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= 010035
         (519 letters)

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

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



>pdb|3FZI|A Chain A, 1.9 Angstrom Structure Of The Thermophilic Exonuclease Iii
           Homologue Mth0212
 pdb|3G0A|A Chain A, Mth0212 With Two Bound Manganese Ions
 pdb|3G1K|A Chain A, Mth0212 (Wt) Crystallized In A Monoclinic Space Group
 pdb|3G1K|B Chain B, Mth0212 (Wt) Crystallized In A Monoclinic Space Group
 pdb|3G2C|A Chain A, Mth0212 In Complex With A Short Ssdna (Cgta)
 pdb|3G2C|B Chain B, Mth0212 In Complex With A Short Ssdna (Cgta)
 pdb|3G3C|A Chain A, Mth0212 (Wt) In Complex With A 6bp Dsdna Containing A
           Single One Nucleotide Long 3'-Overhang
 pdb|3G3C|B Chain B, Mth0212 (Wt) In Complex With A 6bp Dsdna Containing A
           Single One Nucleotide Long 3'-Overhang
 pdb|3G3Y|A Chain A, Mth0212 In Complex With Ssdna In Space Group P32
 pdb|3G3Y|B Chain B, Mth0212 In Complex With Ssdna In Space Group P32
 pdb|3G4T|A Chain A, Mth0212 (Wt) In Complex With A 7bp Dsdna
 pdb|3G4T|B Chain B, Mth0212 (Wt) In Complex With A 7bp Dsdna
          Length = 265

 Score = 55.8 bits (133), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 40/142 (28%), Positives = 65/142 (45%), Gaps = 9/142 (6%)

Query: 14  KIDSEGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQFFHVLQKRWEFLLCQGRRIFV 73
           + D+EGR  I D   F+L+N+Y P     +  R+++KL+F+    +        GR + +
Sbjct: 90  RFDTEGRIQIADFDDFLLYNIYFPNGKMSEE-RLKYKLEFYDAFLEDVNRERDSGRNVII 148

Query: 74  VGDLNIAPAAIDRCDAGPDFAKNEF----RIWFRSMLVESGGSFFDVFRSKHPERREAYT 129
            GD N A   ID      +   + F    R W     +E+G  + D FR  + +  + YT
Sbjct: 149 CGDFNTAHREIDLARPKENSNVSGFLPVERAWI-DKFIENG--YVDTFRMFNSDPGQ-YT 204

Query: 130 CWPSNTGAEQFNYGTRIDHILC 151
            W   T A + N G R+D+   
Sbjct: 205 WWSYRTRARERNVGWRLDYFFV 226


>pdb|3G91|A Chain A, 1.2 Angstrom Structure Of The Exonuclease Iii Homologue
           Mth0212
          Length = 265

 Score = 55.5 bits (132), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 43/143 (30%), Positives = 68/143 (47%), Gaps = 11/143 (7%)

Query: 14  KIDSEGRCVITDHGHFILFNVYGPR-ADSEDTVRIQFKLQFFHVLQKRWEFLLCQGRRIF 72
           + D+EGR  I D   F+L+N+Y P  A SE+  R+++KL+F+    +        GR + 
Sbjct: 90  RFDTEGRIQIADFDDFLLYNIYFPNGAMSEE--RLKYKLEFYDAFLEDVNRERDSGRNVI 147

Query: 73  VVGDLNIAPAAIDRCDAGPDFAKNEF----RIWFRSMLVESGGSFFDVFRSKHPERREAY 128
           + GD N A   ID      +   + F    R W     +E+G  + D FR  + +  + Y
Sbjct: 148 ICGDFNTAHREIDLARPKENSNVSGFLPVERAWI-DKFIENG--YVDTFRMFNSDPGQ-Y 203

Query: 129 TCWPSNTGAEQFNYGTRIDHILC 151
           T W   T A + N G R+D+   
Sbjct: 204 TWWSYRTRARERNVGWRLDYFFV 226


>pdb|3G00|A Chain A, Mth0212 In Complex With A 9bp Blunt End Dsdna At 1.7
           Angstrom
 pdb|3G00|B Chain B, Mth0212 In Complex With A 9bp Blunt End Dsdna At 1.7
           Angstrom
 pdb|3G0R|A Chain A, Complex Of Mth0212 And An 8bp Dsdna With Distorted Ends
 pdb|3G0R|B Chain B, Complex Of Mth0212 And An 8bp Dsdna With Distorted Ends
 pdb|3G2D|A Chain A, Complex Of Mth0212 And A 4 Bp Dsdna With 3'-Overhang
 pdb|3G2D|B Chain B, Complex Of Mth0212 And A 4 Bp Dsdna With 3'-Overhang
 pdb|3G38|A Chain A, The Catalytically Inactive Mutant Mth0212 (D151n) In
           Complex With An 8 Bp Dsdna
 pdb|3G8V|A Chain A, The Rationally Designed Catalytically Inactive Mutant
           Mth0212(D151n)
 pdb|3GA6|A Chain A, Mth0212 In Complex With Two Dna Helices
 pdb|3GA6|B Chain B, Mth0212 In Complex With Two Dna Helices
          Length = 265

 Score = 53.9 bits (128), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 39/142 (27%), Positives = 65/142 (45%), Gaps = 9/142 (6%)

Query: 14  KIDSEGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQFFHVLQKRWEFLLCQGRRIFV 73
           + D+EGR  I D   F+L+N+Y P     +  R+++KL+F+    +        GR + +
Sbjct: 90  RFDTEGRIQIADFDDFLLYNIYFPNGKMSEE-RLKYKLEFYDAFLEDVNRERDSGRNVII 148

Query: 74  VGDLNIAPAAIDRCDAGPDFAKNEF----RIWFRSMLVESGGSFFDVFRSKHPERREAYT 129
            G+ N A   ID      +   + F    R W     +E+G  + D FR  + +  + YT
Sbjct: 149 CGNFNTAHREIDLARPKENSNVSGFLPVERAWI-DKFIENG--YVDTFRMFNSDPGQ-YT 204

Query: 130 CWPSNTGAEQFNYGTRIDHILC 151
            W   T A + N G R+D+   
Sbjct: 205 WWSYRTRARERNVGWRLDYFFV 226


>pdb|1E9N|A Chain A, A Second Divalent Metal Ion In The Active Site Of A New
           Crystal Form Of Human ApurinicAPYRIMIDINIC ENDONUCLEASE,
           Ape1, And Its Implications For The Catalytic Mechanism
 pdb|1E9N|B Chain B, A Second Divalent Metal Ion In The Active Site Of A New
           Crystal Form Of Human ApurinicAPYRIMIDINIC ENDONUCLEASE,
           Ape1, And Its Implications For The Catalytic Mechanism
 pdb|1HD7|A Chain A, A Second Divalent Metal Ion In The Active Site Of A New
           Crystal Form Of Human ApurinicAPYRIDINIMIC ENDONUCLEASE,
           Ape1, And Its Implications For The Catalytic Mechanism
 pdb|3U8U|A Chain A, Crystal Structure Of Human ApurinicAPYRIDINIMIC
           ENDONUCLEASE, APE1 IN A New Crystal Form
 pdb|3U8U|B Chain B, Crystal Structure Of Human ApurinicAPYRIDINIMIC
           ENDONUCLEASE, APE1 IN A New Crystal Form
 pdb|3U8U|C Chain C, Crystal Structure Of Human ApurinicAPYRIDINIMIC
           ENDONUCLEASE, APE1 IN A New Crystal Form
 pdb|3U8U|D Chain D, Crystal Structure Of Human ApurinicAPYRIDINIMIC
           ENDONUCLEASE, APE1 IN A New Crystal Form
 pdb|3U8U|E Chain E, Crystal Structure Of Human ApurinicAPYRIDINIMIC
           ENDONUCLEASE, APE1 IN A New Crystal Form
 pdb|3U8U|F Chain F, Crystal Structure Of Human ApurinicAPYRIDINIMIC
           ENDONUCLEASE, APE1 IN A New Crystal Form
          Length = 318

 Score = 52.4 bits (124), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 43/146 (29%), Positives = 65/146 (44%), Gaps = 18/146 (12%)

Query: 16  DSEGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQFFHVLQKRWEFL--LCQGRRIFV 73
           D EGR ++ +   F+L   Y P A     VR++++ ++    +K   FL  L   + + +
Sbjct: 152 DQEGRVIVAEFDSFVLVTAYVPNA-GRGLVRLEYRQRWDEAFRK---FLKGLASRKPLVL 207

Query: 74  VGDLNIAPAAID-------RCDAGPDFAKNEFRIWFRSMLVESGGSFFDVFRSKHPERRE 126
            GDLN+A   ID       + +AG  F   E R  F  +L        D FR  +P    
Sbjct: 208 CGDLNVAHEEIDLRNPKGNKKNAG--FTPQE-RQGFGELL--QAVPLADSFRHLYPNTPY 262

Query: 127 AYTCWPSNTGAEQFNYGTRIDHILCA 152
           AYT W     A   N G R+D+ L +
Sbjct: 263 AYTFWTYMMNARSKNVGWRLDYFLLS 288


>pdb|2O3C|A Chain A, Crystal Structure Of Zebrafish Ape
 pdb|2O3C|B Chain B, Crystal Structure Of Zebrafish Ape
 pdb|2O3C|C Chain C, Crystal Structure Of Zebrafish Ape
          Length = 282

 Score = 52.0 bits (123), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 50/155 (32%), Positives = 70/155 (45%), Gaps = 29/155 (18%)

Query: 16  DSEGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQFFHVLQKRWEF----LLC--QGR 69
           D EGR +  +   F L   Y P A S   VR+ ++        K W+      LC    R
Sbjct: 117 DKEGRVITAEFPDFFLVTAYVPNA-SRGLVRLDYR--------KTWDVDFRAYLCGLDAR 167

Query: 70  RIFVV-GDLNIAPAAID-------RCDAGPDFAKNEFRIWFRSMLVESGGSFFDVFRSKH 121
           +  V+ GDLN+A   ID       R +AG  F   E R  F + L+E+G  F D FR  +
Sbjct: 168 KPLVLCGDLNVAHQEIDLKNPKGNRKNAG--FTPEE-REGF-TQLLEAG--FTDSFRELY 221

Query: 122 PERREAYTCWPSNTGAEQFNYGTRIDHILCAGPCL 156
           P++  AYT W     A   N G R+D+ + +   L
Sbjct: 222 PDQAYAYTFWTYMMNARSKNVGWRLDYFVLSSALL 256


>pdb|2ISI|A Chain A, Crystal Structure Of Ape1 From Homo Sapiens In A New
           Crystal Form Complexed With A Ligand
 pdb|2ISI|B Chain B, Crystal Structure Of Ape1 From Homo Sapiens In A New
           Crystal Form Complexed With A Ligand
 pdb|2ISI|C Chain C, Crystal Structure Of Ape1 From Homo Sapiens In A New
           Crystal Form Complexed With A Ligand
 pdb|4IEM|A Chain A, Human Apurinic/apyrimidinic Endonuclease (ape1) With
           Product Dna And Mg2+
 pdb|4IEM|B Chain B, Human Apurinic/apyrimidinic Endonuclease (ape1) With
           Product Dna And Mg2+
 pdb|4IEM|C Chain C, Human Apurinic/apyrimidinic Endonuclease (ape1) With
           Product Dna And Mg2+
 pdb|4IEM|D Chain D, Human Apurinic/apyrimidinic Endonuclease (ape1) With
           Product Dna And Mg2+
          Length = 317

 Score = 52.0 bits (123), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 43/146 (29%), Positives = 65/146 (44%), Gaps = 18/146 (12%)

Query: 16  DSEGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQFFHVLQKRWEFL--LCQGRRIFV 73
           D EGR ++ +   F+L   Y P A     VR++++ ++    +K   FL  L   + + +
Sbjct: 151 DQEGRVIVAEFDSFVLVTAYVPNA-GRGLVRLEYRQRWDEAFRK---FLKGLASRKPLVL 206

Query: 74  VGDLNIAPAAID-------RCDAGPDFAKNEFRIWFRSMLVESGGSFFDVFRSKHPERRE 126
            GDLN+A   ID       + +AG  F   E R  F  +L        D FR  +P    
Sbjct: 207 CGDLNVAHEEIDLRNPKGNKKNAG--FTPQE-RQGFGELL--QAVPLADSFRHLYPNTPY 261

Query: 127 AYTCWPSNTGAEQFNYGTRIDHILCA 152
           AYT W     A   N G R+D+ L +
Sbjct: 262 AYTFWTYMMNARSKNVGWRLDYFLLS 287


>pdb|1BIX|A Chain A, The Crystal Structure Of The Human Dna Repair Endonuclease
           Hap1 Suggests The Recognition Of Extra-Helical
           Deoxyribose At Dna Abasic Sites
          Length = 287

 Score = 51.6 bits (122), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 43/146 (29%), Positives = 65/146 (44%), Gaps = 18/146 (12%)

Query: 16  DSEGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQFFHVLQKRWEFL--LCQGRRIFV 73
           D EGR ++ +   F+L   Y P A     VR++++ ++    +K   FL  L   + + +
Sbjct: 121 DQEGRVIVAEFDSFVLVTAYVPNA-GRGLVRLEYRQRWDEAFRK---FLKGLASRKPLVL 176

Query: 74  VGDLNIAPAAID-------RCDAGPDFAKNEFRIWFRSMLVESGGSFFDVFRSKHPERRE 126
            GDLN+A   ID       + +AG  F   E R  F  +L        D FR  +P    
Sbjct: 177 CGDLNVAHEEIDLRNPKGNKKNAG--FTPQE-RQGFGELL--QAVPLADSFRHLYPNTPY 231

Query: 127 AYTCWPSNTGAEQFNYGTRIDHILCA 152
           AYT W     A   N G R+D+ L +
Sbjct: 232 AYTFWTYMMNARSKNVGWRLDYFLLS 257


>pdb|2O3H|A Chain A, Crystal Structure Of The Human C65a Ape
          Length = 285

 Score = 51.6 bits (122), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 43/146 (29%), Positives = 65/146 (44%), Gaps = 18/146 (12%)

Query: 16  DSEGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQFFHVLQKRWEFL--LCQGRRIFV 73
           D EGR ++ +   F+L   Y P A     VR++++ ++    +K   FL  L   + + +
Sbjct: 119 DQEGRVIVAEFDSFVLVTAYVPNA-GRGLVRLEYRQRWDEAFRK---FLKGLASRKPLVL 174

Query: 74  VGDLNIAPAAID-------RCDAGPDFAKNEFRIWFRSMLVESGGSFFDVFRSKHPERRE 126
            GDLN+A   ID       + +AG  F   E R  F  +L        D FR  +P    
Sbjct: 175 CGDLNVAHEEIDLRNPKGNKKNAG--FTPQE-RQGFGELL--QAVPLADSFRHLYPNTPY 229

Query: 127 AYTCWPSNTGAEQFNYGTRIDHILCA 152
           AYT W     A   N G R+D+ L +
Sbjct: 230 AYTFWTYMMNARSKNVGWRLDYFLLS 255


>pdb|1DE8|B Chain B, Human ApurinicAPYRIMIDINIC ENDONUCLEASE-1 (Ape1) Bound To
           Abasic Dna
 pdb|1DE8|A Chain A, Human ApurinicAPYRIMIDINIC ENDONUCLEASE-1 (Ape1) Bound To
           Abasic Dna
 pdb|1DE9|A Chain A, Human Ape1 Endonuclease With Bound Abasic Dna And Mn2+ Ion
 pdb|1DE9|B Chain B, Human Ape1 Endonuclease With Bound Abasic Dna And Mn2+ Ion
          Length = 276

 Score = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 43/146 (29%), Positives = 65/146 (44%), Gaps = 18/146 (12%)

Query: 16  DSEGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQFFHVLQKRWEFL--LCQGRRIFV 73
           D EGR ++ +   F+L   Y P A     VR++++ ++    +K   FL  L   + + +
Sbjct: 110 DQEGRVIVAEFDSFVLVTAYVPNA-GRGLVRLEYRQRWDEAFRK---FLKGLASRKPLVL 165

Query: 74  VGDLNIAPAAID-------RCDAGPDFAKNEFRIWFRSMLVESGGSFFDVFRSKHPERRE 126
            GDLN+A   ID       + +AG  F   E R  F  +L        D FR  +P    
Sbjct: 166 CGDLNVAHEEIDLRNPKGNKKNAG--FTPQE-RQGFGELL--QAVPLADSFRHLYPNTPY 220

Query: 127 AYTCWPSNTGAEQFNYGTRIDHILCA 152
           AYT W     A   N G R+D+ L +
Sbjct: 221 AYTFWTYMMNARSKNVGWRLDYFLLS 246


>pdb|1DEW|A Chain A, Crystal Structure Of Human Ape1 Bound To Abasic Dna
 pdb|1DEW|B Chain B, Crystal Structure Of Human Ape1 Bound To Abasic Dna
          Length = 279

 Score = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 43/146 (29%), Positives = 65/146 (44%), Gaps = 18/146 (12%)

Query: 16  DSEGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQFFHVLQKRWEFL--LCQGRRIFV 73
           D EGR ++ +   F+L   Y P A     VR++++ ++    +K   FL  L   + + +
Sbjct: 113 DQEGRVIVAEFDSFVLVTAYVPNA-GRGLVRLEYRQRWDEAFRK---FLKGLASRKPLVL 168

Query: 74  VGDLNIAPAAID-------RCDAGPDFAKNEFRIWFRSMLVESGGSFFDVFRSKHPERRE 126
            GDLN+A   ID       + +AG  F   E R  F  +L        D FR  +P    
Sbjct: 169 CGDLNVAHEEIDLRNPKGNKKNAG--FTPQE-RQGFGELL--QAVPLADSFRHLYPNTPY 223

Query: 127 AYTCWPSNTGAEQFNYGTRIDHILCA 152
           AYT W     A   N G R+D+ L +
Sbjct: 224 AYTFWTYMMNARSKNVGWRLDYFLLS 249


>pdb|2JC5|A Chain A, Apurinic Apyrimidinic (Ap) Endonuclease (Nape) From
           Neisseria Meningitidis
 pdb|4B5F|A Chain A, Substrate Bound Neisseria Ap Endonuclease In Absence Of
           Metal Ions (Crystal Form 1)
 pdb|4B5G|A Chain A, Substrate Bound Neisseria Ap Endonuclease In Absence Of
           Metal Ions (Crystal Form 2)
 pdb|4B5G|B Chain B, Substrate Bound Neisseria Ap Endonuclease In Absence Of
           Metal Ions (Crystal Form 2)
 pdb|4B5G|C Chain C, Substrate Bound Neisseria Ap Endonuclease In Absence Of
           Metal Ions (Crystal Form 2)
 pdb|4B5I|A Chain A, Product Complex Of Neisseria Ap Endonuclease In Presence
           Of Metal Ions
 pdb|4B5J|A Chain A, Neisseria Ap Endonuclease Bound To The Substrate With An
           Orphan Adenine Base
 pdb|4B5M|A Chain A, Neisseria Ap Endonuclease Bound To The Substrate With A
           Cytosine Orphan Base
 pdb|4B5M|B Chain B, Neisseria Ap Endonuclease Bound To The Substrate With A
           Cytosine Orphan Base
 pdb|4B5M|C Chain C, Neisseria Ap Endonuclease Bound To The Substrate With A
           Cytosine Orphan Base
          Length = 259

 Score = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 69/153 (45%), Gaps = 16/153 (10%)

Query: 3   GLEDFSKDELLKIDSEGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQFFHVLQKRWE 62
           G+E+F        D EGR V  D G   + ++Y P   S +  R Q K +F        E
Sbjct: 85  GIEEF--------DREGRFVRCDFGRLSVISLYLPSGSSAEE-RQQVKYRFLDAFYPMLE 135

Query: 63  FLLCQGRRIFVVGDLNIAPAAIDRCDAGPDFAKNEF----RIWFRSMLVESGGSFFDVFR 118
            +  +GR I V GD NIA   ID  +   +   + F    R W   ++ + G  + D++R
Sbjct: 136 AMKNEGRDIVVCGDWNIAHQNIDLKNWKGNQKNSGFLPEEREWIGKVIHKLG--WTDMWR 193

Query: 119 SKHPERREAYTCWPSNTGAEQFNYGTRIDHILC 151
           + +P+    YT W +   A   + G RID+ + 
Sbjct: 194 TLYPD-VPGYTWWSNRGQAYAKDVGWRIDYQMV 225


>pdb|4B5H|A Chain A, Substate Bound Inactive Mutant Of Neisseria Ap
           Endonuclease In Presence Of Metal Ions
          Length = 259

 Score = 49.3 bits (116), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 43/153 (28%), Positives = 69/153 (45%), Gaps = 16/153 (10%)

Query: 3   GLEDFSKDELLKIDSEGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQFFHVLQKRWE 62
           G+E+F        D EGR V  D G   + ++Y P   S +  R Q K +F        E
Sbjct: 85  GIEEF--------DREGRFVRCDFGRLSVISLYLPSGSSAEE-RQQVKYRFLDAFYPMLE 135

Query: 63  FLLCQGRRIFVVGDLNIAPAAIDRCDAGPDFAKNEF----RIWFRSMLVESGGSFFDVFR 118
            +  +GR I V G+ NIA   ID  +   +   + F    R W   ++ + G  + D++R
Sbjct: 136 AMKNEGRDIVVCGNWNIAHQNIDLKNWKGNQKNSGFLPEEREWIGKVIHKLG--WTDMWR 193

Query: 119 SKHPERREAYTCWPSNTGAEQFNYGTRIDHILC 151
           + +P+    YT W +   A   + G RID+ + 
Sbjct: 194 TLYPD-VPGYTWWSNRGQAYAKDVGWRIDYQMV 225


>pdb|2JC4|A Chain A, 3'-5' Exonuclease (Nexo) From Neisseria Meningitidis
          Length = 256

 Score = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 42/145 (28%), Positives = 65/145 (44%), Gaps = 10/145 (6%)

Query: 13  LKIDSEGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQFFHVLQKRWEFLLCQGRRIF 72
           L  D + R +        + NVY    ++ D+ + ++K Q+F  L +     + +  ++ 
Sbjct: 83  LPDDPQRRVIAATVSGVRVINVYCVNGEALDSPKFKYKEQWFAALTEFVRDEMTRHGKLV 142

Query: 73  VVGDLNIAPAAIDRCDAGPDFAK----NEFRIWFRSMLVESGGSFFDVFRSKHPERREAY 128
           ++GD NIAPA  D  D      K    +  R WF+++L        D  R  HPE   A+
Sbjct: 143 LLGDFNIAPADADCYDPEKWHEKIHCSSVERQWFQNLL---DLGLTDSLRQVHPE--GAF 197

Query: 129 TCWPSNTGAE-QFNYGTRIDHILCA 152
             W    GA  Q   G RIDHIL +
Sbjct: 198 YTWFDYRGAMFQRKLGLRIDHILVS 222


>pdb|2VOA|A Chain A, Structure Of An Ap Endonuclease From Archaeoglobus
           Fulgidus
 pdb|2VOA|B Chain B, Structure Of An Ap Endonuclease From Archaeoglobus
           Fulgidus
          Length = 257

 Score = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 50/151 (33%), Positives = 67/151 (44%), Gaps = 25/151 (16%)

Query: 18  EGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQF----FHVLQKRWEFLLCQGRRIFV 73
           E R +        + N Y P+    D+ + Q+KLQ+    +H LQK  +F      R F 
Sbjct: 88  EDRLIRAKIAGIDVINTYVPQGFKIDSEKYQYKLQWLERLYHYLQKTVDF------RSFA 141

Query: 74  V--GDLNIAPAAIDRCDAGPDFAKN------EFRIWFRSMLVESGGSFFDVFRSKHPERR 125
           V  GD+N+AP  ID     PD  KN      + R  ++ +L E G  F DV R  HP  R
Sbjct: 142 VWCGDMNVAPEPIDV--HSPDKLKNHVXFHEDARRAYKKIL-ELG--FVDVLRKIHPNER 196

Query: 126 EAYTCWPSNT-GAEQFNYGTRIDHILCAGPC 155
             YT +     GA +   G R D IL   P 
Sbjct: 197 -IYTFYDYRVKGAIERGLGWRGDAILATPPL 226


>pdb|1AKO|A Chain A, Exonuclease Iii From Escherichia Coli
          Length = 268

 Score = 46.2 bits (108), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 36/138 (26%), Positives = 60/138 (43%), Gaps = 10/138 (7%)

Query: 27  GHFILFNVYGPRADSED-TVRIQFKLQFFHVLQKRWEFLLCQGRRIFVVGDLNIAPAAID 85
           G+  + N Y P+ +S D  ++   K QF+  LQ   E  L +   + ++GD+NI+P  +D
Sbjct: 101 GNVTVINGYFPQGESRDHPIKFPAKAQFYQNLQNYLETELKRDNPVLIMGDMNISPTDLD 160

Query: 86  RCDAGPDFAKNEFRIWFRSMLVES--------GGSFFDVFRSKHPERREAYTCWPSNTGA 137
               G +  K   R    S L E              D FR  +P+  + ++ +   +  
Sbjct: 161 -IGIGEENRKRWLRTGKCSFLPEEREWMDRLMSWGLVDTFRHANPQTADRFSWFDYRSKG 219

Query: 138 EQFNYGTRIDHILCAGPC 155
              N G RID +L + P 
Sbjct: 220 FDDNRGLRIDLLLASQPL 237


>pdb|2J63|A Chain A, Crystal Structure Of Ap Endonuclease Lmap From Leishmania
           Major
 pdb|2J63|B Chain B, Crystal Structure Of Ap Endonuclease Lmap From Leishmania
           Major
          Length = 467

 Score = 36.2 bits (82), Expect = 0.052,   Method: Compositional matrix adjust.
 Identities = 25/87 (28%), Positives = 37/87 (42%), Gaps = 11/87 (12%)

Query: 74  VGDLNIAPAAIDRCDAGP--------DFAKNEFRIWFRSMLVESGGSFFDVFRSKHPERR 125
            GDLN+A    DR  AG          FA  E R+ FR  +  +     D+FR  +P+  
Sbjct: 353 AGDLNVAERDYDRYYAGTFKSMQECSGFAPEE-RMSFRETMQRTNS--VDIFRQLYPQAG 409

Query: 126 EAYTCWPSNTGAEQFNYGTRIDHILCA 152
             Y+ W         N G R+D+ + +
Sbjct: 410 PVYSFWSQRINGRPRNLGWRLDYFVVS 436


>pdb|4F1R|A Chain A, Structure Analysis Of The Global Metabolic Regulator Crc
           From Pseudomonas Aeruginos
          Length = 293

 Score = 33.1 bits (74), Expect = 0.35,   Method: Compositional matrix adjust.
 Identities = 39/151 (25%), Positives = 57/151 (37%), Gaps = 25/151 (16%)

Query: 16  DSEGRCVITDHGHFILFNVYGPRADSED---TVRIQFKLQFFHVL----QKRWEFLLCQG 68
           D  GR +  D     +  +  P   S D     + +F   F H L    +KR E++ C  
Sbjct: 123 DRYGRYLQADFDKVSIATLLLPSGQSGDESLNQKFKFMDDFTHYLSKQRRKRREYIYC-- 180

Query: 69  RRIFVVGDLNIAPAAID-----RCDAGPDFAKNEFRIWFRSMLVESGGSFFDVFRSKHPE 123
                 G L +A   +D      C   P F   E R W   +    G  + D  R    E
Sbjct: 181 ------GSLYVAHQKMDVKNWRECQQMPGFLAPE-RAWLDEVFGNLG--YADALREVSRE 231

Query: 124 RREAYTCWPSNTGAEQFNYGTRIDH-ILCAG 153
             + ++ WP +  AE  N G R D+ +L  G
Sbjct: 232 G-DQFSWWPDSEQAEMLNLGWRFDYQVLTPG 261


>pdb|1NYP|A Chain A, 4th Lim Domain Of Pinch Protein
 pdb|1U5S|B Chain B, Nmr Structure Of The Complex Between Nck-2 Sh3 Domain And
           Pinch-1 Lim4 Domain
          Length = 66

 Score = 30.4 bits (67), Expect = 2.2,   Method: Composition-based stats.
 Identities = 13/36 (36%), Positives = 18/36 (50%)

Query: 463 IPLCKGHKEPCVARVVKKPGPTFGRRFFVCARAEGP 498
           +P+C   + P   RVV   G  +    FVCA+ E P
Sbjct: 5   VPICGACRRPIEGRVVNAMGKQWHVEHFVCAKCEKP 40


>pdb|3PVL|A Chain A, Structure Of Myosin Viia Myth4-Ferm-Sh3 In Complex With
           The Cen1 Of Sans
          Length = 655

 Score = 29.6 bits (65), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 28/100 (28%), Positives = 46/100 (46%), Gaps = 8/100 (8%)

Query: 212 LGEVPEIPQHSTPSLASRYLPIIRGVQQTLVSVLMKREV-AKQGKSCKFSGSLPAESNST 270
           +G++PE   H+  S  S  +P++  + +TL     KRE+ A QG+          ES   
Sbjct: 85  MGDLPEPKYHTAMSDGSEKIPVMTKIYETLGKKTYKRELQALQGEGEVTKRLNDGESTVQ 144

Query: 271 GDT--EDCSENVDRSLNNYCDSGILQG-----VYCSSSNQ 303
           G++  ED   +    L+    +GIL+      +YC  S Q
Sbjct: 145 GNSMLEDRPTSNLEKLHFIIGNGILRPALRDEIYCQISKQ 184


>pdb|3N75|A Chain A, X-Ray Crystal Structure Of The Escherichia Coli Inducible
           Lysine Decarboxylase Ldci
 pdb|3N75|B Chain B, X-Ray Crystal Structure Of The Escherichia Coli Inducible
           Lysine Decarboxylase Ldci
 pdb|3N75|C Chain C, X-Ray Crystal Structure Of The Escherichia Coli Inducible
           Lysine Decarboxylase Ldci
 pdb|3N75|D Chain D, X-Ray Crystal Structure Of The Escherichia Coli Inducible
           Lysine Decarboxylase Ldci
 pdb|3N75|E Chain E, X-Ray Crystal Structure Of The Escherichia Coli Inducible
           Lysine Decarboxylase Ldci
 pdb|3Q16|A Chain A, Linkage Between The Bacterial Acid Stress And Stringent
           Responses: The Structure Of The Inducible Lysine
           Decarboxylase
 pdb|3Q16|B Chain B, Linkage Between The Bacterial Acid Stress And Stringent
           Responses: The Structure Of The Inducible Lysine
           Decarboxylase
 pdb|3Q16|C Chain C, Linkage Between The Bacterial Acid Stress And Stringent
           Responses: The Structure Of The Inducible Lysine
           Decarboxylase
 pdb|3Q16|D Chain D, Linkage Between The Bacterial Acid Stress And Stringent
           Responses: The Structure Of The Inducible Lysine
           Decarboxylase
 pdb|3Q16|E Chain E, Linkage Between The Bacterial Acid Stress And Stringent
           Responses: The Structure Of The Inducible Lysine
           Decarboxylase
          Length = 715

 Score = 29.3 bits (64), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 3/36 (8%)

Query: 97  EFRIWFRSMLVESGGSFFDVFRSKHPERREAYTCWP 132
           +FR   + +  ES G FFDV++  H +  E   CWP
Sbjct: 434 KFRKEIKRLRTESDGWFFDVWQPDHIDTTE---CWP 466


  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
   0.318    0.133    0.413 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,291,034
Number of Sequences: 62578
Number of extensions: 684847
Number of successful extensions: 1399
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1370
Number of HSP's gapped (non-prelim): 22
length of query: 519
length of database: 14,973,337
effective HSP length: 103
effective length of query: 416
effective length of database: 8,527,803
effective search space: 3547566048
effective search space used: 3547566048
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)