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= 018111
(360 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 = 116 bits (291), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 89/304 (29%), Positives = 146/304 (48%), Gaps = 59/304 (19%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
LK +WN + L +K + +++ PD++ LQE + P QEL
Sbjct: 29 LKIASWNVDGLRAWIKK---KGLDWVKEEAPDILCLQETK---CSENKLPAELQEL---- 78
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSL----EK 156
P ++Q W + +D + Y+G LL ++C P KVS+ +
Sbjct: 79 -----------------PGLSHQYWSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDEEHD 119
Query: 157 TDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWCGD 215
+GRVI+AEF++F L+ Y PN G + R++WD+ ++F+ S KPL+ CGD
Sbjct: 120 QEGRVIVAEFDSFVLVTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGD 177
Query: 216 LNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRF 275
LNV+HEEID+ +P+ NK++ GFT ER+ FG +L+ L D++R
Sbjct: 178 LNVAHEEIDLRNPKG------------NKKN---AGFTPQERQGFGELLQAVPLADSFRH 222
Query: 276 LHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSD 335
L+ F W+ + + R+DYF++S L + +++ + GSD
Sbjct: 223 LYPNTPYAYTF-WTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKAL------GSD 275
Query: 336 HCPV 339
HCP+
Sbjct: 276 HCPI 279
>pdb|1BIX|A Chain A, The Crystal Structure Of The Human Dna Repair Endonuclease
Hap1 Suggests The Recognition Of Extra-Helical
Deoxyribose At Dna Abasic Sites
Length = 287
Score = 116 bits (290), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 89/304 (29%), Positives = 146/304 (48%), Gaps = 59/304 (19%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
LK +WN + L +K + +++ PD++ LQE + P QEL
Sbjct: 31 LKICSWNVDGLRAWIKK---KGLDWVKEEAPDILCLQETK---CSENKLPAELQEL---- 80
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSL----EK 156
P ++Q W + +D + Y+G LL ++C P KVS+ +
Sbjct: 81 -----------------PGLSHQYWSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDEEHD 121
Query: 157 TDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWCGD 215
+GRVI+AEF++F L+ Y PN G + R++WD+ ++F+ S KPL+ CGD
Sbjct: 122 QEGRVIVAEFDSFVLVTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGD 179
Query: 216 LNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRF 275
LNV+HEEID+ +P+ NK++ GFT ER+ FG +L+ L D++R
Sbjct: 180 LNVAHEEIDLRNPKG------------NKKN---AGFTPQERQGFGELLQAVPLADSFRH 224
Query: 276 LHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSD 335
L+ F W+ + + R+DYF++S L + +++ + GSD
Sbjct: 225 LYPNTPYAYTF-WTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKAL------GSD 277
Query: 336 HCPV 339
HCP+
Sbjct: 278 HCPI 281
>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 = 115 bits (289), Expect = 3e-26, Method: Compositional matrix adjust.
Identities = 89/304 (29%), Positives = 146/304 (48%), Gaps = 59/304 (19%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
LK +WN + L +K + +++ PD++ LQE + P QEL
Sbjct: 62 LKICSWNVDGLRAWIKK---KGLDWVKEEAPDILCLQETK---CSENKLPAELQEL---- 111
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSL----EK 156
P ++Q W + +D + Y+G LL ++C P KVS+ +
Sbjct: 112 -----------------PGLSHQYWSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDEEHD 152
Query: 157 TDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWCGD 215
+GRVI+AEF++F L+ Y PN G + R++WD+ ++F+ S KPL+ CGD
Sbjct: 153 QEGRVIVAEFDSFVLVTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGD 210
Query: 216 LNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRF 275
LNV+HEEID+ +P+ NK++ GFT ER+ FG +L+ L D++R
Sbjct: 211 LNVAHEEIDLRNPKG------------NKKN---AGFTPQERQGFGELLQAVPLADSFRH 255
Query: 276 LHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSD 335
L+ F W+ + + R+DYF++S L + +++ + GSD
Sbjct: 256 LYPNTPYAYTF-WTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKAL------GSD 308
Query: 336 HCPV 339
HCP+
Sbjct: 309 HCPI 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 = 115 bits (289), Expect = 3e-26, Method: Compositional matrix adjust.
Identities = 89/304 (29%), Positives = 146/304 (48%), Gaps = 59/304 (19%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
LK +WN + L +K + +++ PD++ LQE + P QEL
Sbjct: 61 LKICSWNVDGLRAWIKK---KGLDWVKEEAPDILCLQETK---CSENKLPAELQEL---- 110
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSL----EK 156
P ++Q W + +D + Y+G LL ++C P KVS+ +
Sbjct: 111 -----------------PGLSHQYWSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDEEHD 151
Query: 157 TDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWCGD 215
+GRVI+AEF++F L+ Y PN G + R++WD+ ++F+ S KPL+ CGD
Sbjct: 152 QEGRVIVAEFDSFVLVTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGD 209
Query: 216 LNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRF 275
LNV+HEEID+ +P+ NK++ GFT ER+ FG +L+ L D++R
Sbjct: 210 LNVAHEEIDLRNPKG------------NKKN---AGFTPQERQGFGELLQAVPLADSFRH 254
Query: 276 LHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSD 335
L+ F W+ + + R+DYF++S L + +++ + GSD
Sbjct: 255 LYPNTPYAYTF-WTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKAL------GSD 307
Query: 336 HCPV 339
HCP+
Sbjct: 308 HCPI 311
>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 = 115 bits (289), Expect = 3e-26, Method: Compositional matrix adjust.
Identities = 89/304 (29%), Positives = 146/304 (48%), Gaps = 59/304 (19%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
LK +WN + L +K + +++ PD++ LQE + P QEL
Sbjct: 23 LKICSWNVDGLRAWIKK---KGLDWVKEEAPDILCLQETK---CSENKLPAELQEL---- 72
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSL----EK 156
P ++Q W + +D + Y+G LL ++C P KVS+ +
Sbjct: 73 -----------------PGLSHQYWSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDEEHD 113
Query: 157 TDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWCGD 215
+GRVI+AEF++F L+ Y PN G + R++WD+ ++F+ S KPL+ CGD
Sbjct: 114 QEGRVIVAEFDSFVLVTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGD 171
Query: 216 LNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRF 275
LNV+HEEID+ +P+ NK++ GFT ER+ FG +L+ L D++R
Sbjct: 172 LNVAHEEIDLRNPKG------------NKKN---AGFTPQERQGFGELLQAVPLADSFRH 216
Query: 276 LHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSD 335
L+ F W+ + + R+DYF++S L + +++ + GSD
Sbjct: 217 LYPNTPYAYTF-WTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKAL------GSD 269
Query: 336 HCPV 339
HCP+
Sbjct: 270 HCPI 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 = 115 bits (289), Expect = 3e-26, Method: Compositional matrix adjust.
Identities = 89/304 (29%), Positives = 146/304 (48%), Gaps = 59/304 (19%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
LK +WN + L +K + +++ PD++ LQE + P QEL
Sbjct: 20 LKICSWNVDGLRAWIKK---KGLDWVKEEAPDILCLQETK---CSENKLPAELQEL---- 69
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSL----EK 156
P ++Q W + +D + Y+G LL ++C P KVS+ +
Sbjct: 70 -----------------PGLSHQYWSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDEEHD 110
Query: 157 TDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWCGD 215
+GRVI+AEF++F L+ Y PN G + R++WD+ ++F+ S KPL+ CGD
Sbjct: 111 QEGRVIVAEFDSFVLVTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGD 168
Query: 216 LNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRF 275
LNV+HEEID+ +P+ NK++ GFT ER+ FG +L+ L D++R
Sbjct: 169 LNVAHEEIDLRNPK------------GNKKN---AGFTPQERQGFGELLQAVPLADSFRH 213
Query: 276 LHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSD 335
L+ F W+ + + R+DYF++S L + +++ + GSD
Sbjct: 214 LYPNTPYAYTF-WTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKAL------GSD 266
Query: 336 HCPV 339
HCP+
Sbjct: 267 HCPI 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 = 99.4 bits (246), Expect = 3e-21, Method: Compositional matrix adjust.
Identities = 83/305 (27%), Positives = 138/305 (45%), Gaps = 62/305 (20%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
+K +WN + L VK N +++ DPD++ LQE + K P +
Sbjct: 27 MKITSWNVDGLRAWVKKNG---LDWVRKEDPDILCLQETK---CAEKALPAD-------- 72
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSK--YAGTALLVKKCFQPKKVSFSLEK--- 156
+ A+ P K +W+ ++ K Y+G A+L K +P V++ + K
Sbjct: 73 ----------ITAMPEYPHK----YWAGSEDKEGYSGVAMLCKT--EPLNVTYGIGKEEH 116
Query: 157 -TDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSG-KPLIWCG 214
+GRVI AEF F+L+ Y PN R+ WD + ++ KPL+ CG
Sbjct: 117 DKEGRVITAEFPDFFLVTAYVPNA--SRGLVRLDYRKTWDVDFRAYLCGLDARKPLVLCG 174
Query: 215 DLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYR 274
DLNV+H+EID+ +P K + GFT ER+ F +L+ G D++R
Sbjct: 175 DLNVAHQEIDLKNP---------------KGNRKNAGFTPEEREGFTQLLEAG-FTDSFR 218
Query: 275 FLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGS 334
L+ ++ F W+ + + R+DYF++S L + +++ + GS
Sbjct: 219 ELYPDQAYAYTF-WTYMMNARSKNVGWRLDYFVLSSALLPGLCDSKIRNTAM------GS 271
Query: 335 DHCPV 339
DHCP+
Sbjct: 272 DHCPI 276
>pdb|3G91|A Chain A, 1.2 Angstrom Structure Of The Exonuclease Iii Homologue
Mth0212
Length = 265
Score = 84.3 bits (207), Expect = 8e-17, Method: Compositional matrix adjust.
Identities = 76/302 (25%), Positives = 130/302 (43%), Gaps = 58/302 (19%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
LK ++WN N L + F + PD++ LQE++ A + P+ + ++
Sbjct: 4 LKIISWNVNGLRAVHRKG---FLKWFMEEKPDILCLQEIK---AAPEQLPRKLRHVE--- 54
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEK--TD 158
Y+ +++ A+ K Y+G A+ K + F +E+ T+
Sbjct: 55 --------------------GYRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVERFDTE 94
Query: 159 GRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQC-SGKPLIWCGDLN 217
GR+ +A+F+ F L N Y PN EE + + +D +++ + SG+ +I CGD N
Sbjct: 95 GRIQIADFDDFLLYNIYFPNGAMSEERLKY-KLEFYDAFLEDVNRERDSGRNVIICGDFN 153
Query: 218 VSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLH 277
+H EID++ P KE+ GF ER ++ G +D +R +
Sbjct: 154 TAHREIDLARP---------------KENSNVSGFLPVERAWIDKFIENG-YVDTFRMFN 197
Query: 278 KEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHC 337
+ WS + R R+DYF V+EE K ++ + L GSDHC
Sbjct: 198 SDPGQYTW--WSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWI------LSDVMGSDHC 249
Query: 338 PV 339
P+
Sbjct: 250 PI 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 = 83.6 bits (205), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 76/302 (25%), Positives = 130/302 (43%), Gaps = 58/302 (19%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
LK ++WN N L + F + PD++ LQE++ A + P+ + ++
Sbjct: 4 LKIISWNVNGLRAVHRKG---FLKWFMEEKPDILCLQEIK---AAPEQLPRKLRHVE--- 54
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEK--TD 158
Y+ +++ A+ K Y+G A+ K + F +E+ T+
Sbjct: 55 --------------------GYRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVERFDTE 94
Query: 159 GRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQC-SGKPLIWCGDLN 217
GR+ +A+F+ F L N Y PN EE + + +D +++ + SG+ +I CGD N
Sbjct: 95 GRIQIADFDDFLLYNIYFPNGKMSEERLKY-KLEFYDAFLEDVNRERDSGRNVIICGDFN 153
Query: 218 VSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLH 277
+H EID++ P KE+ GF ER ++ G +D +R +
Sbjct: 154 TAHREIDLARP---------------KENSNVSGFLPVERAWIDKFIENG-YVDTFRMFN 197
Query: 278 KEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHC 337
+ WS + R R+DYF V+EE K ++ + L GSDHC
Sbjct: 198 SDPGQYTW--WSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWI------LSDVMGSDHC 249
Query: 338 PV 339
P+
Sbjct: 250 PI 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 = 82.0 bits (201), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 75/302 (24%), Positives = 130/302 (43%), Gaps = 58/302 (19%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
LK ++WN N L + F + PD++ LQE++ A + P+ + ++
Sbjct: 4 LKIISWNVNGLRAVHRKG---FLKWFMEEKPDILCLQEIK---AAPEQLPRKLRHVE--- 54
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEK--TD 158
Y+ +++ A+ K Y+G A+ K + F +E+ T+
Sbjct: 55 --------------------GYRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVERFDTE 94
Query: 159 GRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQC-SGKPLIWCGDLN 217
GR+ +A+F+ F L N Y PN EE + + +D +++ + SG+ +I CG+ N
Sbjct: 95 GRIQIADFDDFLLYNIYFPNGKMSEERLKY-KLEFYDAFLEDVNRERDSGRNVIICGNFN 153
Query: 218 VSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLH 277
+H EID++ P KE+ GF ER ++ G +D +R +
Sbjct: 154 TAHREIDLARP---------------KENSNVSGFLPVERAWIDKFIENG-YVDTFRMFN 197
Query: 278 KEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHC 337
+ WS + R R+DYF V+EE K ++ + L GSDHC
Sbjct: 198 SDPGQYTW--WSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWI------LSDVMGSDHC 249
Query: 338 PV 339
P+
Sbjct: 250 PI 251
>pdb|2J63|A Chain A, Crystal Structure Of Ap Endonuclease Lmap From Leishmania
Major
pdb|2J63|B Chain B, Crystal Structure Of Ap Endonuclease Lmap From Leishmania
Major
Length = 467
Score = 60.5 bits (145), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 70/337 (20%), Positives = 118/337 (35%), Gaps = 69/337 (20%)
Query: 43 KFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRM-------------------- 82
KF+TWN L +K N F+ PDV+ LQE ++
Sbjct: 151 KFITWNVAGLRGLLKKNASALRAFMEAEKPDVLCLQETKLNVDEADANATLGVVDGYSFV 210
Query: 83 --PAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALL 140
P A + +K+ T ++ L + + + + AG+ +L
Sbjct: 211 DHPCAFKRGYSGTRTYMKNSTT---------VKGLHARCTRGFALPSEPQADAAAGSRVL 261
Query: 141 VKKCFQPKKVSFSLEKTDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRR------RKW 194
V+ + + + + L+NTY N+G ++ + R++
Sbjct: 262 VEGAGDEEGRVLTTFLSPDPDSASSSSRIALVNTYVANSGMGLTRLPYRVQSFDPSMREY 321
Query: 195 DKRIQEFVLQCSGKP-------------LIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVP 241
R+ + + + P IW GDLNV+ + D + F
Sbjct: 322 LHRLDTWATENAAVPSAAAMGSGSSPHGFIWAGDLNVAERDYDRYYAGTF---------- 371
Query: 242 PNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYRGKRM 301
K GF ER F ++ +D +R L+ + F WS G+ R
Sbjct: 372 --KSMQECSGFAPEERMSFRETMQRTNSVDIFRQLYPQAGPVYSF-WSQRINGRPRNLGW 428
Query: 302 RIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCP 338
R+DYF+VS L ++ C + GSDHCP
Sbjct: 429 RLDYFVVSSRLASYVVDC------FPMPTVMGSDHCP 459
>pdb|2JC4|A Chain A, 3'-5' Exonuclease (Nexo) From Neisseria Meningitidis
Length = 256
Score = 59.3 bits (142), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 74/308 (24%), Positives = 121/308 (39%), Gaps = 68/308 (22%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
+K TWN NSL +R+ P+ N + PD++ LQE+++ D
Sbjct: 1 MKITTWNVNSLNVRL----PQVQNLLADNPPDILVLQELKL-----------------DQ 39
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSL----EKT 157
L +M + WS Y G A++ + P+ V F L +
Sbjct: 40 DKFPAAALQMM---------GWHCVWS-GQKTYNGVAIVSRSV--PQDVHFGLPALPDDP 87
Query: 158 DGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFV---LQCSGKPLIWCG 214
RVI A ++N Y NG + F+ + +W + EFV + GK L+ G
Sbjct: 88 QRRVIAATVSGVRVINVYC-VNGEALDSPKFKYKEQWFAALTEFVRDEMTRHGK-LVLLG 145
Query: 215 DLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQP-GFTIAERKRFGAILKEGRLIDAY 273
D N++ + D P E W + + ER+ F +L G L D+
Sbjct: 146 DFNIAPADADCYDP----------------EKWHEKIHCSSVERQWFQNLLDLG-LTDSL 188
Query: 274 RFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRI--IACEMQGHGIELEGF 331
R +H E F + G + G +RID+ +VS + + + +++ +E
Sbjct: 189 RQVHPEGAFYTWFDYRGAMFQRKLG--LRIDHILVSPAMAAALKDVRVDLETRALE---- 242
Query: 332 YGSDHCPV 339
SDH PV
Sbjct: 243 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 = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 47/179 (26%), Positives = 84/179 (46%), Gaps = 23/179 (12%)
Query: 146 QPKKVSFSLE---KTDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFV 202
+P+ VSF L+ K + R+I A+ ++NTY P G+K + +Q + +W +R+ ++
Sbjct: 73 EPEDVSFGLDSEPKDEDRLIRAKIAGIDVINTYVPQ-GFKIDSEKYQYKLQWLERLYHYL 131
Query: 203 LQCSG--KPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRF 260
+ +WCGD+NV+ E IDV P+ KL +V F R+ +
Sbjct: 132 QKTVDFRSFAVWCGDMNVAPEPIDVHSPD-----KLKNHV----------XFHEDARRAY 176
Query: 261 GAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIAC 319
IL+ G +D R +H + + + + + RG R D + + L +R + C
Sbjct: 177 KKILELG-FVDVLRKIHPNERIYTFYDYRVKGAIE-RGLGWRGDAILATPPLAERCVDC 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 = 55.5 bits (132), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 65/301 (21%), Positives = 121/301 (40%), Gaps = 55/301 (18%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
LK ++ N N + K F +I D++ +QE++ A +L D
Sbjct: 2 LKIISANVNGIRSAYKKG---FYEYIAASGADIVCVQELKAQEA----------DLSADM 48
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTD--G 159
K P + W Y+G A+ K+ ++ +E+ D G
Sbjct: 49 K---------------NPHGMHGHWHCAEKRGYSGVAVYSKRKPDNVQIGMGIEEFDREG 93
Query: 160 RVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVS 219
R + +F +++ Y P+ EE + R ++ G+ ++ CGD N++
Sbjct: 94 RFVRCDFGRLSVISLYLPSGSSAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIA 153
Query: 220 HEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKE 279
H+ ID+ + + K +G++P ER+ G ++ + D +R L+ +
Sbjct: 154 HQNIDLKN--WKGNQKNSGFLPE-------------EREWIGKVIHKLGWTDMWRTLYPD 198
Query: 280 KDMDCGFSWSGNPIGKY-RGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCP 338
G++W N Y + RIDY +V+ EL + ++ H + E F SDH P
Sbjct: 199 VP---GYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSA----HVYKDEKF--SDHAP 249
Query: 339 V 339
+
Sbjct: 250 L 250
>pdb|4B5H|A Chain A, Substate Bound Inactive Mutant Of Neisseria Ap
Endonuclease In Presence Of Metal Ions
Length = 259
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 64/301 (21%), Positives = 121/301 (40%), Gaps = 55/301 (18%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
LK ++ N N + K F +I D++ +QE++ A +L D
Sbjct: 2 LKIISANVNGIRSAYKKG---FYEYIAASGTDIVCVQELKAQEA----------DLSADM 48
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTD--G 159
K P + W Y+G A+ K+ ++ +E+ D G
Sbjct: 49 K---------------NPHGMHGHWHCAEKRGYSGVAVYSKRKPDNVQIGMGIEEFDREG 93
Query: 160 RVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVS 219
R + +F +++ Y P+ EE + R ++ G+ ++ CG+ N++
Sbjct: 94 RFVRCDFGRLSVISLYLPSGSSAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGNWNIA 153
Query: 220 HEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKE 279
H+ ID+ + + K +G++P ER+ G ++ + D +R L+ +
Sbjct: 154 HQNIDLKN--WKGNQKNSGFLPE-------------EREWIGKVIHKLGWTDMWRTLYPD 198
Query: 280 KDMDCGFSWSGNPIGKY-RGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCP 338
G++W N Y + RIDY +V+ EL + ++ H + E F SDH P
Sbjct: 199 VP---GYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSA----HVYKDEKF--SDHAP 249
Query: 339 V 339
+
Sbjct: 250 L 250
>pdb|1AKO|A Chain A, Exonuclease Iii From Escherichia Coli
Length = 268
Score = 48.9 bits (115), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 73/312 (23%), Positives = 121/312 (38%), Gaps = 64/312 (20%)
Query: 42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
+KFV++N N L R + + PDVI LQE + + DD
Sbjct: 1 MKFVSFNINGLRARPH----QLEAIVEKHQPDVIGLQETK---------------VHDD- 40
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSF--SLEKTDG 159
M L Y +++ Y G ALL K+ + F E+
Sbjct: 41 ----------MFPLEEVAKLGYNVFYHGQKGHY-GVALLTKETPIAVRRGFPGDDEEAQR 89
Query: 160 RVILAEFETFY----LLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGK---PLIW 212
R+I+AE + ++N Y P ++ F + ++ + +Q + L+ K P++
Sbjct: 90 RIIMAEIPSLLGNVTVINGYFPQGESRDHPIKFPAKAQFYQNLQNY-LETELKRDNPVLI 148
Query: 213 CGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDW---GQPGFTIAERKRFGAILKEGRL 269
GD+N+S ++D+ G N++ W G+ F ER+ ++ G L
Sbjct: 149 MGDMNISPTDLDI------------GIGEENRKRWLRTGKCSFLPEEREWMDRLMSWG-L 195
Query: 270 IDAYRFLHKEKDMDCGFSWSGNPIGKYRGKR-MRIDYFIVSEELKDRIIACEMQGHGIEL 328
+D +R H FSW + R +RID + S+ L + C G E+
Sbjct: 196 VDTFR--HANPQTADRFSWFDYRSKGFDDNRGLRIDLLLASQPLAE---CCVETGIDYEI 250
Query: 329 EGFYG-SDHCPV 339
SDH PV
Sbjct: 251 RSMEKPSDHAPV 262
>pdb|4F1R|A Chain A, Structure Analysis Of The Global Metabolic Regulator Crc
From Pseudomonas Aeruginos
Length = 293
Score = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 39/160 (24%), Positives = 63/160 (39%), Gaps = 28/160 (17%)
Query: 135 AGTALLVKKCFQPKKV--SFSLEKTD--GRVILAEFETFYLLNTYAPNNGWKEEENSFQR 190
G AL + QPK V E D GR + A+F+ + P+ + + S +
Sbjct: 100 GGVALYSR--LQPKAVISGLGFETADRYGRYLQADFDKVSIATLLLPSG--QSGDESLNQ 155
Query: 191 RRKWDKRIQEFVLQCSGK--PLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWG 248
+ K+ ++ + K I+CG L V+H+++DV + +E
Sbjct: 156 KFKFMDDFTHYLSKQRRKRREYIYCGSLYVAHQKMDVKNW---------------RECQQ 200
Query: 249 QPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSW 288
PGF ER + DA R + +E D FSW
Sbjct: 201 MPGFLAPERAWLDEVFGNLGYADALREVSREGDQ---FSW 237
>pdb|1VYB|A Chain A, Endonuclease Domain Of Human Line1 Orf2p
pdb|1VYB|B Chain B, Endonuclease Domain Of Human Line1 Orf2p
Length = 238
Score = 31.2 bits (69), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 54/226 (23%), Positives = 83/226 (36%), Gaps = 63/226 (27%)
Query: 124 QIWWSLADSKYAGTALLV--KKCFQPKKVSFSLEKTDGRVILA----EFETFYLLNTYAP 177
+I+ + K AG A+LV K F+P K+ E G I+ + E +LN YAP
Sbjct: 61 KIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKE---GHYIMVKGSIQQEELTILNIYAP 117
Query: 178 NNG----WKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAA 233
N G K+ + QR LI GD N +D S
Sbjct: 118 NTGAPRFIKQVLSDLQR-------------DLDSHTLIM-GDFNTPLSTLDRS-----TR 158
Query: 234 AKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPI 293
K+N + + + L + LID YR LH + +++ P
Sbjct: 159 QKVN-----------------KDTQELNSALHQADLIDIYRTLHPK---STEYTFFSAPH 198
Query: 294 GKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 339
Y +ID+ + S+ L + C+ E+ Y SDH +
Sbjct: 199 HTYS----KIDHIVGSKALLSK---CKRT----EIITNYLSDHSAI 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 = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 9/63 (14%)
Query: 124 QIWWSLADSKYAGTALLV--KKCFQPKKVSFSLEKTDGRVILA----EFETFYLLNTYAP 177
+I+ + K AG A+LV K F+P K+ E G I+ + E +LN YAP
Sbjct: 61 KIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKE---GHYIMVKGSIQQEELTILNIYAP 117
Query: 178 NNG 180
N G
Sbjct: 118 NTG 120
>pdb|2V0S|A Chain A, Crystal Structure Of A Hairpin Exchange Variant (Lr1) Of
The Targeting Line-1 Retrotransposon Endonuclease
Length = 236
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 55/226 (24%), Positives = 83/226 (36%), Gaps = 65/226 (28%)
Query: 124 QIWWSLADSKYAGTALLV--KKCFQPKKVSFSLEKTDGRVILA----EFETFYLLNTYAP 177
+I+ + K AG A+LV K F+P K+ E G I+ + E +LN YAP
Sbjct: 61 KIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKE---GHYIMVKGSIQQEELTILNIYAP 117
Query: 178 NNG----WKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAA 233
N G K+ + QR LI GD N +D S +
Sbjct: 118 NTGAPRFIKQVLSDLQR-------------DLDSHTLIM-GDFNTPLSTLDRSTRQ---- 159
Query: 234 AKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPI 293
K+N + + + L + LID YR LH K + FS +
Sbjct: 160 -KVN-----------------KDTQELNSALHQADLIDIYRTLH-PKSTEYTFSTANG-- 198
Query: 294 GKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 339
+ID+ + S+ L + C+ E+ Y SDH +
Sbjct: 199 ------ESKIDHIVGSKALLSK---CKRT----EIITNYLSDHSAI 231
>pdb|3AEV|A Chain A, Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex From
Pyrococcus Horikoshii Ot3
Length = 275
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 29/52 (55%), Gaps = 3/52 (5%)
Query: 263 ILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKD 314
I+KE LI A +KEKD++ F++ G P +YR DY+ E L+D
Sbjct: 194 IIKEA-LIRARDRANKEKDIEVKFTYQGAP--RYRIDITAPDYYKAEEVLED 242
>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 = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 47/197 (23%), Positives = 83/197 (42%), Gaps = 52/197 (26%)
Query: 42 LKFVTWNAN-----SLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQE 96
+ ++WN + SLL R+K ++ + +PD++ LQEV
Sbjct: 14 VSVMSWNIDGLDGRSLLTRMK----AVAHIVKNVNPDILFLQEVV--------------- 54
Query: 97 LKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKK---VSF- 152
D + +KL + Y+I++S +Y TA+LV K F +K + F
Sbjct: 55 ---DRDLAPIDKLQSL----------YKIYYSNKGCQYY-TAILVSKMFDVEKHDVIHFQ 100
Query: 153 ------SLEKTDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCS 206
+L+ +G + + F LLNT+ + + Q DK ++E + Q
Sbjct: 101 NSGMYRTLQILEGSI--GGLKVF-LLNTHLESTREHRPQRCAQFGFCMDK-VREIIAQNP 156
Query: 207 GKPLIWCGDLNVSHEEI 223
G + + GDLN+ EE+
Sbjct: 157 GALVFFGGDLNLRDEEV 173
>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 = 2.4, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 1/60 (1%)
Query: 272 AYRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGF 331
Y +K+K + + S I RGK + +YF + EE+KD++ + G G + F
Sbjct: 206 VYALYNKDKSLFGRYMMSDKVIEPVRGKLIP-NYFKIKEEVKDKVYGITISGSGPSIIAF 264
>pdb|4GEW|A Chain A, Crystal Structure Of Tdp2 From C. Elegans
Length = 362
Score = 29.3 bits (64), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 47/197 (23%), Positives = 82/197 (41%), Gaps = 52/197 (26%)
Query: 42 LKFVTWNAN-----SLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQE 96
+ ++WN + SLL R+K ++ + +PD++ LQEV
Sbjct: 120 VSVMSWNIDGLDGRSLLTRMK----AVAHIVKNVNPDILFLQEVV--------------- 160
Query: 97 LKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKK---VSF- 152
+ L + L S Y+I++S +Y TA+LV K F +K + F
Sbjct: 161 ---------DRDLAPIDKLQSL----YKIYYSNKGCQYY-TAILVSKMFDVEKHDVIHFQ 206
Query: 153 ------SLEKTDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCS 206
+L+ +G + + F LLNT+ + + Q DK ++E + Q
Sbjct: 207 NSGMYRTLQILEGSI--GGLKVF-LLNTHLESTREHRPQRCAQFGFCMDK-VREIIAQNP 262
Query: 207 GKPLIWCGDLNVSHEEI 223
G + + GDLN+ EE+
Sbjct: 263 GALVFFGGDLNLRDEEV 279
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 0.137 0.433
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,457,420
Number of Sequences: 62578
Number of extensions: 446403
Number of successful extensions: 841
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 795
Number of HSP's gapped (non-prelim): 27
length of query: 360
length of database: 14,973,337
effective HSP length: 100
effective length of query: 260
effective length of database: 8,715,537
effective search space: 2266039620
effective search space used: 2266039620
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)