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= psy1207
         (113 letters)

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

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



>pdb|1UL1|X Chain X, Crystal Structure Of The Human Fen1-Pcna Complex
 pdb|1UL1|Y Chain Y, Crystal Structure Of The Human Fen1-Pcna Complex
 pdb|1UL1|Z Chain Z, Crystal Structure Of The Human Fen1-Pcna Complex
          Length = 379

 Score = 98.2 bits (243), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 48/86 (55%), Positives = 59/86 (68%), Gaps = 15/86 (17%)

Query: 15  IDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMV 74
           ++KF +RLV+V+  H  ECK LLSLMGIPY++               AP EAEA CAA+V
Sbjct: 122 VEKFTKRLVKVTKQHNDECKHLLSLMGIPYLD---------------APSEAEASCAALV 166

Query: 75  KAGKVYATATEDMDALTFGTNILLRQ 100
           KAGKVYA ATEDMD LTFG+ +L+R 
Sbjct: 167 KAGKVYAAATEDMDCLTFGSPVLMRH 192


>pdb|3Q8K|A Chain A, Crystal Structure Of Human Flap Endonuclease Fen1 (Wt) In
           Complex With Product 5'-Flap Dna, Sm3+, And K+
 pdb|3Q8L|A Chain A, Crystal Structure Of Human Flap Endonuclease Fen1 (Wt) In
           Complex With Substrate 5'-Flap Dna, Sm3+, And K+
          Length = 341

 Score = 97.8 bits (242), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 48/86 (55%), Positives = 59/86 (68%), Gaps = 15/86 (17%)

Query: 15  IDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMV 74
           ++KF +RLV+V+  H  ECK LLSLMGIPY++               AP EAEA CAA+V
Sbjct: 122 VEKFTKRLVKVTKQHNDECKHLLSLMGIPYLD---------------APSEAEASCAALV 166

Query: 75  KAGKVYATATEDMDALTFGTNILLRQ 100
           KAGKVYA ATEDMD LTFG+ +L+R 
Sbjct: 167 KAGKVYAAATEDMDCLTFGSPVLMRH 192


>pdb|3Q8M|A Chain A, Crystal Structure Of Human Flap Endonuclease Fen1 (D181a)
           In Complex With Substrate 5'-Flap Dna And K+
 pdb|3Q8M|B Chain B, Crystal Structure Of Human Flap Endonuclease Fen1 (D181a)
           In Complex With Substrate 5'-Flap Dna And K+
          Length = 341

 Score = 94.4 bits (233), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 47/86 (54%), Positives = 58/86 (67%), Gaps = 15/86 (17%)

Query: 15  IDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQCAAMV 74
           ++KF +RLV+V+  H  ECK LLSLMGIPY++               AP EAEA CAA+V
Sbjct: 122 VEKFTKRLVKVTKQHNDECKHLLSLMGIPYLD---------------APSEAEASCAALV 166

Query: 75  KAGKVYATATEDMDALTFGTNILLRQ 100
           KAGKVYA ATEDM  LTFG+ +L+R 
Sbjct: 167 KAGKVYAAATEDMACLTFGSPVLMRH 192


>pdb|1B43|A Chain A, Fen-1 From P. Furiosus
 pdb|1B43|B Chain B, Fen-1 From P. Furiosus
          Length = 340

 Score = 65.5 bits (158), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 35/93 (37%), Positives = 52/93 (55%), Gaps = 15/93 (16%)

Query: 7   LLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEA 66
           L  G+ +E  K+ +R  RV+ + +++ K+LL LMGIP ++               AP E 
Sbjct: 109 LEKGEIEEARKYAQRATRVNEMLIEDAKKLLELMGIPIVQ---------------APSEG 153

Query: 67  EAQCAAMVKAGKVYATATEDMDALTFGTNILLR 99
           EAQ A M   G VYA+A++D D+L FG   L+R
Sbjct: 154 EAQAAYMAAKGSVYASASQDYDSLLFGAPRLVR 186


>pdb|1MC8|A Chain A, Crystal Structure Of Flap Endonuclease-1 R42e Mutant From
           Pyrococcus Horikoshii
 pdb|1MC8|B Chain B, Crystal Structure Of Flap Endonuclease-1 R42e Mutant From
           Pyrococcus Horikoshii
          Length = 343

 Score = 65.5 bits (158), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 35/93 (37%), Positives = 52/93 (55%), Gaps = 15/93 (16%)

Query: 7   LLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEA 66
           L  G+ +E  K+ +R  +V+ + +++ K+LL LMGIP I+               AP E 
Sbjct: 109 LAKGNLEEARKYAQRATKVNEMLIEDAKKLLQLMGIPIIQ---------------APSEG 153

Query: 67  EAQCAAMVKAGKVYATATEDMDALTFGTNILLR 99
           EAQ A M   G VYA+A++D D+L FG   L+R
Sbjct: 154 EAQAAYMASKGDVYASASQDYDSLLFGAPRLIR 186


>pdb|1A76|A Chain A, Flap Endonuclease-1 From Methanococcus Jannaschii
 pdb|1A77|A Chain A, Flap Endonuclease-1 From Methanococcus Jannaschii
          Length = 326

 Score = 63.5 bits (153), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 34/90 (37%), Positives = 49/90 (54%), Gaps = 15/90 (16%)

Query: 11  DAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQC 70
           D +E  K+ +R+  ++   V+ CK LLSLMGIPY+E               AP E EAQ 
Sbjct: 113 DFEEAAKYAKRVSYLTPKMVENCKYLLSLMGIPYVE---------------APSEGEAQA 157

Query: 71  AAMVKAGKVYATATEDMDALTFGTNILLRQ 100
           + M K G V+A  ++D DAL +G   ++R 
Sbjct: 158 SYMAKKGDVWAVVSQDYDALLYGAPRVVRN 187


>pdb|2IZO|A Chain A, Structure Of An Archaeal Pcna1-Pcna2-Fen1 Complex
          Length = 346

 Score = 59.7 bits (143), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 31/90 (34%), Positives = 52/90 (57%), Gaps = 15/90 (16%)

Query: 10  GDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEAQ 69
           G  +E+ K+++ ++R+S++ V+E K+LL  MGIP ++               AP E EA+
Sbjct: 109 GKIEELRKYSQAILRLSNIMVEESKKLLRAMGIPIVQ---------------APSEGEAE 153

Query: 70  CAAMVKAGKVYATATEDMDALTFGTNILLR 99
            A + K G  +A A++D DA+ FG   L+R
Sbjct: 154 AAYLNKLGLSWAAASQDYDAILFGAKRLVR 183


>pdb|3ORY|A Chain A, Crystal Structure Of Flap Endonuclease 1 From
           Hyperthermophilic Archaeon Desulfurococcus Amylolyticus
          Length = 363

 Score = 57.0 bits (136), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 30/91 (32%), Positives = 49/91 (53%), Gaps = 15/91 (16%)

Query: 9   TGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEAEA 68
           +GD +   ++     +++   V++ K LL  MGIP+++               AP E EA
Sbjct: 125 SGDLELARRYAMMSAKLTEEMVRDAKSLLDAMGIPWVQ---------------APAEGEA 169

Query: 69  QCAAMVKAGKVYATATEDMDALTFGTNILLR 99
           Q A +VK G  YA+A++D D+L FG+  L+R
Sbjct: 170 QAAYIVKKGDAYASASQDYDSLLFGSPKLVR 200


>pdb|1RXV|A Chain A, Crystal Structure Of A. Fulgidus Fen-1 Bound To Dna
 pdb|1RXV|B Chain B, Crystal Structure Of A. Fulgidus Fen-1 Bound To Dna
 pdb|1RXW|A Chain A, Crystal Structure Of A. Fulgidus Fen-1 Bound To Dna
          Length = 336

 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 33/94 (35%), Positives = 44/94 (46%), Gaps = 16/94 (17%)

Query: 7   LLTGDAQEIDKFNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLGVLAPCEA 66
           L  GD ++  K+ +   RV    V   K LLS MGIP+++               AP E 
Sbjct: 109 LQAGD-KDAKKYAQAAGRVDEYIVDSAKTLLSYMGIPFVD---------------APSEG 152

Query: 67  EAQCAAMVKAGKVYATATEDMDALTFGTNILLRQ 100
           EAQ A M   G V  T ++D D+L FG+  L R 
Sbjct: 153 EAQAAYMAAKGDVEYTGSQDYDSLLFGSPRLARN 186


>pdb|3QEA|Z Chain Z, Crystal Structure Of Human Exonuclease 1 Exo1 (Wt) In
           Complex With Dna (Complex Ii)
 pdb|3QEB|Z Chain Z, Crystal Structure Of Human Exonuclease 1 Exo1 (Wt) In
           Complex With Dna And Mn2+ (Complex Iii)
          Length = 352

 Score = 37.7 bits (86), Expect = 0.001,   Method: Composition-based stats.
 Identities = 19/34 (55%), Positives = 23/34 (67%)

Query: 60  VLAPCEAEAQCAAMVKAGKVYATATEDMDALTFG 93
           ++AP EA+AQ A + KAG V A  TED D L FG
Sbjct: 145 LVAPYEADAQLAYLNKAGIVQAIITEDSDLLAFG 178


>pdb|3QE9|Y Chain Y, Crystal Structure Of Human Exonuclease 1 Exo1 (D173a) In
           Complex With Dna (Complex I)
 pdb|3QE9|Z Chain Z, Crystal Structure Of Human Exonuclease 1 Exo1 (D173a) In
           Complex With Dna (Complex I)
          Length = 352

 Score = 34.7 bits (78), Expect = 0.013,   Method: Composition-based stats.
 Identities = 18/34 (52%), Positives = 22/34 (64%)

Query: 60  VLAPCEAEAQCAAMVKAGKVYATATEDMDALTFG 93
           ++AP EA+AQ A + KAG V A  TED   L FG
Sbjct: 145 LVAPYEADAQLAYLNKAGIVQAIITEDSALLAFG 178


>pdb|1ORU|A Chain A, Crystal Structure Of Apc1665, Yuad Protein From Bacillus
          Subtilis
 pdb|1ORU|B Chain B, Crystal Structure Of Apc1665, Yuad Protein From Bacillus
          Subtilis
          Length = 195

 Score = 29.3 bits (64), Expect = 0.50,   Method: Compositional matrix adjust.
 Identities = 16/42 (38%), Positives = 24/42 (57%), Gaps = 10/42 (23%)

Query: 18 FNRRLVRVSSVHVKECKELLSLMGIPYIEVSRSPRLLPNFLG 59
          FNRR  ++S V ++EC E+    G+        PR+LP +LG
Sbjct: 64 FNRR--QISIVSIEECNEIALKXGV--------PRILPEWLG 95


>pdb|1SY6|A Chain A, Crystal Structure Of Cd3gammaepsilon Heterodimer In
          Complex With Okt3 Fab Fragment
          Length = 204

 Score = 27.7 bits (60), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 14/36 (38%), Positives = 18/36 (50%)

Query: 60 VLAPCEAEAQCAAMVKAGKVYATATEDMDALTFGTN 95
          VL  C+AEA+     K GK+    TED      G+N
Sbjct: 21 VLLTCDAEAKNITWFKDGKMIGFLTEDKKKWNLGSN 56


>pdb|3GG4|A Chain A, The Crystal Structure Of Glycerol Kinase From Yersinia
           Pseudotuberculosis
 pdb|3GG4|B Chain B, The Crystal Structure Of Glycerol Kinase From Yersinia
           Pseudotuberculosis
 pdb|3L0Q|A Chain A, The Crystal Structure Of Xlylulose Kinase From Yersinia
           Pseudotuberculosis
 pdb|3L0Q|B Chain B, The Crystal Structure Of Xlylulose Kinase From Yersinia
           Pseudotuberculosis
          Length = 554

 Score = 26.6 bits (57), Expect = 4.2,   Method: Composition-based stats.
 Identities = 9/20 (45%), Positives = 13/20 (65%)

Query: 42  IPYIEVSRSPRLLPNFLGVL 61
           +PY   +RSPR  PN  G++
Sbjct: 383 LPYFHGNRSPRANPNLTGII 402


>pdb|1C9L|A Chain A, Peptide-In-Groove Interactions Link Target Proteins To The
           B-Propeller Of Clathrin
 pdb|1C9L|B Chain B, Peptide-In-Groove Interactions Link Target Proteins To The
           B-Propeller Of Clathrin
          Length = 357

 Score = 25.8 bits (55), Expect = 5.8,   Method: Compositional matrix adjust.
 Identities = 13/44 (29%), Positives = 23/44 (52%)

Query: 60  VLAPCEAEAQCAAMVKAGKVYATATEDMDALTFGTNILLRQQLS 103
           V AP EA A    + + G+V +   E+ + + + TN+L    L+
Sbjct: 303 VTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLA 346


>pdb|4G55|A Chain A, Clathrin Terminal Domain Complexed With Pitstop 2
          Length = 369

 Score = 25.8 bits (55), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 13/44 (29%), Positives = 23/44 (52%)

Query: 60  VLAPCEAEAQCAAMVKAGKVYATATEDMDALTFGTNILLRQQLS 103
           V AP EA A    + + G+V +   E+ + + + TN+L    L+
Sbjct: 310 VTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLA 353


>pdb|2XZG|A Chain A, Clathrin Terminal Domain Complexed With Pitstop 1
          Length = 365

 Score = 25.8 bits (55), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 13/44 (29%), Positives = 23/44 (52%)

Query: 60  VLAPCEAEAQCAAMVKAGKVYATATEDMDALTFGTNILLRQQLS 103
           V AP EA A    + + G+V +   E+ + + + TN+L    L+
Sbjct: 306 VTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLA 349


>pdb|1C9I|A Chain A, Peptide-In-Groove Interactions Link Target Proteins To The
           B-Propeller Of Clathrin
 pdb|1C9I|B Chain B, Peptide-In-Groove Interactions Link Target Proteins To The
           B-Propeller Of Clathrin
          Length = 359

 Score = 25.8 bits (55), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 13/44 (29%), Positives = 23/44 (52%)

Query: 60  VLAPCEAEAQCAAMVKAGKVYATATEDMDALTFGTNILLRQQLS 103
           V AP EA A    + + G+V +   E+ + + + TN+L    L+
Sbjct: 305 VTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLA 348


>pdb|1UTC|A Chain A, Clathrin Terminal Domain Complexed With Tlpwdlwtt
 pdb|1UTC|B Chain B, Clathrin Terminal Domain Complexed With Tlpwdlwtt
 pdb|3GC3|B Chain B, Crystal Structure Of Arrestin2s And Clathrin
 pdb|3GD1|I Chain I, Structure Of An ArrestinCLATHRIN COMPLEX REVEALS A NOVEL
           Clathrin Binding Domain That Modulates Receptor
           Trafficking
          Length = 363

 Score = 25.8 bits (55), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 13/44 (29%), Positives = 23/44 (52%)

Query: 60  VLAPCEAEAQCAAMVKAGKVYATATEDMDALTFGTNILLRQQLS 103
           V AP EA A    + + G+V +   E+ + + + TN+L    L+
Sbjct: 305 VTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLA 348


>pdb|1XI4|A Chain A, Clathrin D6 Coat
 pdb|1XI4|B Chain B, Clathrin D6 Coat
 pdb|1XI4|C Chain C, Clathrin D6 Coat
 pdb|1XI4|D Chain D, Clathrin D6 Coat
 pdb|1XI4|E Chain E, Clathrin D6 Coat
 pdb|1XI4|F Chain F, Clathrin D6 Coat
 pdb|1XI4|G Chain G, Clathrin D6 Coat
 pdb|1XI4|H Chain H, Clathrin D6 Coat
 pdb|1XI4|I Chain I, Clathrin D6 Coat
 pdb|1XI5|A Chain A, Clathrin D6 Coat With Auxilin J-Domain
 pdb|1XI5|B Chain B, Clathrin D6 Coat With Auxilin J-Domain
 pdb|1XI5|C Chain C, Clathrin D6 Coat With Auxilin J-Domain
 pdb|1XI5|D Chain D, Clathrin D6 Coat With Auxilin J-Domain
 pdb|1XI5|E Chain E, Clathrin D6 Coat With Auxilin J-Domain
 pdb|1XI5|F Chain F, Clathrin D6 Coat With Auxilin J-Domain
 pdb|1XI5|G Chain G, Clathrin D6 Coat With Auxilin J-Domain
 pdb|1XI5|H Chain H, Clathrin D6 Coat With Auxilin J-Domain
 pdb|1XI5|I Chain I, Clathrin D6 Coat With Auxilin J-Domain
 pdb|3IYV|A Chain A, Clathrin D6 Coat As Full-Length Triskelions
 pdb|3IYV|B Chain B, Clathrin D6 Coat As Full-Length Triskelions
 pdb|3IYV|C Chain C, Clathrin D6 Coat As Full-Length Triskelions
 pdb|3IYV|D Chain D, Clathrin D6 Coat As Full-Length Triskelions
 pdb|3IYV|E Chain E, Clathrin D6 Coat As Full-Length Triskelions
 pdb|3IYV|F Chain F, Clathrin D6 Coat As Full-Length Triskelions
 pdb|3IYV|G Chain G, Clathrin D6 Coat As Full-Length Triskelions
 pdb|3IYV|H Chain H, Clathrin D6 Coat As Full-Length Triskelions
 pdb|3IYV|I Chain I, Clathrin D6 Coat As Full-Length Triskelions
          Length = 1630

 Score = 25.8 bits (55), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 13/44 (29%), Positives = 23/44 (52%)

Query: 60  VLAPCEAEAQCAAMVKAGKVYATATEDMDALTFGTNILLRQQLS 103
           V AP EA A    + + G+V +   E+ + + + TN+L    L+
Sbjct: 305 VTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLA 348


>pdb|1BPO|A Chain A, Clathrin Heavy-Chain Terminal Domain And Linker
 pdb|1BPO|B Chain B, Clathrin Heavy-Chain Terminal Domain And Linker
 pdb|1BPO|C Chain C, Clathrin Heavy-Chain Terminal Domain And Linker
          Length = 494

 Score = 25.8 bits (55), Expect = 6.9,   Method: Compositional matrix adjust.
 Identities = 13/44 (29%), Positives = 23/44 (52%)

Query: 60  VLAPCEAEAQCAAMVKAGKVYATATEDMDALTFGTNILLRQQLS 103
           V AP EA A    + + G+V +   E+ + + + TN+L    L+
Sbjct: 305 VTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLA 348


  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
   0.324    0.134    0.406 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,908,427
Number of Sequences: 62578
Number of extensions: 91712
Number of successful extensions: 366
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 339
Number of HSP's gapped (non-prelim): 22
length of query: 113
length of database: 14,973,337
effective HSP length: 77
effective length of query: 36
effective length of database: 10,154,831
effective search space: 365573916
effective search space used: 365573916
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)