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= 023207
(285 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2O3H|A Chain A, Crystal Structure Of The Human C65a Ape
Length = 285
Score = 111 bits (277), Expect = 5e-25, Method: Compositional matrix adjust.
Identities = 74/229 (32%), Positives = 124/229 (54%), Gaps = 30/229 (13%)
Query: 38 PFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYL 96
P ++Q W + +D + Y+G LL ++C P KVS+ + +++ +GRVI+AEF++F L
Sbjct: 79 PGLSHQYWSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDE--EHDQEGRVIVAEFDSFVL 134
Query: 97 LNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWCGDLNVSHEEIDVSHPEF 155
+ Y PN G + R++WD+ ++F+ S KPL+ CGDLNV+HEEID+ +P+
Sbjct: 135 VTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKG 192
Query: 156 FAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSG 215
NK++ GFT ER+ FG +L+ L D++R L+ F W+
Sbjct: 193 ------------NKKN---AGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTF-WTY 236
Query: 216 NPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 264
+ + R+DYF++S L + +++ + GSDHCP+
Sbjct: 237 MMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKAL------GSDHCPI 279
>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 = 110 bits (276), Expect = 6e-25, Method: Compositional matrix adjust.
Identities = 75/233 (32%), Positives = 125/233 (53%), Gaps = 30/233 (12%)
Query: 34 LSSPPFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFE 92
L P ++Q W + +D + Y+G LL ++C P KVS+ + +++ +GRVI+AEF+
Sbjct: 77 LQELPGLSHQYWSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDE--EHDQEGRVIVAEFD 132
Query: 93 TFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWCGDLNVSHEEIDVS 151
+F L+ Y PN G + R++WD+ ++F+ S KPL+ CGDLNV+HEEID+
Sbjct: 133 SFVLVTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLR 190
Query: 152 HPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGF 211
+P+ NK++ GFT ER+ FG +L+ L D++R L+ F
Sbjct: 191 NPKG------------NKKN---AGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTF 235
Query: 212 SWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 264
W+ + + R+DYF++S L + +++ + GSDHCP+
Sbjct: 236 -WTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKAL------GSDHCPI 281
>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 = 110 bits (276), Expect = 6e-25, Method: Compositional matrix adjust.
Identities = 74/229 (32%), Positives = 124/229 (54%), Gaps = 30/229 (13%)
Query: 38 PFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYL 96
P ++Q W + +D + Y+G LL ++C P KVS+ + +++ +GRVI+AEF++F L
Sbjct: 111 PGLSHQYWSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDE--EHDQEGRVIVAEFDSFVL 166
Query: 97 LNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWCGDLNVSHEEIDVSHPEF 155
+ Y PN G + R++WD+ ++F+ S KPL+ CGDLNV+HEEID+ +P+
Sbjct: 167 VTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKG 224
Query: 156 FAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSG 215
NK++ GFT ER+ FG +L+ L D++R L+ F W+
Sbjct: 225 ------------NKKN---AGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTF-WTY 268
Query: 216 NPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 264
+ + R+DYF++S L + +++ + GSDHCP+
Sbjct: 269 MMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKAL------GSDHCPI 311
>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 = 110 bits (276), Expect = 6e-25, Method: Compositional matrix adjust.
Identities = 74/229 (32%), Positives = 124/229 (54%), Gaps = 30/229 (13%)
Query: 38 PFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYL 96
P ++Q W + +D + Y+G LL ++C P KVS+ + +++ +GRVI+AEF++F L
Sbjct: 112 PGLSHQYWSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDE--EHDQEGRVIVAEFDSFVL 167
Query: 97 LNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWCGDLNVSHEEIDVSHPEF 155
+ Y PN G + R++WD+ ++F+ S KPL+ CGDLNV+HEEID+ +P+
Sbjct: 168 VTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKG 225
Query: 156 FAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSG 215
NK++ GFT ER+ FG +L+ L D++R L+ F W+
Sbjct: 226 ------------NKKN---AGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTF-WTY 269
Query: 216 NPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 264
+ + R+DYF++S L + +++ + GSDHCP+
Sbjct: 270 MMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKAL------GSDHCPI 312
>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 = 110 bits (276), Expect = 7e-25, Method: Compositional matrix adjust.
Identities = 74/229 (32%), Positives = 124/229 (54%), Gaps = 30/229 (13%)
Query: 38 PFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYL 96
P ++Q W + +D + Y+G LL ++C P KVS+ + +++ +GRVI+AEF++F L
Sbjct: 73 PGLSHQYWSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDE--EHDQEGRVIVAEFDSFVL 128
Query: 97 LNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWCGDLNVSHEEIDVSHPEF 155
+ Y PN G + R++WD+ ++F+ S KPL+ CGDLNV+HEEID+ +P+
Sbjct: 129 VTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKG 186
Query: 156 FAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSG 215
NK++ GFT ER+ FG +L+ L D++R L+ F W+
Sbjct: 187 ------------NKKN---AGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTF-WTY 230
Query: 216 NPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 264
+ + R+DYF++S L + +++ + GSDHCP+
Sbjct: 231 MMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKAL------GSDHCPI 273
>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 = 110 bits (276), Expect = 7e-25, Method: Compositional matrix adjust.
Identities = 75/233 (32%), Positives = 125/233 (53%), Gaps = 30/233 (12%)
Query: 34 LSSPPFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFE 92
L P ++Q W + +D + Y+G LL ++C P KVS+ + +++ +GRVI+AEF+
Sbjct: 66 LQELPGLSHQYWSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDE--EHDQEGRVIVAEFD 121
Query: 93 TFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWCGDLNVSHEEIDVS 151
+F L+ Y PN G + R++WD+ ++F+ S KPL+ CGDLNV+HEEID+
Sbjct: 122 SFVLVTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLR 179
Query: 152 HPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGF 211
+P+ NK++ GFT ER+ FG +L+ L D++R L+ F
Sbjct: 180 NPK------------GNKKN---AGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTF 224
Query: 212 SWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 264
W+ + + R+DYF++S L + +++ + GSDHCP+
Sbjct: 225 -WTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKAL------GSDHCPI 270
>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 = 92.4 bits (228), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 65/223 (29%), Positives = 111/223 (49%), Gaps = 32/223 (14%)
Query: 45 WWSLADSK--YAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAP 102
+W+ ++ K Y+G A+L K +P V++ + K +++ +GRVI AEF F+L+ Y P
Sbjct: 83 YWAGSEDKEGYSGVAMLCKT--EPLNVTYGIGKE--EHDKEGRVITAEFPDFFLVTAYVP 138
Query: 103 NNGWKEEENSFQRRRKWDKRIQEFVLQCSG-KPLIWCGDLNVSHEEIDVSHPEFFAAAKL 161
N R+ WD + ++ KPL+ CGDLNV+H+EID+ +P
Sbjct: 139 NA--SRGLVRLDYRKTWDVDFRAYLCGLDARKPLVLCGDLNVAHQEIDLKNP-------- 188
Query: 162 NGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKY 221
K + GFT ER+ F +L+ G D++R L+ ++ F W+ +
Sbjct: 189 -------KGNRKNAGFTPEEREGFTQLLEAG-FTDSFRELYPDQAYAYTF-WTYMMNARS 239
Query: 222 RGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 264
+ R+DYF++S L + +++ + GSDHCP+
Sbjct: 240 KNVGWRLDYFVLSSALLPGLCDSKIRNTAM------GSDHCPI 276
>pdb|3G91|A Chain A, 1.2 Angstrom Structure Of The Exonuclease Iii Homologue
Mth0212
Length = 265
Score = 77.4 bits (189), Expect = 8e-15, Method: Compositional matrix adjust.
Identities = 61/225 (27%), Positives = 104/225 (46%), Gaps = 31/225 (13%)
Query: 42 YQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTY 100
Y+ +++ A+ K Y+G A+ K + F +E+ ++ +GR+ +A+F+ F L N Y
Sbjct: 56 YRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVER----FDTEGRIQIADFDDFLLYNIY 111
Query: 101 APNNGWKEEENSFQRRRKWDKRIQEFVLQC-SGKPLIWCGDLNVSHEEIDVSHPEFFAAA 159
PN EE + + +D +++ + SG+ +I CGD N +H EID++ P
Sbjct: 112 FPNGAMSEERLKY-KLEFYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARP------ 164
Query: 160 KLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIG 219
KE+ GF ER ++ G +D +R + + WS
Sbjct: 165 ---------KENSNVSGFLPVERAWIDKFIENG-YVDTFRMFNSDPGQYTW--WSYRTRA 212
Query: 220 KYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 264
+ R R+DYF V+EE K ++ + L GSDHCP+
Sbjct: 213 RERNVGWRLDYFFVNEEFKGKVKRSWI------LSDVMGSDHCPI 251
>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 = 76.3 bits (186), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 61/225 (27%), Positives = 104/225 (46%), Gaps = 31/225 (13%)
Query: 42 YQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTY 100
Y+ +++ A+ K Y+G A+ K + F +E+ ++ +GR+ +A+F+ F L N Y
Sbjct: 56 YRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVER----FDTEGRIQIADFDDFLLYNIY 111
Query: 101 APNNGWKEEENSFQRRRKWDKRIQEFVLQC-SGKPLIWCGDLNVSHEEIDVSHPEFFAAA 159
PN EE + + +D +++ + SG+ +I CGD N +H EID++ P
Sbjct: 112 FPNGKMSEERLKY-KLEFYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARP------ 164
Query: 160 KLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIG 219
KE+ GF ER ++ G +D +R + + WS
Sbjct: 165 ---------KENSNVSGFLPVERAWIDKFIENG-YVDTFRMFNSDPGQYTW--WSYRTRA 212
Query: 220 KYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 264
+ R R+DYF V+EE K ++ + L GSDHCP+
Sbjct: 213 RERNVGWRLDYFFVNEEFKGKVKRSWI------LSDVMGSDHCPI 251
>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 = 74.7 bits (182), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 60/225 (26%), Positives = 104/225 (46%), Gaps = 31/225 (13%)
Query: 42 YQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTY 100
Y+ +++ A+ K Y+G A+ K + F +E+ ++ +GR+ +A+F+ F L N Y
Sbjct: 56 YRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVER----FDTEGRIQIADFDDFLLYNIY 111
Query: 101 APNNGWKEEENSFQRRRKWDKRIQEFVLQC-SGKPLIWCGDLNVSHEEIDVSHPEFFAAA 159
PN EE + + +D +++ + SG+ +I CG+ N +H EID++ P
Sbjct: 112 FPNGKMSEERLKY-KLEFYDAFLEDVNRERDSGRNVIICGNFNTAHREIDLARP------ 164
Query: 160 KLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIG 219
KE+ GF ER ++ G +D +R + + WS
Sbjct: 165 ---------KENSNVSGFLPVERAWIDKFIENG-YVDTFRMFNSDPGQYTW--WSYRTRA 212
Query: 220 KYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 264
+ R R+DYF V+EE K ++ + L GSDHCP+
Sbjct: 213 RERNVGWRLDYFFVNEEFKGKVKRSWI------LSDVMGSDHCPI 251
>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 = 54.3 bits (129), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 46/187 (24%), Positives = 72/187 (38%), Gaps = 38/187 (20%)
Query: 96 LLNTYAPNNGWKEEENSFQRR------RKWDKRIQEFVLQCSGKP-------------LI 136
L+NTY N+G ++ + R++ R+ + + + P I
Sbjct: 292 LVNTYVANSGMGLTRLPYRVQSFDPSMREYLHRLDTWATENAAVPSAAAMGSGSSPHGFI 351
Query: 137 WCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLID 196
W GDLNV+ + D + F K GF ER F ++ +D
Sbjct: 352 WAGDLNVAERDYDRYYAGTF------------KSMQECSGFAPEERMSFRETMQRTNSVD 399
Query: 197 AYRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGF 256
+R L+ + F WS G+ R R+DYF+VS L ++ C +
Sbjct: 400 IFRQLYPQAGPVYSF-WSQRINGRPRNLGWRLDYFVVSSRLASYVVDC------FPMPTV 452
Query: 257 YGSDHCP 263
GSDHCP
Sbjct: 453 MGSDHCP 459
>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 = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 48/184 (26%), Positives = 85/184 (46%), Gaps = 27/184 (14%)
Query: 65 QPKKVSFSLEKTALKYEP--DGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKR 122
+P+ VSF L+ EP + R+I A+ ++NTY P G+K + +Q + +W +R
Sbjct: 73 EPEDVSFGLDS-----EPKDEDRLIRAKIAGIDVINTYVPQ-GFKIDSEKYQYKLQWLER 126
Query: 123 IQEFVLQCSG--KPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIA 180
+ ++ + +WCGD+NV+ E IDV P+ KL +V F
Sbjct: 127 LYHYLQKTVDFRSFAVWCGDMNVAPEPIDVHSPD-----KLKNHV----------XFHED 171
Query: 181 ERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDR 240
R+ + IL+ G +D R +H + + + + + RG R D + + L +R
Sbjct: 172 ARRAYKKILELG-FVDVLRKIHPNERIYTFYDYRVKGAIE-RGLGWRGDAILATPPLAER 229
Query: 241 IIAC 244
+ C
Sbjct: 230 CVDC 233
>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 = 51.6 bits (122), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 50/221 (22%), Positives = 100/221 (45%), Gaps = 30/221 (13%)
Query: 46 WSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNN 104
W A+ + Y+G A+ K+ ++ +E+ ++ +GR + +F +++ Y P+
Sbjct: 58 WHCAEKRGYSGVAVYSKRKPDNVQIGMGIEE----FDREGRFVRCDFGRLSVISLYLPSG 113
Query: 105 GWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGY 164
EE + R ++ G+ ++ CGD N++H+ ID+ + + K +G+
Sbjct: 114 SSAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLKN--WKGNQKNSGF 171
Query: 165 VPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKY-RG 223
+P ER+ G ++ + D +R L+ + G++W N Y +
Sbjct: 172 LPE-------------EREWIGKVIHKLGWTDMWRTLYPDVP---GYTWWSNRGQAYAKD 215
Query: 224 KRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 264
RIDY +V+ EL + ++ H + E F SDH P+
Sbjct: 216 VGWRIDYQMVTPELAAKAVSA----HVYKDEKF--SDHAPL 250
>pdb|4B5H|A Chain A, Substate Bound Inactive Mutant Of Neisseria Ap
Endonuclease In Presence Of Metal Ions
Length = 259
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 49/221 (22%), Positives = 100/221 (45%), Gaps = 30/221 (13%)
Query: 46 WSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNN 104
W A+ + Y+G A+ K+ ++ +E+ ++ +GR + +F +++ Y P+
Sbjct: 58 WHCAEKRGYSGVAVYSKRKPDNVQIGMGIEE----FDREGRFVRCDFGRLSVISLYLPSG 113
Query: 105 GWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGY 164
EE + R ++ G+ ++ CG+ N++H+ ID+ + + K +G+
Sbjct: 114 SSAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGNWNIAHQNIDLKN--WKGNQKNSGF 171
Query: 165 VPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKY-RG 223
+P ER+ G ++ + D +R L+ + G++W N Y +
Sbjct: 172 LPE-------------EREWIGKVIHKLGWTDMWRTLYPDVP---GYTWWSNRGQAYAKD 215
Query: 224 KRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 264
RIDY +V+ EL + ++ H + E F SDH P+
Sbjct: 216 VGWRIDYQMVTPELAAKAVSA----HVYKDEKF--SDHAPL 250
>pdb|1AKO|A Chain A, Exonuclease Iii From Escherichia Coli
Length = 268
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 55/235 (23%), Positives = 96/235 (40%), Gaps = 36/235 (15%)
Query: 42 YQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFY----LL 97
Y +++ Y G ALL K+ + F + E R+I+AE + ++
Sbjct: 52 YNVFYHGQKGHY-GVALLTKETPIAVRRGFPGDDE----EAQRRIIMAEIPSLLGNVTVI 106
Query: 98 NTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGK---PLIWCGDLNVSHEEIDVSHPE 154
N Y P ++ F + ++ + +Q + L+ K P++ GD+N+S ++D+
Sbjct: 107 NGYFPQGESRDHPIKFPAKAQFYQNLQNY-LETELKRDNPVLIMGDMNISPTDLDI---- 161
Query: 155 FFAAAKLNGYVPPNKEDW---GQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGF 211
G N++ W G+ F ER+ ++ G L+D +R H F
Sbjct: 162 --------GIGEENRKRWLRTGKCSFLPEEREWMDRLMSWG-LVDTFR--HANPQTADRF 210
Query: 212 SWSGNPIGKYRGKR-MRIDYFIVSEELKDRIIACEMQGHGIELEGFYG-SDHCPV 264
SW + R +RID + S+ L + C G E+ SDH PV
Sbjct: 211 SWFDYRSKGFDDNRGLRIDLLLASQPLAE---CCVETGIDYEIRSMEKPSDHAPV 262
>pdb|4F1R|A Chain A, Structure Analysis Of The Global Metabolic Regulator Crc
From Pseudomonas Aeruginos
Length = 293
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 41/163 (25%), Positives = 67/163 (41%), Gaps = 28/163 (17%)
Query: 54 AGTALLVKKCFQPKKVSFSLE-KTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENS 112
G AL + QPK V L +TA +Y GR + A+F+ + P+ + + S
Sbjct: 100 GGVALYSR--LQPKAVISGLGFETADRY---GRYLQADFDKVSIATLLLPSG--QSGDES 152
Query: 113 FQRRRKWDKRIQEFVLQCSGK--PLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKE 170
++ K+ ++ + K I+CG L V+H+++DV + +E
Sbjct: 153 LNQKFKFMDDFTHYLSKQRRKRREYIYCGSLYVAHQKMDVKNW---------------RE 197
Query: 171 DWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSW 213
PGF ER + DA R + +E D FSW
Sbjct: 198 CQQMPGFLAPERAWLDEVFGNLGYADALREVSREGDQ---FSW 237
>pdb|1VYB|A Chain A, Endonuclease Domain Of Human Line1 Orf2p
pdb|1VYB|B Chain B, Endonuclease Domain Of Human Line1 Orf2p
Length = 238
Score = 31.6 bits (70), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 54/232 (23%), Positives = 85/232 (36%), Gaps = 69/232 (29%)
Query: 43 QIWWSLADSKYAGTALLV--KKCFQPKKVSFSLEKTALKYEPDGRVILA----EFETFYL 96
+I+ + K AG A+LV K F+P K+ K + +G I+ + E +
Sbjct: 61 KIYQANGKQKKAGVAILVSDKTDFKPTKI---------KRDKEGHYIMVKGSIQQEELTI 111
Query: 97 LNTYAPNNG----WKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSH 152
LN YAPN G K+ + QR LI GD N +D S
Sbjct: 112 LNIYAPNTGAPRFIKQVLSDLQR-------------DLDSHTLIM-GDFNTPLSTLDRS- 156
Query: 153 PEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFS 212
K+N + + + L + LID YR LH + ++
Sbjct: 157 ----TRQKVN-----------------KDTQELNSALHQADLIDIYRTLHPK---STEYT 192
Query: 213 WSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 264
+ P Y +ID+ + S+ L + C+ E+ Y SDH +
Sbjct: 193 FFSAPHHTYS----KIDHIVGSKALLSK---CKRT----EIITNYLSDHSAI 233
>pdb|2V0S|A Chain A, Crystal Structure Of A Hairpin Exchange Variant (Lr1) Of
The Targeting Line-1 Retrotransposon Endonuclease
Length = 236
Score = 31.2 bits (69), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 55/232 (23%), Positives = 85/232 (36%), Gaps = 71/232 (30%)
Query: 43 QIWWSLADSKYAGTALLV--KKCFQPKKVSFSLEKTALKYEPDGRVILA----EFETFYL 96
+I+ + K AG A+LV K F+P K+ K + +G I+ + E +
Sbjct: 61 KIYQANGKQKKAGVAILVSDKTDFKPTKI---------KRDKEGHYIMVKGSIQQEELTI 111
Query: 97 LNTYAPNNG----WKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSH 152
LN YAPN G K+ + QR LI GD N +D S
Sbjct: 112 LNIYAPNTGAPRFIKQVLSDLQR-------------DLDSHTLIM-GDFNTPLSTLDRST 157
Query: 153 PEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFS 212
+ K+N + + + L + LID YR LH K + FS
Sbjct: 158 RQ-----KVN-----------------KDTQELNSALHQADLIDIYRTLH-PKSTEYTFS 194
Query: 213 WSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 264
+ +ID+ + S+ L + C+ E+ Y SDH +
Sbjct: 195 TANG--------ESKIDHIVGSKALLSK---CKRT----EIITNYLSDHSAI 231
>pdb|2V0R|A Chain A, Crystal Structure Of A Hairpin Exchange Variant (Ltx) Of
The Targeting Line-1 Retrotransposon Endonuclease
pdb|2V0R|B Chain B, Crystal Structure Of A Hairpin Exchange Variant (Ltx) Of
The Targeting Line-1 Retrotransposon Endonuclease
Length = 240
Score = 30.8 bits (68), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 15/69 (21%)
Query: 43 QIWWSLADSKYAGTALLV--KKCFQPKKVSFSLEKTALKYEPDGRVILA----EFETFYL 96
+I+ + K AG A+LV K F+P K+ K + +G I+ + E +
Sbjct: 61 KIYQANGKQKKAGVAILVSDKTDFKPTKI---------KRDKEGHYIMVKGSIQQEELTI 111
Query: 97 LNTYAPNNG 105
LN YAPN G
Sbjct: 112 LNIYAPNTG 120
>pdb|3AEV|A Chain A, Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex From
Pyrococcus Horikoshii Ot3
Length = 275
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 29/52 (55%), Gaps = 3/52 (5%)
Query: 188 ILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKD 239
I+KE LI A +KEKD++ F++ G P +YR DY+ E L+D
Sbjct: 194 IIKEA-LIRARDRANKEKDIEVKFTYQGAP--RYRIDITAPDYYKAEEVLED 242
>pdb|1FWK|A Chain A, Crystal Structure Of Homoserine Kinase Complexed With Adp
pdb|1FWK|B Chain B, Crystal Structure Of Homoserine Kinase Complexed With Adp
pdb|1FWK|C Chain C, Crystal Structure Of Homoserine Kinase Complexed With Adp
pdb|1FWK|D Chain D, Crystal Structure Of Homoserine Kinase Complexed With Adp
pdb|1FWL|A Chain A, Crystal Structure Of Homoserine Kinase
pdb|1FWL|B Chain B, Crystal Structure Of Homoserine Kinase
pdb|1FWL|C Chain C, Crystal Structure Of Homoserine Kinase
pdb|1FWL|D Chain D, Crystal Structure Of Homoserine Kinase
pdb|1H72|C Chain C, Crystal Structure Of Homoserine Kinase Complexed With Hse
pdb|1H74|A Chain A, Crystal Structure Of Homoserine Kinase Complexed With Ile
pdb|1H74|B Chain B, Crystal Structure Of Homoserine Kinase Complexed With Ile
pdb|1H74|C Chain C, Crystal Structure Of Homoserine Kinase Complexed With Ile
pdb|1H74|D Chain D, Crystal Structure Of Homoserine Kinase Complexed With Ile
pdb|1H73|A Chain A, Crystal Structure Of Homoserine Kinase Complexed With
Threonine
Length = 296
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 1/60 (1%)
Query: 197 AYRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGF 256
Y +K+K + + S I RGK + +YF + EE+KD++ + G G + F
Sbjct: 206 VYALYNKDKSLFGRYMMSDKVIEPVRGKLIP-NYFKIKEEVKDKVYGITISGSGPSIIAF 264
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 0.137 0.429
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,953,510
Number of Sequences: 62578
Number of extensions: 388280
Number of successful extensions: 746
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 700
Number of HSP's gapped (non-prelim): 23
length of query: 285
length of database: 14,973,337
effective HSP length: 98
effective length of query: 187
effective length of database: 8,840,693
effective search space: 1653209591
effective search space used: 1653209591
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)