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= psy6001
(327 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 = 224 bits (571), Expect = 6e-59, Method: Compositional matrix adjust.
Identities = 112/259 (43%), Positives = 161/259 (62%), Gaps = 6/259 (2%)
Query: 72 VKVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFWI 131
+K+++WNV+GLRA VKKN ++++ +E+PDI+ LQ+ +C E +P + H +W
Sbjct: 27 MKITSWNVDGLRAWVKKNG-LDWVRKEDPDILCLQETKCAEKALPADITAMPEYPHKYWA 85
Query: 132 GSD--KGQGGVGLLTKEKPLTVKYGIPGVSNQR-GRVITAKFKRFTFITVYVPNSGIKLK 188
GS+ +G GV +L K +PL V YGI + + GRVITA+F F +T YVPN+ L
Sbjct: 86 GSEDKEGYSGVAMLCKTEPLNVTYGIGKEEHDKEGRVITAEFPDFFLVTAYVPNASRGLV 145
Query: 189 AIDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYTVEERRN 248
+D+R WD F Y+ L + +++ GDLNV Q IDL NP N K AG+T EER
Sbjct: 146 RLDYRKTWDVDFRAYLCG-LDARKPLVLCGDLNVAHQEIDLKNPKGNRKNAGFTPEEREG 204
Query: 249 FRELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLANNIKDCI 308
F +LL+ G D+FR LYPD+ AYT+W++ +AR N GWRLDY ++S L + D
Sbjct: 205 FTQLLEAGFTDSFRELYPDQAYAYTFWTYM-MNARSKNVGWRLDYFVLSSALLPGLCDSK 263
Query: 309 IRSDVQGSTHCPVVLRLSL 327
IR+ GS HCP+ L L++
Sbjct: 264 IRNTAMGSDHCPITLFLAV 282
>pdb|2O3H|A Chain A, Crystal Structure Of The Human C65a Ape
Length = 285
Score = 223 bits (567), Expect = 1e-58, Method: Compositional matrix adjust.
Identities = 119/268 (44%), Positives = 169/268 (63%), Gaps = 9/268 (3%)
Query: 64 SRKPYTTKVKVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSL 123
S KP T +K+++WNV+GLRA +KK ++++ EE PDI+ LQ+ +C E+++P ++
Sbjct: 23 SGKPAT--LKIASWNVDGLRAWIKKKG-LDWVKEEAPDILCLQETKCSENKLPAELQELP 79
Query: 124 SHYHMFWIG-SDK-GQGGVGLLTKEKPLTVKYGIPGVS-NQRGRVITAKFKRFTFITVYV 180
H +W SDK G GVGLL+++ PL V YGI +Q GRVI A+F F +T YV
Sbjct: 80 GLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYV 139
Query: 181 PNSGIKLKAIDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAG 240
PN+G L +++R WD+ F +++ L S +++ GDLNV + IDL NP N K AG
Sbjct: 140 PNAGRGLVRLEYRQRWDEAFRKFLKG-LASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAG 198
Query: 241 YTVEERRNFRELLDT-GLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQ 299
+T +ER+ F ELL L D+FRHLYP+ AYT+W++ +AR N GWRLDY L+S
Sbjct: 199 FTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYM-MNARSKNVGWRLDYFLLSHS 257
Query: 300 LANNIKDCIIRSDVQGSTHCPVVLRLSL 327
L + D IRS GS HCP+ L L+L
Sbjct: 258 LLPALCDSKIRSKALGSDHCPITLYLAL 285
>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 = 223 bits (567), Expect = 1e-58, Method: Compositional matrix adjust.
Identities = 119/268 (44%), Positives = 168/268 (62%), Gaps = 9/268 (3%)
Query: 64 SRKPYTTKVKVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSL 123
S KP T +K+ +WNV+GLRA +KK ++++ EE PDI+ LQ+ +C E+++P ++
Sbjct: 56 SGKPAT--LKICSWNVDGLRAWIKKKG-LDWVKEEAPDILCLQETKCSENKLPAELQELP 112
Query: 124 SHYHMFWIG-SDK-GQGGVGLLTKEKPLTVKYGIPGVS-NQRGRVITAKFKRFTFITVYV 180
H +W SDK G GVGLL+++ PL V YGI +Q GRVI A+F F +T YV
Sbjct: 113 GLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYV 172
Query: 181 PNSGIKLKAIDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAG 240
PN+G L +++R WD+ F +++ L S +++ GDLNV + IDL NP N K AG
Sbjct: 173 PNAGRGLVRLEYRQRWDEAFRKFLKG-LASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAG 231
Query: 241 YTVEERRNFRELLDT-GLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQ 299
+T +ER+ F ELL L D+FRHLYP+ AYT+W++ +AR N GWRLDY L+S
Sbjct: 232 FTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYM-MNARSKNVGWRLDYFLLSHS 290
Query: 300 LANNIKDCIIRSDVQGSTHCPVVLRLSL 327
L + D IRS GS HCP+ L L+L
Sbjct: 291 LLPALCDSKIRSKALGSDHCPITLYLAL 318
>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 = 223 bits (567), Expect = 2e-58, Method: Compositional matrix adjust.
Identities = 119/268 (44%), Positives = 168/268 (62%), Gaps = 9/268 (3%)
Query: 64 SRKPYTTKVKVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSL 123
S KP T +K+ +WNV+GLRA +KK ++++ EE PDI+ LQ+ +C E+++P ++
Sbjct: 55 SGKPAT--LKICSWNVDGLRAWIKKKG-LDWVKEEAPDILCLQETKCSENKLPAELQELP 111
Query: 124 SHYHMFWIG-SDK-GQGGVGLLTKEKPLTVKYGIPGVS-NQRGRVITAKFKRFTFITVYV 180
H +W SDK G GVGLL+++ PL V YGI +Q GRVI A+F F +T YV
Sbjct: 112 GLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYV 171
Query: 181 PNSGIKLKAIDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAG 240
PN+G L +++R WD+ F +++ L S +++ GDLNV + IDL NP N K AG
Sbjct: 172 PNAGRGLVRLEYRQRWDEAFRKFLKG-LASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAG 230
Query: 241 YTVEERRNFRELLDT-GLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQ 299
+T +ER+ F ELL L D+FRHLYP+ AYT+W++ +AR N GWRLDY L+S
Sbjct: 231 FTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYM-MNARSKNVGWRLDYFLLSHS 289
Query: 300 LANNIKDCIIRSDVQGSTHCPVVLRLSL 327
L + D IRS GS HCP+ L L+L
Sbjct: 290 LLPALCDSKIRSKALGSDHCPITLYLAL 317
>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 = 222 bits (565), Expect = 2e-58, Method: Compositional matrix adjust.
Identities = 119/268 (44%), Positives = 168/268 (62%), Gaps = 9/268 (3%)
Query: 64 SRKPYTTKVKVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSL 123
S KP T +K+ +WNV+GLRA +KK ++++ EE PDI+ LQ+ +C E+++P ++
Sbjct: 25 SGKPAT--LKICSWNVDGLRAWIKKKG-LDWVKEEAPDILCLQETKCSENKLPAELQELP 81
Query: 124 SHYHMFWIG-SDK-GQGGVGLLTKEKPLTVKYGIPGVS-NQRGRVITAKFKRFTFITVYV 180
H +W SDK G GVGLL+++ PL V YGI +Q GRVI A+F F +T YV
Sbjct: 82 GLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYV 141
Query: 181 PNSGIKLKAIDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAG 240
PN+G L +++R WD+ F +++ L S +++ GDLNV + IDL NP N K AG
Sbjct: 142 PNAGRGLVRLEYRQRWDEAFRKFLKG-LASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAG 200
Query: 241 YTVEERRNFRELLDT-GLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQ 299
+T +ER+ F ELL L D+FRHLYP+ AYT+W++ +AR N GWRLDY L+S
Sbjct: 201 FTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYM-MNARSKNVGWRLDYFLLSHS 259
Query: 300 LANNIKDCIIRSDVQGSTHCPVVLRLSL 327
L + D IRS GS HCP+ L L+L
Sbjct: 260 LLPALCDSKIRSKALGSDHCPITLYLAL 287
>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 = 221 bits (564), Expect = 3e-58, Method: Compositional matrix adjust.
Identities = 119/268 (44%), Positives = 168/268 (62%), Gaps = 9/268 (3%)
Query: 64 SRKPYTTKVKVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSL 123
S KP T +K+ +WNV+GLRA +KK ++++ EE PDI+ LQ+ +C E+++P ++
Sbjct: 17 SGKPAT--LKICSWNVDGLRAWIKKKG-LDWVKEEAPDILCLQETKCSENKLPAELQELP 73
Query: 124 SHYHMFWIG-SDK-GQGGVGLLTKEKPLTVKYGIPGVS-NQRGRVITAKFKRFTFITVYV 180
H +W SDK G GVGLL+++ PL V YGI +Q GRVI A+F F +T YV
Sbjct: 74 GLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYV 133
Query: 181 PNSGIKLKAIDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAG 240
PN+G L +++R WD+ F +++ L S +++ GDLNV + IDL NP N K AG
Sbjct: 134 PNAGRGLVRLEYRQRWDEAFRKFLKG-LASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAG 192
Query: 241 YTVEERRNFRELLDT-GLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQ 299
+T +ER+ F ELL L D+FRHLYP+ AYT+W++ +AR N GWRLDY L+S
Sbjct: 193 FTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYM-MNARSKNVGWRLDYFLLSHS 251
Query: 300 LANNIKDCIIRSDVQGSTHCPVVLRLSL 327
L + D IRS GS HCP+ L L+L
Sbjct: 252 LLPALCDSKIRSKALGSDHCPITLYLAL 279
>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 = 221 bits (563), Expect = 4e-58, Method: Compositional matrix adjust.
Identities = 119/268 (44%), Positives = 168/268 (62%), Gaps = 9/268 (3%)
Query: 64 SRKPYTTKVKVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSL 123
S KP T +K+ +WNV+GLRA +KK ++++ EE PDI+ LQ+ +C E+++P ++
Sbjct: 14 SGKPAT--LKICSWNVDGLRAWIKKKG-LDWVKEEAPDILCLQETKCSENKLPAELQELP 70
Query: 124 SHYHMFWIG-SDK-GQGGVGLLTKEKPLTVKYGIPGVS-NQRGRVITAKFKRFTFITVYV 180
H +W SDK G GVGLL+++ PL V YGI +Q GRVI A+F F +T YV
Sbjct: 71 GLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYV 130
Query: 181 PNSGIKLKAIDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAG 240
PN+G L +++R WD+ F +++ L S +++ GDLNV + IDL NP N K AG
Sbjct: 131 PNAGRGLVRLEYRQRWDEAFRKFLKG-LASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAG 189
Query: 241 YTVEERRNFRELLDT-GLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQ 299
+T +ER+ F ELL L D+FRHLYP+ AYT+W++ +AR N GWRLDY L+S
Sbjct: 190 FTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYM-MNARSKNVGWRLDYFLLSHS 248
Query: 300 LANNIKDCIIRSDVQGSTHCPVVLRLSL 327
L + D IRS GS HCP+ L L+L
Sbjct: 249 LLPALCDSKIRSKALGSDHCPITLYLAL 276
>pdb|3G91|A Chain A, 1.2 Angstrom Structure Of The Exonuclease Iii Homologue
Mth0212
Length = 265
Score = 169 bits (427), Expect = 3e-42, Method: Compositional matrix adjust.
Identities = 89/252 (35%), Positives = 138/252 (54%), Gaps = 6/252 (2%)
Query: 72 VKVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFWI 131
+K+ +WNVNGLRA V + +++ +EE PDI+ LQ+I+ +++P R + F
Sbjct: 4 LKIISWNVNGLRA-VHRKGFLKWFMEEKPDILCLQEIKAAPEQLPRKLRHVEGYRSFFTP 62
Query: 132 GSDKGQGGVGLLTKEKPLTVKYGIPGVS--NQRGRVITAKFKRFTFITVYVPNSGIKLKA 189
KG GV + TK P +++ G GV + GR+ A F F +Y PN + +
Sbjct: 63 AERKGYSGVAMYTKVPPSSLREGF-GVERFDTEGRIQIADFDDFLLYNIYFPNGAMSEER 121
Query: 190 IDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYTVEERRNF 249
+ +++ + F + + E S N+II GD N + IDLA P +N +G+ ER
Sbjct: 122 LKYKLEFYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARPKENSNVSGFLPVERAWI 181
Query: 250 RELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLANNIKDCII 309
+ ++ G VD FR ++ + G YT+WS+R + AR N GWRLDY V+E+ +K I
Sbjct: 182 DKFIENGYVDTFR-MFNSDPGQYTWWSYRTR-ARERNVGWRLDYFFVNEEFKGKVKRSWI 239
Query: 310 RSDVQGSTHCPV 321
SDV GS HCP+
Sbjct: 240 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 = 167 bits (424), Expect = 5e-42, Method: Compositional matrix adjust.
Identities = 89/252 (35%), Positives = 138/252 (54%), Gaps = 6/252 (2%)
Query: 72 VKVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFWI 131
+K+ +WNVNGLRA V + +++ +EE PDI+ LQ+I+ +++P R + F
Sbjct: 4 LKIISWNVNGLRA-VHRKGFLKWFMEEKPDILCLQEIKAAPEQLPRKLRHVEGYRSFFTP 62
Query: 132 GSDKGQGGVGLLTKEKPLTVKYGIPGVS--NQRGRVITAKFKRFTFITVYVPNSGIKLKA 189
KG GV + TK P +++ G GV + GR+ A F F +Y PN + +
Sbjct: 63 AERKGYSGVAMYTKVPPSSLREGF-GVERFDTEGRIQIADFDDFLLYNIYFPNGKMSEER 121
Query: 190 IDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYTVEERRNF 249
+ +++ + F + + E S N+II GD N + IDLA P +N +G+ ER
Sbjct: 122 LKYKLEFYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARPKENSNVSGFLPVERAWI 181
Query: 250 RELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLANNIKDCII 309
+ ++ G VD FR ++ + G YT+WS+R + AR N GWRLDY V+E+ +K I
Sbjct: 182 DKFIENGYVDTFR-MFNSDPGQYTWWSYRTR-ARERNVGWRLDYFFVNEEFKGKVKRSWI 239
Query: 310 RSDVQGSTHCPV 321
SDV GS HCP+
Sbjct: 240 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 = 166 bits (420), Expect = 2e-41, Method: Compositional matrix adjust.
Identities = 88/252 (34%), Positives = 138/252 (54%), Gaps = 6/252 (2%)
Query: 72 VKVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFWI 131
+K+ +WNVNGLRA V + +++ +EE PDI+ LQ+I+ +++P R + F
Sbjct: 4 LKIISWNVNGLRA-VHRKGFLKWFMEEKPDILCLQEIKAAPEQLPRKLRHVEGYRSFFTP 62
Query: 132 GSDKGQGGVGLLTKEKPLTVKYGIPGVS--NQRGRVITAKFKRFTFITVYVPNSGIKLKA 189
KG GV + TK P +++ G GV + GR+ A F F +Y PN + +
Sbjct: 63 AERKGYSGVAMYTKVPPSSLREGF-GVERFDTEGRIQIADFDDFLLYNIYFPNGKMSEER 121
Query: 190 IDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYTVEERRNF 249
+ +++ + F + + E S N+II G+ N + IDLA P +N +G+ ER
Sbjct: 122 LKYKLEFYDAFLEDVNRERDSGRNVIICGNFNTAHREIDLARPKENSNVSGFLPVERAWI 181
Query: 250 RELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLANNIKDCII 309
+ ++ G VD FR ++ + G YT+WS+R + AR N GWRLDY V+E+ +K I
Sbjct: 182 DKFIENGYVDTFR-MFNSDPGQYTWWSYRTR-ARERNVGWRLDYFFVNEEFKGKVKRSWI 239
Query: 310 RSDVQGSTHCPV 321
SDV GS HCP+
Sbjct: 240 LSDVMGSDHCPI 251
>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 = 127 bits (319), Expect = 9e-30, Method: Compositional matrix adjust.
Identities = 78/257 (30%), Positives = 137/257 (53%), Gaps = 11/257 (4%)
Query: 72 VKVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFWI 131
+K+ + NVNG+R+ KK EYI DI+ +Q+++ QE ++ + + +
Sbjct: 2 LKIISANVNGIRSAYKK-GFYEYIAASGADIVCVQELKAQEADLSADMKNPHGMHGHWHC 60
Query: 132 GSDKGQGGVGLLTKEKPLTVKYGIPGVS--NQRGRVITAKFKRFTFITVYVPN--SGIKL 187
+G GV + +K KP V+ G+ G+ ++ GR + F R + I++Y+P+ S +
Sbjct: 61 AEKRGYSGVAVYSKRKPDNVQIGM-GIEEFDREGRFVRCDFGRLSVISLYLPSGSSAEER 119
Query: 188 KAIDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYTVEERR 247
+ + +R + FY +++ +I++ GD N+ Q+IDL N N K +G+ EER
Sbjct: 120 QQVKYRFL--DAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLKNWKGNQKNSGFLPEERE 177
Query: 248 NFRELLD-TGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLANNIKD 306
+++ G D +R LYPD G YT+WS R + A + GWR+DY +V+ +LA
Sbjct: 178 WIGKVIHKLGWTDMWRTLYPDVPG-YTWWSNRGQ-AYAKDVGWRIDYQMVTPELAAKAVS 235
Query: 307 CIIRSDVQGSTHCPVVL 323
+ D + S H P+V+
Sbjct: 236 AHVYKDEKFSDHAPLVV 252
>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 = 126 bits (317), Expect = 2e-29, Method: Compositional matrix adjust.
Identities = 77/257 (29%), Positives = 134/257 (52%), Gaps = 12/257 (4%)
Query: 72 VKVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFWI 131
+K++T+NVN +R+ + + + ++ E PDI+ +Q+ + + + PE+ + YH+ +
Sbjct: 2 LKIATFNVNSIRS--RLHIVIPWLKENKPDILCMQETKVENRKFPEADFHRIG-YHVVFS 58
Query: 132 GSDKGQGGVGLLTKEKPLTVKYGIPGVSNQRGRVITAKFKRFTFITVYVPNSGIKLKA-- 189
GS KG+ GV + + E+P V +G+ R+I AK I YVP G K+ +
Sbjct: 59 GS-KGRNGVAIASLEEPEDVSFGLDSEPKDEDRLIRAKIAGIDVINTYVPQ-GFKIDSEK 116
Query: 190 IDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYTVEERRNF 249
+++ W + Y Y+Q + S + GD+NV + ID+ +PDK + + RR +
Sbjct: 117 YQYKLQWLERLYHYLQKTVDFRSFAVWCGDMNVAPEPIDVHSPDKLKNHVXFHEDARRAY 176
Query: 250 RELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLANNIKDCII 309
+++L+ G VD R ++P+E YT++ +R K A GWR D L + LA DC
Sbjct: 177 KKILELGFVDVLRKIHPNER-IYTFYDYRVKGAIERGLGWRGDAILATPPLAERCVDCYA 235
Query: 310 ----RSDVQGSTHCPVV 322
R + S H P+V
Sbjct: 236 DIKPRLAEKPSDHLPLV 252
>pdb|4B5H|A Chain A, Substate Bound Inactive Mutant Of Neisseria Ap
Endonuclease In Presence Of Metal Ions
Length = 259
Score = 125 bits (313), Expect = 5e-29, Method: Compositional matrix adjust.
Identities = 77/257 (29%), Positives = 137/257 (53%), Gaps = 11/257 (4%)
Query: 72 VKVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPESFRKSLSHYHMFWI 131
+K+ + NVNG+R+ KK EYI DI+ +Q+++ QE ++ + + +
Sbjct: 2 LKIISANVNGIRSAYKK-GFYEYIAASGTDIVCVQELKAQEADLSADMKNPHGMHGHWHC 60
Query: 132 GSDKGQGGVGLLTKEKPLTVKYGIPGVS--NQRGRVITAKFKRFTFITVYVPN--SGIKL 187
+G GV + +K KP V+ G+ G+ ++ GR + F R + I++Y+P+ S +
Sbjct: 61 AEKRGYSGVAVYSKRKPDNVQIGM-GIEEFDREGRFVRCDFGRLSVISLYLPSGSSAEER 119
Query: 188 KAIDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYTVEERR 247
+ + +R + FY +++ +I++ G+ N+ Q+IDL N N K +G+ EER
Sbjct: 120 QQVKYRFL--DAFYPMLEAMKNEGRDIVVCGNWNIAHQNIDLKNWKGNQKNSGFLPEERE 177
Query: 248 NFRELLD-TGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLANNIKD 306
+++ G D +R LYPD G YT+WS R + A + GWR+DY +V+ +LA
Sbjct: 178 WIGKVIHKLGWTDMWRTLYPDVPG-YTWWSNRGQ-AYAKDVGWRIDYQMVTPELAAKAVS 235
Query: 307 CIIRSDVQGSTHCPVVL 323
+ D + S H P+V+
Sbjct: 236 AHVYKDEKFSDHAPLVV 252
>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 = 115 bits (289), Expect = 3e-26, Method: Compositional matrix adjust.
Identities = 91/310 (29%), Positives = 138/310 (44%), Gaps = 63/310 (20%)
Query: 73 KVSTWNVNGLRACVKKNACV--EYILEENPDIMALQQIRCQEDEV--------------- 115
K TWNV GLR +KKNA ++ E PD++ LQ+ + DE
Sbjct: 151 KFITWNVAGLRGLLKKNASALRAFMEAEKPDVLCLQETKLNVDEADANATLGVVDGYSFV 210
Query: 116 --PESFRKSLSHYHMFWIGSDKGQG-------GVGLLTK---EKPLTVKYGIPGVSNQRG 163
P +F++ S + S +G G L ++ + + + G ++ G
Sbjct: 211 DHPCAFKRGYSGTRTYMKNSTTVKGLHARCTRGFALPSEPQADAAAGSRVLVEGAGDEEG 270
Query: 164 RVITA----------KFKRFTFITVYVPNSGIKLKAIDFRM-IWDQHFYDYIQ------- 205
RV+T R + YV NSG+ L + +R+ +D +Y+
Sbjct: 271 RVLTTFLSPDPDSASSSSRIALVNTYVANSGMGLTRLPYRVQSFDPSMREYLHRLDTWAT 330
Query: 206 --------SELRSNSN---IIISGDLNVCLQSID--LANPDKNVK-TAGYTVEERRNFRE 251
+ + S S+ I +GDLNV + D A K+++ +G+ EER +FRE
Sbjct: 331 ENAAVPSAAAMGSGSSPHGFIWAGDLNVAERDYDRYYAGTFKSMQECSGFAPEERMSFRE 390
Query: 252 LLD-TGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLANNIKDCIIR 310
+ T VD FR LYP Y++WS R + R N GWRLDY +VS +LA+ + DC
Sbjct: 391 TMQRTNSVDIFRQLYPQAGPVYSFWSQR-INGRPRNLGWRLDYFVVSSRLASYVVDCFPM 449
Query: 311 SDVQGSTHCP 320
V GS HCP
Sbjct: 450 PTVMGSDHCP 459
>pdb|1AKO|A Chain A, Exonuclease Iii From Escherichia Coli
Length = 268
Score = 113 bits (282), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 84/268 (31%), Positives = 139/268 (51%), Gaps = 24/268 (8%)
Query: 72 VKVSTWNVNGLRACVKKNACVEYILEEN-PDIMALQQIRCQEDEVPESFRKSLSHYHMFW 130
+K ++N+NGLRA + +E I+E++ PD++ LQ+ + +D P L Y++F+
Sbjct: 1 MKFVSFNINGLRA---RPHQLEAIVEKHQPDVIGLQETKVHDDMFPLEEVAKLG-YNVFY 56
Query: 131 IGSDKGQGGVGLLTKEKPLTVKYGIPGVSNQ-RGRVITAKFKRF----TFITVYVPNSGI 185
G KG GV LLTKE P+ V+ G PG + + R+I A+ T I Y P
Sbjct: 57 HGQ-KGHYGVALLTKETPIAVRRGFPGDDEEAQRRIIMAEIPSLLGNVTVINGYFPQGES 115
Query: 186 KLKAIDF--RMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVK------ 237
+ I F + + Q+ +Y+++EL+ ++ ++I GD+N+ +D+ ++N K
Sbjct: 116 RDHPIKFPAKAQFYQNLQNYLETELKRDNPVLIMGDMNISPTDLDIGIGEENRKRWLRTG 175
Query: 238 TAGYTVEERRNFRELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVS 297
+ EER L+ GLVD FRH P ++++ +R+K +N+G R+D L S
Sbjct: 176 KCSFLPEEREWMDRLMSWGLVDTFRHANPQTADRFSWFDYRSKGFD-DNRGLRIDLLLAS 234
Query: 298 EQLANNIK----DCIIRSDVQGSTHCPV 321
+ LA D IRS + S H PV
Sbjct: 235 QPLAECCVETGIDYEIRSMEKPSDHAPV 262
>pdb|2JC4|A Chain A, 3'-5' Exonuclease (Nexo) From Neisseria Meningitidis
Length = 256
Score = 112 bits (279), Expect = 4e-25, Method: Compositional matrix adjust.
Identities = 78/261 (29%), Positives = 135/261 (51%), Gaps = 22/261 (8%)
Query: 72 VKVSTWNVNGLRACVKKNACVEYILEENP-DIMALQQIRCQEDEVPESFRKSLSHYHMFW 130
+K++TWNVN L + + V+ +L +NP DI+ LQ+++ +D+ P + + + +H W
Sbjct: 1 MKITTWNVNSLNVRLPQ---VQNLLADNPPDILVLQELKLDQDKFPAAALQMMG-WHCVW 56
Query: 131 IGSDKGQGGVGLLTKEKPLTVKYGIPGVSN--QRGRVITAKFKRFTFITVYVPNS-GIKL 187
G K GV ++++ P V +G+P + + QR RVI A I VY N +
Sbjct: 57 SGQ-KTYNGVAIVSRSVPQDVHFGLPALPDDPQR-RVIAATVSGVRVINVYCVNGEALDS 114
Query: 188 KAIDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYTVEERR 247
++ W ++++ E+ + +++ GD N+ D +P+K + + ER+
Sbjct: 115 PKFKYKEQWFAALTEFVRDEMTRHGKLVLLGDFNIAPADADCYDPEKWHEKIHCSSVERQ 174
Query: 248 NFRELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNK-GWRLDYHLVSEQLANNIKD 306
F+ LLD GL D+ R ++P EGA+ W F + A K G R+D+ LVS +A +KD
Sbjct: 175 WFQNLLDLGLTDSLRQVHP--EGAFYTW-FDYRGAMFQRKLGLRIDHILVSPAMAAALKD 231
Query: 307 CIIRSDVQG------STHCPV 321
+R D++ S H PV
Sbjct: 232 --VRVDLETRALERPSDHAPV 250
>pdb|4F1R|A Chain A, Structure Analysis Of The Global Metabolic Regulator Crc
From Pseudomonas Aeruginos
Length = 293
Score = 82.8 bits (203), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 61/257 (23%), Positives = 125/257 (48%), Gaps = 9/257 (3%)
Query: 71 KVKVSTWNVNGLRACVKKNACVEYILEENPDIMALQQIRCQEDEVPE-SFRKSLSHYHMF 129
++++ + NVNG++A ++ + ++ +N D++ LQ R ++ + SF+ L Y ++
Sbjct: 34 RMRIISVNVNGIQAAAER-GLLSWLQAQNADVICLQDTRASAFDLDDPSFQ--LDGYFLY 90
Query: 130 WIGSD-KGQGGVGLLTKEKPLTVKYGIPGVSNQR-GRVITAKFKRFTFITVYVPNSGIKL 187
++ QGGV L ++ +P V G+ + R GR + A F + + T+ +P+
Sbjct: 91 ACDAELPEQGGVALYSRLQPKAVISGLGFETADRYGRYLQADFDKVSIATLLLPSGQSGD 150
Query: 188 KAIDFRMIWDQHFYDYIQSELRSNSNIIISGDLNVCLQSIDLANPDKNVKTAGYTVEERR 247
++++ + + F Y+ + R I G L V Q +D+ N + + G+ ER
Sbjct: 151 ESLNQKFKFMDDFTHYLSKQRRKRREYIYCGSLYVAHQKMDVKNWRECQQMPGFLAPERA 210
Query: 248 NFRELL-DTGLVDAFRHLYPDEEGAYTYWSFRNKSARLNNKGWRLDYHLVSEQLANNIKD 306
E+ + G DA R + EG W ++ A + N GWR DY +++ L +++
Sbjct: 211 WLDEVFGNLGYADALREV--SREGDQFSWWPDSEQAEMLNLGWRFDYQVLTPGLRRFVRN 268
Query: 307 CIIRSDVQGSTHCPVVL 323
+ + S H P+++
Sbjct: 269 AKLPRQPRFSQHAPLIV 285
>pdb|4F1I|A Chain A, Crystal Structure Of Semet Tdp2 From Caenorhabditis
Elegans
Length = 362
Score = 32.7 bits (73), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 71 KVKVSTWNVNGL--RACVKKNACVEYILEE-NPDIMALQQI 108
+V V +WN++GL R+ + + V +I++ NPDI+ LQ++
Sbjct: 119 EVSVXSWNIDGLDGRSLLTRXKAVAHIVKNVNPDILFLQEV 159
>pdb|4GEW|A Chain A, Crystal Structure Of Tdp2 From C. Elegans
Length = 362
Score = 32.0 bits (71), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 71 KVKVSTWNVNGL--RACVKKNACVEYILEE-NPDIMALQQI 108
+V V +WN++GL R+ + + V +I++ NPDI+ LQ++
Sbjct: 119 EVSVMSWNIDGLDGRSLLTRMKAVAHIVKNVNPDILFLQEV 159
>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 = 31.6 bits (70), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 28/41 (68%), Gaps = 3/41 (7%)
Query: 71 KVKVSTWNVNGL--RACVKKNACVEYILEE-NPDIMALQQI 108
+V V +WN++GL R+ + + V +I++ NPDI+ LQ++
Sbjct: 13 EVSVMSWNIDGLDGRSLLTRMKAVAHIVKNVNPDILFLQEV 53
>pdb|1Z5X|U Chain U, Hemipteran Ecdysone Receptor Ligand-Binding Domain
Complexed With Ponasterone A
Length = 262
Score = 31.6 bits (70), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 36/81 (44%), Gaps = 5/81 (6%)
Query: 223 CLQSIDLANPDKNVKTAGYTVEERRNFRELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSA 282
CL+SI L NP+ + VE N RE + L + R YPD+ G + R +
Sbjct: 170 CLRSIVLFNPEAKGLKSTQQVE---NLREKVYAILEEYCRQTYPDQSGRFAKLLLRLPAL 226
Query: 283 RLNNKGWRLDYHLVSEQLANN 303
R + G + HL +L N
Sbjct: 227 R--SIGLKCLEHLFFFKLVGN 245
>pdb|1XIU|A Chain A, Crystal Structure Of The Agonist-Bound Ligand-Binding
Domain Of Biomphalaria Glabrata Rxr
pdb|1XIU|B Chain B, Crystal Structure Of The Agonist-Bound Ligand-Binding
Domain Of Biomphalaria Glabrata Rxr
Length = 230
Score = 31.2 bits (69), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 3/61 (4%)
Query: 223 CLQSIDLANPDKNVKTAGYTVEERRNFRELLDTGLVDAFRHLYPDEEGAYTYWSFRNKSA 282
CL+++ L NPD TA V+E RE + L + + YP+E G + R +
Sbjct: 137 CLRAVVLFNPDAKGLTA---VQEVEQLREKVYASLEEYTKSRYPEEPGRFAKLLLRLPAL 193
Query: 283 R 283
R
Sbjct: 194 R 194
>pdb|1DHK|B Chain B, Structure Of Porcine Pancreatic Alpha-Amylase
Length = 223
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 37/144 (25%), Positives = 60/144 (41%), Gaps = 37/144 (25%)
Query: 155 IPGVSNQRGRVITAKFKRF-TFITVYVPNSGIKLKAIDFRMIWDQHFYDYIQSELRSNSN 213
+P +G +T +F F + I++ V N+ IK + WD H YD +E+R
Sbjct: 87 VPVQPESKGDTVTVEFDTFLSRISIDVNNNDIK------SVPWDVHDYDGQNAEVR---- 136
Query: 214 IIISGDLNVCLQSIDLANP----DKNVKTAGYTVEERRNFRELLDTGLVDAFRHLYPDEE 269
I+ + + + S+ L+NP NV T TVE + + + G +
Sbjct: 137 --ITYNSSTKVFSVSLSNPSTGKSNNVST---TVELEKEVYDWVSVG--------FSATS 183
Query: 270 GAYTY---------WSFRNKSARL 284
GAY + WSF +K L
Sbjct: 184 GAYQWSYETHDVLSWSFSSKFINL 207
>pdb|1VIW|B Chain B, Tenebrio Molitor Alpha-Amylase-Inhibitor Complex
Length = 205
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 36/140 (25%), Positives = 59/140 (42%), Gaps = 37/140 (26%)
Query: 155 IPGVSNQRGRVITAKFKRF-TFITVYVPNSGIKLKAIDFRMIWDQHFYDYIQSELRSNSN 213
+P +G +T +F F + I++ V N+ IK + WD H YD +E+R
Sbjct: 87 VPVQPESKGDTVTVEFDTFLSRISIDVNNNDIK------SVPWDVHDYDGQNAEVR---- 136
Query: 214 IIISGDLNVCLQSIDLANP----DKNVKTAGYTVEERRNFRELLDTGLVDAFRHLYPDEE 269
I+ + + + S+ L+NP NV T TVE + + + G +
Sbjct: 137 --ITYNSSTKVFSVSLSNPSTGKSNNVST---TVELEKEVYDWVSVG--------FSATS 183
Query: 270 GAYTY---------WSFRNK 280
GAY + WSF +K
Sbjct: 184 GAYQWSYETHDVLSWSFSSK 203
>pdb|1LVG|A Chain A, Crystal Structure Of Mouse Guanylate Kinase In Complex
With Gmp And Adp
Length = 198
Score = 28.5 bits (62), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 71 KVKVSTWNVNGLRACVKKNACVEYILEENPDIMALQQ-IRCQEDEVPESFRKSLS 124
++ V ++ G+R+ K + C YI + P + L+Q +R + E ES K L+
Sbjct: 96 RICVLDVDLQGVRSIKKTDLCPIYIFVQPPSLDVLEQRLRLRNTETEESLAKRLA 150
>pdb|4FPV|A Chain A, Crystal Structure Of D. Rerio Tdp2 Complexed With Single
Strand Dna Product
pdb|4FPV|B Chain B, Crystal Structure Of D. Rerio Tdp2 Complexed With Single
Strand Dna Product
Length = 257
Score = 28.1 bits (61), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 11/72 (15%)
Query: 70 TKVKVSTWNVNG---LRACVKKNACVEYILEENPDIMALQQIRCQEDEVPE--SFRKSLS 124
+K+ + +WNV+G L + Y+ PD++ LQ++ +P + K +
Sbjct: 9 SKLSIISWNVDGLDTLNLADRARGLCSYLALYTPDVVFLQEL------IPAYVQYLKKRA 62
Query: 125 HYHMFWIGSDKG 136
++F+ GSD G
Sbjct: 63 VSYLFFEGSDDG 74
>pdb|4F1H|B Chain B, Crystal Structure Of Tdp2 From Danio Rerio Complexed With
A Single Strand Dna
Length = 251
Score = 28.1 bits (61), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 11/72 (15%)
Query: 70 TKVKVSTWNVNG---LRACVKKNACVEYILEENPDIMALQQIRCQEDEVPE--SFRKSLS 124
+K+ + +WNV+G L + Y+ PD++ LQ++ +P + K +
Sbjct: 3 SKLSIISWNVDGLDTLNLADRARGLCSYLALYTPDVVFLQEL------IPAYVQYLKKRA 56
Query: 125 HYHMFWIGSDKG 136
++F+ GSD G
Sbjct: 57 VSYLFFEGSDDG 68
>pdb|4F1H|A Chain A, Crystal Structure Of Tdp2 From Danio Rerio Complexed With
A Single Strand Dna
Length = 250
Score = 28.1 bits (61), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 11/72 (15%)
Query: 70 TKVKVSTWNVNG---LRACVKKNACVEYILEENPDIMALQQIRCQEDEVPE--SFRKSLS 124
+K+ + +WNV+G L + Y+ PD++ LQ++ +P + K +
Sbjct: 2 SKLSIISWNVDGLDTLNLADRARGLCSYLALYTPDVVFLQEL------IPAYVQYLKKRA 55
Query: 125 HYHMFWIGSDKG 136
++F+ GSD G
Sbjct: 56 VSYLFFEGSDDG 67
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
0.318 0.135 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,903,743
Number of Sequences: 62578
Number of extensions: 420417
Number of successful extensions: 1201
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1108
Number of HSP's gapped (non-prelim): 31
length of query: 327
length of database: 14,973,337
effective HSP length: 99
effective length of query: 228
effective length of database: 8,778,115
effective search space: 2001410220
effective search space used: 2001410220
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)