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= 023088
(287 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 94.7 bits (234), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 73/243 (30%), Positives = 119/243 (48%), Gaps = 50/243 (20%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
LK +WN + L +K + +++ PD++ LQE + P QEL
Sbjct: 62 LKICSWNVDGLRAWIKK---KGLDWVKEEAPDILCLQETK---CSENKLPAELQEL---- 111
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALK 160
P ++Q W + +D + Y+G LL ++C P KVS+ + +
Sbjct: 112 -----------------PGLSHQYWSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDE--E 150
Query: 161 YEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWC 219
++ +GRVI+AEF++F L+ Y PN G + R++WD+ ++F+ S KPL+ C
Sbjct: 151 HDQEGRVIVAEFDSFVLVTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLC 208
Query: 220 GDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEYLIFLCF 279
GDLNV+HEEID+ +P+ NK++ GFT ER+ FG +L+ + F
Sbjct: 209 GDLNVAHEEIDLRNPKG------------NKKN---AGFTPQERQGFGELLQAVPLADSF 253
Query: 280 YEL 282
L
Sbjct: 254 RHL 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 = 94.7 bits (234), Expect = 6e-20, Method: Compositional matrix adjust.
Identities = 73/243 (30%), Positives = 119/243 (48%), Gaps = 50/243 (20%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
LK +WN + L +K + +++ PD++ LQE + P QEL
Sbjct: 61 LKICSWNVDGLRAWIKK---KGLDWVKEEAPDILCLQETK---CSENKLPAELQEL---- 110
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALK 160
P ++Q W + +D + Y+G LL ++C P KVS+ + +
Sbjct: 111 -----------------PGLSHQYWSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDE--E 149
Query: 161 YEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWC 219
++ +GRVI+AEF++F L+ Y PN G + R++WD+ ++F+ S KPL+ C
Sbjct: 150 HDQEGRVIVAEFDSFVLVTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLC 207
Query: 220 GDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEYLIFLCF 279
GDLNV+HEEID+ +P+ NK++ GFT ER+ FG +L+ + F
Sbjct: 208 GDLNVAHEEIDLRNPKG------------NKKN---AGFTPQERQGFGELLQAVPLADSF 252
Query: 280 YEL 282
L
Sbjct: 253 RHL 255
>pdb|2O3H|A Chain A, Crystal Structure Of The Human C65a Ape
Length = 285
Score = 94.4 bits (233), Expect = 7e-20, Method: Compositional matrix adjust.
Identities = 73/243 (30%), Positives = 119/243 (48%), Gaps = 50/243 (20%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
LK +WN + L +K + +++ PD++ LQE + P QEL
Sbjct: 29 LKIASWNVDGLRAWIKK---KGLDWVKEEAPDILCLQETK---CSENKLPAELQEL---- 78
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALK 160
P ++Q W + +D + Y+G LL ++C P KVS+ + +
Sbjct: 79 -----------------PGLSHQYWSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDE--E 117
Query: 161 YEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWC 219
++ +GRVI+AEF++F L+ Y PN G + R++WD+ ++F+ S KPL+ C
Sbjct: 118 HDQEGRVIVAEFDSFVLVTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLC 175
Query: 220 GDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEYLIFLCF 279
GDLNV+HEEID+ +P+ NK++ GFT ER+ FG +L+ + F
Sbjct: 176 GDLNVAHEEIDLRNPKG------------NKKN---AGFTPQERQGFGELLQAVPLADSF 220
Query: 280 YEL 282
L
Sbjct: 221 RHL 223
>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 = 94.0 bits (232), Expect = 8e-20, Method: Compositional matrix adjust.
Identities = 73/243 (30%), Positives = 119/243 (48%), Gaps = 50/243 (20%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
LK +WN + L +K + +++ PD++ LQE + P QEL
Sbjct: 31 LKICSWNVDGLRAWIKK---KGLDWVKEEAPDILCLQETK---CSENKLPAELQEL---- 80
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALK 160
P ++Q W + +D + Y+G LL ++C P KVS+ + +
Sbjct: 81 -----------------PGLSHQYWSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDE--E 119
Query: 161 YEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWC 219
++ +GRVI+AEF++F L+ Y PN G + R++WD+ ++F+ S KPL+ C
Sbjct: 120 HDQEGRVIVAEFDSFVLVTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLC 177
Query: 220 GDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEYLIFLCF 279
GDLNV+HEEID+ +P+ NK++ GFT ER+ FG +L+ + F
Sbjct: 178 GDLNVAHEEIDLRNPKG------------NKKN---AGFTPQERQGFGELLQAVPLADSF 222
Query: 280 YEL 282
L
Sbjct: 223 RHL 225
>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 = 94.0 bits (232), Expect = 8e-20, Method: Compositional matrix adjust.
Identities = 71/232 (30%), Positives = 116/232 (50%), Gaps = 50/232 (21%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
LK +WN + L +K + +++ PD++ LQE + P QEL
Sbjct: 20 LKICSWNVDGLRAWIKK---KGLDWVKEEAPDILCLQETK---CSENKLPAELQEL---- 69
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALK 160
P ++Q W + +D + Y+G LL ++C P KVS+ + +
Sbjct: 70 -----------------PGLSHQYWSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDE--E 108
Query: 161 YEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWC 219
++ +GRVI+AEF++F L+ Y PN G + R++WD+ ++F+ S KPL+ C
Sbjct: 109 HDQEGRVIVAEFDSFVLVTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLC 166
Query: 220 GDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILK 271
GDLNV+HEEID+ +P+ NK++ GFT ER+ FG +L+
Sbjct: 167 GDLNVAHEEIDLRNPK------------GNKKN---AGFTPQERQGFGELLQ 203
>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 = 94.0 bits (232), Expect = 9e-20, Method: Compositional matrix adjust.
Identities = 71/232 (30%), Positives = 116/232 (50%), Gaps = 50/232 (21%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
LK +WN + L +K + +++ PD++ LQE + P QEL
Sbjct: 23 LKICSWNVDGLRAWIKK---KGLDWVKEEAPDILCLQETK---CSENKLPAELQEL---- 72
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALK 160
P ++Q W + +D + Y+G LL ++C P KVS+ + +
Sbjct: 73 -----------------PGLSHQYWSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDE--E 111
Query: 161 YEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWC 219
++ +GRVI+AEF++F L+ Y PN G + R++WD+ ++F+ S KPL+ C
Sbjct: 112 HDQEGRVIVAEFDSFVLVTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLC 169
Query: 220 GDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILK 271
GDLNV+HEEID+ +P+ NK++ GFT ER+ FG +L+
Sbjct: 170 GDLNVAHEEIDLRNPKG------------NKKN---AGFTPQERQGFGELLQ 206
>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 = 82.8 bits (203), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 66/231 (28%), Positives = 110/231 (47%), Gaps = 42/231 (18%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
+K +WN + L VK N +++ DPD++ LQE T
Sbjct: 27 MKITSWNVDGLRAWVKKNG---LDWVRKEDPDILCLQE---------------------T 62
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSK--YAGTALLVKKCFQPKKVSFSLEKTAL 159
K + + + A+ P K +W+ ++ K Y+G A+L K +P V++ + K
Sbjct: 63 KCAEKALPADITAMPEYPHK----YWAGSEDKEGYSGVAMLCKT--EPLNVTYGIGKE-- 114
Query: 160 KYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSG-KPLIW 218
+++ +GRVI AEF F+L+ Y PN R+ WD + ++ KPL+
Sbjct: 115 EHDKEGRVITAEFPDFFLVTAYVPNA--SRGLVRLDYRKTWDVDFRAYLCGLDARKPLVL 172
Query: 219 CGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQ---PGFTIAERKRF 266
CGDLNV+H+EID+ +P+ K G+ P +E + Q GFT + R+ +
Sbjct: 173 CGDLNVAHQEIDLKNPK--GNRKNAGFTPEEREGFTQLLEAGFTDSFRELY 221
>pdb|3G91|A Chain A, 1.2 Angstrom Structure Of The Exonuclease Iii Homologue
Mth0212
Length = 265
Score = 62.8 bits (151), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 50/208 (24%), Positives = 98/208 (47%), Gaps = 38/208 (18%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
LK ++WN N L + F + PD++ LQE++ A + P+ + ++
Sbjct: 4 LKIISWNVNGLRAVHRKG---FLKWFMEEKPDILCLQEIK---AAPEQLPRKLRHVE--- 54
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALK 160
Y+ +++ A+ K Y+G A+ K + F +E+
Sbjct: 55 --------------------GYRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVER---- 90
Query: 161 YEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWC 219
++ +GR+ +A+F+ F L N Y PN EE + + +D +++ + SG+ +I C
Sbjct: 91 FDTEGRIQIADFDDFLLYNIYFPNGAMSEERLKY-KLEFYDAFLEDVNRERDSGRNVIIC 149
Query: 220 GDLNVSHEEIDVSHPEFFAAAKLNGYVP 247
GD N +H EID++ P+ + ++G++P
Sbjct: 150 GDFNTAHREIDLARPK--ENSNVSGFLP 175
>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 = 62.0 bits (149), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 50/208 (24%), Positives = 98/208 (47%), Gaps = 38/208 (18%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
LK ++WN N L + F + PD++ LQE++ A + P+ + ++
Sbjct: 4 LKIISWNVNGLRAVHRKG---FLKWFMEEKPDILCLQEIK---AAPEQLPRKLRHVE--- 54
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALK 160
Y+ +++ A+ K Y+G A+ K + F +E+
Sbjct: 55 --------------------GYRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVER---- 90
Query: 161 YEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWC 219
++ +GR+ +A+F+ F L N Y PN EE + + +D +++ + SG+ +I C
Sbjct: 91 FDTEGRIQIADFDDFLLYNIYFPNGKMSEERLKY-KLEFYDAFLEDVNRERDSGRNVIIC 149
Query: 220 GDLNVSHEEIDVSHPEFFAAAKLNGYVP 247
GD N +H EID++ P+ + ++G++P
Sbjct: 150 GDFNTAHREIDLARPK--ENSNVSGFLP 175
>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 = 60.1 bits (144), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 49/208 (23%), Positives = 98/208 (47%), Gaps = 38/208 (18%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
LK ++WN N L + F + PD++ LQE++ A + P+ + ++
Sbjct: 4 LKIISWNVNGLRAVHRKG---FLKWFMEEKPDILCLQEIK---AAPEQLPRKLRHVE--- 54
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALK 160
Y+ +++ A+ K Y+G A+ K + F +E+
Sbjct: 55 --------------------GYRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVER---- 90
Query: 161 YEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWC 219
++ +GR+ +A+F+ F L N Y PN EE + + +D +++ + SG+ +I C
Sbjct: 91 FDTEGRIQIADFDDFLLYNIYFPNGKMSEERLKY-KLEFYDAFLEDVNRERDSGRNVIIC 149
Query: 220 GDLNVSHEEIDVSHPEFFAAAKLNGYVP 247
G+ N +H EID++ P+ + ++G++P
Sbjct: 150 GNFNTAHREIDLARPK--ENSNVSGFLP 175
>pdb|2JC4|A Chain A, 3'-5' Exonuclease (Nexo) From Neisseria Meningitidis
Length = 256
Score = 53.9 bits (128), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 52/197 (26%), Positives = 81/197 (41%), Gaps = 40/197 (20%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
+K TWN NSL +R+ P+ N + PD++ LQE+++ D
Sbjct: 1 MKITTWNVNSLNVRL----PQVQNLLADNPPDILVLQELKL-----------------DQ 39
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKY 161
L +M + WS Y G A++ + P+ V F L AL
Sbjct: 40 DKFPAAALQMM---------GWHCVWS-GQKTYNGVAIVSRSV--PQDVHFGL--PALPD 85
Query: 162 EPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFV---LQCSGKPLIW 218
+P RVI A ++N Y NG + F+ + +W + EFV + GK L+
Sbjct: 86 DPQRRVIAATVSGVRVINVYCV-NGEALDSPKFKYKEQWFAALTEFVRDEMTRHGK-LVL 143
Query: 219 CGDLNVSHEEIDVSHPE 235
GD N++ + D PE
Sbjct: 144 LGDFNIAPADADCYDPE 160
>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 = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 31/116 (26%), Positives = 60/116 (51%), Gaps = 7/116 (6%)
Query: 123 YQIWWSLADSKYAG-TALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTY 181
++I + + S G + + +P+ VSF L+ + + R+I A+ ++NTY
Sbjct: 49 HRIGYHVVFSGSKGRNGVAIASLEEPEDVSFGLDSEP---KDEDRLIRAKIAGIDVINTY 105
Query: 182 APNNGWKEEENSFQRRRKWDKRIQEFVLQCSG--KPLIWCGDLNVSHEEIDVSHPE 235
P G+K + +Q + +W +R+ ++ + +WCGD+NV+ E IDV P+
Sbjct: 106 VPQ-GFKIDSEKYQYKLQWLERLYHYLQKTVDFRSFAVWCGDMNVAPEPIDVHSPD 160
>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 = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 42/215 (19%), Positives = 86/215 (40%), Gaps = 44/215 (20%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
LK ++ N N + K F +I D++ +QE++ A +L D
Sbjct: 2 LKIISANVNGIRSAYKKG---FYEYIAASGADIVCVQELKAQEA----------DLSADM 48
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKY 161
K P + W Y+G A+ K+ ++ +E+ +
Sbjct: 49 K---------------NPHGMHGHWHCAEKRGYSGVAVYSKRKPDNVQIGMGIEE----F 89
Query: 162 EPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEF-----VLQCSGKPL 216
+ +GR + +F +++ Y P+ EE + R + F ++ G+ +
Sbjct: 90 DREGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYRF-----LDAFYPMLEAMKNEGRDI 144
Query: 217 IWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKE 251
+ CGD N++H+ ID+ + + K +G++P +E
Sbjct: 145 VVCGDWNIAHQNIDLKN--WKGNQKNSGFLPEERE 177
>pdb|4B5H|A Chain A, Substate Bound Inactive Mutant Of Neisseria Ap
Endonuclease In Presence Of Metal Ions
Length = 259
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 41/215 (19%), Positives = 86/215 (40%), Gaps = 44/215 (20%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
LK ++ N N + K F +I D++ +QE++ A +L D
Sbjct: 2 LKIISANVNGIRSAYKKG---FYEYIAASGTDIVCVQELKAQEA----------DLSADM 48
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKY 161
K P + W Y+G A+ K+ ++ +E+ +
Sbjct: 49 K---------------NPHGMHGHWHCAEKRGYSGVAVYSKRKPDNVQIGMGIEE----F 89
Query: 162 EPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEF-----VLQCSGKPL 216
+ +GR + +F +++ Y P+ EE + R + F ++ G+ +
Sbjct: 90 DREGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYRF-----LDAFYPMLEAMKNEGRDI 144
Query: 217 IWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKE 251
+ CG+ N++H+ ID+ + + K +G++P +E
Sbjct: 145 VVCGNWNIAHQNIDLKN--WKGNQKNSGFLPEERE 177
>pdb|1AKO|A Chain A, Exonuclease Iii From Escherichia Coli
Length = 268
Score = 37.0 bits (84), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 44/198 (22%), Positives = 78/198 (39%), Gaps = 43/198 (21%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
+KFV++N N L R + + PDVI LQE + + DD
Sbjct: 1 MKFVSFNINGLRARPH----QLEAIVEKHQPDVIGLQETK---------------VHDD- 40
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKY 161
M L Y +++ Y G ALL K+ + F +
Sbjct: 41 ----------MFPLEEVAKLGYNVFYHGQKGHY-GVALLTKETPIAVRRGFPGDDE---- 85
Query: 162 EPDGRVILAEFETFY----LLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGK--- 214
E R+I+AE + ++N Y P ++ F + ++ + +Q + L+ K
Sbjct: 86 EAQRRIIMAEIPSLLGNVTVINGYFPQGESRDHPIKFPAKAQFYQNLQNY-LETELKRDN 144
Query: 215 PLIWCGDLNVSHEEIDVS 232
P++ GD+N+S ++D+
Sbjct: 145 PVLIMGDMNISPTDLDIG 162
>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 = 33.9 bits (76), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 43 KFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRM 82
KF+TWN L +K N F+ PDV+ LQE ++
Sbjct: 151 KFITWNVAGLRGLLKKNASALRAFMEAEKPDVLCLQETKL 190
>pdb|4F1R|A Chain A, Structure Analysis Of The Global Metabolic Regulator Crc
From Pseudomonas Aeruginos
Length = 293
Score = 32.3 bits (72), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 34/137 (24%), Positives = 65/137 (47%), Gaps = 16/137 (11%)
Query: 135 AGTALLVKKCFQPKKVSFSLE-KTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENS 193
G AL + QPK V L +TA +Y GR + A+F+ + P+ + + S
Sbjct: 100 GGVALYSR--LQPKAVISGLGFETADRY---GRYLQADFDKVSIATLLLPSG--QSGDES 152
Query: 194 FQRRRKWDKRIQEFVLQCSGK--PLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNK- 250
++ K+ ++ + K I+CG L V+H+++DV + + ++ G++ P +
Sbjct: 153 LNQKFKFMDDFTHYLSKQRRKRREYIYCGSLYVAHQKMDVKN--WRECQQMPGFLAPERA 210
Query: 251 ---EDWGQPGFTIAERK 264
E +G G+ A R+
Sbjct: 211 WLDEVFGNLGYADALRE 227
>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 = 31.6 bits (70), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 15/69 (21%)
Query: 124 QIWWSLADSKYAGTALLV--KKCFQPKKVSFSLEKTALKYEPDGRVILA----EFETFYL 177
+I+ + K AG A+LV K F+P K+ K + +G I+ + E +
Sbjct: 61 KIYQANGKQKKAGVAILVSDKTDFKPTKI---------KRDKEGHYIMVKGSIQQEELTI 111
Query: 178 LNTYAPNNG 186
LN YAPN G
Sbjct: 112 LNIYAPNTG 120
>pdb|2V0S|A Chain A, Crystal Structure Of A Hairpin Exchange Variant (Lr1) Of
The Targeting Line-1 Retrotransposon Endonuclease
Length = 236
Score = 31.6 bits (70), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 15/69 (21%)
Query: 124 QIWWSLADSKYAGTALLV--KKCFQPKKVSFSLEKTALKYEPDGRVILA----EFETFYL 177
+I+ + K AG A+LV K F+P K+ K + +G I+ + E +
Sbjct: 61 KIYQANGKQKKAGVAILVSDKTDFKPTKI---------KRDKEGHYIMVKGSIQQEELTI 111
Query: 178 LNTYAPNNG 186
LN YAPN G
Sbjct: 112 LNIYAPNTG 120
>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 = 31.2 bits (69), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 15/69 (21%)
Query: 124 QIWWSLADSKYAGTALLV--KKCFQPKKVSFSLEKTALKYEPDGRVILA----EFETFYL 177
+I+ + K AG A+LV K F+P K+ K + +G I+ + E +
Sbjct: 61 KIYQANGKQKKAGVAILVSDKTDFKPTKI---------KRDKEGHYIMVKGSIQQEELTI 111
Query: 178 LNTYAPNNG 186
LN YAPN G
Sbjct: 112 LNIYAPNTG 120
>pdb|1ZH8|A Chain A, Crystal Structure Of Oxidoreductase (tm0312) From
Thermotoga Maritima At 2.50 A Resolution
pdb|1ZH8|B Chain B, Crystal Structure Of Oxidoreductase (tm0312) From
Thermotoga Maritima At 2.50 A Resolution
Length = 340
Score = 29.3 bits (64), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 5/70 (7%)
Query: 105 REEKLILMRALSSPPFKNYQIWWSL-ADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEP 163
+ ++L+ A+ P F N+QIW ++KY T K PK V L + +
Sbjct: 150 KAKELVESGAIGDPVFXNWQIWVGXDENNKYVHTDWRKK----PKHVGGFLSDGGVHHAA 205
Query: 164 DGRVILAEFE 173
R+IL E E
Sbjct: 206 AXRLILGEIE 215
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
0.320 0.136 0.430
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,232,775
Number of Sequences: 62578
Number of extensions: 337677
Number of successful extensions: 712
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 684
Number of HSP's gapped (non-prelim): 23
length of query: 287
length of database: 14,973,337
effective HSP length: 98
effective length of query: 189
effective length of database: 8,840,693
effective search space: 1670890977
effective search space used: 1670890977
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)