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= psy6130
(295 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 223 bits (568), Expect = 1e-58, Method: Compositional matrix adjust.
Identities = 122/234 (52%), Positives = 150/234 (64%), Gaps = 8/234 (3%)
Query: 65 NKLGEEPNFKIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFP 124
+K G N KI SWNV GLRA VKK GLD+++KED DI CLQETKC E LP ++ P
Sbjct: 19 SKDGRAANMKITSWNVDGLRAWVKKNGLDWVRKEDPDILCLQETKCAEKALPADIT-AMP 77
Query: 125 EY-KTYWLSSP-KAGYAGVGLYTKVKPNKVTYGLGTKNEH--YGRNCNSNIVNTFYIRKN 180
EY YW S K GY+GV + K +P VTYG+G K EH GR + + F +
Sbjct: 78 EYPHKYWAGSEDKEGYSGVAMLCKTEPLNVTYGIG-KEEHDKEGRVITAEFPDFFLVTAY 136
Query: 181 VPNAGAGLKTLDKRLEWDKLFHEHLVKLDAEKPVILIGDLNVSHKPIDLANPTTNTRSAG 240
VPNA GL LD R WD F +L LDA KP++L GDLNV+H+ IDL NP N ++AG
Sbjct: 137 VPNASRGLVRLDYRKTWDVDFRAYLCGLDARKPLVLCGDLNVAHQEIDLKNPKGNRKNAG 196
Query: 241 FTIEERDSFSSLLDKGFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTGC-TNYF 293
FT EER+ F+ LL+ GFTDSFR LYP + AYT+W+YM ARS+N G +YF
Sbjct: 197 FTPEEREGFTQLLEAGFTDSFRELYPDQAYAYTFWTYM-MNARSKNVGWRLDYF 249
>pdb|2O3H|A Chain A, Crystal Structure Of The Human C65a Ape
Length = 285
Score = 200 bits (508), Expect = 1e-51, Method: Compositional matrix adjust.
Identities = 110/237 (46%), Positives = 149/237 (62%), Gaps = 7/237 (2%)
Query: 62 NKKNKLGEEPNFKIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKM 121
K + G+ KIASWNV GLRA +KK+GLD++K+E DI CLQETKC E +LP E++
Sbjct: 18 QKTSPSGKPATLKIASWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQ- 76
Query: 122 KFPEYKTYWLSSP--KAGYAGVGLYTKVKPNKVTYGLG-TKNEHYGRNCNSNIVNTFYIR 178
+ P + S+P K GY+GVGL ++ P KV+YG+G +++ GR + + +
Sbjct: 77 ELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVT 136
Query: 179 KNVPNAGAGLKTLDKRLEWDKLFHEHLVKLDAEKPVILIGDLNVSHKPIDLANPTTNTRS 238
VPNAG GL L+ R WD+ F + L L + KP++L GDLNV+H+ IDL NP N ++
Sbjct: 137 AYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKN 196
Query: 239 AGFTIEERDSFSSLLDK-GFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTGC-TNYF 293
AGFT +ER F LL DSFRHLYP AYT+W+YM ARS+N G +YF
Sbjct: 197 AGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYM-MNARSKNVGWRLDYF 252
>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 = 198 bits (503), Expect = 3e-51, Method: Compositional matrix adjust.
Identities = 109/237 (45%), Positives = 148/237 (62%), Gaps = 7/237 (2%)
Query: 62 NKKNKLGEEPNFKIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKM 121
K + G+ KI SWNV GLRA +KK+GLD++K+E DI CLQETKC E +LP E++
Sbjct: 51 QKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQ- 109
Query: 122 KFPEYKTYWLSSP--KAGYAGVGLYTKVKPNKVTYGLG-TKNEHYGRNCNSNIVNTFYIR 178
+ P + S+P K GY+GVGL ++ P KV+YG+G +++ GR + + +
Sbjct: 110 ELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVT 169
Query: 179 KNVPNAGAGLKTLDKRLEWDKLFHEHLVKLDAEKPVILIGDLNVSHKPIDLANPTTNTRS 238
VPNAG GL L+ R WD+ F + L L + KP++L GDLNV+H+ IDL NP N ++
Sbjct: 170 AYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKN 229
Query: 239 AGFTIEERDSFSSLLDK-GFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTGC-TNYF 293
AGFT +ER F LL DSFRHLYP AYT+W+YM ARS+N G +YF
Sbjct: 230 AGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYM-MNARSKNVGWRLDYF 285
>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 = 198 bits (503), Expect = 4e-51, Method: Compositional matrix adjust.
Identities = 109/237 (45%), Positives = 148/237 (62%), Gaps = 7/237 (2%)
Query: 62 NKKNKLGEEPNFKIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKM 121
K + G+ KI SWNV GLRA +KK+GLD++K+E DI CLQETKC E +LP E++
Sbjct: 20 QKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQ- 78
Query: 122 KFPEYKTYWLSSP--KAGYAGVGLYTKVKPNKVTYGLG-TKNEHYGRNCNSNIVNTFYIR 178
+ P + S+P K GY+GVGL ++ P KV+YG+G +++ GR + + +
Sbjct: 79 ELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVT 138
Query: 179 KNVPNAGAGLKTLDKRLEWDKLFHEHLVKLDAEKPVILIGDLNVSHKPIDLANPTTNTRS 238
VPNAG GL L+ R WD+ F + L L + KP++L GDLNV+H+ IDL NP N ++
Sbjct: 139 AYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKN 198
Query: 239 AGFTIEERDSFSSLLDK-GFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTGC-TNYF 293
AGFT +ER F LL DSFRHLYP AYT+W+YM ARS+N G +YF
Sbjct: 199 AGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYM-MNARSKNVGWRLDYF 254
>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 = 198 bits (503), Expect = 4e-51, Method: Compositional matrix adjust.
Identities = 109/237 (45%), Positives = 149/237 (62%), Gaps = 7/237 (2%)
Query: 62 NKKNKLGEEPNFKIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKM 121
+K + G+ KI SWNV GLRA +KK+GLD++K+E DI CLQETKC E +LP E++
Sbjct: 9 HKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQ- 67
Query: 122 KFPEYKTYWLSSP--KAGYAGVGLYTKVKPNKVTYGLG-TKNEHYGRNCNSNIVNTFYIR 178
+ P + S+P K GY+GVGL ++ P KV+YG+G +++ GR + + +
Sbjct: 68 ELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVT 127
Query: 179 KNVPNAGAGLKTLDKRLEWDKLFHEHLVKLDAEKPVILIGDLNVSHKPIDLANPTTNTRS 238
VPNAG GL L+ R WD+ F + L L + KP++L GDLNV+H+ IDL NP N ++
Sbjct: 128 AYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKN 187
Query: 239 AGFTIEERDSFSSLLDK-GFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTGC-TNYF 293
AGFT +ER F LL DSFRHLYP AYT+W+YM ARS+N G +YF
Sbjct: 188 AGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYM-MNARSKNVGWRLDYF 243
>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 = 197 bits (502), Expect = 4e-51, Method: Compositional matrix adjust.
Identities = 109/237 (45%), Positives = 148/237 (62%), Gaps = 7/237 (2%)
Query: 62 NKKNKLGEEPNFKIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKM 121
K + G+ KI SWNV GLRA +KK+GLD++K+E DI CLQETKC E +LP E++
Sbjct: 50 QKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQ- 108
Query: 122 KFPEYKTYWLSSP--KAGYAGVGLYTKVKPNKVTYGLG-TKNEHYGRNCNSNIVNTFYIR 178
+ P + S+P K GY+GVGL ++ P KV+YG+G +++ GR + + +
Sbjct: 109 ELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVT 168
Query: 179 KNVPNAGAGLKTLDKRLEWDKLFHEHLVKLDAEKPVILIGDLNVSHKPIDLANPTTNTRS 238
VPNAG GL L+ R WD+ F + L L + KP++L GDLNV+H+ IDL NP N ++
Sbjct: 169 AYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKN 228
Query: 239 AGFTIEERDSFSSLLDK-GFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTGC-TNYF 293
AGFT +ER F LL DSFRHLYP AYT+W+YM ARS+N G +YF
Sbjct: 229 AGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYM-MNARSKNVGWRLDYF 284
>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 = 197 bits (502), Expect = 4e-51, Method: Compositional matrix adjust.
Identities = 109/237 (45%), Positives = 149/237 (62%), Gaps = 7/237 (2%)
Query: 62 NKKNKLGEEPNFKIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKM 121
+K + G+ KI SWNV GLRA +KK+GLD++K+E DI CLQETKC E +LP E++
Sbjct: 12 HKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQ- 70
Query: 122 KFPEYKTYWLSSP--KAGYAGVGLYTKVKPNKVTYGLG-TKNEHYGRNCNSNIVNTFYIR 178
+ P + S+P K GY+GVGL ++ P KV+YG+G +++ GR + + +
Sbjct: 71 ELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVT 130
Query: 179 KNVPNAGAGLKTLDKRLEWDKLFHEHLVKLDAEKPVILIGDLNVSHKPIDLANPTTNTRS 238
VPNAG GL L+ R WD+ F + L L + KP++L GDLNV+H+ IDL NP N ++
Sbjct: 131 AYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKN 190
Query: 239 AGFTIEERDSFSSLLDK-GFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTGC-TNYF 293
AGFT +ER F LL DSFRHLYP AYT+W+YM ARS+N G +YF
Sbjct: 191 AGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYM-MNARSKNVGWRLDYF 246
>pdb|3G91|A Chain A, 1.2 Angstrom Structure Of The Exonuclease Iii Homologue
Mth0212
Length = 265
Score = 130 bits (327), Expect = 9e-31, Method: Compositional matrix adjust.
Identities = 78/224 (34%), Positives = 121/224 (54%), Gaps = 6/224 (2%)
Query: 73 FKIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPEYKTYWLS 132
KI SWNV GLRA +K L + +E DI CLQE K QLP +++ Y++++
Sbjct: 4 LKIISWNVNGLRAVHRKGFLKWFMEEKPDILCLQEIKAAPEQLPRKLR-HVEGYRSFFTP 62
Query: 133 SPKAGYAGVGLYTKVKPNKVTYGLGTKN-EHYGRNCNSNIVNTFYIRKNVPNAGAGLKTL 191
+ + GY+GV +YTKV P+ + G G + + GR ++ + PN + L
Sbjct: 63 AERKGYSGVAMYTKVPPSSLREGFGVERFDTEGRIQIADFDDFLLYNIYFPNGAMSEERL 122
Query: 192 DKRLEWDKLFHEHLVK-LDAEKPVILIGDLNVSHKPIDLANPTTNTRSAGFTIEERDSFS 250
+LE+ F E + + D+ + VI+ GD N +H+ IDLA P N+ +GF ER
Sbjct: 123 KYKLEFYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARPKENSNVSGFLPVERAWID 182
Query: 251 SLLDKGFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTGC-TNYF 293
++ G+ D+FR ++ G YT+WSY ++ AR RN G +YF
Sbjct: 183 KFIENGYVDTFR-MFNSDPGQYTWWSYRTR-ARERNVGWRLDYF 224
>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 = 129 bits (324), Expect = 2e-30, Method: Compositional matrix adjust.
Identities = 78/224 (34%), Positives = 121/224 (54%), Gaps = 6/224 (2%)
Query: 73 FKIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPEYKTYWLS 132
KI SWNV GLRA +K L + +E DI CLQE K QLP +++ Y++++
Sbjct: 4 LKIISWNVNGLRAVHRKGFLKWFMEEKPDILCLQEIKAAPEQLPRKLR-HVEGYRSFFTP 62
Query: 133 SPKAGYAGVGLYTKVKPNKVTYGLGTKN-EHYGRNCNSNIVNTFYIRKNVPNAGAGLKTL 191
+ + GY+GV +YTKV P+ + G G + + GR ++ + PN + L
Sbjct: 63 AERKGYSGVAMYTKVPPSSLREGFGVERFDTEGRIQIADFDDFLLYNIYFPNGKMSEERL 122
Query: 192 DKRLEWDKLFHEHLVK-LDAEKPVILIGDLNVSHKPIDLANPTTNTRSAGFTIEERDSFS 250
+LE+ F E + + D+ + VI+ GD N +H+ IDLA P N+ +GF ER
Sbjct: 123 KYKLEFYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARPKENSNVSGFLPVERAWID 182
Query: 251 SLLDKGFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTGC-TNYF 293
++ G+ D+FR ++ G YT+WSY ++ AR RN G +YF
Sbjct: 183 KFIENGYVDTFR-MFNSDPGQYTWWSYRTR-ARERNVGWRLDYF 224
>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 = 127 bits (319), Expect = 8e-30, Method: Compositional matrix adjust.
Identities = 77/224 (34%), Positives = 121/224 (54%), Gaps = 6/224 (2%)
Query: 73 FKIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPEYKTYWLS 132
KI SWNV GLRA +K L + +E DI CLQE K QLP +++ Y++++
Sbjct: 4 LKIISWNVNGLRAVHRKGFLKWFMEEKPDILCLQEIKAAPEQLPRKLR-HVEGYRSFFTP 62
Query: 133 SPKAGYAGVGLYTKVKPNKVTYGLGTKN-EHYGRNCNSNIVNTFYIRKNVPNAGAGLKTL 191
+ + GY+GV +YTKV P+ + G G + + GR ++ + PN + L
Sbjct: 63 AERKGYSGVAMYTKVPPSSLREGFGVERFDTEGRIQIADFDDFLLYNIYFPNGKMSEERL 122
Query: 192 DKRLEWDKLFHEHLVK-LDAEKPVILIGDLNVSHKPIDLANPTTNTRSAGFTIEERDSFS 250
+LE+ F E + + D+ + VI+ G+ N +H+ IDLA P N+ +GF ER
Sbjct: 123 KYKLEFYDAFLEDVNRERDSGRNVIICGNFNTAHREIDLARPKENSNVSGFLPVERAWID 182
Query: 251 SLLDKGFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTGC-TNYF 293
++ G+ D+FR ++ G YT+WSY ++ AR RN G +YF
Sbjct: 183 KFIENGYVDTFR-MFNSDPGQYTWWSYRTR-ARERNVGWRLDYF 224
>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 = 108 bits (271), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 70/208 (33%), Positives = 109/208 (52%), Gaps = 7/208 (3%)
Query: 73 FKIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPE-YKTYWL 131
KI S NV G+R+ KK +YI ADI C+QE K E L + MK P +W
Sbjct: 2 LKIISANVNGIRSAYKKGFYEYIAASGADIVCVQELKAQEADLSAD--MKNPHGMHGHWH 59
Query: 132 SSPKAGYAGVGLYTKVKPNKVTYGLGTKN-EHYGRNCNSNIVNTFYIRKNVPNAGAGLKT 190
+ K GY+GV +Y+K KP+ V G+G + + GR + I +P+ + +
Sbjct: 60 CAEKRGYSGVAVYSKRKPDNVQIGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSSAEER 119
Query: 191 LDKRLEWDKLFHEHLVKLDAE-KPVILIGDLNVSHKPIDLANPTTNTRSAGFTIEERDSF 249
+ + F+ L + E + +++ GD N++H+ IDL N N +++GF EER+
Sbjct: 120 QQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLKNWKGNQKNSGFLPEEREWI 179
Query: 250 SSLLDK-GFTDSFRHLYPKRTGAYTYWS 276
++ K G+TD +R LYP G YT+WS
Sbjct: 180 GKVIHKLGWTDMWRTLYPDVPG-YTWWS 206
>pdb|4B5H|A Chain A, Substate Bound Inactive Mutant Of Neisseria Ap
Endonuclease In Presence Of Metal Ions
Length = 259
Score = 105 bits (261), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 68/208 (32%), Positives = 108/208 (51%), Gaps = 7/208 (3%)
Query: 73 FKIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPE-YKTYWL 131
KI S NV G+R+ KK +YI DI C+QE K E L + MK P +W
Sbjct: 2 LKIISANVNGIRSAYKKGFYEYIAASGTDIVCVQELKAQEADLSAD--MKNPHGMHGHWH 59
Query: 132 SSPKAGYAGVGLYTKVKPNKVTYGLGTKN-EHYGRNCNSNIVNTFYIRKNVPNAGAGLKT 190
+ K GY+GV +Y+K KP+ V G+G + + GR + I +P+ + +
Sbjct: 60 CAEKRGYSGVAVYSKRKPDNVQIGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSSAEER 119
Query: 191 LDKRLEWDKLFHEHLVKLDAE-KPVILIGDLNVSHKPIDLANPTTNTRSAGFTIEERDSF 249
+ + F+ L + E + +++ G+ N++H+ IDL N N +++GF EER+
Sbjct: 120 QQVKYRFLDAFYPMLEAMKNEGRDIVVCGNWNIAHQNIDLKNWKGNQKNSGFLPEEREWI 179
Query: 250 SSLLDK-GFTDSFRHLYPKRTGAYTYWS 276
++ K G+TD +R LYP G YT+WS
Sbjct: 180 GKVIHKLGWTDMWRTLYPDVPG-YTWWS 206
>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 = 81.6 bits (200), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 59/221 (26%), Positives = 104/221 (47%), Gaps = 13/221 (5%)
Query: 73 FKIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPEYKTYWLS 132
KIA++NV +R+ + + ++K+ DI C+QETK + P + F + +
Sbjct: 2 LKIATFNVNSIRSRLHI-VIPWLKENKPDILCMQETKVENRKFP---EADFHRIGYHVVF 57
Query: 133 SPKAGYAGVGLYTKVKPNKVTYGLGTKNEHYGRNCNSNIVNTFYIRKNVPNAGAGLKTLD 192
S G GV + + +P V++GL ++ + R + I I VP G K
Sbjct: 58 SGSKGRNGVAIASLEEPEDVSFGLDSEPKDEDRLIRAKIAGIDVINTYVPQ---GFKIDS 114
Query: 193 KR----LEW-DKLFHEHLVKLDAEKPVILIGDLNVSHKPIDLANPTTNTRSAGFTIEERD 247
++ L+W ++L+H +D + GD+NV+ +PID+ +P F + R
Sbjct: 115 EKYQYKLQWLERLYHYLQKTVDFRSFAVWCGDMNVAPEPIDVHSPDKLKNHVXFHEDARR 174
Query: 248 SFSSLLDKGFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTG 288
++ +L+ GF D R ++P YT++ Y K A R G
Sbjct: 175 AYKKILELGFVDVLRKIHPNER-IYTFYDYRVKGAIERGLG 214
>pdb|4F1R|A Chain A, Structure Analysis Of The Global Metabolic Regulator Crc
From Pseudomonas Aeruginos
Length = 293
Score = 73.9 bits (180), Expect = 9e-14, Method: Compositional matrix adjust.
Identities = 55/219 (25%), Positives = 103/219 (47%), Gaps = 6/219 (2%)
Query: 73 FKIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPEYKTYWLS 132
+I S NV G++A ++ L +++ ++AD+ CLQ+T+ L + + Y Y
Sbjct: 35 MRIISVNVNGIQAAAERGLLSWLQAQNADVICLQDTRASAFDL-DDPSFQLDGYFLYACD 93
Query: 133 SPKAGYAGVGLYTKVKPNKVTYGLGTKN-EHYGRNCNSNIVNTFYIRKNVPNAGAGLKTL 191
+ GV LY++++P V GLG + + YGR ++ +P+ +G ++L
Sbjct: 94 AELPEQGGVALYSRLQPKAVISGLGFETADRYGRYLQADFDKVSIATLLLPSGQSGDESL 153
Query: 192 DKRLEWDKLFHEHLVKLDAE-KPVILIGDLNVSHKPIDLANPTTNTRSAGFTIEERDSFS 250
+++ ++ F +L K + + I G L V+H+ +D+ N + GF ER
Sbjct: 154 NQKFKFMDDFTHYLSKQRRKRREYIYCGSLYVAHQKMDVKNWRECQQMPGFLAPERAWLD 213
Query: 251 SLL-DKGFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTG 288
+ + G+ D+ R + R G W S+ A N G
Sbjct: 214 EVFGNLGYADALREV--SREGDQFSWWPDSEQAEMLNLG 250
>pdb|1AKO|A Chain A, Exonuclease Iii From Escherichia Coli
Length = 268
Score = 72.8 bits (177), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 62/232 (26%), Positives = 97/232 (41%), Gaps = 38/232 (16%)
Query: 73 FKIASWNVAGLRACVKKEGLDYI-KKEDADIFCLQETKCHETQLPPEVKMKFPEYKTYWL 131
K S+N+ GLRA + L+ I +K D+ LQETK H+ P E K Y ++
Sbjct: 1 MKFVSFNINGLRA--RPHQLEAIVEKHQPDVIGLQETKVHDDMFPLEEVAKL-GYNVFYH 57
Query: 132 SSPKAGYAGVGLYTKVKPNKVTYGLGTKNEHYGRNC----------NSNIVNTFYIRKN- 180
+ G+ GV L TK P V G +E R N ++N ++ +
Sbjct: 58 G--QKGHYGVALLTKETPIAVRRGFPGDDEEAQRRIIMAEIPSLLGNVTVINGYFPQGES 115
Query: 181 ------VPNAGAGLKTLDKRLEWDKLFHEHLVKLDAEKPVILIGDLNVSHKPIDLANPTT 234
P + L LE +L + PV+++GD+N+S +D+
Sbjct: 116 RDHPIKFPAKAQFYQNLQNYLE---------TELKRDNPVLIMGDMNISPTDLDIGIGEE 166
Query: 235 N------TRSAGFTIEERDSFSSLLDKGFTDSFRHLYPKRTGAYTYWSYMSK 280
N T F EER+ L+ G D+FRH P+ ++++ Y SK
Sbjct: 167 NRKRWLRTGKCSFLPEEREWMDRLMSWGLVDTFRHANPQTADRFSWFDYRSK 218
>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 = 62.8 bits (151), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 72/280 (25%), Positives = 107/280 (38%), Gaps = 66/280 (23%)
Query: 73 FKIASWNVAGLRACVKKEG---LDYIKKEDADIFCLQETKCHETQLPPEVKMKFPEYKTY 129
+K +WNVAGLR +KK +++ E D+ CLQETK + + + + ++
Sbjct: 150 YKFITWNVAGLRGLLKKNASALRAFMEAEKPDVLCLQETKLNVDEADANATLGVVDGYSF 209
Query: 130 WLSSP---KAGYAGVGLYTKVKPN------KVTYGLGTKNEHYGRNCNSN---------- 170
+ P K GY+G Y K + T G +E +
Sbjct: 210 -VDHPCAFKRGYSGTRTYMKNSTTVKGLHARCTRGFALPSEPQADAAAGSRVLVEGAGDE 268
Query: 171 ---IVNTFY---------------IRKNVPNAGAGLKTLDKRLE-WDKLFHEHLVKLD-- 209
++ TF + V N+G GL L R++ +D E+L +LD
Sbjct: 269 EGRVLTTFLSPDPDSASSSSRIALVNTYVANSGMGLTRLPYRVQSFDPSMREYLHRLDTW 328
Query: 210 ----AEKP-------------VILIGDLNVSHKPIDLANPTT---NTRSAGFTIEERDSF 249
A P I GDLNV+ + D T +GF EER SF
Sbjct: 329 ATENAAVPSAAAMGSGSSPHGFIWAGDLNVAERDYDRYYAGTFKSMQECSGFAPEERMSF 388
Query: 250 SSLLDK-GFTDSFRHLYPKRTGAYTYWSYMSKTARSRNTG 288
+ + D FR LYP+ Y++WS R RN G
Sbjct: 389 RETMQRTNSVDIFRQLYPQAGPVYSFWS-QRINGRPRNLG 427
>pdb|2JC4|A Chain A, 3'-5' Exonuclease (Nexo) From Neisseria Meningitidis
Length = 256
Score = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 49/206 (23%), Positives = 86/206 (41%), Gaps = 9/206 (4%)
Query: 73 FKIASWNVAGLRACVKKEGLDYIKKEDADIFCLQETKCHETQLPPEVKMKFPEYKTYWLS 132
KI +WNV L + + + + DI LQE K + + P ++ + W
Sbjct: 1 MKITTWNVNSLNVRLPQVQ-NLLADNPPDILVLQELKLDQDKFP-AAALQMMGWHCVW-- 56
Query: 133 SPKAGYAGVGLYTKVKPNKVTYGLGTKNEHYGRNCNSNIVNTFYIRKNVPNAGAGLKT-- 190
S + Y GV + ++ P V +GL + R + V+ + G L +
Sbjct: 57 SGQKTYNGVAIVSRSVPQDVHFGLPALPDDPQRRVIAATVSGVRVINVYCVNGEALDSPK 116
Query: 191 LDKRLEWDKLFHEHLV-KLDAEKPVILIGDLNVSHKPIDLANPTTNTRSAGFTIEERDSF 249
+ +W E + ++ ++L+GD N++ D +P + ER F
Sbjct: 117 FKYKEQWFAALTEFVRDEMTRHGKLVLLGDFNIAPADADCYDPEKWHEKIHCSSVERQWF 176
Query: 250 SSLLDKGFTDSFRHLYPKRTGAYTYW 275
+LLD G TDS R ++P+ GA+ W
Sbjct: 177 QNLLDLGLTDSLRQVHPE--GAFYTW 200
>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 = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 56/222 (25%), Positives = 95/222 (42%), Gaps = 42/222 (18%)
Query: 68 GEEPNFKIASWNVAGLRACVKKEGL-DYIKKEDADIFCLQETK--CHETQLPPEVKMKFP 124
G + I + N+ GL + +K+ L +IK +D + C+QET C +T ++K
Sbjct: 3 GSNSHITILTLNINGLNSAIKRHRLASWIKSQDPSVCCIQETHLTCRDTH-----RLKIK 57
Query: 125 EYKTYWLSSPKAGYAGVGLY----TKVKPNKVTYGLGTKNEHYGRNCNS------NIVNT 174
++ + ++ K AGV + T KP K+ K HY S I+N
Sbjct: 58 GWRKIYQANGKQKKAGVAILVSDKTDFKPTKIKRD---KEGHYIMVKGSIQQEELTILNI 114
Query: 175 FYIRKNVPNAGAGLKTLDKRLEWDKLFHEHLVKLDAEKPVILIGDLNVSHKPIDLANPTT 234
+ PN GA K++ D ++ D + +++GD N P+ + +T
Sbjct: 115 Y-----APNTGA--PRFIKQVLSD-------LQRDLDSHTLIMGDFNT---PLSTLDRST 157
Query: 235 NTRSAGFTIEERDSFSSLLDKGFTDSFRHLYPKRTGAYTYWS 276
+ T E S+L D +R L+PK T YT++S
Sbjct: 158 RQKVNKDTQELN---SALHQADLIDIYRTLHPKST-EYTFFS 195
>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 = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 56/220 (25%), Positives = 93/220 (42%), Gaps = 42/220 (19%)
Query: 68 GEEPNFKIASWNVAGLRACVKKEGL-DYIKKEDADIFCLQETK--CHETQLPPEVKMKFP 124
G + I + N+ GL + +K+ L +IK +D + C+QET C +T ++K
Sbjct: 3 GSNSHITILTLNINGLNSAIKRHRLASWIKSQDPSVCCIQETHLTCRDTH-----RLKIK 57
Query: 125 EYKTYWLSSPKAGYAGVGLY----TKVKPNKVTYGLGTKNEHYGRNCNS------NIVNT 174
++ + ++ K AGV + T KP K+ K HY S I+N
Sbjct: 58 GWRKIYQANGKQKKAGVAILVSDKTDFKPTKIKRD---KEGHYIMVKGSIQQEELTILNI 114
Query: 175 FYIRKNVPNAGAGLKTLDKRLEWDKLFHEHLVKLDAEKPVILIGDLNVSHKPIDLANPTT 234
+ PN GA K++ D ++ D + +++GD N P+ + +T
Sbjct: 115 Y-----APNTGA--PRFIKQVLSD-------LQRDLDSHTLIMGDFNT---PLSTLDRST 157
Query: 235 NTRSAGFTIEERDSFSSLLDKGFTDSFRHLYPKRTGAYTY 274
+ T E S+L D +R L+PK T YTY
Sbjct: 158 RQKVNKDTQELN---SALHQADLIDIYRTLHPKST-EYTY 193
>pdb|2V0S|A Chain A, Crystal Structure Of A Hairpin Exchange Variant (Lr1) Of
The Targeting Line-1 Retrotransposon Endonuclease
Length = 236
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 55/220 (25%), Positives = 93/220 (42%), Gaps = 42/220 (19%)
Query: 68 GEEPNFKIASWNVAGLRACVKKEGL-DYIKKEDADIFCLQETK--CHETQLPPEVKMKFP 124
G + I + N+ GL + +K+ L +IK +D + C+QET C +T ++K
Sbjct: 3 GSNSHITILTLNINGLNSAIKRHRLASWIKSQDPSVCCIQETHLTCRDTH-----RLKIK 57
Query: 125 EYKTYWLSSPKAGYAGVGLY----TKVKPNKVTYGLGTKNEHYGRNCNS------NIVNT 174
++ + ++ K AGV + T KP K+ K HY S I+N
Sbjct: 58 GWRKIYQANGKQKKAGVAILVSDKTDFKPTKIKRD---KEGHYIMVKGSIQQEELTILNI 114
Query: 175 FYIRKNVPNAGAGLKTLDKRLEWDKLFHEHLVKLDAEKPVILIGDLNVSHKPIDLANPTT 234
+ PN GA K++ D ++ D + +++GD N P+ + +T
Sbjct: 115 Y-----APNTGA--PRFIKQVLSD-------LQRDLDSHTLIMGDFNT---PLSTLDRST 157
Query: 235 NTRSAGFTIEERDSFSSLLDKGFTDSFRHLYPKRTGAYTY 274
+ T E S+L D +R L+PK T YT+
Sbjct: 158 RQKVNKDTQELN---SALHQADLIDIYRTLHPKST-EYTF 193
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
0.314 0.133 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,778,399
Number of Sequences: 62578
Number of extensions: 384394
Number of successful extensions: 715
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 658
Number of HSP's gapped (non-prelim): 24
length of query: 295
length of database: 14,973,337
effective HSP length: 98
effective length of query: 197
effective length of database: 8,840,693
effective search space: 1741616521
effective search space used: 1741616521
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (24.3 bits)