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= 025844
         (247 letters)

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

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



>pdb|1YR6|A Chain A, Pab0955 Crystal Structure : A Gtpase In Apo Form From
           Pyrococcus Abyssi
 pdb|1YR7|A Chain A, Pab0955 Crystal Structure : A Gtpase In Gtp-Gamma-S Bound
           Form From Pyrococcus Abyssi
 pdb|1YR8|A Chain A, Pab0955 Crystal Structure : A Gtpase In Gtp Bound Form
           From Pyrococcus Abyssi
 pdb|1YR9|A Chain A, Pab0955 Crystal Structure : A Gtpase In Gdp And Po4 Bound
           Form From Pyrococcus Abyssi
 pdb|1YRA|A Chain A, Pab0955 Crystal Structure : A Gtpase In Gdp Bound Form
           From Pyrococcus Abyssi
 pdb|1YRA|B Chain B, Pab0955 Crystal Structure : A Gtpase In Gdp Bound Form
           From Pyrococcus Abyssi
 pdb|1YRB|A Chain A, Pab0955 Crystal Structure : A Gtpase In Gdp And Mg Bound
           Form From Pyrococcus Abyssi
 pdb|1YRB|B Chain B, Pab0955 Crystal Structure : A Gtpase In Gdp And Mg Bound
           Form From Pyrococcus Abyssi
 pdb|2OXR|A Chain A, Pab0955 Crystal Structure : A Gtpase In Gdp And Mg Bound
           Form From Pyrococcus Abyssi (After Gtp Hydrolysis)
          Length = 262

 Score = 65.1 bits (157), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 46/181 (25%), Positives = 84/181 (46%), Gaps = 12/181 (6%)

Query: 6   LVIGPAGSGKSTYCSSLYRHCETVRRTMHIVNLDPAAENFDYPVAMDIRELISLEDVMEE 65
           + +G AGSGK+T      R+ E   +  + VNLD   +   Y  ++D+RE +++E++M E
Sbjct: 18  VFVGTAGSGKTTLTGEFGRYLEDNYKVAY-VNLDTGVKELPYEPSIDVREFVTVEEIMRE 76

Query: 66  LGLGPNGGLIYCMEHLEDNLDDWXXXXXXXXXXXXXXVFDCPGQIELFTHVPVLRNFVDH 125
            G GPNG ++   + L +  +++              + D PGQ+E F    +   F   
Sbjct: 77  -GYGPNGAIVESYDRLMEKFNEYLNKILRLEKENDYVLIDTPGQMETF----LFHEFGVR 131

Query: 126 LKSRNFNVCAVYLLDSQFITDVTKFISGCMASLSA-MVQLELPHVNI--LSKMDLVTNKK 182
           L         VY+ D + +     +   C     A ++ L L    I  L+K+DL++ ++
Sbjct: 132 LMENLPYPLVVYISDPEILKKPNDY---CFVRFFALLIDLRLGATTIPALNKVDLLSEEE 188

Query: 183 E 183
           +
Sbjct: 189 K 189


>pdb|4E2I|A Chain A, The Complex Structure Of The Sv40 Helicase Large T Antigen
           And P68 Subunit Of Dna Polymerase Alpha-Primase
 pdb|4E2I|B Chain B, The Complex Structure Of The Sv40 Helicase Large T Antigen
           And P68 Subunit Of Dna Polymerase Alpha-Primase
 pdb|4E2I|C Chain C, The Complex Structure Of The Sv40 Helicase Large T Antigen
           And P68 Subunit Of Dna Polymerase Alpha-Primase
 pdb|4E2I|D Chain D, The Complex Structure Of The Sv40 Helicase Large T Antigen
           And P68 Subunit Of Dna Polymerase Alpha-Primase
 pdb|4E2I|E Chain E, The Complex Structure Of The Sv40 Helicase Large T Antigen
           And P68 Subunit Of Dna Polymerase Alpha-Primase
 pdb|4E2I|F Chain F, The Complex Structure Of The Sv40 Helicase Large T Antigen
           And P68 Subunit Of Dna Polymerase Alpha-Primase
 pdb|4E2I|G Chain G, The Complex Structure Of The Sv40 Helicase Large T Antigen
           And P68 Subunit Of Dna Polymerase Alpha-Primase
 pdb|4E2I|H Chain H, The Complex Structure Of The Sv40 Helicase Large T Antigen
           And P68 Subunit Of Dna Polymerase Alpha-Primase
 pdb|4E2I|I Chain I, The Complex Structure Of The Sv40 Helicase Large T Antigen
           And P68 Subunit Of Dna Polymerase Alpha-Primase
 pdb|4E2I|J Chain J, The Complex Structure Of The Sv40 Helicase Large T Antigen
           And P68 Subunit Of Dna Polymerase Alpha-Primase
 pdb|4E2I|K Chain K, The Complex Structure Of The Sv40 Helicase Large T Antigen
           And P68 Subunit Of Dna Polymerase Alpha-Primase
 pdb|4E2I|L Chain L, The Complex Structure Of The Sv40 Helicase Large T Antigen
           And P68 Subunit Of Dna Polymerase Alpha-Primase
          Length = 362

 Score = 31.6 bits (70), Expect = 0.39,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 43/84 (51%), Gaps = 7/84 (8%)

Query: 6   LVIGPAGSGKSTYCSSLYRHCETVRRTMHIVNLDPAAENFDYPVAMDIRELISLEDVMEE 65
           L  GP  SGK+T  ++L   C    + ++ VNL     NF+  VA+D + L+  EDV   
Sbjct: 158 LFKGPIDSGKTTLAAALLELCGG--KALN-VNLPLDRLNFELGVAID-QFLVVFEDVKGT 213

Query: 66  LGLG---PNGGLIYCMEHLEDNLD 86
            G     P+G  I  +++L D LD
Sbjct: 214 GGESRDLPSGQGINNLDNLRDYLD 237


>pdb|1N25|A Chain A, Crystal Structure Of The Sv40 Large T Antigen Helicase
           Domain
 pdb|1N25|B Chain B, Crystal Structure Of The Sv40 Large T Antigen Helicase
           Domain
          Length = 368

 Score = 31.6 bits (70), Expect = 0.44,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 43/84 (51%), Gaps = 7/84 (8%)

Query: 6   LVIGPAGSGKSTYCSSLYRHCETVRRTMHIVNLDPAAENFDYPVAMDIRELISLEDVMEE 65
           L  GP  SGK+T  ++L   C    + ++ VNL     NF+  VA+D + L+  EDV   
Sbjct: 164 LFKGPIDSGKTTLAAALLELCGG--KALN-VNLPLDRLNFELGVAID-QFLVVFEDVKGT 219

Query: 66  LGLG---PNGGLIYCMEHLEDNLD 86
            G     P+G  I  +++L D LD
Sbjct: 220 GGESRDLPSGQGINNLDNLRDYLD 243


>pdb|2H1L|A Chain A, The Structure Of The Oncoprotein Sv40 Large T Antigen And
           P53 Tumor Suppressor Complex
 pdb|2H1L|B Chain B, The Structure Of The Oncoprotein Sv40 Large T Antigen And
           P53 Tumor Suppressor Complex
 pdb|2H1L|C Chain C, The Structure Of The Oncoprotein Sv40 Large T Antigen And
           P53 Tumor Suppressor Complex
 pdb|2H1L|D Chain D, The Structure Of The Oncoprotein Sv40 Large T Antigen And
           P53 Tumor Suppressor Complex
 pdb|2H1L|E Chain E, The Structure Of The Oncoprotein Sv40 Large T Antigen And
           P53 Tumor Suppressor Complex
 pdb|2H1L|F Chain F, The Structure Of The Oncoprotein Sv40 Large T Antigen And
           P53 Tumor Suppressor Complex
 pdb|2H1L|G Chain G, The Structure Of The Oncoprotein Sv40 Large T Antigen And
           P53 Tumor Suppressor Complex
 pdb|2H1L|H Chain H, The Structure Of The Oncoprotein Sv40 Large T Antigen And
           P53 Tumor Suppressor Complex
 pdb|2H1L|I Chain I, The Structure Of The Oncoprotein Sv40 Large T Antigen And
           P53 Tumor Suppressor Complex
 pdb|2H1L|J Chain J, The Structure Of The Oncoprotein Sv40 Large T Antigen And
           P53 Tumor Suppressor Complex
 pdb|2H1L|K Chain K, The Structure Of The Oncoprotein Sv40 Large T Antigen And
           P53 Tumor Suppressor Complex
 pdb|2H1L|L Chain L, The Structure Of The Oncoprotein Sv40 Large T Antigen And
           P53 Tumor Suppressor Complex
          Length = 370

 Score = 31.6 bits (70), Expect = 0.47,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 43/84 (51%), Gaps = 7/84 (8%)

Query: 6   LVIGPAGSGKSTYCSSLYRHCETVRRTMHIVNLDPAAENFDYPVAMDIRELISLEDVMEE 65
           L  GP  SGK+T  ++L   C    + ++ VNL     NF+  VA+D + L+  EDV   
Sbjct: 166 LFKGPIDSGKTTLAAALLELCGG--KALN-VNLPLDRLNFELGVAID-QFLVVFEDVKGT 221

Query: 66  LGLG---PNGGLIYCMEHLEDNLD 86
            G     P+G  I  +++L D LD
Sbjct: 222 GGESRDLPSGQGINNLDNLRDYLD 245


>pdb|1SVL|A Chain A, Co-Crystal Structure Of Sv40 Large T Antigen Helicase
           Domain And Adp
 pdb|1SVL|B Chain B, Co-Crystal Structure Of Sv40 Large T Antigen Helicase
           Domain And Adp
 pdb|1SVL|C Chain C, Co-Crystal Structure Of Sv40 Large T Antigen Helicase
           Domain And Adp
 pdb|1SVM|A Chain A, Co-Crystal Structure Of Sv40 Large T Antigen Helicase
           Domain And Atp
 pdb|1SVM|B Chain B, Co-Crystal Structure Of Sv40 Large T Antigen Helicase
           Domain And Atp
 pdb|1SVM|C Chain C, Co-Crystal Structure Of Sv40 Large T Antigen Helicase
           Domain And Atp
 pdb|1SVM|D Chain D, Co-Crystal Structure Of Sv40 Large T Antigen Helicase
           Domain And Atp
 pdb|1SVM|E Chain E, Co-Crystal Structure Of Sv40 Large T Antigen Helicase
           Domain And Atp
 pdb|1SVM|F Chain F, Co-Crystal Structure Of Sv40 Large T Antigen Helicase
           Domain And Atp
 pdb|1SVO|A Chain A, Structure Of Sv40 Large T Antigen Helicase Domain
 pdb|1SVO|B Chain B, Structure Of Sv40 Large T Antigen Helicase Domain
          Length = 377

 Score = 31.2 bits (69), Expect = 0.50,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 43/84 (51%), Gaps = 7/84 (8%)

Query: 6   LVIGPAGSGKSTYCSSLYRHCETVRRTMHIVNLDPAAENFDYPVAMDIRELISLEDVMEE 65
           L  GP  SGK+T  ++L   C    + ++ VNL     NF+  VA+D + L+  EDV   
Sbjct: 173 LFKGPIDSGKTTLAAALLELCGG--KALN-VNLPLDRLNFELGVAID-QFLVVFEDVKGT 228

Query: 66  LGLG---PNGGLIYCMEHLEDNLD 86
            G     P+G  I  +++L D LD
Sbjct: 229 GGESRDLPSGQGINNLDNLRDYLD 252


>pdb|2EWV|A Chain A, Crystal Structure Of The Pilus Retraction Motor Pilt And
           Bound Adp
          Length = 372

 Score = 30.0 bits (66), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 2/36 (5%)

Query: 6   LVIGPAGSGKSTYCSSLYRHCETVRRTMHIVNL-DP 40
           LV GP GSGKST  +S+  +     ++ HI+ + DP
Sbjct: 140 LVTGPTGSGKSTTIASMIDYINQT-KSYHIITIEDP 174


>pdb|3C41|J Chain J, Abc Protein Artp In Complex With Amp-PnpMG2+
 pdb|3C41|K Chain K, Abc Protein Artp In Complex With Amp-PnpMG2+
          Length = 242

 Score = 29.3 bits (64), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 12/21 (57%), Positives = 15/21 (71%)

Query: 2  GYAQLVIGPAGSGKSTYCSSL 22
          G   +VIGP+GSGKST+   L
Sbjct: 29 GEVVVVIGPSGSGKSTFLRCL 49


>pdb|2OLJ|A Chain A, Abc Protein Artp In Complex With AdpMG2+
 pdb|2OLJ|B Chain B, Abc Protein Artp In Complex With AdpMG2+
 pdb|2OLK|A Chain A, Abc Protein Artp In Complex With Adp-Beta-S
 pdb|2OLK|B Chain B, Abc Protein Artp In Complex With Adp-Beta-S
 pdb|2OLK|C Chain C, Abc Protein Artp In Complex With Adp-Beta-S
 pdb|2OLK|D Chain D, Abc Protein Artp In Complex With Adp-Beta-S
 pdb|2OUK|A Chain A, Abc Protein Artp In Complex With Sulphate
 pdb|2OUK|B Chain B, Abc Protein Artp In Complex With Sulphate
 pdb|2OUK|C Chain C, Abc Protein Artp In Complex With Sulphate
 pdb|2OUK|D Chain D, Abc Protein Artp In Complex With Sulphate
 pdb|2Q0H|A Chain A, Abc Protein Artp In Complex With AdpMG2+, ATP-Gamma-S
          Hydrolyzed
 pdb|2Q0H|B Chain B, Abc Protein Artp In Complex With AdpMG2+, ATP-Gamma-S
          Hydrolyzed
 pdb|3C4J|A Chain A, Abc Protein Artp In Complex With Atp-Gamma-S
 pdb|3C4J|B Chain B, Abc Protein Artp In Complex With Atp-Gamma-S
          Length = 263

 Score = 28.9 bits (63), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 12/21 (57%), Positives = 15/21 (71%)

Query: 2  GYAQLVIGPAGSGKSTYCSSL 22
          G   +VIGP+GSGKST+   L
Sbjct: 50 GEVVVVIGPSGSGKSTFLRCL 70


>pdb|2EWW|A Chain A, Crystal Structure Of The Pilus Retraction Motor Pilt And
           Bound Atp
          Length = 372

 Score = 28.9 bits (63), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 2/36 (5%)

Query: 6   LVIGPAGSGKSTYCSSLYRHCETVRRTMHIVNL-DP 40
           LV GP GSGKST  +S   +     ++ HI+ + DP
Sbjct: 140 LVTGPTGSGKSTTIASXIDYINQT-KSYHIITIEDP 174


>pdb|2CXX|A Chain A, Crystal Structure Of A Probable Gtp-binding Protein Engb
 pdb|2CXX|B Chain B, Crystal Structure Of A Probable Gtp-binding Protein Engb
 pdb|2CXX|C Chain C, Crystal Structure Of A Probable Gtp-binding Protein Engb
          Length = 190

 Score = 28.9 bits (63), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 13/52 (25%), Positives = 32/52 (61%)

Query: 163 QLELPHVNILSKMDLVTNKKEIEDYLNPESQFLLSELNQHMAPQFAKLNKSL 214
           +L++P +  ++K+D + N +E+ ++L  + +  LSE+++   P  AK   ++
Sbjct: 120 ELDIPTIVAVNKLDKIKNVQEVINFLAEKFEVPLSEIDKVFIPISAKFGDNI 171


>pdb|2GSZ|A Chain A, Structure Of A. Aeolicus Pilt With 6 Monomers Per
           Asymmetric Unit
 pdb|2GSZ|B Chain B, Structure Of A. Aeolicus Pilt With 6 Monomers Per
           Asymmetric Unit
 pdb|2GSZ|C Chain C, Structure Of A. Aeolicus Pilt With 6 Monomers Per
           Asymmetric Unit
 pdb|2GSZ|D Chain D, Structure Of A. Aeolicus Pilt With 6 Monomers Per
           Asymmetric Unit
 pdb|2GSZ|E Chain E, Structure Of A. Aeolicus Pilt With 6 Monomers Per
           Asymmetric Unit
 pdb|2GSZ|F Chain F, Structure Of A. Aeolicus Pilt With 6 Monomers Per
           Asymmetric Unit
          Length = 363

 Score = 28.9 bits (63), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 2/36 (5%)

Query: 6   LVIGPAGSGKSTYCSSLYRHCETVRRTMHIVNL-DP 40
           LV GP GSGKST  +S   +     ++ HI+ + DP
Sbjct: 129 LVTGPTGSGKSTTIASXIDYINQT-KSYHIITIEDP 163


>pdb|2EYU|A Chain A, The Crystal Structure Of The C-Terminal Domain Of
          Aquifex Aeolicus Pilt
 pdb|2EYU|B Chain B, The Crystal Structure Of The C-Terminal Domain Of
          Aquifex Aeolicus Pilt
          Length = 261

 Score = 28.5 bits (62), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 2/36 (5%)

Query: 6  LVIGPAGSGKSTYCSSLYRHCETVRRTMHIVNL-DP 40
          LV GP GSGKST  +S   +     ++ HI+ + DP
Sbjct: 29 LVTGPTGSGKSTTIASXIDYINQT-KSYHIITIEDP 63


  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
   0.322    0.137    0.403 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,496,046
Number of Sequences: 62578
Number of extensions: 235365
Number of successful extensions: 756
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 750
Number of HSP's gapped (non-prelim): 14
length of query: 247
length of database: 14,973,337
effective HSP length: 96
effective length of query: 151
effective length of database: 8,965,849
effective search space: 1353843199
effective search space used: 1353843199
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)