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= 006881
(627 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 93.6 bits (231), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 80/266 (30%), Positives = 122/266 (45%), Gaps = 50/266 (18%)
Query: 1 MKIVTYNVNGLRQRVSQFGSLRKLLDSFDADIICFQETKLRRQELKSDLVMADGYESFFS 60
+KI+++NVNGLR V + G L+ ++ DI+C QE K ++L L +GY SFF+
Sbjct: 4 LKIISWNVNGLRA-VHRKGFLKWFMEE-KPDILCLQEIKAAPEQLPRKLRHVEGYRSFFT 61
Query: 61 CTRTSDKGRTGYSGVATFCRVKSPFSSTEVALPVAAEEGFTGLLETSGSKIMEGLEDFSK 120
R GYSGVA + +V P + EGF G+E F
Sbjct: 62 PAE-----RKGYSGVAMYTKVP----------PSSLREGF-------------GVERF-- 91
Query: 121 DELLKIDSEGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQFFHKRWEFLLCQ---GR 177
D+EGR I D F+L+N+Y P + R+++KL+F+ E + + GR
Sbjct: 92 ------DTEGRIQIADFDDFLLYNIYFPNGKMSEE-RLKYKLEFYDAFLEDVNRERDSGR 144
Query: 178 RIFVVGDLNIAPAAIDRCDAGPDFAKNEF----RIWFRSMLVESGGSFFDVFRSKHPERR 233
+ + GD N A ID + + F R W +E+G + D FR + +
Sbjct: 145 NVIICGDFNTAHREIDLARPKENSNVSGFLPVERAWI-DKFIENG--YVDTFRMFNSDPG 201
Query: 234 EAYTCWPSNTGAEQFNYGTRIDHILC 259
+ YT W T A + N G R+D+
Sbjct: 202 Q-YTWWSYRTRARERNVGWRLDYFFV 226
>pdb|3G91|A Chain A, 1.2 Angstrom Structure Of The Exonuclease Iii Homologue
Mth0212
Length = 265
Score = 93.6 bits (231), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 83/267 (31%), Positives = 125/267 (46%), Gaps = 52/267 (19%)
Query: 1 MKIVTYNVNGLRQRVSQFGSLRKLLDSFDADIICFQETKLRRQELKSDLVMADGYESFFS 60
+KI+++NVNGLR V + G L+ ++ DI+C QE K ++L L +GY SFF+
Sbjct: 4 LKIISWNVNGLRA-VHRKGFLKWFMEE-KPDILCLQEIKAAPEQLPRKLRHVEGYRSFFT 61
Query: 61 CTRTSDKGRTGYSGVATFCRVKSPFSSTEVALPVAAEEGFTGLLETSGSKIMEGLEDFSK 120
R GYSGVA + +V P + EGF G+E F
Sbjct: 62 PAE-----RKGYSGVAMYTKVP----------PSSLREGF-------------GVERF-- 91
Query: 121 DELLKIDSEGRCVITDHGHFILFNVYGPR-ADSEDTVRIQFKLQFFHKRWEFLLCQ---G 176
D+EGR I D F+L+N+Y P A SE+ R+++KL+F+ E + + G
Sbjct: 92 ------DTEGRIQIADFDDFLLYNIYFPNGAMSEE--RLKYKLEFYDAFLEDVNRERDSG 143
Query: 177 RRIFVVGDLNIAPAAIDRCDAGPDFAKNEF----RIWFRSMLVESGGSFFDVFRSKHPER 232
R + + GD N A ID + + F R W +E+G + D FR + +
Sbjct: 144 RNVIICGDFNTAHREIDLARPKENSNVSGFLPVERAWI-DKFIENG--YVDTFRMFNSDP 200
Query: 233 REAYTCWPSNTGAEQFNYGTRIDHILC 259
+ YT W T A + N G R+D+
Sbjct: 201 GQ-YTWWSYRTRARERNVGWRLDYFFV 226
>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 = 92.0 bits (227), Expect = 9e-19, Method: Compositional matrix adjust.
Identities = 79/266 (29%), Positives = 122/266 (45%), Gaps = 50/266 (18%)
Query: 1 MKIVTYNVNGLRQRVSQFGSLRKLLDSFDADIICFQETKLRRQELKSDLVMADGYESFFS 60
+KI+++NVNGLR V + G L+ ++ DI+C QE K ++L L +GY SFF+
Sbjct: 4 LKIISWNVNGLRA-VHRKGFLKWFMEE-KPDILCLQEIKAAPEQLPRKLRHVEGYRSFFT 61
Query: 61 CTRTSDKGRTGYSGVATFCRVKSPFSSTEVALPVAAEEGFTGLLETSGSKIMEGLEDFSK 120
R GYSGVA + +V P + EGF G+E F
Sbjct: 62 PAE-----RKGYSGVAMYTKVP----------PSSLREGF-------------GVERF-- 91
Query: 121 DELLKIDSEGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQFFHKRWEFLLCQ---GR 177
D+EGR I D F+L+N+Y P + R+++KL+F+ E + + GR
Sbjct: 92 ------DTEGRIQIADFDDFLLYNIYFPNGKMSEE-RLKYKLEFYDAFLEDVNRERDSGR 144
Query: 178 RIFVVGDLNIAPAAIDRCDAGPDFAKNEF----RIWFRSMLVESGGSFFDVFRSKHPERR 233
+ + G+ N A ID + + F R W +E+G + D FR + +
Sbjct: 145 NVIICGNFNTAHREIDLARPKENSNVSGFLPVERAWI-DKFIENG--YVDTFRMFNSDPG 201
Query: 234 EAYTCWPSNTGAEQFNYGTRIDHILC 259
+ YT W T A + N G R+D+
Sbjct: 202 Q-YTWWSYRTRARERNVGWRLDYFFV 226
>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 = 80.1 bits (196), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 81/278 (29%), Positives = 116/278 (41%), Gaps = 62/278 (22%)
Query: 1 MKIVTYNVNGLRQRVSQFGSLRKLLDSFDADIICFQETKLRRQELKSDLVMADGYESFFS 60
MKI ++NV+GLR V + G + D DI+C QETK + L +D+ Y +
Sbjct: 27 MKITSWNVDGLRAWVKKNG--LDWVRKEDPDILCLQETKCAEKALPADITAMPEYPHKY- 83
Query: 61 CTRTSDKGRTGYSGVATFCRVKSPFSSTEVALPVAAEEGFTGLLETSGSKIMEGLEDFSK 120
+ + GYSGVA C+ + V + EE
Sbjct: 84 --WAGSEDKEGYSGVAMLCKTE----PLNVTYGIGKEEH--------------------- 116
Query: 121 DELLKIDSEGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQFFHKRWEF----LLC-- 174
D EGR + + F L Y P A S VR+ ++ K W+ LC
Sbjct: 117 ------DKEGRVITAEFPDFFLVTAYVPNA-SRGLVRLDYR-----KTWDVDFRAYLCGL 164
Query: 175 QGRRIFVV-GDLNIAPAAID-------RCDAGPDFAKNEFRIWFRSMLVESGGSFFDVFR 226
R+ V+ GDLN+A ID R +AG F E R F + L+E+G F D FR
Sbjct: 165 DARKPLVLCGDLNVAHQEIDLKNPKGNRKNAG--FTPEE-REGF-TQLLEAG--FTDSFR 218
Query: 227 SKHPERREAYTCWPSNTGAEQFNYGTRIDHILCAGPCL 264
+P++ AYT W A N G R+D+ + + L
Sbjct: 219 ELYPDQAYAYTFWTYMMNARSKNVGWRLDYFVLSSALL 256
>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 = 77.4 bits (189), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 71/266 (26%), Positives = 115/266 (43%), Gaps = 49/266 (18%)
Query: 1 MKIVTYNVNGLRQRVSQFGSLRKLLDSFDADIICFQETKLRRQELKSDLVMADGYESFFS 60
+KI++ NVNG+R + + + + ADI+C QE K + +L +D+ G +
Sbjct: 2 LKIISANVNGIRSAYKK--GFYEYIAASGADIVCVQELKAQEADLSADMKNPHGMHGHWH 59
Query: 61 CTRTSDKGRTGYSGVATFCRVKSPFSSTEVALPVAAEEGFTGLLETSGSKIMEGLEDFSK 120
C + GYSGVA + + K +I G+E+F
Sbjct: 60 CAE-----KRGYSGVAVYSKRK-----------------------PDNVQIGMGIEEF-- 89
Query: 121 DELLKIDSEGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQF---FHKRWEFLLCQGR 177
D EGR V D G + ++Y P S + R Q K +F F+ E + +GR
Sbjct: 90 ------DREGRFVRCDFGRLSVISLYLPSGSSAEE-RQQVKYRFLDAFYPMLEAMKNEGR 142
Query: 178 RIFVVGDLNIAPAAIDRCDAGPDFAKNEF----RIWFRSMLVESGGSFFDVFRSKHPERR 233
I V GD NIA ID + + + F R W ++ + G + D++R+ +P+
Sbjct: 143 DIVVCGDWNIAHQNIDLKNWKGNQKNSGFLPEEREWIGKVIHKLG--WTDMWRTLYPD-V 199
Query: 234 EAYTCWPSNTGAEQFNYGTRIDHILC 259
YT W + A + G RID+ +
Sbjct: 200 PGYTWWSNRGQAYAKDVGWRIDYQMV 225
>pdb|4B5H|A Chain A, Substate Bound Inactive Mutant Of Neisseria Ap
Endonuclease In Presence Of Metal Ions
Length = 259
Score = 73.9 bits (180), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 69/266 (25%), Positives = 114/266 (42%), Gaps = 49/266 (18%)
Query: 1 MKIVTYNVNGLRQRVSQFGSLRKLLDSFDADIICFQETKLRRQELKSDLVMADGYESFFS 60
+KI++ NVNG+R + + + + DI+C QE K + +L +D+ G +
Sbjct: 2 LKIISANVNGIRSAYKK--GFYEYIAASGTDIVCVQELKAQEADLSADMKNPHGMHGHWH 59
Query: 61 CTRTSDKGRTGYSGVATFCRVKSPFSSTEVALPVAAEEGFTGLLETSGSKIMEGLEDFSK 120
C + GYSGVA + + K +I G+E+F
Sbjct: 60 CAE-----KRGYSGVAVYSKRK-----------------------PDNVQIGMGIEEF-- 89
Query: 121 DELLKIDSEGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQF---FHKRWEFLLCQGR 177
D EGR V D G + ++Y P S + R Q K +F F+ E + +GR
Sbjct: 90 ------DREGRFVRCDFGRLSVISLYLPSGSSAEE-RQQVKYRFLDAFYPMLEAMKNEGR 142
Query: 178 RIFVVGDLNIAPAAIDRCDAGPDFAKNEF----RIWFRSMLVESGGSFFDVFRSKHPERR 233
I V G+ NIA ID + + + F R W ++ + G + D++R+ +P+
Sbjct: 143 DIVVCGNWNIAHQNIDLKNWKGNQKNSGFLPEEREWIGKVIHKLG--WTDMWRTLYPD-V 199
Query: 234 EAYTCWPSNTGAEQFNYGTRIDHILC 259
YT W + A + G RID+ +
Sbjct: 200 PGYTWWSNRGQAYAKDVGWRIDYQMV 225
>pdb|1AKO|A Chain A, Exonuclease Iii From Escherichia Coli
Length = 268
Score = 72.8 bits (177), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 69/275 (25%), Positives = 114/275 (41%), Gaps = 50/275 (18%)
Query: 1 MKIVTYNVNGLRQRVSQFGSLRKLLDSFDADIICFQETKLRRQELKSDLVMADGYESFFS 60
MK V++N+NGLR R Q L +++ D+I QETK+ + V GY F+
Sbjct: 1 MKFVSFNINGLRARPHQ---LEAIVEKHQPDVIGLQETKVHDDMFPLEEVAKLGYNVFYH 57
Query: 61 CTRTSDKGRTGYSGVATFCRVKSPFSSTEVALPVAAEEGFTGLLETSGSKIMEGLEDFSK 120
G+ G+ GVA + P+A GF G E + +I
Sbjct: 58 -------GQKGHYGVALLTK----------ETPIAVRRGFPGDDEEAQRRI--------- 91
Query: 121 DELLKIDSEGRCVITDHGHFILFNVYGPRADSED-TVRIQFKLQFFHKRWEFLLCQGRR- 178
I +E ++ G+ + N Y P+ +S D ++ K QF+ +L + +R
Sbjct: 92 -----IMAEIPSLL---GNVTVINGYFPQGESRDHPIKFPAKAQFYQNLQNYLETELKRD 143
Query: 179 --IFVVGDLNIAPAAIDRCDAGPDFAKNEFRIWFRSMLVES--------GGSFFDVFRSK 228
+ ++GD+NI+P +D G + K R S L E D FR
Sbjct: 144 NPVLIMGDMNISPTDLD-IGIGEENRKRWLRTGKCSFLPEEREWMDRLMSWGLVDTFRHA 202
Query: 229 HPERREAYTCWPSNTGAEQFNYGTRIDHILCAGPC 263
+P+ + ++ + + N G RID +L + P
Sbjct: 203 NPQTADRFSWFDYRSKGFDDNRGLRIDLLLASQPL 237
>pdb|2O3H|A Chain A, Crystal Structure Of The Human C65a Ape
Length = 285
Score = 70.9 bits (172), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 73/269 (27%), Positives = 112/269 (41%), Gaps = 51/269 (18%)
Query: 1 MKIVTYNVNGLRQRVSQFGSLRKLLDSFDADIICFQETKLRRQELKSDLVMADGYESFFS 60
+KI ++NV+GLR + + G + DI+C QETK +L ++L G +
Sbjct: 29 LKIASWNVDGLRAWIKKKG--LDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQY- 85
Query: 61 CTRTSDKGRTGYSGVATFCRVKSPFSSTEVALPVAAEEGFTGLLETSGSKIMEGLEDFSK 120
+ SDK GYSGV R + P K+ G+ D
Sbjct: 86 WSAPSDK--EGYSGVGLLSR-QCPL------------------------KVSYGIGDEEH 118
Query: 121 DELLKIDSEGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQFFHKRWEFL--LCQGRR 178
D+ EGR ++ + F+L Y P A VR++++ ++ +FL L +
Sbjct: 119 DQ------EGRVIVAEFDSFVLVTAYVPNA-GRGLVRLEYRQRWDEAFRKFLKGLASRKP 171
Query: 179 IFVVGDLNIAPAAID-------RCDAGPDFAKNEFRIWFRSMLVESGGSFFDVFRSKHPE 231
+ + GDLN+A ID + +AG F E R F +L D FR +P
Sbjct: 172 LVLCGDLNVAHEEIDLRNPKGNKKNAG--FTPQE-RQGFGELL--QAVPLADSFRHLYPN 226
Query: 232 RREAYTCWPSNTGAEQFNYGTRIDHILCA 260
AYT W A N G R+D+ L +
Sbjct: 227 TPYAYTFWTYMMNARSKNVGWRLDYFLLS 255
>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 = 70.5 bits (171), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 73/269 (27%), Positives = 112/269 (41%), Gaps = 51/269 (18%)
Query: 1 MKIVTYNVNGLRQRVSQFGSLRKLLDSFDADIICFQETKLRRQELKSDLVMADGYESFFS 60
+KI ++NV+GLR + + G + DI+C QETK +L ++L G +
Sbjct: 62 LKICSWNVDGLRAWIKKKG--LDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQY- 118
Query: 61 CTRTSDKGRTGYSGVATFCRVKSPFSSTEVALPVAAEEGFTGLLETSGSKIMEGLEDFSK 120
+ SDK GYSGV R + P K+ G+ D
Sbjct: 119 WSAPSDK--EGYSGVGLLSR-QCPL------------------------KVSYGIGDEEH 151
Query: 121 DELLKIDSEGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQFFHKRWEFL--LCQGRR 178
D+ EGR ++ + F+L Y P A VR++++ ++ +FL L +
Sbjct: 152 DQ------EGRVIVAEFDSFVLVTAYVPNA-GRGLVRLEYRQRWDEAFRKFLKGLASRKP 204
Query: 179 IFVVGDLNIAPAAID-------RCDAGPDFAKNEFRIWFRSMLVESGGSFFDVFRSKHPE 231
+ + GDLN+A ID + +AG F E R F +L D FR +P
Sbjct: 205 LVLCGDLNVAHEEIDLRNPKGNKKNAG--FTPQE-RQGFGELL--QAVPLADSFRHLYPN 259
Query: 232 RREAYTCWPSNTGAEQFNYGTRIDHILCA 260
AYT W A N G R+D+ L +
Sbjct: 260 TPYAYTFWTYMMNARSKNVGWRLDYFLLS 288
>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 = 70.1 bits (170), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 73/269 (27%), Positives = 112/269 (41%), Gaps = 51/269 (18%)
Query: 1 MKIVTYNVNGLRQRVSQFGSLRKLLDSFDADIICFQETKLRRQELKSDLVMADGYESFFS 60
+KI ++NV+GLR + + G + DI+C QETK +L ++L G +
Sbjct: 61 LKICSWNVDGLRAWIKKKG--LDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQY- 117
Query: 61 CTRTSDKGRTGYSGVATFCRVKSPFSSTEVALPVAAEEGFTGLLETSGSKIMEGLEDFSK 120
+ SDK GYSGV R + P K+ G+ D
Sbjct: 118 WSAPSDK--EGYSGVGLLSR-QCPL------------------------KVSYGIGDEEH 150
Query: 121 DELLKIDSEGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQFFHKRWEFL--LCQGRR 178
D+ EGR ++ + F+L Y P A VR++++ ++ +FL L +
Sbjct: 151 DQ------EGRVIVAEFDSFVLVTAYVPNA-GRGLVRLEYRQRWDEAFRKFLKGLASRKP 203
Query: 179 IFVVGDLNIAPAAID-------RCDAGPDFAKNEFRIWFRSMLVESGGSFFDVFRSKHPE 231
+ + GDLN+A ID + +AG F E R F +L D FR +P
Sbjct: 204 LVLCGDLNVAHEEIDLRNPKGNKKNAG--FTPQE-RQGFGELL--QAVPLADSFRHLYPN 258
Query: 232 RREAYTCWPSNTGAEQFNYGTRIDHILCA 260
AYT W A N G R+D+ L +
Sbjct: 259 TPYAYTFWTYMMNARSKNVGWRLDYFLLS 287
>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 = 70.1 bits (170), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 73/269 (27%), Positives = 112/269 (41%), Gaps = 51/269 (18%)
Query: 1 MKIVTYNVNGLRQRVSQFGSLRKLLDSFDADIICFQETKLRRQELKSDLVMADGYESFFS 60
+KI ++NV+GLR + + G + DI+C QETK +L ++L G +
Sbjct: 31 LKICSWNVDGLRAWIKKKG--LDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQY- 87
Query: 61 CTRTSDKGRTGYSGVATFCRVKSPFSSTEVALPVAAEEGFTGLLETSGSKIMEGLEDFSK 120
+ SDK GYSGV R + P K+ G+ D
Sbjct: 88 WSAPSDK--EGYSGVGLLSR-QCPL------------------------KVSYGIGDEEH 120
Query: 121 DELLKIDSEGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQFFHKRWEFL--LCQGRR 178
D+ EGR ++ + F+L Y P A VR++++ ++ +FL L +
Sbjct: 121 DQ------EGRVIVAEFDSFVLVTAYVPNA-GRGLVRLEYRQRWDEAFRKFLKGLASRKP 173
Query: 179 IFVVGDLNIAPAAID-------RCDAGPDFAKNEFRIWFRSMLVESGGSFFDVFRSKHPE 231
+ + GDLN+A ID + +AG F E R F +L D FR +P
Sbjct: 174 LVLCGDLNVAHEEIDLRNPKGNKKNAG--FTPQE-RQGFGELL--QAVPLADSFRHLYPN 228
Query: 232 RREAYTCWPSNTGAEQFNYGTRIDHILCA 260
AYT W A N G R+D+ L +
Sbjct: 229 TPYAYTFWTYMMNARSKNVGWRLDYFLLS 257
>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 = 69.7 bits (169), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 73/269 (27%), Positives = 112/269 (41%), Gaps = 51/269 (18%)
Query: 1 MKIVTYNVNGLRQRVSQFGSLRKLLDSFDADIICFQETKLRRQELKSDLVMADGYESFFS 60
+KI ++NV+GLR + + G + DI+C QETK +L ++L G +
Sbjct: 23 LKICSWNVDGLRAWIKKKG--LDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQY- 79
Query: 61 CTRTSDKGRTGYSGVATFCRVKSPFSSTEVALPVAAEEGFTGLLETSGSKIMEGLEDFSK 120
+ SDK GYSGV R + P K+ G+ D
Sbjct: 80 WSAPSDK--EGYSGVGLLSR-QCPL------------------------KVSYGIGDEEH 112
Query: 121 DELLKIDSEGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQFFHKRWEFL--LCQGRR 178
D+ EGR ++ + F+L Y P A VR++++ ++ +FL L +
Sbjct: 113 DQ------EGRVIVAEFDSFVLVTAYVPNA-GRGLVRLEYRQRWDEAFRKFLKGLASRKP 165
Query: 179 IFVVGDLNIAPAAID-------RCDAGPDFAKNEFRIWFRSMLVESGGSFFDVFRSKHPE 231
+ + GDLN+A ID + +AG F E R F +L D FR +P
Sbjct: 166 LVLCGDLNVAHEEIDLRNPKGNKKNAG--FTPQE-RQGFGELL--QAVPLADSFRHLYPN 220
Query: 232 RREAYTCWPSNTGAEQFNYGTRIDHILCA 260
AYT W A N G R+D+ L +
Sbjct: 221 TPYAYTFWTYMMNARSKNVGWRLDYFLLS 249
>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 = 69.7 bits (169), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 73/269 (27%), Positives = 112/269 (41%), Gaps = 51/269 (18%)
Query: 1 MKIVTYNVNGLRQRVSQFGSLRKLLDSFDADIICFQETKLRRQELKSDLVMADGYESFFS 60
+KI ++NV+GLR + + G + DI+C QETK +L ++L G +
Sbjct: 20 LKICSWNVDGLRAWIKKKG--LDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQY- 76
Query: 61 CTRTSDKGRTGYSGVATFCRVKSPFSSTEVALPVAAEEGFTGLLETSGSKIMEGLEDFSK 120
+ SDK GYSGV R + P K+ G+ D
Sbjct: 77 WSAPSDK--EGYSGVGLLSR-QCPL------------------------KVSYGIGDEEH 109
Query: 121 DELLKIDSEGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQFFHKRWEFL--LCQGRR 178
D+ EGR ++ + F+L Y P A VR++++ ++ +FL L +
Sbjct: 110 DQ------EGRVIVAEFDSFVLVTAYVPNA-GRGLVRLEYRQRWDEAFRKFLKGLASRKP 162
Query: 179 IFVVGDLNIAPAAID-------RCDAGPDFAKNEFRIWFRSMLVESGGSFFDVFRSKHPE 231
+ + GDLN+A ID + +AG F E R F +L D FR +P
Sbjct: 163 LVLCGDLNVAHEEIDLRNPKGNKKNAG--FTPQE-RQGFGELL--QAVPLADSFRHLYPN 217
Query: 232 RREAYTCWPSNTGAEQFNYGTRIDHILCA 260
AYT W A N G R+D+ L +
Sbjct: 218 TPYAYTFWTYMMNARSKNVGWRLDYFLLS 246
>pdb|2JC4|A Chain A, 3'-5' Exonuclease (Nexo) From Neisseria Meningitidis
Length = 256
Score = 68.9 bits (167), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 71/268 (26%), Positives = 110/268 (41%), Gaps = 54/268 (20%)
Query: 1 MKIVTYNVNGLRQRVSQFGSLRKLLDSFDADIICFQETKLRRQELKSDLVMADGYESFFS 60
MKI T+NVN L R+ Q ++ LL DI+ QE KL + + + + G+ +S
Sbjct: 1 MKITTWNVNSLNVRLPQ---VQNLLADNPPDILVLQELKLDQDKFPAAALQMMGWHCVWS 57
Query: 61 CTRTSDKGRTGYSGVATFCRVKSPFSSTEVALPVAAEEGFTGLLETSGSKIMEGLEDFSK 120
G+ Y+GVA R ++P G L +
Sbjct: 58 -------GQKTYNGVAIVSR----------SVPQDVHFGLPALPD--------------- 85
Query: 121 DELLKIDSEGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQFFHKRWEFL---LCQGR 177
D + R + + NVY ++ D+ + ++K Q+F EF+ + +
Sbjct: 86 ------DPQRRVIAATVSGVRVINVYCVNGEALDSPKFKYKEQWFAALTEFVRDEMTRHG 139
Query: 178 RIFVVGDLNIAPAAIDRCDAGPDFAK----NEFRIWFRSMLVESGGSFFDVFRSKHPERR 233
++ ++GD NIAPA D D K + R WF+++L D R HPE
Sbjct: 140 KLVLLGDFNIAPADADCYDPEKWHEKIHCSSVERQWFQNLL---DLGLTDSLRQVHPE-- 194
Query: 234 EAYTCWPSNTGAE-QFNYGTRIDHILCA 260
A+ W GA Q G RIDHIL +
Sbjct: 195 GAFYTWFDYRGAMFQRKLGLRIDHILVS 222
>pdb|2VOA|A Chain A, Structure Of An Ap Endonuclease From Archaeoglobus
Fulgidus
pdb|2VOA|B Chain B, Structure Of An Ap Endonuclease From Archaeoglobus
Fulgidus
Length = 257
Score = 60.8 bits (146), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 80/275 (29%), Positives = 112/275 (40%), Gaps = 62/275 (22%)
Query: 1 MKIVTYNVNGLRQRVSQFGSLRKLLDSFDADIICFQETKLRRQELKSDLVMADGYESFFS 60
+KI T+NVN +R R+ + L DI+C QETK+ ++ GY FS
Sbjct: 2 LKIATFNVNSIRSRLH---IVIPWLKENKPDILCMQETKVENRKFPEADFHRIGYHVVFS 58
Query: 61 CTRTSDKGRTGYSGVATFCRVKSPFSSTEVALPVAAEEGFTGLLETSGSKIMEGLEDFSK 120
G G +GVA +A+ E + GL+ K
Sbjct: 59 -------GSKGRNGVA-----------------IASLE--------EPEDVSFGLDSEPK 86
Query: 121 DE--LLKIDSEGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQFFHKRWEFLL-CQGR 177
DE L++ G VI N Y P+ D+ + Q+KLQ+ + + +L
Sbjct: 87 DEDRLIRAKIAGIDVI---------NTYVPQGFKIDSEKYQYKLQWLERLYHYLQKTVDF 137
Query: 178 RIFVV--GDLNIAPAAIDRCDAGPDFAKN------EFRIWFRSMLVESGGSFFDVFRSKH 229
R F V GD+N+AP ID PD KN + R ++ +L E G F DV R H
Sbjct: 138 RSFAVWCGDMNVAPEPIDV--HSPDKLKNHVXFHEDARRAYKKIL-ELG--FVDVLRKIH 192
Query: 230 PERREAYTCWPSNT-GAEQFNYGTRIDHILCAGPC 263
P R YT + GA + G R D IL P
Sbjct: 193 PNER-IYTFYDYRVKGAIERGLGWRGDAILATPPL 226
>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 = 55.5 bits (132), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 77/303 (25%), Positives = 117/303 (38%), Gaps = 61/303 (20%)
Query: 2 KIVTYNVNGLRQRVSQFGS-LRKLLDSFDADIICFQETKLRRQELKSD--LVMADGYESF 58
K +T+NV GLR + + S LR +++ D++C QETKL E ++ L + DGY SF
Sbjct: 151 KFITWNVAGLRGLLKKNASALRAFMEAEKPDVLCLQETKLNVDEADANATLGVVDGY-SF 209
Query: 59 ----------FSCTRTSDKGRTGYSGVATFCRVKSPFSSTEVALPVAAEEGFTGLLETSG 108
+S TRT K T G+ C + ALP + +G
Sbjct: 210 VDHPCAFKRGYSGTRTYMKNSTTVKGLHARC-------TRGFALPSEPQAD-----AAAG 257
Query: 109 SKIM-EGLEDFSKDELLKIDSEGRCVITDHGHFILFNVYGPRADSEDTVRIQFKLQFFHK 167
S+++ EG D L S + L N Y + T R+ +++Q F
Sbjct: 258 SRVLVEGAGDEEGRVLTTFLSPDPDSASSSSRIALVNTYVANSGMGLT-RLPYRVQSFDP 316
Query: 168 RW-EFL------------------LCQGRR---IFVVGDLNIAPAAIDRCDAGP------ 199
E+L + G GDLN+A DR AG
Sbjct: 317 SMREYLHRLDTWATENAAVPSAAAMGSGSSPHGFIWAGDLNVAERDYDRYYAGTFKSMQE 376
Query: 200 --DFAKNEFRIWFRSMLVESGGSFFDVFRSKHPERREAYTCWPSNTGAEQFNYGTRIDHI 257
FA E R+ FR + + D+FR +P+ Y+ W N G R+D+
Sbjct: 377 CSGFAPEE-RMSFRETMQRTNS--VDIFRQLYPQAGPVYSFWSQRINGRPRNLGWRLDYF 433
Query: 258 LCA 260
+ +
Sbjct: 434 VVS 436
>pdb|4F1R|A Chain A, Structure Analysis Of The Global Metabolic Regulator Crc
From Pseudomonas Aeruginos
Length = 293
Score = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 66/277 (23%), Positives = 102/277 (36%), Gaps = 66/277 (23%)
Query: 1 MKIVTYNVNGLRQRVSQFGSLRKLLDSFDADIICFQETKLRRQELKSDLVMADGYESFFS 60
M+I++ NVNG++ + L L + +AD+IC Q+T+ +L DGY +
Sbjct: 35 MRIISVNVNGIQAAAER--GLLSWLQAQNADVICLQDTRASAFDLDDPSFQLDGYFLYAC 92
Query: 61 CTRTSDKGRTGYSGVATFCRVKSPFSSTEVALPVAAEEGFTGLLETSGSKIMEGLEDFSK 120
++G GVA + R++ P A G ET+
Sbjct: 93 DAELPEQG-----GVALYSRLQ----------PKAVISGLG--FETA------------- 122
Query: 121 DELLKIDSEGRCVITDHGHFILFNVYGPRADSED---TVRIQFKLQFFH-------KRWE 170
D GR + D + + P S D + +F F H KR E
Sbjct: 123 ------DRYGRYLQADFDKVSIATLLLPSGQSGDESLNQKFKFMDDFTHYLSKQRRKRRE 176
Query: 171 FLLCQGRRIFVVGDLNIAPAAID-----RCDAGPDFAKNEFRIWFRSMLVESGGSFFDVF 225
++ C G L +A +D C P F E R W + G + D
Sbjct: 177 YIYC--------GSLYVAHQKMDVKNWRECQQMPGFLAPE-RAWLDEVFGNLG--YADAL 225
Query: 226 RSKHPERREAYTCWPSNTGAEQFNYGTRIDH-ILCAG 261
R E + ++ WP + AE N G R D+ +L G
Sbjct: 226 REVSRE-GDQFSWWPDSEQAEMLNLGWRFDYQVLTPG 261
>pdb|1NYP|A Chain A, 4th Lim Domain Of Pinch Protein
pdb|1U5S|B Chain B, Nmr Structure Of The Complex Between Nck-2 Sh3 Domain And
Pinch-1 Lim4 Domain
Length = 66
Score = 30.8 bits (68), Expect = 2.2, Method: Composition-based stats.
Identities = 13/36 (36%), Positives = 18/36 (50%)
Query: 571 IPLCKGHKEPCVARVVKKPGPTFGRRFFVCARAEGP 606
+P+C + P RVV G + FVCA+ E P
Sbjct: 5 VPICGACRRPIEGRVVNAMGKQWHVEHFVCAKCEKP 40
>pdb|3PVL|A Chain A, Structure Of Myosin Viia Myth4-Ferm-Sh3 In Complex With
The Cen1 Of Sans
Length = 655
Score = 29.6 bits (65), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 46/100 (46%), Gaps = 8/100 (8%)
Query: 320 LGEVPEIPQHSTPSLASRYLPIIRGVQQTLVSVLMKREV-AKQGKSCKFSGSLPAESNST 378
+G++PE H+ S S +P++ + +TL KRE+ A QG+ ES
Sbjct: 85 MGDLPEPKYHTAMSDGSEKIPVMTKIYETLGKKTYKRELQALQGEGEVTKRLNDGESTVQ 144
Query: 379 GDT--EDCSENVDRSLNNYCDSGILQG-----VYCSSSNQ 411
G++ ED + L+ +GIL+ +YC S Q
Sbjct: 145 GNSMLEDRPTSNLEKLHFIIGNGILRPALRDEIYCQISKQ 184
>pdb|3N75|A Chain A, X-Ray Crystal Structure Of The Escherichia Coli Inducible
Lysine Decarboxylase Ldci
pdb|3N75|B Chain B, X-Ray Crystal Structure Of The Escherichia Coli Inducible
Lysine Decarboxylase Ldci
pdb|3N75|C Chain C, X-Ray Crystal Structure Of The Escherichia Coli Inducible
Lysine Decarboxylase Ldci
pdb|3N75|D Chain D, X-Ray Crystal Structure Of The Escherichia Coli Inducible
Lysine Decarboxylase Ldci
pdb|3N75|E Chain E, X-Ray Crystal Structure Of The Escherichia Coli Inducible
Lysine Decarboxylase Ldci
pdb|3Q16|A Chain A, Linkage Between The Bacterial Acid Stress And Stringent
Responses: The Structure Of The Inducible Lysine
Decarboxylase
pdb|3Q16|B Chain B, Linkage Between The Bacterial Acid Stress And Stringent
Responses: The Structure Of The Inducible Lysine
Decarboxylase
pdb|3Q16|C Chain C, Linkage Between The Bacterial Acid Stress And Stringent
Responses: The Structure Of The Inducible Lysine
Decarboxylase
pdb|3Q16|D Chain D, Linkage Between The Bacterial Acid Stress And Stringent
Responses: The Structure Of The Inducible Lysine
Decarboxylase
pdb|3Q16|E Chain E, Linkage Between The Bacterial Acid Stress And Stringent
Responses: The Structure Of The Inducible Lysine
Decarboxylase
Length = 715
Score = 29.6 bits (65), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 205 EFRIWFRSMLVESGGSFFDVFRSKHPERREAYTCWP 240
+FR + + ES G FFDV++ H + E CWP
Sbjct: 434 KFRKEIKRLRTESDGWFFDVWQPDHIDTTE---CWP 466
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 0.133 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,302,322
Number of Sequences: 62578
Number of extensions: 817977
Number of successful extensions: 1756
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1693
Number of HSP's gapped (non-prelim): 31
length of query: 627
length of database: 14,973,337
effective HSP length: 105
effective length of query: 522
effective length of database: 8,402,647
effective search space: 4386181734
effective search space used: 4386181734
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: 54 (25.4 bits)