84


>pdb|1G9L|A Chain A, Solution Structure Of The Pabc Domain Of Human Poly(A)
           Binding Protein
          Length = 144

 Score = 30.4 bits (67), Expect = 0.27,   Method: Compositional matrix adjust.
 Identities = 19/54 (35%), Positives = 33/54 (61%), Gaps = 5/54 (9%)

Query: 1   MLLELSPAQLLMLLASDEALRQKVEEAMDIVMNLSGHDL--SSENLLGSSDGID 52
           MLLE+  ++LL +L S E+LR KV+EA+ +   L  H    +++  + S+ G+ 
Sbjct: 92  MLLEIDNSELLHMLESPESLRSKVDEAVAV---LQAHQAKEAAQKAVNSATGVP 142


>pdb|1JGN|A Chain A, Solution Structure Of The C-Terminal Pabc Domain Of
          Human Poly(A)-Binding Protein In Complex With The
          Peptide From Paip2
 pdb|1JH4|A Chain A, Solution Structure Of The C-Terminal Pabc Domain Of
          Human Poly(A)-Binding Protein In Complex With The
          Peptide From Paip1
          Length = 98

 Score = 29.6 bits (65), Expect = 0.46,   Method: Compositional matrix adjust.
 Identities = 17/52 (32%), Positives = 33/52 (63%), Gaps = 1/52 (1%)

Query: 1  MLLELSPAQLLMLLASDEALRQKVEEAMDIVMNLSGHDLSSENLLGSSDGID 52
          MLLE+  ++LL +L S E+LR KV+EA+ ++      + +++  + S+ G+ 
Sbjct: 46 MLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKE-AAQKAVNSATGVP 96


>pdb|3KUR|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
          Protein
 pdb|3KUR|B Chain B, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
          Protein
 pdb|3KUR|C Chain C, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
          Protein
 pdb|3KUR|D Chain D, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
          Protein
 pdb|3KUR|E Chain E, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
          Protein
 pdb|3KUR|F Chain F, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
          Protein
 pdb|3KUR|G Chain G, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
          Protein
 pdb|3KUR|H Chain H, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
          Protein
          Length = 79

 Score = 28.9 bits (63), Expect = 0.81,   Method: Compositional matrix adjust.
 Identities = 15/31 (48%), Positives = 24/31 (77%)

Query: 1  MLLELSPAQLLMLLASDEALRQKVEEAMDIV 31
          MLLE+  ++LL +L S E+LR KV+EA+ ++
Sbjct: 46 MLLEIDNSELLHMLESPESLRSKVDEAVAVL 76


>pdb|2X04|A Chain A, Crystal Structure Of The Pabc-Tnrc6c Complex
 pdb|2X04|B Chain B, Crystal Structure Of The Pabc-Tnrc6c Complex
          Length = 80

 Score = 28.9 bits (63), Expect = 0.83,   Method: Compositional matrix adjust.
 Identities = 15/31 (48%), Positives = 24/31 (77%)

Query: 1  MLLELSPAQLLMLLASDEALRQKVEEAMDIV 31
          MLLE+  ++LL +L S E+LR KV+EA+ ++
Sbjct: 45 MLLEIDNSELLHMLESPESLRSKVDEAVAVL 75


>pdb|3KUS|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
          Protein In Complex With The Binding Region Of Paip2
 pdb|3KUS|B Chain B, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
          Protein In Complex With The Binding Region Of Paip2
 pdb|3KUT|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(a)-binding
          Protein In Complex With The Binding Region Of Paip2
 pdb|3KUT|B Chain B, Crystal Structure Of The Mlle Domain Of Poly(a)-binding
          Protein In Complex With The Binding Region Of Paip2
 pdb|3KTP|A Chain A, Structural Basis Of Gw182 Recognition By Poly(a)-binding
          Protein
 pdb|3KTR|A Chain A, Structural Basis Of Ataxin-2 Recognition By
          Poly(A)-Binding
 pdb|3KUI|A Chain A, Crystal Structure Of C-Terminal Domain Of Pabpc1 In
          Complex Binding Region Of Erf3a
 pdb|3KUJ|A Chain A, Crystal Structure Of C-Terminal Domain Of Pabpc1 In
          Complex With Binding Region Of Erf3a
 pdb|3PKN|A Chain A, Crystal Structure Of Mlle Domain Of Poly(A) Binding
          Protein In Complex With Pam2 Motif Of La-Related
          Protein 4 (Larp4)
          Length = 88

 Score = 28.5 bits (62), Expect = 0.99,   Method: Compositional matrix adjust.
 Identities = 15/31 (48%), Positives = 24/31 (77%)

Query: 1  MLLELSPAQLLMLLASDEALRQKVEEAMDIV 31
          MLLE+  ++LL +L S E+LR KV+EA+ ++
Sbjct: 46 MLLEIDNSELLHMLESPESLRSKVDEAVAVL 76


>pdb|3PTH|A Chain A, The Pabc1 Mlle Domain Bound To The Variant Pam2 Motif Of
          Larp4b
          Length = 82

 Score = 28.5 bits (62), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 15/31 (48%), Positives = 24/31 (77%)

Query: 1  MLLELSPAQLLMLLASDEALRQKVEEAMDIV 31
          MLLE+  ++LL +L S E+LR KV+EA+ ++
Sbjct: 45 MLLEIDNSELLHMLESPESLRSKVDEAVAVL 75


>pdb|2RQG|B Chain B, Structure Of Gspt1ERF3A-Pabc
 pdb|2RQH|B Chain B, Structure Of Gspt1ERF3A-Pabc
          Length = 83

 Score = 28.5 bits (62), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 15/31 (48%), Positives = 24/31 (77%)

Query: 1  MLLELSPAQLLMLLASDEALRQKVEEAMDIV 31
          MLLE+  ++LL +L S E+LR KV+EA+ ++
Sbjct: 44 MLLEIDNSELLHMLESPESLRSKVDEAVAVL 74


>pdb|4IVE|A Chain A, Crystal Structure Of A Polyadenylate-binding Protein 3
          (pabpc3) From Homo Sapiens At 2.30 A Resolution
 pdb|4IVE|B Chain B, Crystal Structure Of A Polyadenylate-binding Protein 3
          (pabpc3) From Homo Sapiens At 2.30 A Resolution
 pdb|4IVE|C Chain C, Crystal Structure Of A Polyadenylate-binding Protein 3
          (pabpc3) From Homo Sapiens At 2.30 A Resolution
 pdb|4IVE|D Chain D, Crystal Structure Of A Polyadenylate-binding Protein 3
          (pabpc3) From Homo Sapiens At 2.30 A Resolution
          Length = 98

 Score = 27.7 bits (60), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 16/51 (31%), Positives = 31/51 (60%), Gaps = 1/51 (1%)

Query: 2  LLELSPAQLLMLLASDEALRQKVEEAMDIVMNLSGHDLSSENLLGSSDGID 52
          LLE+  ++LL  L S E+LR KV+EA+ ++      + +++  + S+ G+ 
Sbjct: 47 LLEIDNSELLYXLESPESLRSKVDEAVAVLQAHQAKE-ATQKAVNSATGVP 96


>pdb|1IFW|A Chain A, Solution Structure Of C-Terminal Domain Of Poly(A)
          Binding Protein From Saccharomyces Cerevisiae
          Length = 92

 Score = 26.2 bits (56), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 12/27 (44%), Positives = 17/27 (62%)

Query: 1  MLLELSPAQLLMLLASDEALRQKVEEA 27
          M+L+L P ++  LL SDE   Q  +EA
Sbjct: 48 MILDLPPQEVFPLLESDELFEQHYKEA 74


>pdb|3BH1|A Chain A, Crystal Structure Of Protein Dip2346 From Corynebacterium
           Diphtheriae
 pdb|3BH1|B Chain B, Crystal Structure Of Protein Dip2346 From Corynebacterium
           Diphtheriae
 pdb|3BH1|C Chain C, Crystal Structure Of Protein Dip2346 From Corynebacterium
           Diphtheriae
 pdb|3BH1|D Chain D, Crystal Structure Of Protein Dip2346 From Corynebacterium
           Diphtheriae
          Length = 507

 Score = 26.2 bits (56), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 13/41 (31%), Positives = 24/41 (58%)

Query: 9   QLLMLLASDEALRQKVEEAMDIVMNLSGHDLSSENLLGSSD 49
           ++L+ L+   A     ++A+D + NL G D+ +  +LGS D
Sbjct: 433 EVLIALSVSAATDSNAQKALDQLKNLRGCDVHTTTILGSVD 473


>pdb|3FC3|A Chain A, Crystal Structure Of The Beta-Beta-Alpha-Me Type Ii
           Restriction Endonuclease Hpy99i
 pdb|3FC3|B Chain B, Crystal Structure Of The Beta-Beta-Alpha-Me Type Ii
           Restriction Endonuclease Hpy99i
 pdb|3GOX|A Chain A, Crystal Structure Of The Beta-Beta-Alpha-Me Type Ii
           Restriction Endonuclease Hpy99i In The Absence Of Edta
 pdb|3GOX|B Chain B, Crystal Structure Of The Beta-Beta-Alpha-Me Type Ii
           Restriction Endonuclease Hpy99i In The Absence Of Edta
          Length = 200

 Score = 25.4 bits (54), Expect = 7.3,   Method: Composition-based stats.
 Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 3/43 (6%)

Query: 26  EAMDIVMNLSGHDLSSENL---LGSSDGIDIHSSTVKGELTLR 65
           EA+DI     G+D    N+   L ++DG +I+ +  KG  T R
Sbjct: 62  EAIDIYRTGKGYDKKICNICHILKNTDGFEINQTDAKGRKTTR 104


>pdb|2D5K|A Chain A, Crystal Structure Of Dps From Staphylococcus Aureus
 pdb|2D5K|B Chain B, Crystal Structure Of Dps From Staphylococcus Aureus
 pdb|2D5K|C Chain C, Crystal Structure Of Dps From Staphylococcus Aureus
 pdb|2D5K|D Chain D, Crystal Structure Of Dps From Staphylococcus Aureus
          Length = 156

 Score = 25.0 bits (53), Expect = 9.9,   Method: Compositional matrix adjust.
 Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 2/62 (3%)

Query: 5   LSPAQLLMLLASD-EALRQKVEEAMDIVMNLSGHDLSSENLLGSSDGIDIHSSTVKGELT 63
            S  Q++  L+ D   + +++E A++I  N +G D+S +  +G    +D H+   K  L+
Sbjct: 90  YSAEQMVEELSQDFTNISKQLENAIEIAGN-AGDDVSEDMFIGMQTSVDKHNWMFKSYLS 148

Query: 64  LR 65
           L 
Sbjct: 149 LE 150


  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
   0.312    0.130    0.330 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,541,022
Number of Sequences: 62578
Number of extensions: 42588
Number of successful extensions: 140
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 126
Number of HSP's gapped (non-prelim): 16
length of query: 65
length of database: 14,973,337
effective HSP length: 36
effective length of query: 29
effective length of database: 12,720,529
effective search space: 368895341
effective search space used: 368895341
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 45 (21.9 bits)