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= 027283
(225 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 = 74.3 bits (181), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 55/185 (29%), Positives = 91/185 (49%), Gaps = 35/185 (18%)
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 GDLNV 224
GDLNV
Sbjct: 176 GDLNV 180
>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 = 74.3 bits (181), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 55/185 (29%), Positives = 91/185 (49%), Gaps = 35/185 (18%)
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 GDLNV 224
GDLNV
Sbjct: 209 GDLNV 213
>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 = 74.3 bits (181), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 55/185 (29%), Positives = 91/185 (49%), Gaps = 35/185 (18%)
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 GDLNV 224
GDLNV
Sbjct: 208 GDLNV 212
>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 = 74.3 bits (181), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 55/185 (29%), Positives = 91/185 (49%), Gaps = 35/185 (18%)
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 GDLNV 224
GDLNV
Sbjct: 178 GDLNV 182
>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 = 74.3 bits (181), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 55/185 (29%), Positives = 91/185 (49%), Gaps = 35/185 (18%)
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 GDLNV 224
GDLNV
Sbjct: 170 GDLNV 174
>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 = 73.9 bits (180), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 55/185 (29%), Positives = 91/185 (49%), Gaps = 35/185 (18%)
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 GDLNV 224
GDLNV
Sbjct: 167 GDLNV 171
>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 = 64.7 bits (156), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 52/186 (27%), Positives = 85/186 (45%), Gaps = 37/186 (19%)
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 CGDLNV 224
CGDLNV
Sbjct: 173 CGDLNV 178
>pdb|2JC4|A Chain A, 3'-5' Exonuclease (Nexo) From Neisseria Meningitidis
Length = 256
Score = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 49/186 (26%), Positives = 76/186 (40%), Gaps = 40/186 (21%)
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 CGDLNV 224
GD N+
Sbjct: 144 LGDFNI 149
>pdb|3G91|A Chain A, 1.2 Angstrom Structure Of The Exonuclease Iii Homologue
Mth0212
Length = 265
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 43/185 (23%), Positives = 82/185 (44%), Gaps = 36/185 (19%)
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 GDLNV 224
GD N
Sbjct: 150 GDFNT 154
>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 = 47.8 bits (112), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 43/185 (23%), Positives = 82/185 (44%), Gaps = 36/185 (19%)
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 GDLNV 224
GD N
Sbjct: 150 GDFNT 154
>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 = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 42/185 (22%), Positives = 82/185 (44%), Gaps = 36/185 (19%)
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 GDLNV 224
G+ N
Sbjct: 150 GNFNT 154
>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 = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 28/107 (26%), Positives = 54/107 (50%), Gaps = 11/107 (10%)
Query: 123 YQIWWSLADSKYAG-TALLVKKCFQPKKVSFSLEKTALKYEP--DGRVILAEFETFYLLN 179
++I + + S G + + +P+ VSF L+ EP + R+I A+ ++N
Sbjct: 49 HRIGYHVVFSGSKGRNGVAIASLEEPEDVSFGLDS-----EPKDEDRLIRAKIAGIDVIN 103
Query: 180 TYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSG--KPLIWCGDLNV 224
TY P G+K + +Q + +W +R+ ++ + +WCGD+NV
Sbjct: 104 TYVPQ-GFKIDSEKYQYKLQWLERLYHYLQKTVDFRSFAVWCGDMNV 149
>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 = 35.0 bits (79), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 35/188 (18%), Positives = 70/188 (37%), Gaps = 42/188 (22%)
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 DREGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYR-----FLDAFYPMLEAMKNEGRDI 144
Query: 217 IWCGDLNV 224
+ CGD N+
Sbjct: 145 VVCGDWNI 152
>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 = 0.081, 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|4B5H|A Chain A, Substate Bound Inactive Mutant Of Neisseria Ap
Endonuclease In Presence Of Metal Ions
Length = 259
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 34/188 (18%), Positives = 70/188 (37%), Gaps = 42/188 (22%)
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 DREGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYR-----FLDAFYPMLEAMKNEGRDI 144
Query: 217 IWCGDLNV 224
+ CG+ N+
Sbjct: 145 VVCGNWNI 152
>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 = 32.0 bits (71), Expect = 0.30, 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 = 32.0 bits (71), Expect = 0.31, 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 = 31.6 bits (70), Expect = 0.34, 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 = 1.9, 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
0.319 0.135 0.424
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,187,922
Number of Sequences: 62578
Number of extensions: 237700
Number of successful extensions: 540
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 519
Number of HSP's gapped (non-prelim): 22
length of query: 225
length of database: 14,973,337
effective HSP length: 95
effective length of query: 130
effective length of database: 9,028,427
effective search space: 1173695510
effective search space used: 1173695510
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: 50 (23.9 bits)