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= psy12564
(1033 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 = 191 bits (484), Expect = 2e-48, Method: Composition-based stats.
Identities = 119/330 (36%), Positives = 162/330 (49%), Gaps = 61/330 (18%)
Query: 709 EVPIIDFNDPFRILEHKRRQDQYPWNFKIGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSF 768
E PI+ + DP L K D N KI SWNV+G+RAW + K+G +
Sbjct: 5 EAPIL-YEDPPEKLTSK---DGRAANMKITSWNVDGLRAWVK------------KNGLDW 48
Query: 769 MRQHDLNVFCIQEIRCPLEKLPE----CPEGYHAFWFPGT-RQGYAGVAVLSKTKPVRVT 823
+R+ D ++ C+QE +C + LP PE H +W ++GY+GVA+L KT+P+ VT
Sbjct: 49 VRKEDPDILCLQETKCAEKALPADITAMPEYPHKYWAGSEDKEGYSGVAMLCKTEPLNVT 108
Query: 824 HGFSMKVGGVVHTHGFNRGSNEHGSDMESGPSHPELTTIQYADASGIDDGRVMTVEYEQF 883
+G G EH + GRV+T E+ F
Sbjct: 109 YGI---------------GKEEHDKE-----------------------GRVITAEFPDF 130
Query: 884 YLVNVYAPAAKEDLSMLSVKLLWNSFLRGHLKSLNEIKPVVLAGDLNVAHNHIDVALPLT 943
+LV Y P A L L + W+ R +L L+ KP+VL GDLNVAH ID+ P
Sbjct: 131 FLVTAYVPNASRGLVRLDYRKTWDVDFRAYLCGLDARKPLVLCGDLNVAHQEIDLKNPKG 190
Query: 944 NLGKSGFTIQERNYFSNFLDLGFLDVHRHLYPNHR-IYTYWPY-YDRPSKMKGWRLDYFL 1001
N +GFT +ER F+ L+ GF D R LYP+ YT+W Y + SK GWRLDYF+
Sbjct: 191 NRKNAGFTPEEREGFTQLLEAGFTDSFRELYPDQAYAYTFWTYMMNARSKNVGWRLDYFV 250
Query: 1002 ISKQLKSHLSDLEIHGDVEGSDHAPQILYL 1031
+S L L D +I GSDH P L+L
Sbjct: 251 LSSALLPGLCDSKIRNTAMGSDHCPITLFL 280
>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 = 179 bits (453), Expect = 1e-44, Method: Compositional matrix adjust.
Identities = 116/319 (36%), Positives = 151/319 (47%), Gaps = 58/319 (18%)
Query: 723 EHKRRQDQYPWNFKIGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEI 782
+HK P KI SWNV+G+RAW + K G ++++ ++ C+QE
Sbjct: 8 DHKTSPSGKPATLKICSWNVDGLRAWIK------------KKGLDWVKEEAPDILCLQET 55
Query: 783 RCPLEKLP----ECPEGYHAFW-FPGTRQGYAGVAVLSKTKPVRVTHGFSMKVGGVVHTH 837
+C KLP E P H +W P ++GY+GV +LS+ P++V++G
Sbjct: 56 KCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGI----------- 104
Query: 838 GFNRGSNEHGSDMESGPSHPELTTIQYADASGIDDGRVMTVEYEQFYLVNVYAPAAKEDL 897
G EH D E GRV+ E++ F LV Y P A L
Sbjct: 105 ----GDEEH--DQE---------------------GRVIVAEFDSFVLVTAYVPNAGRGL 137
Query: 898 SMLSVKLLWNSFLRGHLKSLNEIKPVVLAGDLNVAHNHIDVALPLTNLGKSGFTIQERNY 957
L + W+ R LK L KP+VL GDLNVAH ID+ P N +GFT QER
Sbjct: 138 VRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQG 197
Query: 958 FSNFLD-LGFLDVHRHLYPNH-RIYTYWPY-YDRPSKMKGWRLDYFLISKQLKSHLSDLE 1014
F L + D RHLYPN YT+W Y + SK GWRLDYFL+S L L D +
Sbjct: 198 FGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSK 257
Query: 1015 IHGDVEGSDHAPQILYLNL 1033
I GSDH P LYL L
Sbjct: 258 IRSKALGSDHCPITLYLAL 276
>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 = 178 bits (452), Expect = 1e-44, Method: Compositional matrix adjust.
Identities = 116/319 (36%), Positives = 151/319 (47%), Gaps = 58/319 (18%)
Query: 723 EHKRRQDQYPWNFKIGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEI 782
+HK P KI SWNV+G+RAW + K G ++++ ++ C+QE
Sbjct: 11 DHKTSPSGKPATLKICSWNVDGLRAWIK------------KKGLDWVKEEAPDILCLQET 58
Query: 783 RCPLEKLP----ECPEGYHAFW-FPGTRQGYAGVAVLSKTKPVRVTHGFSMKVGGVVHTH 837
+C KLP E P H +W P ++GY+GV +LS+ P++V++G
Sbjct: 59 KCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGI----------- 107
Query: 838 GFNRGSNEHGSDMESGPSHPELTTIQYADASGIDDGRVMTVEYEQFYLVNVYAPAAKEDL 897
G EH D E GRV+ E++ F LV Y P A L
Sbjct: 108 ----GDEEH--DQE---------------------GRVIVAEFDSFVLVTAYVPNAGRGL 140
Query: 898 SMLSVKLLWNSFLRGHLKSLNEIKPVVLAGDLNVAHNHIDVALPLTNLGKSGFTIQERNY 957
L + W+ R LK L KP+VL GDLNVAH ID+ P N +GFT QER
Sbjct: 141 VRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQG 200
Query: 958 FSNFLD-LGFLDVHRHLYPNH-RIYTYWPY-YDRPSKMKGWRLDYFLISKQLKSHLSDLE 1014
F L + D RHLYPN YT+W Y + SK GWRLDYFL+S L L D +
Sbjct: 201 FGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSK 260
Query: 1015 IHGDVEGSDHAPQILYLNL 1033
I GSDH P LYL L
Sbjct: 261 IRSKALGSDHCPITLYLAL 279
>pdb|2O3H|A Chain A, Crystal Structure Of The Human C65a Ape
Length = 285
Score = 178 bits (451), Expect = 2e-44, Method: Compositional matrix adjust.
Identities = 114/310 (36%), Positives = 148/310 (47%), Gaps = 58/310 (18%)
Query: 732 PWNFKIGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEIRCPLEKLP- 790
P KI SWNV+G+RAW + K G ++++ ++ C+QE +C KLP
Sbjct: 26 PATLKIASWNVDGLRAWIK------------KKGLDWVKEEAPDILCLQETKCSENKLPA 73
Query: 791 ---ECPEGYHAFW-FPGTRQGYAGVAVLSKTKPVRVTHGFSMKVGGVVHTHGFNRGSNEH 846
E P H +W P ++GY+GV +LS+ P++V++G G EH
Sbjct: 74 ELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGI---------------GDEEH 118
Query: 847 GSDMESGPSHPELTTIQYADASGIDDGRVMTVEYEQFYLVNVYAPAAKEDLSMLSVKLLW 906
D E GRV+ E++ F LV Y P A L L + W
Sbjct: 119 --DQE---------------------GRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRW 155
Query: 907 NSFLRGHLKSLNEIKPVVLAGDLNVAHNHIDVALPLTNLGKSGFTIQERNYFSNFLD-LG 965
+ R LK L KP+VL GDLNVAH ID+ P N +GFT QER F L +
Sbjct: 156 DEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVP 215
Query: 966 FLDVHRHLYPNH-RIYTYWPY-YDRPSKMKGWRLDYFLISKQLKSHLSDLEIHGDVEGSD 1023
D RHLYPN YT+W Y + SK GWRLDYFL+S L L D +I GSD
Sbjct: 216 LADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSD 275
Query: 1024 HAPQILYLNL 1033
H P LYL L
Sbjct: 276 HCPITLYLAL 285
>pdb|1BIX|A Chain A, The Crystal Structure Of The Human Dna Repair Endonuclease
Hap1 Suggests The Recognition Of Extra-Helical
Deoxyribose At Dna Abasic Sites
Length = 287
Score = 177 bits (449), Expect = 2e-44, Method: Compositional matrix adjust.
Identities = 114/310 (36%), Positives = 148/310 (47%), Gaps = 58/310 (18%)
Query: 732 PWNFKIGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEIRCPLEKLP- 790
P KI SWNV+G+RAW + K G ++++ ++ C+QE +C KLP
Sbjct: 28 PATLKICSWNVDGLRAWIK------------KKGLDWVKEEAPDILCLQETKCSENKLPA 75
Query: 791 ---ECPEGYHAFW-FPGTRQGYAGVAVLSKTKPVRVTHGFSMKVGGVVHTHGFNRGSNEH 846
E P H +W P ++GY+GV +LS+ P++V++G G EH
Sbjct: 76 ELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGI---------------GDEEH 120
Query: 847 GSDMESGPSHPELTTIQYADASGIDDGRVMTVEYEQFYLVNVYAPAAKEDLSMLSVKLLW 906
D E GRV+ E++ F LV Y P A L L + W
Sbjct: 121 --DQE---------------------GRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRW 157
Query: 907 NSFLRGHLKSLNEIKPVVLAGDLNVAHNHIDVALPLTNLGKSGFTIQERNYFSNFLD-LG 965
+ R LK L KP+VL GDLNVAH ID+ P N +GFT QER F L +
Sbjct: 158 DEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVP 217
Query: 966 FLDVHRHLYPNH-RIYTYWPY-YDRPSKMKGWRLDYFLISKQLKSHLSDLEIHGDVEGSD 1023
D RHLYPN YT+W Y + SK GWRLDYFL+S L L D +I GSD
Sbjct: 218 LADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSD 277
Query: 1024 HAPQILYLNL 1033
H P LYL L
Sbjct: 278 HCPITLYLAL 287
>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 = 176 bits (447), Expect = 4e-44, Method: Composition-based stats.
Identities = 112/310 (36%), Positives = 147/310 (47%), Gaps = 58/310 (18%)
Query: 732 PWNFKIGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEIRCPLEKLP- 790
P KI SWNV+G+RAW + K G ++++ ++ C+QE +C KLP
Sbjct: 59 PATLKICSWNVDGLRAWIK------------KKGLDWVKEEAPDILCLQETKCSENKLPA 106
Query: 791 ---ECPEGYHAFW-FPGTRQGYAGVAVLSKTKPVRVTHGFSMKVGGVVHTHGFNRGSNEH 846
E P H +W P ++GY+GV +LS+ P++V++G G EH
Sbjct: 107 ELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGI---------------GDEEH 151
Query: 847 GSDMESGPSHPELTTIQYADASGIDDGRVMTVEYEQFYLVNVYAPAAKEDLSMLSVKLLW 906
+ GRV+ E++ F LV Y P A L L + W
Sbjct: 152 DQE-----------------------GRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRW 188
Query: 907 NSFLRGHLKSLNEIKPVVLAGDLNVAHNHIDVALPLTNLGKSGFTIQERNYFSNFLD-LG 965
+ R LK L KP+VL GDLNVAH ID+ P N +GFT QER F L +
Sbjct: 189 DEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVP 248
Query: 966 FLDVHRHLYPNH-RIYTYWPY-YDRPSKMKGWRLDYFLISKQLKSHLSDLEIHGDVEGSD 1023
D RHLYPN YT+W Y + SK GWRLDYFL+S L L D +I GSD
Sbjct: 249 LADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSD 308
Query: 1024 HAPQILYLNL 1033
H P LYL L
Sbjct: 309 HCPITLYLAL 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 = 176 bits (447), Expect = 5e-44, Method: Composition-based stats.
Identities = 112/310 (36%), Positives = 147/310 (47%), Gaps = 58/310 (18%)
Query: 732 PWNFKIGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEIRCPLEKLP- 790
P KI SWNV+G+RAW + K G ++++ ++ C+QE +C KLP
Sbjct: 58 PATLKICSWNVDGLRAWIK------------KKGLDWVKEEAPDILCLQETKCSENKLPA 105
Query: 791 ---ECPEGYHAFW-FPGTRQGYAGVAVLSKTKPVRVTHGFSMKVGGVVHTHGFNRGSNEH 846
E P H +W P ++GY+GV +LS+ P++V++G G EH
Sbjct: 106 ELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGI---------------GDEEH 150
Query: 847 GSDMESGPSHPELTTIQYADASGIDDGRVMTVEYEQFYLVNVYAPAAKEDLSMLSVKLLW 906
+ GRV+ E++ F LV Y P A L L + W
Sbjct: 151 DQE-----------------------GRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRW 187
Query: 907 NSFLRGHLKSLNEIKPVVLAGDLNVAHNHIDVALPLTNLGKSGFTIQERNYFSNFLD-LG 965
+ R LK L KP+VL GDLNVAH ID+ P N +GFT QER F L +
Sbjct: 188 DEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVP 247
Query: 966 FLDVHRHLYPNH-RIYTYWPY-YDRPSKMKGWRLDYFLISKQLKSHLSDLEIHGDVEGSD 1023
D RHLYPN YT+W Y + SK GWRLDYFL+S L L D +I GSD
Sbjct: 248 LADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSD 307
Query: 1024 HAPQILYLNL 1033
H P LYL L
Sbjct: 308 HCPITLYLAL 317
>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 = 139 bits (350), Expect = 8e-33, Method: Compositional matrix adjust.
Identities = 93/296 (31%), Positives = 137/296 (46%), Gaps = 55/296 (18%)
Query: 736 KIGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEIRCPLEKLPEC--- 792
KI SWNVNG+RA + K F F+++K ++ C+QEI+ E+LP
Sbjct: 5 KIISWNVNGLRAVHR--KGFLKWFMEEKP----------DILCLQEIKAAPEQLPRKLRH 52
Query: 793 PEGYHAFWFPGTRQGYAGVAVLSKTKPVRVTHGFSMKVGGVVHTHGFNRGSNEHGSDMES 852
EGY +F+ P R+GY+GVA+ +K P + GF G R E
Sbjct: 53 VEGYRSFFTPAERKGYSGVAMYTKVPPSSLREGF-----------GVERFDTE------- 94
Query: 853 GPSHPELTTIQYADASGIDDGRVMTVEYEQFYLVNVYAPAAKEDLSMLSVKL-LWNSFLR 911
GR+ +++ F L N+Y P K L KL +++FL
Sbjct: 95 --------------------GRIQIADFDDFLLYNIYFPNGKMSEERLKYKLEFYDAFLE 134
Query: 912 GHLKSLNEIKPVVLAGDLNVAHNHIDVALPLTNLGKSGFTIQERNYFSNFLDLGFLDVHR 971
+ + + V++ GD N AH ID+A P N SGF ER + F++ G++D R
Sbjct: 135 DVNRERDSGRNVIICGDFNTAHREIDLARPKENSNVSGFLPVERAWIDKFIENGYVDTFR 194
Query: 972 HLYPNHRIYTYWPYYDRPSKMK-GWRLDYFLISKQLKSHLSDLEIHGDVEGSDHAP 1026
+ YT+W Y R + GWRLDYF ++++ K + I DV GSDH P
Sbjct: 195 MFNSDPGQYTWWSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWILSDVMGSDHCP 250
>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 = 137 bits (345), Expect = 3e-32, Method: Compositional matrix adjust.
Identities = 92/296 (31%), Positives = 137/296 (46%), Gaps = 55/296 (18%)
Query: 736 KIGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEIRCPLEKLPEC--- 792
KI SWNVNG+RA + K F F+++K ++ C+QEI+ E+LP
Sbjct: 5 KIISWNVNGLRAVHR--KGFLKWFMEEKP----------DILCLQEIKAAPEQLPRKLRH 52
Query: 793 PEGYHAFWFPGTRQGYAGVAVLSKTKPVRVTHGFSMKVGGVVHTHGFNRGSNEHGSDMES 852
EGY +F+ P R+GY+GVA+ +K P + GF G R E
Sbjct: 53 VEGYRSFFTPAERKGYSGVAMYTKVPPSSLREGF-----------GVERFDTE------- 94
Query: 853 GPSHPELTTIQYADASGIDDGRVMTVEYEQFYLVNVYAPAAKEDLSMLSVKL-LWNSFLR 911
GR+ +++ F L N+Y P K L KL +++FL
Sbjct: 95 --------------------GRIQIADFDDFLLYNIYFPNGKMSEERLKYKLEFYDAFLE 134
Query: 912 GHLKSLNEIKPVVLAGDLNVAHNHIDVALPLTNLGKSGFTIQERNYFSNFLDLGFLDVHR 971
+ + + V++ G+ N AH ID+A P N SGF ER + F++ G++D R
Sbjct: 135 DVNRERDSGRNVIICGNFNTAHREIDLARPKENSNVSGFLPVERAWIDKFIENGYVDTFR 194
Query: 972 HLYPNHRIYTYWPYYDRPSKMK-GWRLDYFLISKQLKSHLSDLEIHGDVEGSDHAP 1026
+ YT+W Y R + GWRLDYF ++++ K + I DV GSDH P
Sbjct: 195 MFNSDPGQYTWWSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWILSDVMGSDHCP 250
>pdb|3G91|A Chain A, 1.2 Angstrom Structure Of The Exonuclease Iii Homologue
Mth0212
Length = 265
Score = 137 bits (344), Expect = 4e-32, Method: Compositional matrix adjust.
Identities = 92/296 (31%), Positives = 136/296 (45%), Gaps = 55/296 (18%)
Query: 736 KIGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEIRCPLEKLPEC--- 792
KI SWNVNG+RA + K F F+++K ++ C+QEI+ E+LP
Sbjct: 5 KIISWNVNGLRAVHR--KGFLKWFMEEKP----------DILCLQEIKAAPEQLPRKLRH 52
Query: 793 PEGYHAFWFPGTRQGYAGVAVLSKTKPVRVTHGFSMKVGGVVHTHGFNRGSNEHGSDMES 852
EGY +F+ P R+GY+GVA+ +K P + GF G R E
Sbjct: 53 VEGYRSFFTPAERKGYSGVAMYTKVPPSSLREGF-----------GVERFDTE------- 94
Query: 853 GPSHPELTTIQYADASGIDDGRVMTVEYEQFYLVNVYAPAAKEDLSMLSVKL-LWNSFLR 911
GR+ +++ F L N+Y P L KL +++FL
Sbjct: 95 --------------------GRIQIADFDDFLLYNIYFPNGAMSEERLKYKLEFYDAFLE 134
Query: 912 GHLKSLNEIKPVVLAGDLNVAHNHIDVALPLTNLGKSGFTIQERNYFSNFLDLGFLDVHR 971
+ + + V++ GD N AH ID+A P N SGF ER + F++ G++D R
Sbjct: 135 DVNRERDSGRNVIICGDFNTAHREIDLARPKENSNVSGFLPVERAWIDKFIENGYVDTFR 194
Query: 972 HLYPNHRIYTYWPYYDRPSKMK-GWRLDYFLISKQLKSHLSDLEIHGDVEGSDHAP 1026
+ YT+W Y R + GWRLDYF ++++ K + I DV GSDH P
Sbjct: 195 MFNSDPGQYTWWSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWILSDVMGSDHCP 250
>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 = 103 bits (256), Expect = 7e-22, Method: Composition-based stats.
Identities = 78/301 (25%), Positives = 135/301 (44%), Gaps = 56/301 (18%)
Query: 735 FKIGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEIRCPLEKLP---E 791
KI S NVNGIR+ +K + ++ ++ C+QE++ L +
Sbjct: 2 LKIISANVNGIRS------------AYKKGFYEYIAASGADIVCVQELKAQEADLSADMK 49
Query: 792 CPEGYHAFWFPGTRQGYAGVAVLSKTKPVRVTHGFSMKVGGVVHTHGFNRGSNEHGSDME 851
P G H W ++GY+GVAV SK KP V G ++ F+R
Sbjct: 50 NPHGMHGHWHCAEKRGYSGVAVYSKRKPDNVQIGMGIE--------EFDR---------- 91
Query: 852 SGPSHPELTTIQYADASGIDDGRVMTVEYEQFYLVNVYAPAAKEDLSMLSVKLLWNSFLR 911
+GR + ++ + ++++Y P+ VK +
Sbjct: 92 --------------------EGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYRFLDAFY 131
Query: 912 GHLKSL-NEIKPVVLAGDLNVAHNHIDVALPLTNLGKSGFTIQERNYFSNFL-DLGFLDV 969
L+++ NE + +V+ GD N+AH +ID+ N SGF +ER + + LG+ D+
Sbjct: 132 PMLEAMKNEGRDIVVCGDWNIAHQNIDLKNWKGNQKNSGFLPEEREWIGKVIHKLGWTDM 191
Query: 970 HRHLYPNHRIYTYWPYYDRP-SKMKGWRLDYFLISKQLKSHLSDLEIHGDVEGSDHAPQI 1028
R LYP+ YT+W + +K GWR+DY +++ +L + ++ D + SDHAP +
Sbjct: 192 WRTLYPDVPGYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVYKDEKFSDHAPLV 251
Query: 1029 L 1029
+
Sbjct: 252 V 252
>pdb|4B5H|A Chain A, Substate Bound Inactive Mutant Of Neisseria Ap Endonuclease
In Presence Of Metal Ions
Length = 259
Score = 100 bits (250), Expect = 3e-21, Method: Composition-based stats.
Identities = 77/301 (25%), Positives = 135/301 (44%), Gaps = 56/301 (18%)
Query: 735 FKIGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEIRCPLEKLP---E 791
KI S NVNGIR+ +K + ++ ++ C+QE++ L +
Sbjct: 2 LKIISANVNGIRS------------AYKKGFYEYIAASGTDIVCVQELKAQEADLSADMK 49
Query: 792 CPEGYHAFWFPGTRQGYAGVAVLSKTKPVRVTHGFSMKVGGVVHTHGFNRGSNEHGSDME 851
P G H W ++GY+GVAV SK KP V G ++ F+R
Sbjct: 50 NPHGMHGHWHCAEKRGYSGVAVYSKRKPDNVQIGMGIE--------EFDR---------- 91
Query: 852 SGPSHPELTTIQYADASGIDDGRVMTVEYEQFYLVNVYAPAAKEDLSMLSVKLLWNSFLR 911
+GR + ++ + ++++Y P+ VK +
Sbjct: 92 --------------------EGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYRFLDAFY 131
Query: 912 GHLKSL-NEIKPVVLAGDLNVAHNHIDVALPLTNLGKSGFTIQERNYFSNFL-DLGFLDV 969
L+++ NE + +V+ G+ N+AH +ID+ N SGF +ER + + LG+ D+
Sbjct: 132 PMLEAMKNEGRDIVVCGNWNIAHQNIDLKNWKGNQKNSGFLPEEREWIGKVIHKLGWTDM 191
Query: 970 HRHLYPNHRIYTYWPYYDRP-SKMKGWRLDYFLISKQLKSHLSDLEIHGDVEGSDHAPQI 1028
R LYP+ YT+W + +K GWR+DY +++ +L + ++ D + SDHAP +
Sbjct: 192 WRTLYPDVPGYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVYKDEKFSDHAPLV 251
Query: 1029 L 1029
+
Sbjct: 252 V 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 = 75.5 bits (184), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 80/312 (25%), Positives = 128/312 (41%), Gaps = 69/312 (22%)
Query: 735 FKIGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEIRCPLEKLPECP- 793
KI ++NVN IR+ +L I +++++ ++ C+QE + K PE
Sbjct: 2 LKIATFNVNSIRS-----RLHIVI--------PWLKENKPDILCMQETKVENRKFPEADF 48
Query: 794 --EGYHAFWFPGTRQGYAGVAVLSKTKPVRVTHGFSMKVGGVVHTHGFNRGSNEHGSDME 851
GYH F G++ G GVA+ S +P V+ G ++
Sbjct: 49 HRIGYHVV-FSGSK-GRNGVAIASLEEPEDVSFG------------------------LD 82
Query: 852 SGPSHPELTTIQYADASGIDDGRVMTVEYEQFYLVNVYAPAA-KEDLSMLSVKLLWNSFL 910
S P D+ R++ + ++N Y P K D KL W L
Sbjct: 83 SEPK---------------DEDRLIRAKIAGIDVINTYVPQGFKIDSEKYQYKLQWLERL 127
Query: 911 RGHLKSLNEIKP-VVLAGDLNVAHNHIDVALPLTNLGKSGFTIQERNYFSNFLDLGFLDV 969
+L+ + + V GD+NVA IDV P F R + L+LGF+DV
Sbjct: 128 YHYLQKTVDFRSFAVWCGDMNVAPEPIDVHSPDKLKNHVXFHEDARRAYKKILELGFVDV 187
Query: 970 HRHLYPNHRIYTYWPYYDRPS--KMKGWRLDYFLISKQLKSHLSDLEIHGDV------EG 1021
R ++PN RIYT++ Y + + + GWR D L + L D + D+ +
Sbjct: 188 LRKIHPNERIYTFYDYRVKGAIERGLGWRGDAILATPPLAERCVDC--YADIKPRLAEKP 245
Query: 1022 SDHAPQILYLNL 1033
SDH P + ++
Sbjct: 246 SDHLPLVAVFDV 257
>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 = 69.7 bits (169), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 86/348 (24%), Positives = 139/348 (39%), Gaps = 84/348 (24%)
Query: 735 FKIGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEIRCPLEKLPE--- 791
+K +WNV G+R + N +FM +V C+QE + +++
Sbjct: 150 YKFITWNVAGLRGLLKKNASALR---------AFMEAEKPDVLCLQETKLNVDEADANAT 200
Query: 792 --CPEGYHAFWFPGT-RQGYAGVAVLSKTKP------VRVTHGFSMKVGGVVHTHGFNRG 842
+GY P ++GY+G K R T GF++
Sbjct: 201 LGVVDGYSFVDHPCAFKRGYSGTRTYMKNSTTVKGLHARCTRGFALP------------- 247
Query: 843 SNEHGSDMESGPSHPELTTIQYADASGIDDGRVMTV----------EYEQFYLVNVYAPA 892
+E +D +G + + +G ++GRV+T + LVN Y
Sbjct: 248 -SEPQADAAAG-------SRVLVEGAGDEEGRVLTTFLSPDPDSASSSSRIALVNTYVAN 299
Query: 893 AKEDLSMLSVKLLWNSF---LRGHLKSL------NEIKP-------------VVLAGDLN 930
+ L+ L ++ SF +R +L L N P + AGDLN
Sbjct: 300 SGMGLTRLPYRV--QSFDPSMREYLHRLDTWATENAAVPSAAAMGSGSSPHGFIWAGDLN 357
Query: 931 VAHNHID--VALPLTNLGK-SGFTIQERNYFSNFLD-LGFLDVHRHLYPNHR-IYTYWPY 985
VA D A ++ + SGF +ER F + +D+ R LYP +Y++W
Sbjct: 358 VAERDYDRYYAGTFKSMQECSGFAPEERMSFRETMQRTNSVDIFRQLYPQAGPVYSFWSQ 417
Query: 986 Y--DRPSKMKGWRLDYFLISKQLKSHLSDLEIHGDVEGSDHAPQILYL 1031
RP + GWRLDYF++S +L S++ D V GSDH P +++
Sbjct: 418 RINGRPRNL-GWRLDYFVVSSRLASYVVDCFPMPTVMGSDHCPFQMWM 464
>pdb|2JC4|A Chain A, 3'-5' Exonuclease (Nexo) From Neisseria Meningitidis
Length = 256
Score = 67.0 bits (162), Expect = 6e-11, Method: Composition-based stats.
Identities = 77/301 (25%), Positives = 120/301 (39%), Gaps = 63/301 (20%)
Query: 736 KIGSWNVNGIRA-WSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEIRCPLEKLPECP- 793
KI +WNVN + QV L + + ++ +QE++ +K P
Sbjct: 2 KITTWNVNSLNVRLPQVQNL--------------LADNPPDILVLQELKLDQDKFPAAAL 47
Query: 794 --EGYHAFWFPGTRQGYAGVAVLSKTKPVRVTHGFSMKVGGVVHTHGFNRGSNEHGSDME 851
G+H W ++ Y GVA++S++ P V G +
Sbjct: 48 QMMGWHCVW--SGQKTYNGVAIVSRSVPQDVHFG------------------------LP 81
Query: 852 SGPSHPELTTIQYADASGIDDGRVMTVEYEQFYLVNVYAPAAKEDLSMLSVKLLWNSFLR 911
+ P P+ I A SG+ RV+ V Y VN A D K W + L
Sbjct: 82 ALPDDPQRRVIA-ATVSGV---RVINV-----YCVNGEAL----DSPKFKYKEQWFAALT 128
Query: 912 GHLK-SLNEIKPVVLAGDLNVAHNHIDVALPLTNLGKSGFTIQERNYFSNFLDLGFLDVH 970
++ + +VL GD N+A D P K + ER +F N LDLG D
Sbjct: 129 EFVRDEMTRHGKLVLLGDFNIAPADADCYDPEKWHEKIHCSSVERQWFQNLLDLGLTDSL 188
Query: 971 RHLYPNHRIYTYWPYYDRPSKMK-GWRLDYFLISKQLKSHLSDLEIHGDVEG----SDHA 1025
R ++P YT++ Y + K G R+D+ L+S + + L D+ + + SDHA
Sbjct: 189 RQVHPEGAFYTWFDYRGAMFQRKLGLRIDHILVSPAMAAALKDVRVDLETRALERPSDHA 248
Query: 1026 P 1026
P
Sbjct: 249 P 249
>pdb|1AKO|A Chain A, Exonuclease Iii From Escherichia Coli
Length = 268
Score = 57.4 bits (137), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 74/318 (23%), Positives = 124/318 (38%), Gaps = 83/318 (26%)
Query: 735 FKIGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEIRC-----PLEKL 789
K S+N+NG+RA + + + +H +V +QE + PLE++
Sbjct: 1 MKFVSFNINGLRARPHQLE-------------AIVEKHQPDVIGLQETKVHDDMFPLEEV 47
Query: 790 PECPEGYHAFWFPGTRQGYAGVAVLSKTKPVRVTHGFSMKVGGVVHTHGFNRGSNEHGSD 849
+ GY+ F+ ++G+ GVA+L+K P+ V GF G D
Sbjct: 48 AKL--GYNVFYH--GQKGHYGVALLTKETPIAVRRGFP-------------------GDD 84
Query: 850 MESGPSHPELTTIQYADASGIDDGRVMTVEYEQFY----LVNVYAPAA--KEDLSMLSVK 903
E+ R++ E ++N Y P ++ K
Sbjct: 85 EEA-------------------QRRIIMAEIPSLLGNVTVINGYFPQGESRDHPIKFPAK 125
Query: 904 LLWNSFLRGHLKS-LNEIKPVVLAGDLNVAHNHIDVALPLTN------LGKSGFTIQERN 956
+ L+ +L++ L PV++ GD+N++ +D+ + N GK F +ER
Sbjct: 126 AQFYQNLQNYLETELKRDNPVLIMGDMNISPTDLDIGIGEENRKRWLRTGKCSFLPEERE 185
Query: 957 YFSNFLDLGFLDVHRHLYPNHRIYTYWPYYDRPSKM----KGWRLDYFLISKQLKSHLS- 1011
+ + G +D RH P W +D SK +G R+D L S+ L
Sbjct: 186 WMDRLMSWGLVDTFRHANPQTADRFSW--FDYRSKGFDDNRGLRIDLLLASQPLAECCVE 243
Query: 1012 ---DLEIHGDVEGSDHAP 1026
D EI + SDHAP
Sbjct: 244 TGIDYEIRSMEKPSDHAP 261
>pdb|4F1R|A Chain A, Structure Analysis Of The Global Metabolic Regulator Crc
From Pseudomonas Aeruginos
Length = 293
Score = 54.3 bits (129), Expect = 4e-07, Method: Composition-based stats.
Identities = 64/300 (21%), Positives = 116/300 (38%), Gaps = 56/300 (18%)
Query: 736 KIGSWNVNGIRAWSQVNKLFTSIFLQQKDGFSFMRQHDLNVFCIQEIRCPLEKLPECP-- 793
+I S NVNGI+A ++ L S+++ + +V C+Q+ R L +
Sbjct: 36 RIISVNVNGIQAAAERGLL------------SWLQAQNADVICLQDTRASAFDLDDPSFQ 83
Query: 794 -EGYHAFWFPGTRQGYAGVAVLSKTKPVRVTHGFSMKVGGVVHTHGFNRGSNEHGSDMES 852
+GY + GVA+ S+ +P V G GF
Sbjct: 84 LDGYFLYACDAELPEQGGVALYSRLQPKAVISGL-----------GFE------------ 120
Query: 853 GPSHPELTTIQYADASGIDDGRVMTVEYEQFYLVNVYAPAAKEDLSMLSVKL-LWNSFLR 911
T +Y GR + ++++ + + P+ + L+ K + F
Sbjct: 121 -------TADRY--------GRYLQADFDKVSIATLLLPSGQSGDESLNQKFKFMDDFTH 165
Query: 912 GHLKSLNEIKPVVLAGDLNVAHNHIDVALPLTNLGKSGFTIQERNYFSN-FLDLGFLDVH 970
K + + + G L VAH +DV GF ER + F +LG+ D
Sbjct: 166 YLSKQRRKRREYIYCGSLYVAHQKMDVKNWRECQQMPGFLAPERAWLDEVFGNLGYADAL 225
Query: 971 RHLYPNHRIYTYWPYYDRPSKMK-GWRLDYFLISKQLKSHLSDLEIHGDVEGSDHAPQIL 1029
R + +++WP ++ + GWR DY +++ L+ + + ++ S HAP I+
Sbjct: 226 REVSREGDQFSWWPDSEQAEMLNLGWRFDYQVLTPGLRRFVRNAKLPRQPRFSQHAPLIV 285
>pdb|1VI7|A Chain A, Crystal Structure Of An Hypothetical Protein
Length = 217
Score = 31.2 bits (69), Expect = 3.4, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 10/61 (16%)
Query: 863 QYADASGID------DGRVMTVEYEQFYLVNVYAPAAKEDLSMLSVKLLWNSFLRGHLKS 916
+Y +GI+ DG+++ +Y+ F L+ V PAAK ++ S KL F RG L+
Sbjct: 147 EYHQLTGIEALLGQCDGKIINSDYQAFVLLRVALPAAK--VAEFSAKLA--DFSRGSLQL 202
Query: 917 L 917
L
Sbjct: 203 L 203
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.314 0.131 0.379
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 29,688,290
Number of Sequences: 62578
Number of extensions: 1261496
Number of successful extensions: 2020
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 1949
Number of HSP's gapped (non-prelim): 45
length of query: 1033
length of database: 14,973,337
effective HSP length: 109
effective length of query: 924
effective length of database: 8,152,335
effective search space: 7532757540
effective search space used: 7532757540
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 56 (26.2 bits)