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= 019834
(335 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 = 118 bits (295), Expect = 6e-27, Method: Compositional matrix adjust.
Identities = 86/282 (30%), Positives = 145/282 (51%), Gaps = 40/282 (14%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQ-------ILMRALSSPPFKNYQI 94
LK +WN + L +K + +++ PD++ LQ L L P ++Q
Sbjct: 29 LKIASWNVDGLRAWIKK---KGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQY 85
Query: 95 WWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPN 153
W + +D + Y+G LL ++C P KVS+ + +++ +GRVI+AEF++F L+ Y PN
Sbjct: 86 WSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDE--EHDQEGRVIVAEFDSFVLVTAYVPN 141
Query: 154 NGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLN 212
G + R++WD+ ++F+ S KPL+ CGDLNV+HEEID+ +P+
Sbjct: 142 AG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKG------- 192
Query: 213 GYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYR 272
NK++ GFT ER+ FG +L+ L D++R L+ F W+ + +
Sbjct: 193 -----NKKN---AGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTF-WTYMMNARSK 243
Query: 273 GKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 314
R+DYF++S L + +++ + GSDHCP+
Sbjct: 244 NVGWRLDYFLLSHSLLPALCDSKIRSKAL------GSDHCPI 279
>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 = 117 bits (294), Expect = 7e-27, Method: Compositional matrix adjust.
Identities = 86/282 (30%), Positives = 145/282 (51%), Gaps = 40/282 (14%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQ-------ILMRALSSPPFKNYQI 94
LK +WN + L +K + +++ PD++ LQ L L P ++Q
Sbjct: 62 LKICSWNVDGLRAWIKK---KGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQY 118
Query: 95 WWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPN 153
W + +D + Y+G LL ++C P KVS+ + +++ +GRVI+AEF++F L+ Y PN
Sbjct: 119 WSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDE--EHDQEGRVIVAEFDSFVLVTAYVPN 174
Query: 154 NGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLN 212
G + R++WD+ ++F+ S KPL+ CGDLNV+HEEID+ +P+
Sbjct: 175 AG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKG------- 225
Query: 213 GYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYR 272
NK++ GFT ER+ FG +L+ L D++R L+ F W+ + +
Sbjct: 226 -----NKKN---AGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTF-WTYMMNARSK 276
Query: 273 GKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 314
R+DYF++S L + +++ + GSDHCP+
Sbjct: 277 NVGWRLDYFLLSHSLLPALCDSKIRSKAL------GSDHCPI 312
>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 = 117 bits (294), Expect = 7e-27, Method: Compositional matrix adjust.
Identities = 86/282 (30%), Positives = 145/282 (51%), Gaps = 40/282 (14%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQ-------ILMRALSSPPFKNYQI 94
LK +WN + L +K + +++ PD++ LQ L L P ++Q
Sbjct: 61 LKICSWNVDGLRAWIKK---KGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQY 117
Query: 95 WWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPN 153
W + +D + Y+G LL ++C P KVS+ + +++ +GRVI+AEF++F L+ Y PN
Sbjct: 118 WSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDE--EHDQEGRVIVAEFDSFVLVTAYVPN 173
Query: 154 NGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLN 212
G + R++WD+ ++F+ S KPL+ CGDLNV+HEEID+ +P+
Sbjct: 174 AG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKG------- 224
Query: 213 GYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYR 272
NK++ GFT ER+ FG +L+ L D++R L+ F W+ + +
Sbjct: 225 -----NKKN---AGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTF-WTYMMNARSK 275
Query: 273 GKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 314
R+DYF++S L + +++ + GSDHCP+
Sbjct: 276 NVGWRLDYFLLSHSLLPALCDSKIRSKAL------GSDHCPI 311
>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 = 117 bits (293), Expect = 8e-27, Method: Compositional matrix adjust.
Identities = 86/282 (30%), Positives = 145/282 (51%), Gaps = 40/282 (14%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQ-------ILMRALSSPPFKNYQI 94
LK +WN + L +K + +++ PD++ LQ L L P ++Q
Sbjct: 31 LKICSWNVDGLRAWIKK---KGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQY 87
Query: 95 WWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPN 153
W + +D + Y+G LL ++C P KVS+ + +++ +GRVI+AEF++F L+ Y PN
Sbjct: 88 WSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDE--EHDQEGRVIVAEFDSFVLVTAYVPN 143
Query: 154 NGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLN 212
G + R++WD+ ++F+ S KPL+ CGDLNV+HEEID+ +P+
Sbjct: 144 AG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKG------- 194
Query: 213 GYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYR 272
NK++ GFT ER+ FG +L+ L D++R L+ F W+ + +
Sbjct: 195 -----NKKN---AGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTF-WTYMMNARSK 245
Query: 273 GKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 314
R+DYF++S L + +++ + GSDHCP+
Sbjct: 246 NVGWRLDYFLLSHSLLPALCDSKIRSKAL------GSDHCPI 281
>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 = 117 bits (293), Expect = 8e-27, Method: Compositional matrix adjust.
Identities = 86/282 (30%), Positives = 145/282 (51%), Gaps = 40/282 (14%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQ-------ILMRALSSPPFKNYQI 94
LK +WN + L +K + +++ PD++ LQ L L P ++Q
Sbjct: 23 LKICSWNVDGLRAWIKK---KGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQY 79
Query: 95 WWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPN 153
W + +D + Y+G LL ++C P KVS+ + +++ +GRVI+AEF++F L+ Y PN
Sbjct: 80 WSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDE--EHDQEGRVIVAEFDSFVLVTAYVPN 135
Query: 154 NGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLN 212
G + R++WD+ ++F+ S KPL+ CGDLNV+HEEID+ +P+
Sbjct: 136 AG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKG------- 186
Query: 213 GYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYR 272
NK++ GFT ER+ FG +L+ L D++R L+ F W+ + +
Sbjct: 187 -----NKKN---AGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTF-WTYMMNARSK 237
Query: 273 GKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 314
R+DYF++S L + +++ + GSDHCP+
Sbjct: 238 NVGWRLDYFLLSHSLLPALCDSKIRSKAL------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 = 117 bits (293), Expect = 9e-27, Method: Compositional matrix adjust.
Identities = 86/282 (30%), Positives = 145/282 (51%), Gaps = 40/282 (14%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQ-------ILMRALSSPPFKNYQI 94
LK +WN + L +K + +++ PD++ LQ L L P ++Q
Sbjct: 20 LKICSWNVDGLRAWIKK---KGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQY 76
Query: 95 WWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPN 153
W + +D + Y+G LL ++C P KVS+ + +++ +GRVI+AEF++F L+ Y PN
Sbjct: 77 WSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDE--EHDQEGRVIVAEFDSFVLVTAYVPN 132
Query: 154 NGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLN 212
G + R++WD+ ++F+ S KPL+ CGDLNV+HEEID+ +P+
Sbjct: 133 AG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKG------- 183
Query: 213 GYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYR 272
NK++ GFT ER+ FG +L+ L D++R L+ F W+ + +
Sbjct: 184 -----NKKN---AGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTF-WTYMMNARSK 234
Query: 273 GKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 314
R+DYF++S L + +++ + GSDHCP+
Sbjct: 235 NVGWRLDYFLLSHSLLPALCDSKIRSKAL------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 = 103 bits (256), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 79/282 (28%), Positives = 135/282 (47%), Gaps = 41/282 (14%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQ-------ILMRALSSPPFKNYQI 94
+K +WN + L VK N +++ DPD++ LQ L +++ P ++
Sbjct: 27 MKITSWNVDGLRAWVKKNG---LDWVRKEDPDILCLQETKCAEKALPADITAMPEYPHKY 83
Query: 95 WWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPN 153
W D + Y+G A+L K +P V++ + K +++ +GRVI AEF F+L+ Y PN
Sbjct: 84 WAGSEDKEGYSGVAMLCKT--EPLNVTYGIGKE--EHDKEGRVITAEFPDFFLVTAYVPN 139
Query: 154 NGWKEEENSFQRRRKWDKRIQEFVLQCSG-KPLIWCGDLNVSHEEIDVSHPEFFAAAKLN 212
R+ WD + ++ KPL+ CGDLNV+H+EID+ +P
Sbjct: 140 A--SRGLVRLDYRKTWDVDFRAYLCGLDARKPLVLCGDLNVAHQEIDLKNP--------- 188
Query: 213 GYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYR 272
K + GFT ER+ F +L+ G D++R L+ ++ F W+ + +
Sbjct: 189 ------KGNRKNAGFTPEEREGFTQLLEAG-FTDSFRELYPDQAYAYTF-WTYMMNARSK 240
Query: 273 GKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 314
R+DYF++S L + +++ + GSDHCP+
Sbjct: 241 NVGWRLDYFVLSSALLPGLCDSKIRNTAM------GSDHCPI 276
>pdb|3G91|A Chain A, 1.2 Angstrom Structure Of The Exonuclease Iii Homologue
Mth0212
Length = 265
Score = 88.2 bits (217), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 75/280 (26%), Positives = 125/280 (44%), Gaps = 39/280 (13%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQILMRALSSPPFK-----NYQIWW 96
LK ++WN N L + F + PD++ LQ + A P K Y+ ++
Sbjct: 4 LKIISWNVNGLRAVHRKG---FLKWFMEEKPDILCLQEIKAAPEQLPRKLRHVEGYRSFF 60
Query: 97 SLADSK-YAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNG 155
+ A+ K Y+G A+ K + F +E+ ++ +GR+ +A+F+ F L N Y PN
Sbjct: 61 TPAERKGYSGVAMYTKVPPSSLREGFGVER----FDTEGRIQIADFDDFLLYNIYFPNGA 116
Query: 156 WKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGY 214
EE + + +D +++ + SG+ +I CGD N +H EID++ P
Sbjct: 117 MSEERLKY-KLEFYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARP----------- 164
Query: 215 VPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYRGK 274
KE+ GF ER ++ G +D +R + + WS + R
Sbjct: 165 ----KENSNVSGFLPVERAWIDKFIENG-YVDTFRMFNSDPGQYTW--WSYRTRARERNV 217
Query: 275 RMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 314
R+DYF V+EE K ++ + L GSDHCP+
Sbjct: 218 GWRLDYFFVNEEFKGKVKRSWI------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 = 87.4 bits (215), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 75/280 (26%), Positives = 125/280 (44%), Gaps = 39/280 (13%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQILMRALSSPPFK-----NYQIWW 96
LK ++WN N L + F + PD++ LQ + A P K Y+ ++
Sbjct: 4 LKIISWNVNGLRAVHRKG---FLKWFMEEKPDILCLQEIKAAPEQLPRKLRHVEGYRSFF 60
Query: 97 SLADSK-YAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNG 155
+ A+ K Y+G A+ K + F +E+ ++ +GR+ +A+F+ F L N Y PN
Sbjct: 61 TPAERKGYSGVAMYTKVPPSSLREGFGVER----FDTEGRIQIADFDDFLLYNIYFPNGK 116
Query: 156 WKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGY 214
EE + + +D +++ + SG+ +I CGD N +H EID++ P
Sbjct: 117 MSEERLKY-KLEFYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARP----------- 164
Query: 215 VPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYRGK 274
KE+ GF ER ++ G +D +R + + WS + R
Sbjct: 165 ----KENSNVSGFLPVERAWIDKFIENG-YVDTFRMFNSDPGQYTW--WSYRTRARERNV 217
Query: 275 RMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 314
R+DYF V+EE K ++ + L GSDHCP+
Sbjct: 218 GWRLDYFFVNEEFKGKVKRSWI------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 = 85.9 bits (211), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 74/280 (26%), Positives = 125/280 (44%), Gaps = 39/280 (13%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQILMRALSSPPFK-----NYQIWW 96
LK ++WN N L + F + PD++ LQ + A P K Y+ ++
Sbjct: 4 LKIISWNVNGLRAVHRKG---FLKWFMEEKPDILCLQEIKAAPEQLPRKLRHVEGYRSFF 60
Query: 97 SLADSK-YAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNG 155
+ A+ K Y+G A+ K + F +E+ ++ +GR+ +A+F+ F L N Y PN
Sbjct: 61 TPAERKGYSGVAMYTKVPPSSLREGFGVER----FDTEGRIQIADFDDFLLYNIYFPNGK 116
Query: 156 WKEEENSFQRRRKWDKRIQEFVLQC-SGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGY 214
EE + + +D +++ + SG+ +I CG+ N +H EID++ P
Sbjct: 117 MSEERLKY-KLEFYDAFLEDVNRERDSGRNVIICGNFNTAHREIDLARP----------- 164
Query: 215 VPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYRGK 274
KE+ GF ER ++ G +D +R + + WS + R
Sbjct: 165 ----KENSNVSGFLPVERAWIDKFIENG-YVDTFRMFNSDPGQYTW--WSYRTRARERNV 217
Query: 275 RMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 314
R+DYF V+EE K ++ + L GSDHCP+
Sbjct: 218 GWRLDYFFVNEEFKGKVKRSWI------LSDVMGSDHCPI 251
>pdb|2JC4|A Chain A, 3'-5' Exonuclease (Nexo) From Neisseria Meningitidis
Length = 256
Score = 70.1 bits (170), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 77/284 (27%), Positives = 120/284 (42%), Gaps = 45/284 (15%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQILMRALSSPPFKNYQI--W---W 96
+K TWN NSL +R+ P+ N + PD++ LQ L P Q+ W W
Sbjct: 1 MKITTWNVNSLNVRL----PQVQNLLADNPPDILVLQELKLDQDKFPAAALQMMGWHCVW 56
Query: 97 SLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGW 156
S Y G A++ + P+ V F L AL +P RVI A ++N Y NG
Sbjct: 57 S-GQKTYNGVAIVSRSV--PQDVHFGL--PALPDDPQRRVIAATVSGVRVINVYC-VNGE 110
Query: 157 KEEENSFQRRRKWDKRIQEFV---LQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNG 213
+ F+ + +W + EFV + GK L+ GD N++ + D P
Sbjct: 111 ALDSPKFKYKEQWFAALTEFVRDEMTRHGK-LVLLGDFNIAPADADCYDP---------- 159
Query: 214 YVPPNKEDWGQP-GFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYR 272
E W + + ER+ F +L G L D+ R +H E F + G +
Sbjct: 160 ------EKWHEKIHCSSVERQWFQNLLDLG-LTDSLRQVHPEGAFYTWFDYRGAMFQRKL 212
Query: 273 GKRMRIDYFIVSEELKDRI--IACEMQGHGIELEGFYGSDHCPV 314
G +RID+ +VS + + + +++ +E SDH PV
Sbjct: 213 G--LRIDHILVSPAMAAALKDVRVDLETRALE----RPSDHAPV 250
>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 = 60.1 bits (144), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 61/257 (23%), Positives = 114/257 (44%), Gaps = 29/257 (11%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQ-ILMRALSSPPFKNYQIWWSLAD 100
LK T+N NS+ R+ P ++ PD++ +Q + P ++I + +
Sbjct: 2 LKIATFNVNSIRSRLHIVIP----WLKENKPDILCMQETKVENRKFPEADFHRIGYHVVF 57
Query: 101 SKYAG-TALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEE 159
S G + + +P+ VSF L+ + + R+I A+ ++NTY P G+K +
Sbjct: 58 SGSKGRNGVAIASLEEPEDVSFGLDSEP---KDEDRLIRAKIAGIDVINTYVPQ-GFKID 113
Query: 160 ENSFQRRRKWDKRIQEFVLQCSG--KPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPP 217
+Q + +W +R+ ++ + +WCGD+NV+ E IDV P+ KL +V
Sbjct: 114 SEKYQYKLQWLERLYHYLQKTVDFRSFAVWCGDMNVAPEPIDVHSPD-----KLKNHV-- 166
Query: 218 NKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYRGKRMR 277
F R+ + IL+ G +D R +H + + + + + RG R
Sbjct: 167 --------XFHEDARRAYKKILELG-FVDVLRKIHPNERIYTFYDYRVKGAIE-RGLGWR 216
Query: 278 IDYFIVSEELKDRIIAC 294
D + + L +R + C
Sbjct: 217 GDAILATPPLAERCVDC 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 = 57.8 bits (138), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 61/280 (21%), Positives = 118/280 (42%), Gaps = 38/280 (13%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQIL------MRALSSPPFKNYQIW 95
LK ++ N N + K F +I D++ +Q L + A P + W
Sbjct: 2 LKIISANVNGIRSAYKKG---FYEYIAASGADIVCVQELKAQEADLSADMKNPHGMHGHW 58
Query: 96 WSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNG 155
Y+G A+ K+ ++ +E+ ++ +GR + +F +++ Y P+
Sbjct: 59 HCAEKRGYSGVAVYSKRKPDNVQIGMGIEE----FDREGRFVRCDFGRLSVISLYLPSGS 114
Query: 156 WKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYV 215
EE + R ++ G+ ++ CGD N++H+ ID+ + + K +G++
Sbjct: 115 SAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLKN--WKGNQKNSGFL 172
Query: 216 PPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKY-RGK 274
P ER+ G ++ + D +R L+ + G++W N Y +
Sbjct: 173 PE-------------EREWIGKVIHKLGWTDMWRTLYPDVP---GYTWWSNRGQAYAKDV 216
Query: 275 RMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 314
RIDY +V+ EL + ++ H + E F SDH P+
Sbjct: 217 GWRIDYQMVTPELAAKAVSA----HVYKDEKF--SDHAPL 250
>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 = 57.4 bits (137), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 76/328 (23%), Positives = 115/328 (35%), Gaps = 76/328 (23%)
Query: 43 KFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQ---ILMRALSSPPFKNYQIWWSLA 99
KF+TWN L +K N F+ PDV+ LQ + + + +S
Sbjct: 151 KFITWNVAGLRGLLKKNASALRAFMEAEKPDVLCLQETKLNVDEADANATLGVVDGYSFV 210
Query: 100 DS------KYAGTALLVKKCFQPKKVSFSLEKT-ALKYEPD-----GRVILAE------- 140
D Y+GT +K K + + AL EP G +L E
Sbjct: 211 DHPCAFKRGYSGTRTYMKNSTTVKGLHARCTRGFALPSEPQADAAAGSRVLVEGAGDEEG 270
Query: 141 --FETFY--------------LLNTYAPNNGWKEEENSFQRR------RKWDKRIQEFVL 178
TF L+NTY N+G ++ + R++ R+ +
Sbjct: 271 RVLTTFLSPDPDSASSSSRIALVNTYVANSGMGLTRLPYRVQSFDPSMREYLHRLDTWAT 330
Query: 179 QCSGKP-------------LIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQP 225
+ + P IW GDLNV+ + D + F K
Sbjct: 331 ENAAVPSAAAMGSGSSPHGFIWAGDLNVAERDYDRYYAGTF------------KSMQECS 378
Query: 226 GFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSE 285
GF ER F ++ +D +R L+ + F WS G+ R R+DYF+VS
Sbjct: 379 GFAPEERMSFRETMQRTNSVDIFRQLYPQAGPVYSF-WSQRINGRPRNLGWRLDYFVVSS 437
Query: 286 ELKDRIIACEMQGHGIELEGFYGSDHCP 313
L ++ C + GSDHCP
Sbjct: 438 RLASYVVDC------FPMPTVMGSDHCP 459
>pdb|4B5H|A Chain A, Substate Bound Inactive Mutant Of Neisseria Ap
Endonuclease In Presence Of Metal Ions
Length = 259
Score = 55.8 bits (133), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 60/280 (21%), Positives = 118/280 (42%), Gaps = 38/280 (13%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQIL------MRALSSPPFKNYQIW 95
LK ++ N N + K F +I D++ +Q L + A P + W
Sbjct: 2 LKIISANVNGIRSAYKKG---FYEYIAASGTDIVCVQELKAQEADLSADMKNPHGMHGHW 58
Query: 96 WSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNG 155
Y+G A+ K+ ++ +E+ ++ +GR + +F +++ Y P+
Sbjct: 59 HCAEKRGYSGVAVYSKRKPDNVQIGMGIEE----FDREGRFVRCDFGRLSVISLYLPSGS 114
Query: 156 WKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYV 215
EE + R ++ G+ ++ CG+ N++H+ ID+ + + K +G++
Sbjct: 115 SAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGNWNIAHQNIDLKN--WKGNQKNSGFL 172
Query: 216 PPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKY-RGK 274
P ER+ G ++ + D +R L+ + G++W N Y +
Sbjct: 173 PE-------------EREWIGKVIHKLGWTDMWRTLYPDVP---GYTWWSNRGQAYAKDV 216
Query: 275 RMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 314
RIDY +V+ EL + ++ H + E F SDH P+
Sbjct: 217 GWRIDYQMVTPELAAKAVSA----HVYKDEKF--SDHAPL 250
>pdb|1AKO|A Chain A, Exonuclease Iii From Escherichia Coli
Length = 268
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 70/290 (24%), Positives = 116/290 (40%), Gaps = 45/290 (15%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQIL-----MRALSSPPFKNYQIWW 96
+KFV++N N L R + + PDVI LQ M L Y +++
Sbjct: 1 MKFVSFNINGLRARPH----QLEAIVEKHQPDVIGLQETKVHDDMFPLEEVAKLGYNVFY 56
Query: 97 SLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFY----LLNTYAP 152
Y G ALL K+ + F + E R+I+AE + ++N Y P
Sbjct: 57 HGQKGHY-GVALLTKETPIAVRRGFPGDDE----EAQRRIIMAEIPSLLGNVTVINGYFP 111
Query: 153 NNGWKEEENSFQRRRKWDKRIQEFVLQCSGK---PLIWCGDLNVSHEEIDVSHPEFFAAA 209
++ F + ++ + +Q + L+ K P++ GD+N+S ++D+
Sbjct: 112 QGESRDHPIKFPAKAQFYQNLQNY-LETELKRDNPVLIMGDMNISPTDLDI--------- 161
Query: 210 KLNGYVPPNKEDW---GQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGN 266
G N++ W G+ F ER+ ++ G L+D +R H FSW
Sbjct: 162 ---GIGEENRKRWLRTGKCSFLPEEREWMDRLMSWG-LVDTFR--HANPQTADRFSWFDY 215
Query: 267 PIGKYRGKR-MRIDYFIVSEELKDRIIACEMQGHGIELEGFYG-SDHCPV 314
+ R +RID + S+ L + C G E+ SDH PV
Sbjct: 216 RSKGFDDNRGLRIDLLLASQPLAE---CCVETGIDYEIRSMEKPSDHAPV 262
>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 = 35.8 bits (81), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 66/287 (22%), Positives = 108/287 (37%), Gaps = 75/287 (26%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQ---ILMRALSSPPFKNY-QIWWS 97
+ +T N N L +K + +++I + DP V +Q + R K + +I+ +
Sbjct: 8 ITILTLNINGLNSAIKRH--RLASWIKSQDPSVCCIQETHLTCRDTHRLKIKGWRKIYQA 65
Query: 98 LADSKYAGTALLV--KKCFQPKKVSFSLEKTALKYEPDGRVILA----EFETFYLLNTYA 151
K AG A+LV K F+P K+ K + +G I+ + E +LN YA
Sbjct: 66 NGKQKKAGVAILVSDKTDFKPTKI---------KRDKEGHYIMVKGSIQQEELTILNIYA 116
Query: 152 PNNG----WKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFA 207
PN G K+ + QR LI GD N +D S
Sbjct: 117 PNTGAPRFIKQVLSDLQR-------------DLDSHTLIM-GDFNTPLSTLDRS-----T 157
Query: 208 AAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNP 267
K+N + + + L + LID YR LH + +++ P
Sbjct: 158 RQKVN-----------------KDTQELNSALHQADLIDIYRTLHPK---STEYTFFSAP 197
Query: 268 IGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 314
Y +ID+ + S+ L + C+ E+ Y SDH +
Sbjct: 198 HHTYS----KIDHIVGSKALLSK---CKR----TEIITNYLSDHSAI 233
>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 = 35.4 bits (80), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 34/124 (27%), Positives = 56/124 (45%), Gaps = 21/124 (16%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQ---ILMRALSSPPFKNY-QIWWS 97
+ +T N N L +K + +++I + DP V +Q + R K + +I+ +
Sbjct: 8 ITILTLNINGLNSAIKRH--RLASWIKSQDPSVCCIQETHLTCRDTHRLKIKGWRKIYQA 65
Query: 98 LADSKYAGTALLV--KKCFQPKKVSFSLEKTALKYEPDGRVILA----EFETFYLLNTYA 151
K AG A+LV K F+P K+ K + +G I+ + E +LN YA
Sbjct: 66 NGKQKKAGVAILVSDKTDFKPTKI---------KRDKEGHYIMVKGSIQQEELTILNIYA 116
Query: 152 PNNG 155
PN G
Sbjct: 117 PNTG 120
>pdb|2V0S|A Chain A, Crystal Structure Of A Hairpin Exchange Variant (Lr1) Of
The Targeting Line-1 Retrotransposon Endonuclease
Length = 236
Score = 35.4 bits (80), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 67/287 (23%), Positives = 108/287 (37%), Gaps = 77/287 (26%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQ---ILMRALSSPPFKNY-QIWWS 97
+ +T N N L +K + +++I + DP V +Q + R K + +I+ +
Sbjct: 8 ITILTLNINGLNSAIKRH--RLASWIKSQDPSVCCIQETHLTCRDTHRLKIKGWRKIYQA 65
Query: 98 LADSKYAGTALLV--KKCFQPKKVSFSLEKTALKYEPDGRVILA----EFETFYLLNTYA 151
K AG A+LV K F+P K+ K + +G I+ + E +LN YA
Sbjct: 66 NGKQKKAGVAILVSDKTDFKPTKI---------KRDKEGHYIMVKGSIQQEELTILNIYA 116
Query: 152 PNNG----WKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFA 207
PN G K+ + QR LI GD N +D S +
Sbjct: 117 PNTGAPRFIKQVLSDLQR-------------DLDSHTLIM-GDFNTPLSTLDRSTRQ--- 159
Query: 208 AAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNP 267
K+N + + + L + LID YR LH K + FS +
Sbjct: 160 --KVN-----------------KDTQELNSALHQADLIDIYRTLH-PKSTEYTFSTANG- 198
Query: 268 IGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 314
+ID+ + S+ L + C+ E+ Y SDH +
Sbjct: 199 -------ESKIDHIVGSKALLSK---CKR----TEIITNYLSDHSAI 231
>pdb|4FVA|A Chain A, Crystal Structure Of Truncated Caenorhabditis Elegans Tdp2
pdb|4FVA|B Chain B, Crystal Structure Of Truncated Caenorhabditis Elegans Tdp2
pdb|4FVA|C Chain C, Crystal Structure Of Truncated Caenorhabditis Elegans Tdp2
pdb|4FVA|D Chain D, Crystal Structure Of Truncated Caenorhabditis Elegans Tdp2
Length = 256
Score = 35.0 bits (79), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 43/169 (25%), Positives = 78/169 (46%), Gaps = 21/169 (12%)
Query: 42 LKFVTWNAN-----SLLLRVKNNWPEFSNFITTFDPDVIALQILMRALSSPPFKN---YQ 93
+ ++WN + SLL R+K ++ + +PD++ LQ ++ +P K Y+
Sbjct: 14 VSVMSWNIDGLDGRSLLTRMK----AVAHIVKNVNPDILFLQEVVDRDLAPIDKLQSLYK 69
Query: 94 IWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEP----DGRVILAEFETFYLLNT 149
I++S +Y TA+LV K F +K + + Y +G + + F LLNT
Sbjct: 70 IYYSNKGCQYY-TAILVSKMFDVEKHDVIHFQNSGMYRTLQILEGSI--GGLKVF-LLNT 125
Query: 150 YAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEI 198
+ + + Q DK ++E + Q G + + GDLN+ EE+
Sbjct: 126 HLESTREHRPQRCAQFGFCMDK-VREIIAQNPGALVFFGGDLNLRDEEV 173
>pdb|4F1R|A Chain A, Structure Analysis Of The Global Metabolic Regulator Crc
From Pseudomonas Aeruginos
Length = 293
Score = 35.0 bits (79), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 52/230 (22%), Positives = 93/230 (40%), Gaps = 35/230 (15%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQILMRA---LSSPPFK--NYQIWW 96
++ ++ N N + + +++ + DVI LQ + L P F+ Y ++
Sbjct: 35 MRIISVNVNGIQAAAERG---LLSWLQAQNADVICLQDTRASAFDLDDPSFQLDGYFLYA 91
Query: 97 SLADSKYAGTALLVKKCFQPKKVSFSLE-KTALKYEPDGRVILAEFETFYLLNTYAPNNG 155
A+ G L + QPK V L +TA +Y GR + A+F+ + P+
Sbjct: 92 CDAELPEQGGVALYSR-LQPKAVISGLGFETADRY---GRYLQADFDKVSIATLLLPSG- 146
Query: 156 WKEEENSFQRRRKWDKRIQEFVLQCSGK--PLIWCGDLNVSHEEIDVSHPEFFAAAKLNG 213
+ + S ++ K+ ++ + K I+CG L V+H+++DV +
Sbjct: 147 -QSGDESLNQKFKFMDDFTHYLSKQRRKRREYIYCGSLYVAHQKMDVKNW---------- 195
Query: 214 YVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSW 263
+E PGF ER + DA R + +E D FSW
Sbjct: 196 -----RECQQMPGFLAPERAWLDEVFGNLGYADALREVSREGDQ---FSW 237
>pdb|4GEW|A Chain A, Crystal Structure Of Tdp2 From C. Elegans
Length = 362
Score = 35.0 bits (79), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 43/172 (25%), Positives = 77/172 (44%), Gaps = 27/172 (15%)
Query: 42 LKFVTWNAN-----SLLLRVKNNWPEFSNFITTFDPDVIALQILMRALSSPPFKN---YQ 93
+ ++WN + SLL R+K ++ + +PD++ LQ ++ +P K Y+
Sbjct: 120 VSVMSWNIDGLDGRSLLTRMK----AVAHIVKNVNPDILFLQEVVDRDLAPIDKLQSLYK 175
Query: 94 IWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRV-ILAEFE------TFYL 146
I++S +Y TA+LV K F +K + ++ G L E +L
Sbjct: 176 IYYSNKGCQYY-TAILVSKMFDVEK------HDVIHFQNSGMYRTLQILEGSIGGLKVFL 228
Query: 147 LNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEI 198
LNT+ + + Q DK ++E + Q G + + GDLN+ EE+
Sbjct: 229 LNTHLESTREHRPQRCAQFGFCMDK-VREIIAQNPGALVFFGGDLNLRDEEV 279
>pdb|4F1I|A Chain A, Crystal Structure Of Semet Tdp2 From Caenorhabditis
Elegans
Length = 362
Score = 32.7 bits (73), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 41/163 (25%), Positives = 74/163 (45%), Gaps = 17/163 (10%)
Query: 46 TWNAN-----SLLLRVKNNWPEFSNFITTFDPDVIALQILMRALSSPPFKN---YQIWWS 97
+WN + SLL R K ++ + +PD++ LQ ++ +P K Y+I++S
Sbjct: 124 SWNIDGLDGRSLLTRXK----AVAHIVKNVNPDILFLQEVVDRDLAPIDKLQSLYKIYYS 179
Query: 98 LADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETF--YLLNTYAPNNG 155
+Y TA+LV K F +K + + Y +++ +LLNT+ +
Sbjct: 180 NKGCQYY-TAILVSKXFDVEKHDVIHFQNSGXYRT-LQILEGSIGGLKVFLLNTHLESTR 237
Query: 156 WKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEI 198
+ Q DK ++E + Q G + + GDLN+ EE+
Sbjct: 238 EHRPQRCAQFGFCXDK-VREIIAQNPGALVFFGGDLNLRDEEV 279
>pdb|3AEV|A Chain A, Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex From
Pyrococcus Horikoshii Ot3
Length = 275
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 29/52 (55%), Gaps = 3/52 (5%)
Query: 238 ILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKD 289
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 = 2.7, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 1/60 (1%)
Query: 247 AYRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGF 306
Y +K+K + + S I RGK + +YF + EE+KD++ + G G + F
Sbjct: 206 VYALYNKDKSLFGRYMMSDKVIEPVRGKLIP-NYFKIKEEVKDKVYGITISGSGPSIIAF 264
>pdb|3T6A|A Chain A, Structure Of The C-Terminal Domain Of Bcar3
pdb|3T6A|B Chain B, Structure Of The C-Terminal Domain Of Bcar3
pdb|3T6A|C Chain C, Structure Of The C-Terminal Domain Of Bcar3
pdb|3T6A|D Chain D, Structure Of The C-Terminal Domain Of Bcar3
Length = 333
Score = 29.3 bits (64), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 22/44 (50%)
Query: 73 DVIALQILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQP 116
D+ + LM+AL P + W+ +Y TA+L +K +P
Sbjct: 143 DLYSFSALMKALEMPQITRLEKTWTALRHQYTQTAILYEKQLKP 186
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
0.321 0.139 0.445
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,726,943
Number of Sequences: 62578
Number of extensions: 412007
Number of successful extensions: 777
Number of sequences better than 100.0: 27
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 730
Number of HSP's gapped (non-prelim): 28
length of query: 335
length of database: 14,973,337
effective HSP length: 99
effective length of query: 236
effective length of database: 8,778,115
effective search space: 2071635140
effective search space used: 2071635140
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: 52 (24.6 bits)