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= 024924
(260 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3TWL|A Chain A, Crystal Structure Of Arabidopsis Thaliana Fpg
pdb|3TWM|A Chain A, Crystal Structure Of Arabidopsis Thaliana Fpg
pdb|3TWM|B Chain B, Crystal Structure Of Arabidopsis Thaliana Fpg
Length = 310
Score = 423 bits (1088), Expect = e-119, Method: Compositional matrix adjust.
Identities = 209/258 (81%), Positives = 228/258 (88%), Gaps = 3/258 (1%)
Query: 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGK 60
MPELPEVEAARRAIEE+C+GKKI + IIADDNKVI G+S SDF+ S+LGK I+SA RKGK
Sbjct: 1 MPELPEVEAARRAIEENCLGKKIKRVIIADDNKVIHGISPSDFQTSILGKTIISARRKGK 60
Query: 61 NLWLRLDSPPFPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLEL 120
NLWL LDSPPFPSFQFGM GAIYIKGVAVT+YKRSAVKD++EWPSKYSKFFVELDDGLEL
Sbjct: 61 NLWLELDSPPFPSFQFGMAGAIYIKGVAVTKYKRSAVKDSEEWPSKYSKFFVELDDGLEL 120
Query: 121 SFTDKRRFAKVRLLNDPTSVPPISELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQSY 180
SFTDKRRFAKVRLL +PTSV PISELGPDALLEPMTVDEF +SL+KKKITIK LLLDQ Y
Sbjct: 121 SFTDKRRFAKVRLLANPTSVSPISELGPDALLEPMTVDEFAESLAKKKITIKPLLLDQGY 180
Query: 181 ISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAVEVDADCSRFPLEW 240
ISGIGNW+ADEVLYQA+IHPLQTA SLSKE C L IKEVI+ AVEVDAD S+FP W
Sbjct: 181 ISGIGNWIADEVLYQARIHPLQTASSLSKEQCEALHTSIKEVIEKAVEVDADSSQFPSNW 240
Query: 241 LFHFRWGKKPGK--VNGK 256
+FH R KKPGK V+GK
Sbjct: 241 IFHNR-EKKPGKAFVDGK 257
>pdb|3TWK|A Chain A, Crystal Structure Of Arabidopsis Thaliana Fpg
pdb|3TWK|B Chain B, Crystal Structure Of Arabidopsis Thaliana Fpg
Length = 297
Score = 415 bits (1066), Expect = e-116, Method: Compositional matrix adjust.
Identities = 206/257 (80%), Positives = 225/257 (87%), Gaps = 3/257 (1%)
Query: 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKN 61
PELPEVEAARRAIEE+C+GKKI + IIADDNKVI G+S SDF+ S+LGK I+SA RKGKN
Sbjct: 2 PELPEVEAARRAIEENCLGKKIKRVIIADDNKVIHGISPSDFQTSILGKTIISARRKGKN 61
Query: 62 LWLRLDSPPFPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELS 121
LWL LDSPPFPSFQFG GAIYIKGVAVT+YKRSAVKD++EWPSKYSKFFVELDDGLELS
Sbjct: 62 LWLELDSPPFPSFQFGXAGAIYIKGVAVTKYKRSAVKDSEEWPSKYSKFFVELDDGLELS 121
Query: 122 FTDKRRFAKVRLLNDPTSVPPISELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQSYI 181
FTDKRRFAKVRLL +PTSV PISELGPDALLEP TVDEF +SL+KKKITIK LLLDQ YI
Sbjct: 122 FTDKRRFAKVRLLANPTSVSPISELGPDALLEPXTVDEFAESLAKKKITIKPLLLDQGYI 181
Query: 182 SGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAVEVDADCSRFPLEWL 241
SGIGNW+ADEVLYQA+IHPLQTA SLSKE C L IKEVI+ AVEVDAD S+FP W+
Sbjct: 182 SGIGNWIADEVLYQARIHPLQTASSLSKEQCEALHTSIKEVIEKAVEVDADSSQFPSNWI 241
Query: 242 FHFRWGKKPGK--VNGK 256
FH R KKPGK V+GK
Sbjct: 242 FHNR-EKKPGKAFVDGK 257
>pdb|1EE8|A Chain A, Crystal Structure Of Mutm (Fpg) Protein From Thermus
Thermophilus Hb8
pdb|1EE8|B Chain B, Crystal Structure Of Mutm (Fpg) Protein From Thermus
Thermophilus Hb8
Length = 266
Score = 99.8 bits (247), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 71/234 (30%), Positives = 109/234 (46%), Gaps = 30/234 (12%)
Query: 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKN 61
PELPEVE RR + +G+ + + + D + + A G+ IL R+GK
Sbjct: 1 PELPEVETTRRRLRPLVLGQTLRQVVHRDPARYRNTALAE-------GRRILEVDRRGKF 53
Query: 62 LWLRLDSPPFPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELS 121
L L+ GMTG ++ T + R+A+ + +G L
Sbjct: 54 LLFALEGGVELVAHLGMTGGFRLE---PTPHTRAAL----------------VLEGRTLY 94
Query: 122 FTDKRRFAK---VRLLNDPTSVPPISELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQ 178
F D RRF + VR D +P + LGP+ L E F L + +KALLLDQ
Sbjct: 95 FHDPRRFGRLFGVRR-GDYREIPLLLRLGPEPLSEAFAFPGFFRGLKESARPLKALLLDQ 153
Query: 179 SYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAVEVDAD 232
+G+GN ADE L++A++ P + A SL++E L + ++EV+ AVE+
Sbjct: 154 RLAAGVGNIYADEALFRARLSPFRPARSLTEEEARRLYRALREVLAEAVELGGS 207
>pdb|1K82|A Chain A, Crystal Structure Of E.Coli Formamidopyrimidine-Dna
Glycosylase (Fpg) Covalently Trapped With Dna
pdb|1K82|B Chain B, Crystal Structure Of E.Coli Formamidopyrimidine-Dna
Glycosylase (Fpg) Covalently Trapped With Dna
pdb|1K82|C Chain C, Crystal Structure Of E.Coli Formamidopyrimidine-Dna
Glycosylase (Fpg) Covalently Trapped With Dna
pdb|1K82|D Chain D, Crystal Structure Of E.Coli Formamidopyrimidine-Dna
Glycosylase (Fpg) Covalently Trapped With Dna
Length = 268
Score = 95.5 bits (236), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 68/227 (29%), Positives = 107/227 (47%), Gaps = 17/227 (7%)
Query: 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKN 61
PELPEVE +RR IE H +G I+ +++ + ++ VS + S + +LS R+ K
Sbjct: 1 PELPEVETSRRGIEPHLVGATILHAVV-RNGRLRWPVSEEIYRLS--DQPVLSVQRRAKY 57
Query: 62 LWLRLDSPPFPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELS 121
L L L + GM+G++ I + P K+ + + +G L
Sbjct: 58 LLLELPEG-WIIIHLGMSGSLRILPEELP-------------PEKHDHVDLVMSNGKVLR 103
Query: 122 FTDKRRFAKVRLLNDPTSVPPISELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQSYI 181
+TD RRF + ++ LGP+ L + + +KKK IK L+D +
Sbjct: 104 YTDPRRFGAWLWTKELEGHNVLTHLGPEPLSDDFNGEYLHQKCAKKKTAIKPWLMDNKLV 163
Query: 182 SGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAVE 228
G+GN A E L+ A IHP + A SLS C L + IK V+ ++E
Sbjct: 164 VGVGNIYASESLFAAGIHPDRLASSLSLAECELLARVIKAVLLRSIE 210
>pdb|1L1T|A Chain A, Mutm (Fpg) Bound To Abasic-Site Containing Dna
pdb|1L1Z|A Chain A, Mutm (Fpg) Covalent-Dna Intermediate
pdb|1L2B|A Chain A, Mutm (Fpg) Dna End-Product Structure
pdb|1L2C|A Chain A, Mutm (Fpg)-Dna Estranged Thymine Mismatch Recognition
Complex
pdb|1L2D|A Chain A, Mutm (fpg)-dna Estranged Guanine Mismatch Recognition
Complex
Length = 274
Score = 91.7 bits (226), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 71/229 (31%), Positives = 103/229 (44%), Gaps = 16/229 (6%)
Query: 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGK 60
MPELPEVE RR + +GK I I N + + F A ++G+ + R+GK
Sbjct: 1 MPELPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGK 60
Query: 61 NLWLRLDSPPFPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLEL 120
L LD S M G R AV E ++ DG EL
Sbjct: 61 FLKFLLDRDALIS-HLRMEG-------------RYAVASALEPLEPHTHVVFCFTDGSEL 106
Query: 121 SFTDKRRFAKVRLL--NDPTSVPPISELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQ 178
+ D R+F + + + PP++ELGP+ L + + K K ++KALLLDQ
Sbjct: 107 RYRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVKALLLDQ 166
Query: 179 SYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAV 227
+ ++G GN DE L++A I P + A SLS + L + + I AV
Sbjct: 167 TVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAV 215
>pdb|1R2Y|A Chain A, Mutm (Fpg) Bound To 8-Oxoguanine (Oxog) Containing Dna
pdb|1R2Z|A Chain A, Mutm (Fpg) Bound To 5,6-Dihydrouracil (Dhu) Containing Dna
Length = 274
Score = 90.1 bits (222), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 70/229 (30%), Positives = 103/229 (44%), Gaps = 16/229 (6%)
Query: 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGK 60
MP+LPEVE RR + +GK I I N + + F A ++G+ + R+GK
Sbjct: 1 MPQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGK 60
Query: 61 NLWLRLDSPPFPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLEL 120
L LD S M G R AV E ++ DG EL
Sbjct: 61 FLKFLLDRDALIS-HLRMEG-------------RYAVASALEPLEPHTHVVFCFTDGSEL 106
Query: 121 SFTDKRRFAKVRLL--NDPTSVPPISELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQ 178
+ D R+F + + + PP++ELGP+ L + + K K ++KALLLDQ
Sbjct: 107 RYRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVKALLLDQ 166
Query: 179 SYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAV 227
+ ++G GN DE L++A I P + A SLS + L + + I AV
Sbjct: 167 TVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAV 215
>pdb|1TDZ|A Chain A, Crystal Structure Complex Between The Lactococcus Lactis
Fpg (Mutm) And A Fapy-Dg Containing Dna
Length = 272
Score = 89.0 bits (219), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 67/237 (28%), Positives = 111/237 (46%), Gaps = 18/237 (7%)
Query: 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGK 60
MPELPEVE RR +E+ +G+KI+ V+ G + + GK I R+GK
Sbjct: 1 MPELPEVETVRRELEKRIVGQKIISIEATYPRMVLTGFE--QLKKELTGKTIQGISRRGK 58
Query: 61 NLWLRLDSPPFPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLEL 120
L + F + + ++G +Y+ + + D K+ ++ DG +L
Sbjct: 59 YLIFEIGD------DFRLISHLRMEG----KYRLATL---DAPREKHDHLTMKFADG-QL 104
Query: 121 SFTDKRRFAKVRLLNDPTSVPPI--SELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQ 178
+ D R+F L++ +P ++GP+ E F + L K IK LL+Q
Sbjct: 105 IYADVRKFGTWELISTDQVLPYFLKKKIGPEPTYEDFDEKLFREKLRKSTKKIKPYLLEQ 164
Query: 179 SYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAVEVDADCSR 235
+ ++G+GN DEVL+ AKIHP + L + S L I E++Q A+++ R
Sbjct: 165 TLVAGLGNIYVDEVLWLAKIHPEKETNQLIESSIHLLHDSIIEILQKAIKLGGSSIR 221
>pdb|2F5N|A Chain A, Mutm Crosslinked To Undamaged Dna Sampling A:t Base Pair
Ic1
pdb|2F5O|A Chain A, Mutm Crosslinked To Undamaged Dna Sampling G:c Base Pair
Ic3
pdb|2F5P|A Chain A, Mutm Crosslinked To Undamaged Dna Sampling A:t Base Pair
Ic2
Length = 274
Score = 88.2 bits (217), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 70/229 (30%), Positives = 102/229 (44%), Gaps = 16/229 (6%)
Query: 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGK 60
MPELPEVE RR + +GK I I N + + F A ++G+ + R+GK
Sbjct: 1 MPELPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGK 60
Query: 61 NLWLRLDSPPFPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLEL 120
L LD S M G R AV E ++ DG EL
Sbjct: 61 FLKFLLDRDALIS-HLRMEG-------------RYAVASALEPLEPHTHVVFCFTDGSEL 106
Query: 121 SFTDKRRFAKVRLL--NDPTSVPPISELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQ 178
+ D R+F + + + PP++ELGP+ L + + K K ++KALLLD
Sbjct: 107 RYRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVKALLLDC 166
Query: 179 SYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAV 227
+ ++G GN DE L++A I P + A SLS + L + + I AV
Sbjct: 167 TVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAV 215
>pdb|2F5Q|A Chain A, Catalytically Inactive (E3q) Mutm Crosslinked To Oxog:c
Containing Dna Cc2
pdb|2F5S|A Chain A, Catalytically Inactive (e3q) Mutm Crosslinked To Oxog:c
Containing Dna Cc1
Length = 274
Score = 87.0 bits (214), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 69/229 (30%), Positives = 102/229 (44%), Gaps = 16/229 (6%)
Query: 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGK 60
MP+LPEVE RR + +GK I I N + + F A ++G+ + R+GK
Sbjct: 1 MPQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGK 60
Query: 61 NLWLRLDSPPFPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLEL 120
L LD S M G R AV E ++ DG EL
Sbjct: 61 FLKFLLDRDALIS-HLRMEG-------------RYAVASALEPLEPHTHVVFCFTDGSEL 106
Query: 121 SFTDKRRFAKVRLL--NDPTSVPPISELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQ 178
+ D R+F + + + PP++ELGP+ L + + K K ++KALLLD
Sbjct: 107 RYRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVKALLLDC 166
Query: 179 SYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAV 227
+ ++G GN DE L++A I P + A SLS + L + + I AV
Sbjct: 167 TVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAV 215
>pdb|1PJI|A Chain A, Crystal Structure Of Wild Type Lactococcus Lactis Fpg
Complexed To A 1,3 Propanediol Containing Dna
pdb|1PM5|A Chain A, Crystal Structure Of Wild Type Lactococcus Lactis Fpg
Complexed To A Tetrahydrofuran Containing Dna
pdb|1XC8|A Chain A, Crystal Structure Complex Between The Wild-Type
Lactococcus Lactis Fpg (Mutm) And A Fapy-Dg Containing
Dna
pdb|3C58|A Chain A, Crystal Structure Of A Complex Between The Wild-Type
Lactococcus Lactis Fpg (Mutm) And A N7-Benzyl-Fapy-Dg
Containing Dna
pdb|2XZF|A Chain A, Crystal Structure Of A Complex Between The Wild-Type
Lactococcus Lactis Fpg (Mutm) And An Oxidized Pyrimidine
Containing Dna At 293k
pdb|2XZU|A Chain A, Crystal Structure Of A Complex Between The Wild-Type
Lactococcus Lactis Fpg (Mutm) And An Oxidized Pyrimidine
Containing Dna At 310k
Length = 271
Score = 86.7 bits (213), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 66/236 (27%), Positives = 110/236 (46%), Gaps = 18/236 (7%)
Query: 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKN 61
PELPEVE RR +E+ +G+KI+ V+ G + + GK I R+GK
Sbjct: 1 PELPEVETVRRELEKRIVGQKIISIEATYPRMVLTGFE--QLKKELTGKTIQGISRRGKY 58
Query: 62 LWLRLDSPPFPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELS 121
L + F + + ++G +Y+ + + D K+ ++ DG +L
Sbjct: 59 LIFEIGD------DFRLISHLRMEG----KYRLATL---DAPREKHDHLTMKFADG-QLI 104
Query: 122 FTDKRRFAKVRLLNDPTSVPPI--SELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQS 179
+ D R+F L++ +P ++GP+ E F + L K IK LL+Q+
Sbjct: 105 YADVRKFGTWELISTDQVLPYFLKKKIGPEPTYEDFDEKLFREKLRKSTKKIKPYLLEQT 164
Query: 180 YISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAVEVDADCSR 235
++G+GN DEVL+ AKIHP + L + S L I E++Q A+++ R
Sbjct: 165 LVAGLGNIYVDEVLWLAKIHPEKETNQLIESSIHLLHDSIIEILQKAIKLGGSSIR 220
>pdb|3GPX|A Chain A, Sequence-Matched Mutm Interrogation Complex 4 (Ic4)
pdb|3GQ3|A Chain A, Mutm Encountering An Intrahelical 8-Oxoguanine (Oxog)
Lesion In Ec5- Loop Deletion Complex
Length = 257
Score = 85.9 bits (211), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 69/228 (30%), Positives = 101/228 (44%), Gaps = 16/228 (7%)
Query: 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKN 61
PELPEVE RR + +GK I I N + + F A ++G+ + R+GK
Sbjct: 1 PELPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGKF 60
Query: 62 LWLRLDSPPFPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELS 121
L LD S M G R AV E ++ DG EL
Sbjct: 61 LKFLLDRDALIS-HLRMEG-------------RYAVASALEPLEPHTHVVFCFTDGSELR 106
Query: 122 FTDKRRFAKVRLL--NDPTSVPPISELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQS 179
+ D R+F + + + PP++ELGP+ L + + K K ++KALLLD +
Sbjct: 107 YRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVKALLLDCT 166
Query: 180 YISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAV 227
++G GN DE L++A I P + A SLS + L + + I AV
Sbjct: 167 VVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAV 214
>pdb|3GO8|A Chain A, Mutm Encountering An Intrahelical 8-Oxoguanine (Oxog)
Lesion In Ec3- Loop Deletion Complex
Length = 257
Score = 85.9 bits (211), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 69/228 (30%), Positives = 101/228 (44%), Gaps = 16/228 (7%)
Query: 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKN 61
PELPEVE RR + +GK I I N + + F A ++G+ + R+GK
Sbjct: 1 PELPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGKF 60
Query: 62 LWLRLDSPPFPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELS 121
L LD S M G R AV E ++ DG EL
Sbjct: 61 LKFLLDRDALIS-HLRMEG-------------RYAVASALEPLEPHTHVVFCFTDGSELR 106
Query: 122 FTDKRRFAKVRLL--NDPTSVPPISELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQS 179
+ D R+F + + + PP++ELGP+ L + + K K ++KALLLD +
Sbjct: 107 YRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVKALLLDCT 166
Query: 180 YISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAV 227
++G GN DE L++A I P + A SLS + L + + I AV
Sbjct: 167 VVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAV 214
>pdb|3SAR|A Chain A, Mutm Slanted Complex 1
pdb|3SAU|A Chain A, Mutm Interrogation Complex 6
pdb|3SAV|A Chain A, Mutm Slanted Complex 8
Length = 273
Score = 85.9 bits (211), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 69/228 (30%), Positives = 101/228 (44%), Gaps = 16/228 (7%)
Query: 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKN 61
PELPEVE RR + +GK I I N + + F A ++G+ + R+GK
Sbjct: 1 PELPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGKF 60
Query: 62 LWLRLDSPPFPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELS 121
L LD S M G R AV E ++ DG EL
Sbjct: 61 LKFLLDRDALIS-HLRMEG-------------RYAVASALEPLEPHTHVVFCFTDGSELR 106
Query: 122 FTDKRRFAKVRLL--NDPTSVPPISELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQS 179
+ D R+F + + + PP++ELGP+ L + + K K ++KALLLD +
Sbjct: 107 YRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVKALLLDCT 166
Query: 180 YISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAV 227
++G GN DE L++A I P + A SLS + L + + I AV
Sbjct: 167 VVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAV 214
>pdb|3GPU|A Chain A, Mutm Encountering An Intrahelical 8-Oxoguanine (Oxog)
Lesion In Ec4- Loop Deletion Complex
Length = 256
Score = 85.9 bits (211), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 69/228 (30%), Positives = 101/228 (44%), Gaps = 16/228 (7%)
Query: 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKN 61
PELPEVE RR + +GK I I N + + F A ++G+ + R+GK
Sbjct: 1 PELPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGKF 60
Query: 62 LWLRLDSPPFPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELS 121
L LD S M G R AV E ++ DG EL
Sbjct: 61 LKFLLDRDALIS-HLRMEG-------------RYAVASALEPLEPHTHVVFCFTDGSELR 106
Query: 122 FTDKRRFAKVRLL--NDPTSVPPISELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQS 179
+ D R+F + + + PP++ELGP+ L + + K K ++KALLLD +
Sbjct: 107 YRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVKALLLDCT 166
Query: 180 YISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAV 227
++G GN DE L++A I P + A SLS + L + + I AV
Sbjct: 167 VVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAV 214
>pdb|3GPP|A Chain A, Mutm Encountering An Intrahelical 8-Oxoguanine (Oxog)
Lesion In Ec3- T224p Complex
pdb|3GQ5|A Chain A, Sequence-Matched Mutm Interrogation Complex 5 (Ic5)
Length = 273
Score = 85.5 bits (210), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 69/228 (30%), Positives = 101/228 (44%), Gaps = 16/228 (7%)
Query: 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKN 61
PELPEVE RR + +GK I I N + + F A ++G+ + R+GK
Sbjct: 1 PELPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGKF 60
Query: 62 LWLRLDSPPFPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELS 121
L LD S M G R AV E ++ DG EL
Sbjct: 61 LKFLLDRDALIS-HLRMEG-------------RYAVASALEPLEPHTHVVFCFTDGSELR 106
Query: 122 FTDKRRFAKVRLL--NDPTSVPPISELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQS 179
+ D R+F + + + PP++ELGP+ L + + K K ++KALLLD +
Sbjct: 107 YRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVKALLLDCT 166
Query: 180 YISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAV 227
++G GN DE L++A I P + A SLS + L + + I AV
Sbjct: 167 VVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAV 214
>pdb|3GP1|A Chain A, Mutm Encountering An Intrahelical 8-Oxoguanine (Oxog)
Lesion In Ec3- V222p Complex
pdb|3SBJ|A Chain A, Mutm Slanted Complex 7
Length = 273
Score = 85.5 bits (210), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 69/228 (30%), Positives = 101/228 (44%), Gaps = 16/228 (7%)
Query: 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKN 61
PELPEVE RR + +GK I I N + + F A ++G+ + R+GK
Sbjct: 1 PELPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGKF 60
Query: 62 LWLRLDSPPFPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELS 121
L LD S M G R AV E ++ DG EL
Sbjct: 61 LKFLLDRDALIS-HLRMEG-------------RYAVASALEPLEPHTHVVFCFTDGSELR 106
Query: 122 FTDKRRFAKVRLL--NDPTSVPPISELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQS 179
+ D R+F + + + PP++ELGP+ L + + K K ++KALLLD +
Sbjct: 107 YRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVKALLLDCT 166
Query: 180 YISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAV 227
++G GN DE L++A I P + A SLS + L + + I AV
Sbjct: 167 VVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAV 214
>pdb|3GPY|A Chain A, Sequence-Matched Mutm Lesion Recognition Complex 3 (Lrc3)
pdb|3GQ4|A Chain A, Sequence-matched Mutm Lesion Recognition Complex 5 (lrc5)
Length = 273
Score = 84.7 bits (208), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 68/228 (29%), Positives = 101/228 (44%), Gaps = 16/228 (7%)
Query: 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKN 61
P+LPEVE RR + +GK I I N + + F A ++G+ + R+GK
Sbjct: 1 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGKF 60
Query: 62 LWLRLDSPPFPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELS 121
L LD S M G R AV E ++ DG EL
Sbjct: 61 LKFLLDRDALIS-HLRMEG-------------RYAVASALEPLEPHTHVVFCFTDGSELR 106
Query: 122 FTDKRRFAKVRLL--NDPTSVPPISELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQS 179
+ D R+F + + + PP++ELGP+ L + + K K ++KALLLD +
Sbjct: 107 YRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVKALLLDCT 166
Query: 180 YISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAV 227
++G GN DE L++A I P + A SLS + L + + I AV
Sbjct: 167 VVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAV 214
>pdb|3U6C|A Chain A, Mutm Set 1 Apgo
pdb|3U6D|A Chain A, Mutm Set 1 Gpgo
pdb|3U6E|A Chain A, Mutm Set 1 Tpgo
pdb|3U6L|A Chain A, Mutm Set 2 Cpgo
pdb|3U6M|A Chain A, Structural Effects Of Sequence Context On Lesion
Recognition By Mutm
pdb|3U6O|A Chain A, Mutm Set 1 Apg
pdb|3U6P|A Chain A, Mutm Set 1 Gpg
pdb|3U6Q|A Chain A, Mutm Set 2 Apgo
pdb|3U6S|A Chain A, Mutm Set 1 Tpg
Length = 273
Score = 84.7 bits (208), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 68/228 (29%), Positives = 101/228 (44%), Gaps = 16/228 (7%)
Query: 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKN 61
P+LPEVE RR + +GK I I N + + F A ++G+ + R+GK
Sbjct: 1 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGKF 60
Query: 62 LWLRLDSPPFPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELS 121
L LD S M G R AV E ++ DG EL
Sbjct: 61 LKFLLDRDALIS-HLRMEG-------------RYAVASALEPLEPHTHVVFCFTDGSELR 106
Query: 122 FTDKRRFAKVRLL--NDPTSVPPISELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQS 179
+ D R+F + + + PP++ELGP+ L + + K K ++KALLLD +
Sbjct: 107 YRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVKALLLDCT 166
Query: 180 YISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAV 227
++G GN DE L++A I P + A SLS + L + + I AV
Sbjct: 167 VVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAV 214
>pdb|3JR4|A Chain A, Mutm Interrogating An Extrahelical G
pdb|3JR5|A Chain A, Mutm Lesion Recognition Control Complex With N174c
Crosslinking Site
Length = 273
Score = 84.3 bits (207), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 68/228 (29%), Positives = 101/228 (44%), Gaps = 16/228 (7%)
Query: 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKN 61
P+LPEVE RR + +GK I I N + + F A ++G+ + R+GK
Sbjct: 1 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGKF 60
Query: 62 LWLRLDSPPFPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELS 121
L LD S M G R AV E ++ DG EL
Sbjct: 61 LKFLLDRDALIS-HLRMEG-------------RYAVASALEPLEPHTHVVFCFTDGSELR 106
Query: 122 FTDKRRFAKVRLL--NDPTSVPPISELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQS 179
+ D R+F + + + PP++ELGP+ L + + K K ++KALLLDQ+
Sbjct: 107 YRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVKALLLDQT 166
Query: 180 YISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAV 227
++G G DE L++A I P + A SLS + L + + I AV
Sbjct: 167 VVAGFGCIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAV 214
>pdb|4G4N|A Chain A, Mutm Containing M77a Mutation Bound To Undamaged Dna
Length = 273
Score = 84.0 bits (206), Expect = 7e-17, Method: Compositional matrix adjust.
Identities = 67/228 (29%), Positives = 103/228 (45%), Gaps = 16/228 (7%)
Query: 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKN 61
PELPEVE RR + +GK I I N + + F A ++G+ + R+GK
Sbjct: 1 PELPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGKF 60
Query: 62 LWLRLDSPPFPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELS 121
L LD + + + +G R AV E ++ DG EL
Sbjct: 61 LKFLLD-------RDALISHLRAEG-------RYAVASALEPLEPHTHVVFCFTDGSELR 106
Query: 122 FTDKRRFAKVRLL--NDPTSVPPISELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQS 179
+ D R+F + + + PP++ELGP+ L + + K K ++KALLLD +
Sbjct: 107 YRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVKALLLDCT 166
Query: 180 YISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAV 227
++G GN DE L++A I P + A SLS + L + + I AV
Sbjct: 167 VVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAV 214
>pdb|1NNJ|A Chain A, Crystal Structure Complex Between The Lactococcus Lactis
Fpg And An Abasic Site Containing Dna
pdb|1PJJ|A Chain A, Complex Between The Lactococcus Lactis Fpg And An Abasic
Site Containing Dna
Length = 271
Score = 83.6 bits (205), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 65/235 (27%), Positives = 109/235 (46%), Gaps = 18/235 (7%)
Query: 3 ELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNL 62
ELPEVE RR +E+ +G+KI+ V+ G + + GK I R+GK L
Sbjct: 2 ELPEVETVRRELEKRIVGQKIISIEATYPRMVLTGFE--QLKKELTGKTIQGISRRGKYL 59
Query: 63 WLRLDSPPFPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSF 122
+ F + + ++G +Y+ + + D K+ ++ DG +L +
Sbjct: 60 IFEIGD------DFRLISHLRMEG----KYRLATL---DAPREKHDHLTMKFADG-QLIY 105
Query: 123 TDKRRFAKVRLLNDPTSVPPI--SELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQSY 180
D R+F L++ +P ++GP+ E F + L K IK LL+Q+
Sbjct: 106 ADVRKFGTWELISTDQVLPYFLKKKIGPEPTYEDFDEKLFREKLRKSTKKIKPYLLEQTL 165
Query: 181 ISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAVEVDADCSR 235
++G+GN DEVL+ AKIHP + L + S L I E++Q A+++ R
Sbjct: 166 VAGLGNIYVDEVLWLAKIHPEKETNQLIESSIHLLHDSIIEILQKAIKLGGSSIR 220
>pdb|4G4O|A Chain A, Mutm Containing M77a Mutation Bound To Oxog-containing Dna
Length = 273
Score = 83.2 bits (204), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 66/228 (28%), Positives = 103/228 (45%), Gaps = 16/228 (7%)
Query: 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKN 61
P+LPEVE RR + +GK I I N + + F A ++G+ + R+GK
Sbjct: 1 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGKF 60
Query: 62 LWLRLDSPPFPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELS 121
L LD + + + +G R AV E ++ DG EL
Sbjct: 61 LKFLLD-------RDALISHLRAEG-------RYAVASALEPLEPHTHVVFCFTDGSELR 106
Query: 122 FTDKRRFAKVRLL--NDPTSVPPISELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQS 179
+ D R+F + + + PP++ELGP+ L + + K K ++KALLLD +
Sbjct: 107 YRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVKALLLDCT 166
Query: 180 YISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAV 227
++G GN DE L++A I P + A SLS + L + + I AV
Sbjct: 167 VVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAV 214
>pdb|3SAS|A Chain A, Mutm Slanted Complex 4 With R112a Mutation
pdb|3SAT|A Chain A, Mutm Slanted Complex 6 With R112a Mutation
pdb|3SAW|A Chain A, Mutm Slanted Complex 8 With R112a Mutation
Length = 273
Score = 82.8 bits (203), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 68/228 (29%), Positives = 100/228 (43%), Gaps = 16/228 (7%)
Query: 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKN 61
PELPEVE RR + +GK I I N + + F A ++G+ + R+GK
Sbjct: 1 PELPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGKF 60
Query: 62 LWLRLDSPPFPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELS 121
L LD S M G R AV E ++ DG EL
Sbjct: 61 LKFLLDRDALIS-HLRMEG-------------RYAVASALEPLEPHTHVVFCFTDGSELR 106
Query: 122 FTDKRRFAKVRLL--NDPTSVPPISELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQS 179
+ D +F + + + PP++ELGP+ L + + K K ++KALLLD +
Sbjct: 107 YRDVAKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVKALLLDCT 166
Query: 180 YISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAV 227
++G GN DE L++A I P + A SLS + L + + I AV
Sbjct: 167 VVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAV 214
>pdb|4G4Q|A Chain A, Mutm Containing F114a Mutation Bound To Undamaged Dna
Length = 273
Score = 82.4 bits (202), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 68/228 (29%), Positives = 100/228 (43%), Gaps = 16/228 (7%)
Query: 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKN 61
PELPEVE RR + +GK I I N + + F A ++G+ + R+GK
Sbjct: 1 PELPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGKF 60
Query: 62 LWLRLDSPPFPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELS 121
L LD S M G R AV E ++ DG EL
Sbjct: 61 LKFLLDRDALIS-HLRMEG-------------RYAVASALEPLEPHTHVVFCFTDGSELR 106
Query: 122 FTDKRRFAKVRLL--NDPTSVPPISELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQS 179
+ D R+ + + + PP++ELGP+ L + + K K ++KALLLD +
Sbjct: 107 YRDVRKAGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVKALLLDCT 166
Query: 180 YISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAV 227
++G GN DE L++A I P + A SLS + L + + I AV
Sbjct: 167 VVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAV 214
>pdb|1KFV|A Chain A, Crystal Structure Of Lactococcus Lactis
Formamido-Pyrimidine Dna Glycosylase (Alias Fpg Or Mutm)
Non Covalently Bound To An Ap Site Containing Dna.
pdb|1KFV|B Chain B, Crystal Structure Of Lactococcus Lactis
Formamido-Pyrimidine Dna Glycosylase (Alias Fpg Or Mutm)
Non Covalently Bound To An Ap Site Containing Dna
Length = 271
Score = 81.6 bits (200), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 65/235 (27%), Positives = 107/235 (45%), Gaps = 18/235 (7%)
Query: 3 ELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKNL 62
ELPEVE RR +E+ +G+KI+ V+ G + + GK I R+GK L
Sbjct: 2 ELPEVETVRRELEKRIVGQKIISIEATYPRXVLTGFE--QLKKELTGKTIQGISRRGKYL 59
Query: 63 WLRLDSPPFPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELSF 122
+ F + + +G +Y+ + + D K+ + DG +L +
Sbjct: 60 IFEIGD------DFRLISHLRXEG----KYRLATL---DAPREKHDHLTXKFADG-QLIY 105
Query: 123 TDKRRFAKVRLLNDPTSVPPI--SELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQSY 180
D R+F L++ +P ++GP+ E F + L K IK LL+Q+
Sbjct: 106 ADVRKFGTWELISTDQVLPYFLKKKIGPEPTYEDFDEKLFREKLRKSTKKIKPYLLEQTL 165
Query: 181 ISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAVEVDADCSR 235
++G+GN DEVL+ AKIHP + L + S L I E++Q A+++ R
Sbjct: 166 VAGLGNIYVDEVLWLAKIHPEKETNQLIESSIHLLHDSIIEILQKAIKLGGSSIR 220
>pdb|4G4R|A Chain A, Mutm Containing F114a Mutation Bound To Oxog-containing
Dna
Length = 273
Score = 80.9 bits (198), Expect = 6e-16, Method: Compositional matrix adjust.
Identities = 67/228 (29%), Positives = 100/228 (43%), Gaps = 16/228 (7%)
Query: 2 PELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAHRKGKN 61
P+LPEVE RR + +GK I I N + + F A ++G+ + R+GK
Sbjct: 1 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGKF 60
Query: 62 LWLRLDSPPFPSFQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPSKYSKFFVELDDGLELS 121
L LD S M G R AV E ++ DG EL
Sbjct: 61 LKFLLDRDALIS-HLRMEG-------------RYAVASALEPLEPHTHVVFCFTDGSELR 106
Query: 122 FTDKRRFAKVRLL--NDPTSVPPISELGPDALLEPMTVDEFTDSLSKKKITIKALLLDQS 179
+ D R+ + + + PP++ELGP+ L + + K K ++KALLLD +
Sbjct: 107 YRDVRKAGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVKALLLDCT 166
Query: 180 YISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAV 227
++G GN DE L++A I P + A SLS + L + + I AV
Sbjct: 167 VVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAV 214
>pdb|3A45|A Chain A, Crystal Structure Of Mvnei1_2
pdb|3A45|B Chain B, Crystal Structure Of Mvnei1_2
pdb|3A46|A Chain A, Crystal Structure Of Mvnei1/thf Complex
pdb|3A46|B Chain B, Crystal Structure Of Mvnei1/thf Complex
Length = 289
Score = 67.8 bits (164), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 68/238 (28%), Positives = 105/238 (44%), Gaps = 49/238 (20%)
Query: 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSA----------SDFEASVLGK 50
MPE PEV +E++ GK + + ID +S DF A++ K
Sbjct: 1 MPEGPEVALTADILEKYFKGKTL---------EYIDFISGRYSKSEPEGYDDFIANLPLK 51
Query: 51 AILSAHRKGKNLWLRLDSPPFPSFQ------FGMTGAIYIKGVAVTQYKRSAVKDTDEWP 104
+ + KGK LW L P S + FG+TG + +
Sbjct: 52 -VSNVDTKGKFLWFELFDPNDKSNKWYIWNTFGLTGMWSL------------------FE 92
Query: 105 SKYSKFFVELDDGLELSFTDKRRFAKVRLLNDPTSVP-PISELGPDALLEPMTVDEFTDS 163
+KY++ + D+ L F+D R F + N + ++ELGPD L+ +D
Sbjct: 93 AKYTRAVLSFDNELMAYFSDMRNFGTFKFSNSEKELKRKLNELGPD-FLKNDDID--ISK 149
Query: 164 LSKKKITIKALLLDQSYI-SGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIK 220
+ K K I ALL+DQ I SG+GN++ E+LY+AKI P + +L+ + L IK
Sbjct: 150 IKKYKQPIVALLMDQKKIGSGLGNYLVAEILYRAKIDPHKLGSNLTDQEIENLWYWIK 207
>pdb|3A42|A Chain A, Crystal Structure Of Mvnei1
Length = 295
Score = 67.8 bits (164), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 68/238 (28%), Positives = 105/238 (44%), Gaps = 49/238 (20%)
Query: 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSA----------SDFEASVLGK 50
MPE PEV +E++ GK + + ID +S DF A++ K
Sbjct: 1 MPEGPEVALTADILEKYFKGKTL---------EYIDFISGRYSKSEPEGYDDFIANLPLK 51
Query: 51 AILSAHRKGKNLWLRLDSPPFPSFQ------FGMTGAIYIKGVAVTQYKRSAVKDTDEWP 104
+ + KGK LW L P S + FG+TG + +
Sbjct: 52 -VSNVDTKGKFLWFELFDPNDKSNKWYIWNTFGLTGMWSL------------------FE 92
Query: 105 SKYSKFFVELDDGLELSFTDKRRFAKVRLLNDPTSVP-PISELGPDALLEPMTVDEFTDS 163
+KY++ + D+ L F+D R F + N + ++ELGPD L+ +D
Sbjct: 93 AKYTRAVLSFDNELMAYFSDMRNFGTFKFSNSEKELKRKLNELGPD-FLKNDDID--ISK 149
Query: 164 LSKKKITIKALLLDQSYI-SGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIK 220
+ K K I ALL+DQ I SG+GN++ E+LY+AKI P + +L+ + L IK
Sbjct: 150 IKKYKQPIVALLMDQKKIGSGLGNYLVAEILYRAKIDPHKLGSNLTDQEIENLWYWIK 207
>pdb|3VK7|A Chain A, Crystal Structure Of Dna-glycosylase Bound To Dna
Containing 5- Hydroxyuracil
pdb|3VK7|B Chain B, Crystal Structure Of Dna-glycosylase Bound To Dna
Containing 5- Hydroxyuracil
pdb|3VK8|A Chain A, Crystal Structure Of Dna-glycosylase Bound To Dna
Containing Thymine Glycol
pdb|3VK8|B Chain B, Crystal Structure Of Dna-glycosylase Bound To Dna
Containing Thymine Glycol
Length = 295
Score = 66.6 bits (161), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 67/238 (28%), Positives = 105/238 (44%), Gaps = 49/238 (20%)
Query: 1 MPELPEVEAARRAIEEHCIGKKIVKSIIADDNKVIDGVSA----------SDFEASVLGK 50
MP+ PEV +E++ GK + + ID +S DF A++ K
Sbjct: 1 MPQGPEVALTADILEKYFKGKTL---------EYIDFISGRYSKSEPEGYDDFIANLPLK 51
Query: 51 AILSAHRKGKNLWLRLDSPPFPSFQ------FGMTGAIYIKGVAVTQYKRSAVKDTDEWP 104
+ + KGK LW L P S + FG+TG + +
Sbjct: 52 -VSNVDTKGKFLWFELFDPNDKSNKWYIWNTFGLTGMWSL------------------FE 92
Query: 105 SKYSKFFVELDDGLELSFTDKRRFAKVRLLNDPTSVP-PISELGPDALLEPMTVDEFTDS 163
+KY++ + D+ L F+D R F + N + ++ELGPD L+ +D
Sbjct: 93 AKYTRAVLSFDNELMAYFSDMRNFGTFKFSNSEKELKRKLNELGPD-FLKNDDID--ISK 149
Query: 164 LSKKKITIKALLLDQSYI-SGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIK 220
+ K K I ALL+DQ I SG+GN++ E+LY+AKI P + +L+ + L IK
Sbjct: 150 IKKYKQPIVALLMDQKKIGSGLGNYLVAEILYRAKIDPHKLGSNLTDQEIENLWYWIK 207
>pdb|1TDH|A Chain A, Crystal Structure Of Human Endonuclease Viii-Like 1
(Neil1)
Length = 364
Score = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 66/233 (28%), Positives = 96/233 (41%), Gaps = 62/233 (26%)
Query: 1 MPELPEVEAARRAIEEHC----IGKKIVKSIIADDNKVIDGVSASDFEASVLGKAILSAH 56
MPE PE+ A + + E C G + KS ++ + +V FE+S +SA
Sbjct: 1 MPEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEV-------PFESSAY---RISAS 50
Query: 57 RKGKNLWLRLDSPPFPS-----------FQFGMTGAIYIKGVAVTQYKRSAVKDTDEWPS 105
+GK L L L P P F+FGM+G+ + +E P
Sbjct: 51 ARGKELRLILS--PLPGAQPQQEPLALVFRFGMSGSFQLV-------------PREELPR 95
Query: 106 KYSKFFVELDDG--LELSFTDKRRFAKVRLLN--DPTSVPPISELGPDALLEPMTVDEFT 161
F G L L F D RRF + L P GP L E +F
Sbjct: 96 HAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGR-------GPCVLQE---YQQFR 145
Query: 162 DSLSKKKITIKAL-------LLDQSYISGIGNWVADEVLYQAKIHPLQTAVSL 207
+S+ + + KA LLDQ + +GIGN++ E+LY+ KI P + A S+
Sbjct: 146 ESVLRN-LADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSV 197
>pdb|2OQ4|A Chain A, Crystal Structure Of The Dna Repair Enzyme Endonuclease-
Viii (Nei) From E. Coli (E2q) In Complex With Ap-Site
Containing Dna Substrate
pdb|2OQ4|B Chain B, Crystal Structure Of The Dna Repair Enzyme Endonuclease-
Viii (Nei) From E. Coli (E2q) In Complex With Ap-Site
Containing Dna Substrate
Length = 262
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 43/88 (48%), Gaps = 3/88 (3%)
Query: 138 TSVPPISELGPDAL---LEPMTVDEFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLY 194
T+ P + +GPD L L P V E S + LLLDQ++++G+GN++ E+L+
Sbjct: 117 TTHPFLQRVGPDVLDPNLTPEVVKERLLSPRFRNRQFAGLLLDQAFLAGLGNYLRVEILW 176
Query: 195 QAKIHPLQTAVSLSKESCATLLKCIKEV 222
Q + A L+ L + E+
Sbjct: 177 QVGLTGNHKAKDLNAAQLDALAHALLEI 204
>pdb|1Q3C|A Chain A, Crystal Structure Of The Dna Repair Enzyme
Endonuclease-Viii (Nei) From E. Coli: The E2a Mutant At
2.3 Resolution
Length = 262
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 43/88 (48%), Gaps = 3/88 (3%)
Query: 138 TSVPPISELGPDAL---LEPMTVDEFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLY 194
T+ P + +GPD L L P V E S + LLLDQ++++G+GN++ E+L+
Sbjct: 117 TTHPFLQRVGPDVLDPNLTPEVVKERLLSPRFRNRQFAGLLLDQAFLAGLGNYLRVEILW 176
Query: 195 QAKIHPLQTAVSLSKESCATLLKCIKEV 222
Q + A L+ L + E+
Sbjct: 177 QVGLTGNHKAKDLNAAQLDALAHALLEI 204
>pdb|1K3W|A Chain A, Crystal Structure Of A Trapped Reaction Intermediate Of
The Dna Repair Enzyme Endonuclease Viii With Dna
pdb|1K3X|A Chain A, Crystal Structure Of A Trapped Reaction Intermediate Of
The Dna Repair Enzyme Endonuclease Viii With
Brominated-Dna
pdb|1Q39|A Chain A, Crystal Structure Of The Dna Repair Enzyme
Endonuclease-Viii (Nei) From E. Coli: The Wt Enzyme At
2.8 Resolution.
pdb|2EA0|A Chain A, Crystal Structure Of The Dna Repair Enzyme
Endonuclease-viii (nei) From E. Coli In Complex With
Ap-site Containing Dna Substrate
Length = 262
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 43/88 (48%), Gaps = 3/88 (3%)
Query: 138 TSVPPISELGPDAL---LEPMTVDEFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLY 194
T+ P + +GPD L L P V E S + LLLDQ++++G+GN++ E+L+
Sbjct: 117 TTHPFLQRVGPDVLDPNLTPEVVKERLLSPRFRNRQFAGLLLDQAFLAGLGNYLRVEILW 176
Query: 195 QAKIHPLQTAVSLSKESCATLLKCIKEV 222
Q + A L+ L + E+
Sbjct: 177 QVGLTGNHKAKDLNAAQLDALAHALLEI 204
>pdb|1Q3B|A Chain A, Crystal Structure Of The Dna Repair Enzyme
Endonuclease-Viii (Nei) From E. Coli: The R252a Mutant
At 2.05 Resolution.
pdb|2OPF|A Chain A, Crystal Structure Of The Dna Repair Enzyme
Endonuclease-Viii (Nei) From E. Coli (R252a) In Complex
With Ap-Site Containing Dna Substrate
Length = 262
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 43/88 (48%), Gaps = 3/88 (3%)
Query: 138 TSVPPISELGPDAL---LEPMTVDEFTDSLSKKKITIKALLLDQSYISGIGNWVADEVLY 194
T+ P + +GPD L L P V E S + LLLDQ++++G+GN++ E+L+
Sbjct: 117 TTHPFLQRVGPDVLDPNLTPEVVKERLLSPRFRNRQFAGLLLDQAFLAGLGNYLRVEILW 176
Query: 195 QAKIHPLQTAVSLSKESCATLLKCIKEV 222
Q + A L+ L + E+
Sbjct: 177 QVGLTGNHKAKDLNAAQLDALAHALLEI 204
>pdb|3W0F|A Chain A, Crystal Structure Of Mouse Endonuclease Viii-like 3
(mneil3)
Length = 287
Score = 36.2 bits (82), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 25/44 (56%)
Query: 174 LLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLK 217
+LLDQ + G+GN + +E L+ + +HP LS + L+K
Sbjct: 180 VLLDQRVLPGVGNIIKNEALFDSGLHPAVKVCQLSDKQACHLVK 223
>pdb|2IKS|A Chain A, Crystal Structure Of N-Terminal Truncated Dna-Binding
Transcriptional Dual Regulator From Escherichia Coli K12
pdb|2IKS|B Chain B, Crystal Structure Of N-Terminal Truncated Dna-Binding
Transcriptional Dual Regulator From Escherichia Coli K12
Length = 293
Score = 30.8 bits (68), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 4/75 (5%)
Query: 176 LDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKEVIQSAVEVDADCSR 235
L+ + + I N++ QA+ Q ++ S++ +CI+ ++Q V+ +
Sbjct: 30 LENTSYTRIANYLE----RQARQRGYQLLIACSEDQPDNEXRCIEHLLQRQVDAIIVSTS 85
Query: 236 FPLEWLFHFRWGKKP 250
P E F+ RW P
Sbjct: 86 LPPEHPFYQRWANDP 100
>pdb|1Z59|A Chain A, Topoisomerase Vi-B, Adp-Bound Monomer Form
pdb|1Z5C|A Chain A, Topoisomerase Vi-B, Adp Pi Bound Dimer Form
pdb|1Z5C|B Chain B, Topoisomerase Vi-B, Adp Pi Bound Dimer Form
Length = 469
Score = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 166 KKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKE 221
K+ TIK L+++ IG+ AD++L A + P + +L++E L++ K+
Sbjct: 248 KRDYTIKEFLVNE--FQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKK 301
>pdb|1MU5|A Chain A, Structure Of Topoisomerase Subunit
Length = 471
Score = 28.9 bits (63), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 166 KKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKE 221
K+ TIK L+++ IG+ AD++L A + P + +L++E L++ K+
Sbjct: 250 KRDYTIKEFLVNE--FQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKK 303
>pdb|1MX0|A Chain A, Structure Of Topoisomerase Subunit
pdb|1MX0|B Chain B, Structure Of Topoisomerase Subunit
pdb|1MX0|C Chain C, Structure Of Topoisomerase Subunit
pdb|1MX0|D Chain D, Structure Of Topoisomerase Subunit
pdb|1MX0|E Chain E, Structure Of Topoisomerase Subunit
pdb|1MX0|F Chain F, Structure Of Topoisomerase Subunit
Length = 472
Score = 28.9 bits (63), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 166 KKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKE 221
K+ TIK L+++ IG+ AD++L A + P + +L++E L++ K+
Sbjct: 251 KRDYTIKEFLVNE--FQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKK 304
>pdb|1Z5A|A Chain A, Topoisomerase Vi-B, Adp-Bound Dimer Form
pdb|1Z5A|B Chain B, Topoisomerase Vi-B, Adp-Bound Dimer Form
pdb|1Z5B|A Chain A, Topoisomerase Vi-B, Adp Alf4- Bound Dimer Form
pdb|1Z5B|B Chain B, Topoisomerase Vi-B, Adp Alf4- Bound Dimer Form
pdb|2HKJ|A Chain A, Topoisomerase Vi-B Bound To Radicicol
Length = 469
Score = 28.9 bits (63), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 166 KKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKE 221
K+ TIK L+++ IG+ AD++L A + P + +L++E L++ K+
Sbjct: 248 KRDYTIKEFLVNE--FQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKK 301
>pdb|2ZBK|B Chain B, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
pdb|2ZBK|D Chain D, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
pdb|2ZBK|F Chain F, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
pdb|2ZBK|H Chain H, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
Length = 530
Score = 28.9 bits (63), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 166 KKKITIKALLLDQSYISGIGNWVADEVLYQAKIHPLQTAVSLSKESCATLLKCIKE 221
K+ TIK L+++ IG+ AD++L A + P + +L++E L++ K+
Sbjct: 249 KRDYTIKEFLVNE--FQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKK 302
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 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,673,408
Number of Sequences: 62578
Number of extensions: 296946
Number of successful extensions: 781
Number of sequences better than 100.0: 67
Number of HSP's better than 100.0 without gapping: 36
Number of HSP's successfully gapped in prelim test: 31
Number of HSP's that attempted gapping in prelim test: 715
Number of HSP's gapped (non-prelim): 67
length of query: 260
length of database: 14,973,337
effective HSP length: 97
effective length of query: 163
effective length of database: 8,903,271
effective search space: 1451233173
effective search space used: 1451233173
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)