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= 009729
(527 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MR6|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex With A Cpd
2bp Upstream Of The Active Site (Tt4)
pdb|3TQ1|A Chain A, Human Dna Polymerase Eta In Binary Complex With Dna
pdb|4EEY|A Chain A, Crystal Structure Of Human Dna Polymerase Eta In Ternary
Complex With A Cisplatin Dna Adduct
Length = 435
Score = 162 bits (409), Expect = 5e-40, Method: Compositional matrix adjust.
Identities = 87/203 (42%), Positives = 117/203 (57%), Gaps = 5/203 (2%)
Query: 5 KETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTS 64
+ET F CSAGI+HNK+LAKLA G+NKP +QT V SV L +PI+K++ LGGKLG S
Sbjct: 209 RETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGAS 268
Query: 65 LQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSF 124
+ LG+ +G+L +F+E +LQ +G G+WL+ + RGI + V+ R LPK+ G K+F
Sbjct: 269 VIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNF 328
Query: 125 PGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHXXXXXXXXXXXXXXXX 184
PG AL T VQ WL QL +EL ERL D N R+A L +
Sbjct: 329 PGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVV----SIRVQGDKRLSSL 384
Query: 185 XXXCPL-RYGTAKIQEDTFNLFQ 206
C L RY K+ D F + +
Sbjct: 385 RRCCALTRYDAHKMSHDAFTVIK 407
>pdb|3MR2|A Chain A, Human Dna Polymerase Eta In Complex With Normal Dna And
Incoming Nucleotide (Nrm)
pdb|3MR3|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex With The
3't Of A Cpd In The Active Site (Tt1)
pdb|3MR5|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex With A Cpd
1bp Upstream Of The Active Site (Tt3)
pdb|3SI8|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex With The
5't Of A Cpd In The Active Site (Tt2)
pdb|4DL2|A Chain A, Human Dna Polymerase Eta Inserting Dcmpnpp Opposite Cg
Template (Gg0a)
pdb|4DL3|A Chain A, Human Dna Polymerase Eta Inserting Dcmpnpp Opposite Gg
Template (Gg0b).
pdb|4DL4|A Chain A, Human Dna Polymerase Eta Inserting Dcmpnpp Opposite The
3'g Of Cisplatin Crosslinked Gs (Pt-Gg1).
pdb|4DL5|A Chain A, Human Dna Polymerase Eta Inserting Dcmpnpp Opposite The
5'g Of Cisplatin Crosslinked Gs (Pt-Gg2).
pdb|4DL6|A Chain A, Human Dna Polymerase Eta Extending Primer Immediately
After Cisplatin Crosslink (Pt-Gg3).
pdb|4DL7|A Chain A, Human Dna Polymerase Eta Fails To Extend Primer 2
Nucleotide After Cisplatin Crosslink (Pt-Gg4).
pdb|4ECQ|A Chain A, Human Dna Polymerase Eta- Dna Ternary Complex: At Crystal
At Ph6.8(K+ Mes) With 1 Ca2+ Ion
pdb|4ECR|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction
In The At Crystal At Ph 7.0 For 40 Sec
pdb|4ECS|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction
In The At Crystal At Ph 7.0 For 80 Sec
pdb|4ECT|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction
In The At Crystal At Ph 7.0 For 140 Sec
pdb|4ECU|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction
In The At Crystal At Ph 7.0 For 200 Sec
pdb|4ECV|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction
In The At Crystal At Ph 7.0 For 230 Sec
pdb|4ECW|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction
In The At Crystal At Ph 7.0 For 250 Sec
pdb|4ECX|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction
In The At Crystal At Ph 7.0 For 300 Sec
pdb|4ECY|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: At Crystal
At Ph 6.0 (Na+ Mes) With 1 Ca2+ Ion
pdb|4ECZ|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: At Crystal
At Ph 6.5 (Na+ Mes) With 1 Ca2+ Ion
pdb|4ED0|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: At Crystal
At Ph 6.8 (Na+ Mes) With 1 Ca2+ Ion
pdb|4ED1|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: At Crystal
At Ph 7.0 (Na+ Mes) With 1 Ca2+ Ion
pdb|4ED2|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: At Crystal
At Ph 7.2 (Na+ Hepes) With 1 Ca2+ Ion
pdb|4ED3|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: At Crystal
At Ph 7.5 (Na+ Hepes) With 1 Ca2+ Ion
pdb|4ED6|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction
In The At Crystal At Ph 6.7 For 15 Hr, Sideway
Translocation
pdb|4ED7|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Tg Crystal
At Ph 7.0 (K+ Mes) With 1 Ca2+ Ion
pdb|4ED8|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction
In The Tg Crystal At Ph 7.0, Normal Translocation
Length = 435
Score = 162 bits (409), Expect = 6e-40, Method: Compositional matrix adjust.
Identities = 87/203 (42%), Positives = 117/203 (57%), Gaps = 5/203 (2%)
Query: 5 KETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTS 64
+ET F CSAGI+HNK+LAKLA G+NKP +QT V SV L +PI+K++ LGGKLG S
Sbjct: 209 RETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGAS 268
Query: 65 LQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSF 124
+ LG+ +G+L +F+E +LQ +G G+WL+ + RGI + V+ R LPK+ G K+F
Sbjct: 269 VIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNF 328
Query: 125 PGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHXXXXXXXXXXXXXXXX 184
PG AL T VQ WL QL +EL ERL D N R+A L +
Sbjct: 329 PGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVV----SIRVQGDKRLSSL 384
Query: 185 XXXCPL-RYGTAKIQEDTFNLFQ 206
C L RY K+ D F + +
Sbjct: 385 RRCCALTRYDAHKMSHDAFTVIK 407
>pdb|3GV5|B Chain B, Human Dna Polymerase Iota In Complex With T Template Dna
And Incoming Ddadp
pdb|3GV5|D Chain D, Human Dna Polymerase Iota In Complex With T Template Dna
And Incoming Ddadp
Length = 420
Score = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 50/160 (31%), Positives = 78/160 (48%), Gaps = 9/160 (5%)
Query: 9 FTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL-PIKKMKQLGGKLGTSLQN 67
T AG+A NK+LAKL SG+ KP QQT + S + L+ SL IK++ +G K L+
Sbjct: 193 LTGCAGVASNKLLAKLVSGVFKPNQQTVLLPESCQHLIHSLNHIKEIPGIGYKTAKCLE- 251
Query: 68 ELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGP 127
LG+ +V DL FS L++ G + + ++ G V P+S SF
Sbjct: 252 ALGINSVRDLQTFSPKILEKELGISVAQRIQKLSFGEDNSPVILSGPPQSFSEEDSF--- 308
Query: 128 RALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTL 167
+ + ++ + +L L R+C Q+ R HT+ L
Sbjct: 309 KKCSSEVEAKNKIEELLASLLNRVC----QDGRKPHTVRL 344
>pdb|2DPI|A Chain A, Ternary Complex Of Hpoli With Dna And Dctp
pdb|2DPJ|A Chain A, Structure Of Hpoli With Dna And Dttp
pdb|2FLN|A Chain A, Binary Complex Of Catalytic Core Of Human Dna Polymerase
Iota With Dna (Template A)
pdb|2FLP|A Chain A, Binary Complex Of The Catalytic Core Of Human Dna
Polymerase Iota With Dna (Template G)
pdb|2FLL|A Chain A, Ternary Complex Of Human Dna Polymerase Iota With Dna And
Dttp
pdb|3EPG|A Chain A, Structure Of Human Dna Polymerase Iota Complexed With
N2-Ethylguanine
pdb|3EPI|A Chain A, Structure Of Human Dna Polymerase Iota Complexed With
N2-Ethylguanine And Incoming Ttp
pdb|3G6V|A Chain A, Dna Synthesis Across An Abasic Lesion By Human Dna
Polymerase-Iota
pdb|3G6X|A Chain A, Ternary Complex Of Dna Polymerase Iota:dna:dgtp With An
Abasic Site At The Templating Position
pdb|3G6Y|A Chain A, Ternary Complex Of Dna Polymerase Iota:dna:dttp With An
Abasic Site At The Templating Position
pdb|3GV7|B Chain B, Human Dna Polymerase Iota In Complex With T Template Dna
And Incoming Dttp
pdb|3GV8|B Chain B, Human Dna Polymerase Iota In Complex With T Template Dna
And Incoming Dgtp
pdb|3NGD|A Chain A, Structural Basis For Proficient Incorporation Of Dttp
Opposite O6- Methylguanine By Human Dna Polymerase Iota
pdb|3OSN|A Chain A, Structural Basis For Proficient Incorporation Of Dttp
Opposite O6- Methylguanine By Human Dna Polymerase Iota
pdb|3Q8P|B Chain B, Human Dna Polymerase Iota Incorporating Dctp Opposite
8-Oxo-Guanine
pdb|3Q8Q|B Chain B, Human Dna Polymerase Iota Incorporating Datp Opposite
8-Oxo-Guanine
pdb|3Q8R|B Chain B, Human Dna Polymerase Iota Incorporating Dgtp Opposite
8-Oxo-Guanine
pdb|3Q8S|B Chain B, Human Dna Polymerase Iota Incorporating Dttp Opposite
8-Oxo-Guanine
pdb|4EBC|A Chain A, Conformationally Restrained
North-Methanocarba-2'-Deoxyadenosine Corrects The
Error-Prone Nature Of Human Dna Polymerase Iota
pdb|4EBD|A Chain A, Conformationally Restrained
North-Methanocarba-2'-Deoxyadenosine Corrects The
Error-Prone Nature Of Human Dna Polymerase Iota
pdb|4EBE|A Chain A, Conformationally Restrained
North-Methanocarba-2'-Deoxyadenosine Corrects The
Error-Prone Nature Of Human Dna Polymerase Iota
pdb|4FS1|A Chain A, Base Pairing Mechanism Of N2,3-Ethenoguanine With Dttp By
Human Polymerase Iota
pdb|4FS2|A Chain A, Base Pairing Mechanism Of N2,3-Ethenoguanine With Dctp By
Human Polymerase Iota
pdb|4EYH|B Chain B, Human Dna Polymerase Iota Incorporating Dctp Opposite N-
(deoxyguanosin-8-yl)-1-aminopyrene Lesion
pdb|4EYI|B Chain B, Human Dna Polymerase Iota Incorporating Datp Opposite N-
(deoxyguanosin-8-yl)-1-aminopyrene Lesion
Length = 420
Score = 59.7 bits (143), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 50/160 (31%), Positives = 78/160 (48%), Gaps = 9/160 (5%)
Query: 9 FTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL-PIKKMKQLGGKLGTSLQN 67
T AG+A NK+LAKL SG+ KP QQT + S + L+ SL IK++ +G K L+
Sbjct: 193 LTGCAGVASNKLLAKLVSGVFKPNQQTVLLPESCQHLIHSLNHIKEIPGIGYKTAKCLE- 251
Query: 68 ELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGP 127
LG+ +V DL FS L++ G + + ++ G V P+S SF
Sbjct: 252 ALGINSVRDLQTFSPKILEKELGISVAQRIQKLSFGEDNSPVILSGPPQSFSEEDSF--- 308
Query: 128 RALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTL 167
+ + ++ + +L L R+C Q+ R HT+ L
Sbjct: 309 KKCSSEVEAKNKIEELLASLLNRVC----QDGRKPHTVRL 344
>pdb|2ALZ|A Chain A, Ternary Complex Of Hpoli With Dna And Dctp
pdb|3H4B|A Chain A, Ternary Complex Of Human Dna Polymerase Iota With Template
UT AND Incoming Datp
pdb|3H4D|A Chain A, Ternary Complex Of Human Dna Polymerase Iota With Template
UT AND Incoming Dgtp
Length = 390
Score = 59.7 bits (143), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 50/160 (31%), Positives = 78/160 (48%), Gaps = 9/160 (5%)
Query: 9 FTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL-PIKKMKQLGGKLGTSLQN 67
T AG+A NK+LAKL SG+ KP QQT + S + L+ SL IK++ +G K L+
Sbjct: 169 LTGCAGVASNKLLAKLVSGVFKPNQQTVLLPESCQHLIHSLNHIKEIPGIGYKTAKCLE- 227
Query: 68 ELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGP 127
LG+ +V DL FS L++ G + + ++ G V P+S SF
Sbjct: 228 ALGINSVRDLQTFSPKILEKELGISVAQRIQKLSFGEDNSPVILSGPPQSFSEEDSF--- 284
Query: 128 RALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTL 167
+ + ++ + +L L R+C Q+ R HT+ L
Sbjct: 285 KKCSSEVEAKNKIEELLASLLNRVC----QDGRKPHTVRL 320
>pdb|3H40|A Chain A, Binary Complex Of Human Dna Polymerase Iota With Template
UT
Length = 389
Score = 59.7 bits (143), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 50/160 (31%), Positives = 78/160 (48%), Gaps = 9/160 (5%)
Query: 9 FTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL-PIKKMKQLGGKLGTSLQN 67
T AG+A NK+LAKL SG+ KP QQT + S + L+ SL IK++ +G K L+
Sbjct: 168 LTGCAGVASNKLLAKLVSGVFKPNQQTVLLPESCQHLIHSLNHIKEIPGIGYKTAKCLE- 226
Query: 68 ELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGP 127
LG+ +V DL FS L++ G + + ++ G V P+S SF
Sbjct: 227 ALGINSVRDLQTFSPKILEKELGISVAQRIQKLSFGEDNSPVILSGPPQSFSEEDSF--- 283
Query: 128 RALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTL 167
+ + ++ + +L L R+C Q+ R HT+ L
Sbjct: 284 KKCSSEVEAKNKIEELLASLLNRVC----QDGRKPHTVRL 319
>pdb|4DEZ|A Chain A, Structure Of Msdpo4
Length = 356
Score = 59.7 bits (143), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 40/124 (32%), Positives = 62/124 (50%), Gaps = 2/124 (1%)
Query: 3 VLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLG 62
V ET +CS GI+ NK AK+A+G KPA + ++ ++ P + +G K
Sbjct: 132 VAAETGLSCSVGISDNKQRAKVATGFAKPAGIYVLTEANWMTVMGDRPPDALWGVGPKTT 191
Query: 63 TSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQAR-LLPKSHGSG 121
L +G+TTV DL L ++G +TG WL +A+G EV + +P+S
Sbjct: 192 KKLAA-MGITTVADLAVTDPSVLTTAFGPSTGLWLLLLAKGGGDTEVSSEPWVPRSRSHV 250
Query: 122 KSFP 125
+FP
Sbjct: 251 VTFP 254
>pdb|1T3N|A Chain A, Structure Of The Catalytic Core Of Dna Polymerase Iota In
Complex With Dna And Dttp
pdb|1T3N|B Chain B, Structure Of The Catalytic Core Of Dna Polymerase Iota In
Complex With Dna And Dttp
pdb|1ZET|A Chain A, X-Ray Data Do Not Support Hoogsteen Base-Pairing During
Replication By Human Polymerase Iota
Length = 388
Score = 59.3 bits (142), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 50/160 (31%), Positives = 78/160 (48%), Gaps = 9/160 (5%)
Query: 9 FTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL-PIKKMKQLGGKLGTSLQN 67
T AG+A NK+LAKL SG+ KP QQT + S + L+ SL IK++ +G K L+
Sbjct: 167 LTGCAGVASNKLLAKLVSGVFKPNQQTVLLPESCQHLIHSLNHIKEIPGIGYKTAKCLE- 225
Query: 68 ELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGP 127
LG+ +V DL FS L++ G + + ++ G V P+S SF
Sbjct: 226 ALGINSVRDLQTFSPKILEKELGISVAQRIQKLSFGEDNSPVILSGPPQSFSEEDSF--- 282
Query: 128 RALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTL 167
+ + ++ + +L L R+C Q+ R HT+ L
Sbjct: 283 KKCSSEVEAKNKIEELLASLLNRVC----QDGRKPHTVRL 318
>pdb|3GQC|A Chain A, Structure Of Human Rev1-Dna-Dntp Ternary Complex
pdb|3GQC|B Chain B, Structure Of Human Rev1-Dna-Dntp Ternary Complex
pdb|3GQC|C Chain C, Structure Of Human Rev1-Dna-Dntp Ternary Complex
pdb|3GQC|D Chain D, Structure Of Human Rev1-Dna-Dntp Ternary Complex
Length = 504
Score = 55.1 bits (131), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 44/165 (26%), Positives = 75/165 (45%), Gaps = 11/165 (6%)
Query: 1 MQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGK 60
M++ +T+ S GI N +LA++A+ KP Q + V + + + +G
Sbjct: 267 MEIKDQTKCAASVGIGSNILLARMATRKAKPDGQYHLKPEEVDDFIRGQLVTNLPGVGHS 326
Query: 61 LGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGS 120
+ + L + LG+ T GDL + KLQ+ +G TG L+ RG+ V+ KS +
Sbjct: 327 MESKLAS-LGIKTCGDLQYMTMAKLQKEFGPKTGQMLYRFCRGLDDRPVRTEKERKSVSA 385
Query: 121 ----GKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRI 161
G F P+ + +L L EE+ RL + + KR+
Sbjct: 386 EINYGIRFTQPK------EAEAFLLSLSEEIQRRLEATGMKGKRL 424
>pdb|1T94|A Chain A, Crystal Structure Of The Catalytic Core Of Human Dna
Polymerase Kappa
pdb|1T94|B Chain B, Crystal Structure Of The Catalytic Core Of Human Dna
Polymerase Kappa
Length = 459
Score = 54.7 bits (130), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 47/171 (27%), Positives = 80/171 (46%), Gaps = 15/171 (8%)
Query: 1 MQVLKETEFTCSAGIAHNKMLAKLASGMNKP-AQQTTVP-FSSVKGLLDSLPIKKMKQLG 58
++ ++T T SAGIA N MLAK+ S NKP Q +P +V + LPI+K+ +
Sbjct: 232 FRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGI- 290
Query: 59 GKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLW--NIARGISGEEVQARLLPK 116
GK+ + LG+ T +L + + S F+ +W + +I+ G+ +
Sbjct: 291 GKVTEKMLKALGIITCTELY---QQRALLSLLFSETSWHYFLHISLGLGSTHL------T 341
Query: 117 SHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTL 167
G KS R + + + LC+EL L DL++ + T+T+
Sbjct: 342 RDGERKSMSVERTFSEINKAEEQYS-LCQELCSELAQDLQKERLKGRTVTI 391
>pdb|3PZP|A Chain A, Human Dna Polymerase Kappa Extending Opposite A Cis-Syn
Thymine Dimer
pdb|3PZP|B Chain B, Human Dna Polymerase Kappa Extending Opposite A Cis-Syn
Thymine Dimer
Length = 517
Score = 54.7 bits (130), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 47/171 (27%), Positives = 80/171 (46%), Gaps = 15/171 (8%)
Query: 1 MQVLKETEFTCSAGIAHNKMLAKLASGMNKP-AQQTTVP-FSSVKGLLDSLPIKKMKQLG 58
++ ++T T SAGIA N MLAK+ S NKP Q +P +V + LPI+K+ +
Sbjct: 288 FRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGI- 346
Query: 59 GKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLW--NIARGISGEEVQARLLPK 116
GK+ + LG+ T +L + + S F+ +W + +I+ G+ +
Sbjct: 347 GKVTEKMLKALGIITCTELY---QQRALLSLLFSETSWHYFLHISLGLGSTHL------T 397
Query: 117 SHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTL 167
G KS R + + + LC+EL L DL++ + T+T+
Sbjct: 398 RDGERKSMSVERTFSEINKAEEQYS-LCQELCSELAQDLQKERLKGRTVTI 447
>pdb|2OH2|A Chain A, Ternary Complex Of Human Dna Polymerase
pdb|2OH2|B Chain B, Ternary Complex Of Human Dna Polymerase
pdb|2W7O|A Chain A, Structure And Activity Of Bypass Synthesis By Human Dna
Polymerase Kappa Opposite The 7,8-Dihydro-8-
Oxodeoxyguanosine Adduct
pdb|2W7O|B Chain B, Structure And Activity Of Bypass Synthesis By Human Dna
Polymerase Kappa Opposite The 7,8-Dihydro-8-
Oxodeoxyguanosine Adduct
pdb|2W7P|A Chain A, Structure And Activity Of Bypass Synthesis By Human Dna
Polymerase Kappa Opposite The 7,8-Dihydro-8-
Oxodeoxyguanosine Adduct
pdb|2W7P|B Chain B, Structure And Activity Of Bypass Synthesis By Human Dna
Polymerase Kappa Opposite The 7,8-Dihydro-8-
Oxodeoxyguanosine Adduct
pdb|3IN5|A Chain A, Structure Of Human Dna Polymerase Kappa Inserting Datp
Opposite An 8-Oxog Dna Lesion
pdb|3IN5|B Chain B, Structure Of Human Dna Polymerase Kappa Inserting Datp
Opposite An 8-Oxog Dna Lesion
Length = 508
Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 47/171 (27%), Positives = 80/171 (46%), Gaps = 15/171 (8%)
Query: 1 MQVLKETEFTCSAGIAHNKMLAKLASGMNKP-AQQTTVP-FSSVKGLLDSLPIKKMKQLG 58
++ ++T T SAGIA N MLAK+ S NKP Q +P +V + LPI+K+ +
Sbjct: 281 FRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGI- 339
Query: 59 GKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLW--NIARGISGEEVQARLLPK 116
GK+ + LG+ T +L + + S F+ +W + +I+ G+ +
Sbjct: 340 GKVTEKMLKALGIITCTELY---QQRALLSLLFSETSWHYFLHISLGLGSTHL------T 390
Query: 117 SHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTL 167
G KS R + + + LC+EL L DL++ + T+T+
Sbjct: 391 RDGERKSMSVERTFSEINKAEEQYS-LCQELCSELAQDLQKERLKGRTVTI 440
>pdb|3V6H|A Chain A, Replication Of N2,3-Ethenoguanine By Dna Polymerases
pdb|3V6H|B Chain B, Replication Of N2,3-Ethenoguanine By Dna Polymerases
pdb|3V6J|A Chain A, Replication Of N2,3-Ethenoguanine By Dna Polymerases
pdb|3V6J|J Chain J, Replication Of N2,3-Ethenoguanine By Dna Polymerases
Length = 348
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 37/145 (25%), Positives = 69/145 (47%), Gaps = 4/145 (2%)
Query: 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKL 61
++L++ + T + GI+ NK+ AK+A+ M KP + VK L+ L I + +G
Sbjct: 137 KILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNIT 196
Query: 62 GTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSG 121
L+ +LG+ + D L DKL+ G +L ++AR E ++ R+ G
Sbjct: 197 AEKLK-KLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRV---RKSIG 252
Query: 122 KSFPGPRALKTVASVQHWLNQLCEE 146
+ R + + ++ +L + EE
Sbjct: 253 RIVTMKRNSRNLEEIKPYLFRAIEE 277
>pdb|2AGO|A Chain A, Fidelity Of Dpo4: Effect Of Metal Ions, Nucleotide
Selection And Pyrophosphorolysis
pdb|2AGP|A Chain A, Fidelity Of Dpo4: Effect Of Metal Ions, Nucleotide
Selection And Pyrophosphorolysis
pdb|2AGP|B Chain B, Fidelity Of Dpo4: Effect Of Metal Ions, Nucleotide
Selection And Pyrophosphorolysis
pdb|2AGQ|A Chain A, Fidelity Of Dpo4: Effect Of Metal Ions, Nucleotide
Selection And Pyrophosphorolysis
pdb|3T5H|A Chain A, Ternary Complex Of Hne Adduct Modified Dna (5'-Cxg-3' Vs
13-Mer) With Dpo4 And Incoming Ddgt
pdb|3T5J|A Chain A, Ternary Complex Of Hne Adduct Modified Dna (5'-Txg-3' Vs
13-Mer) With Dpo4 And Incoming Ddtp
pdb|3T5K|A Chain A, Ternary Complex Of Hne Adduct Modified Dna (5'-Txg-3' Vs
14-Mer) With Dpo4 And Incoming Ddtp
pdb|3T5L|A Chain A, Ternary Complex Of Hne Adduct Modified Dna (5'-Cxg-3' Vs
14-Mer) With Dpo4 And Incoming Ddgt
Length = 341
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 37/145 (25%), Positives = 69/145 (47%), Gaps = 4/145 (2%)
Query: 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKL 61
++L++ + T + GI+ NK+ AK+A+ M KP + VK L+ L I + +G
Sbjct: 131 KILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNIT 190
Query: 62 GTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSG 121
L+ +LG+ + D L DKL+ G +L ++AR E ++ R+ G
Sbjct: 191 AEKLK-KLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRV---RKSIG 246
Query: 122 KSFPGPRALKTVASVQHWLNQLCEE 146
+ R + + ++ +L + EE
Sbjct: 247 RIVTMKRNSRNLEEIKPYLFRAIEE 271
>pdb|3PVX|A Chain A, Binary Complex Of Aflatoxin B1 Adduct Modified Dna
(Afb1-Fapy) With Dna Polymerase Iv
pdb|3PW0|A Chain A, Ternary Complex Of Aflatoxin B1 Adduct Modified Dna
(Afb1-Fapy) With Dna Polymerase Iv And Incoming Datp
pdb|3PW2|A Chain A, Ternary Complex Of Aflatoxin B1 Adduct Modified Dna
(Afb1-Fapy) With Dna Polymerase Iv And Incoming Dttp
pdb|3PW4|A Chain A, Ternary Complex Of Aflatoxin B1 Adduct Modified Dna
(Afb1-N7-Gua) With Dna Polymerase Iv And Incoming Datp
pdb|3PW5|A Chain A, Ternary Complex Of Aflatoxin B1 Adduct Modified Dna
(Afb1-N7-Gua) With Dna Polymerase Iv And Incoming Dttp
pdb|3PW7|A Chain A, Ternary Complex Of Aflatoxin B1 Adduct Modified Dna
(Afb1-N7-Gua) With Dna Polymerase Iv And Incoming Dctp
pdb|3PW7|E Chain E, Ternary Complex Of Aflatoxin B1 Adduct Modified Dna
(Afb1-N7-Gua) With Dna Polymerase Iv And Incoming Dctp
Length = 347
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 37/145 (25%), Positives = 69/145 (47%), Gaps = 4/145 (2%)
Query: 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKL 61
++L++ + T + GI+ NK+ AK+A+ M KP + VK L+ L I + +G
Sbjct: 137 KILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNIT 196
Query: 62 GTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSG 121
L+ +LG+ + D L DKL+ G +L ++AR E ++ R+ G
Sbjct: 197 AEKLK-KLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRV---RKSIG 252
Query: 122 KSFPGPRALKTVASVQHWLNQLCEE 146
+ R + + ++ +L + EE
Sbjct: 253 RIVTMKRNSRNLEEIKPYLFRAIEE 277
>pdb|2IMW|P Chain P, Mechanism Of Template-Independent Nucleotide Incorporation
Catalyzed By A Template-Dependent Dna Polymerase
Length = 348
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 37/145 (25%), Positives = 69/145 (47%), Gaps = 4/145 (2%)
Query: 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKL 61
++L++ + T + GI+ NK+ AK+A+ M KP + VK L+ L I + +G
Sbjct: 131 KILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNIT 190
Query: 62 GTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSG 121
L+ +LG+ + D L DKL+ G +L ++AR E ++ R+ G
Sbjct: 191 AEKLK-KLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRV---RKSIG 246
Query: 122 KSFPGPRALKTVASVQHWLNQLCEE 146
+ R + + ++ +L + EE
Sbjct: 247 RIVTMKRNSRNLEEIKPYLFRAIEE 271
>pdb|3V6K|A Chain A, Replication Of N2,3-Ethenoguanine By Dna Polymerases
pdb|3V6K|J Chain J, Replication Of N2,3-Ethenoguanine By Dna Polymerases
Length = 347
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 37/145 (25%), Positives = 69/145 (47%), Gaps = 4/145 (2%)
Query: 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKL 61
++L++ + T + GI+ NK+ AK+A+ M KP + VK L+ L I + +G
Sbjct: 136 KILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNIT 195
Query: 62 GTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSG 121
L+ +LG+ + D L DKL+ G +L ++AR E ++ R+ G
Sbjct: 196 AEKLK-KLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRV---RKSIG 251
Query: 122 KSFPGPRALKTVASVQHWLNQLCEE 146
+ R + + ++ +L + EE
Sbjct: 252 RIVTMKRNSRNLEEIKPYLFRAIEE 276
>pdb|3PR4|A Chain A, Dpo4 Y12a Mutant Incorporating Dadp Opposite Template Dt
pdb|3PR5|B Chain B, Dpo4 Y12a Mutant Incorporating Adp Opposite Template Dt
Length = 341
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 37/145 (25%), Positives = 69/145 (47%), Gaps = 4/145 (2%)
Query: 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKL 61
++L++ + T + GI+ NK+ AK+A+ M KP + VK L+ L I + +G
Sbjct: 131 KILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNIT 190
Query: 62 GTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSG 121
L+ +LG+ + D L DKL+ G +L ++AR E ++ R+ G
Sbjct: 191 AEKLK-KLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRV---RKSIG 246
Query: 122 KSFPGPRALKTVASVQHWLNQLCEE 146
+ R + + ++ +L + EE
Sbjct: 247 RIVTMKRNSRNLEEIKPYLFRAIEE 271
>pdb|2UVV|A Chain A, Crystal Structures Of Mutant Dpo4 Dna Polymerases With 8-
Oxog Containing Dna Template-Primer Constructs
pdb|2UVW|A Chain A, Crystal Structures Of Mutant Dpo4 Dna Polymerases With 8-
Oxog Containing Dna Template-Primer Constructs
Length = 358
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 37/145 (25%), Positives = 69/145 (47%), Gaps = 4/145 (2%)
Query: 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKL 61
++L++ + T + GI+ NK+ AK+A+ M KP + VK L+ L I + +G
Sbjct: 137 KILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNIT 196
Query: 62 GTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSG 121
L+ +LG+ + D L DKL+ G +L ++AR E ++ R+ G
Sbjct: 197 AEKLK-KLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRV---RKSIG 252
Query: 122 KSFPGPRALKTVASVQHWLNQLCEE 146
+ R + + ++ +L + EE
Sbjct: 253 RIVTMKRNSRNLEEIKPYLFRAIEE 277
>pdb|2RDI|A Chain A, Snapshots Of A Y-family Dna Polymerase In Replication:
Dpo4 In Apo And Binary/ternary Complex Forms
Length = 342
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 37/145 (25%), Positives = 69/145 (47%), Gaps = 4/145 (2%)
Query: 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKL 61
++L++ + T + GI+ NK+ AK+A+ M KP + VK L+ L I + +G
Sbjct: 131 KILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNIT 190
Query: 62 GTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSG 121
L+ +LG+ + D L DKL+ G +L ++AR E ++ R+ G
Sbjct: 191 AEKLK-KLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRV---RKSIG 246
Query: 122 KSFPGPRALKTVASVQHWLNQLCEE 146
+ R + + ++ +L + EE
Sbjct: 247 RIVTMKRNSRNLEEIKPYLFRAIEE 271
>pdb|2BQ3|A Chain A, Dna Adduct Bypass Polymerization By Sulfolobus
Solfataricus Dpo4. Analysis And Crystal Structures Of
Multiple Base- Pair Substitution And Frameshift Products
With The Adduct 1,N2-Ethenoguanine
pdb|2BQR|A Chain A, Dna Adduct Bypass Polymerization By Sulfolobus
Solfataricus Dpo4. Analysis And Crystal Structures Of
Multiple Base- Pair Substitution And Frameshift Products
With The Adduct 1,N2-Ethenoguanine
pdb|2BQU|A Chain A, Dna Adduct Bypass Polymerization By Sulfolobus
Solfataricus Dpo4. Analysis And Crystal Structures Of
Multiple Base- Pair Substitution And Frameshift Products
With The Adduct 1,N2-Ethenoguanine
pdb|2BR0|A Chain A, Dna Adduct Bypass Polymerization By Sulfolobus
Solfataricus Dpo4. Analysis And Crystal Structures Of
Multiple Base- Pair Substitution And Frameshift Products
With The Adduct 1,N2-Ethenoguanine
pdb|2C22|A Chain A, Efficient And High Fidelity Incorporation Of Dctp Opposite
7,8-Dihydro-8-Oxodeoxyguanosine By Sulfolobus
Solfataricus Dna Polymerase Dpo4
pdb|2C28|A Chain A, Efficient And High Fidelity Incorporation Of Dctp Opposite
7,8-Dihydro-8-Oxodeoxyguanosine By Sulfolobus
Solfataricus Dna Polymerase Dpo4
pdb|2C2D|A Chain A, Efficient And High Fidelity Incorporation Of Dctp Opposite
7,8-Dihydro-8-Oxodeoxyguanosine By Sulfolobus
Solfataricus Dna Polymerase Dpo4
pdb|2C2E|A Chain A, Efficient And High Fidelity Incorporation Of Dctp Opposite
7,8-Dihydro-8-Oxodeoxyguanosine By Sulfolobus
Solfataricus Dna Polymerase Dpo4
pdb|2C2R|A Chain A, Efficient And High Fidelity Incorporation Of Dctp Opposite
7,8-Dihydro-8-Oxodeoxyguanosine By Sulfolobus
Solfataricus Dna Polymerase Dpo4
pdb|2J6S|A Chain A, Ternary Complex Of Sulfolobus Solfataricus Dpo4 Dna
Polymerase, O6-Methylguanine Modified Dna, And Datp.
pdb|2J6T|A Chain A, Ternary Complex Of Sulfolobus Solfataricus Dpo4 Dna
Polymerase, O6-Methylguanine Modified Dna, And Datp.
pdb|2J6U|A Chain A, Ternary Complex Of Sulfolobus Solfataricus Dpo4 Dna
Polymerase, O6-methylguanine Modified Dna, And Dgtp.
pdb|2JEF|A Chain A, The Molecular Basis Of Selectivity Of Nucleotide
Triphosphate Incorporation Opposite O6-benzylguanine By
Sulfolobus Solfataricus Dna Polymerase Iv: Steady-state
And Pre-steady-state And X-ray Crystallography Of
Correct And Incorrect Pairing
pdb|2JEG|A Chain A, The Molecular Basis Of Selectivity Of Nucleoside
Triphosphate Incorporation Opposite O6-Benzylguanine By
Sulfolobus Solfataricus Dna Polymerase Iv: Steady-State
And Pre-Steady-State Kinetics And X-Ray Crystallography
Of Correct And Incorrect Pairing
pdb|2JEI|A Chain A, The Molecular Basis Of Selectivity Of Nucleoside
Triphosphate Incorporation Opposite O6-benzylguanine By
Sulfolobus Solfataricus Dna Polymerase Iv: Steady-state
And Pre-steady-state Kinetics And X-ray Crystallography
Of Correct And Incorrect Pairing
pdb|2JEJ|A Chain A, The Molecular Basis Of Selectivity Of Nucleoside
Triphosphate Incorporation Opposite O6-Benzylguanine By
Sulfolobus Solfataricus Dna Polymerase Iv: Steady-State
And Pre-Steady-State Kinetics And X-Ray Crystallography
Of Correct And Incorrect Pairing
pdb|2V9W|A Chain A, Complex Structure Of Sulfolobus Solfataricus Dpo4 And Dna
Duplex Containing A Hydrophobic Thymine Isostere 2,4-
Difluorotoluene Nucleotide In The Template Strand
pdb|2V9W|B Chain B, Complex Structure Of Sulfolobus Solfataricus Dpo4 And Dna
Duplex Containing A Hydrophobic Thymine Isostere 2,4-
Difluorotoluene Nucleotide In The Template Strand
pdb|2VA2|A Chain A, Complex Structure Of Sulfolobus Solfataricus Dpo4 And Dna
Duplex Containing A Hydrophobic Thymine Isostere 2,4-
Difluorotoluene Nucleotide In The Template Strand
pdb|2VA2|B Chain B, Complex Structure Of Sulfolobus Solfataricus Dpo4 And Dna
Duplex Containing A Hydrophobic Thymine Isostere 2,4-
Difluorotoluene Nucleotide In The Template Strand
pdb|2VA3|A Chain A, Complex Structure Of Sulfolobus Solfataricus Dpo4 And Dna
Duplex Containing A Hydrophobic Thymine Isostere 2,4-
Difluorotoluene Nucleotide In The Template Strand
pdb|2W8K|A Chain A, Y-Family Dna Polymerase Dpo4 Bypassing N2-Naphthyl-Guanine
Adduct In Syn Orientation
pdb|2W8L|A Chain A, Y-Family Dna Polymerase Dpo4 Bypassing N2-Naphthyl-Guanine
Adduct In Anti Orientation
pdb|2W9A|A Chain A, Ternary Complex Of Dpo4 Bound To N2,N2-Dimethyl-
Deoxyguanosine Modified Dna With Incoming Dgtp
pdb|2W9B|B Chain B, Binary Complex Of Dpo4 Bound To N2,N2-Dimethyl-
Deoxyguanosine Modified Dna
pdb|2W9C|B Chain B, Ternary Complex Of Dpo4 Bound To N2,N2-Dimethyl-
Deoxyguanosine Modified Dna With Incoming Dttp
pdb|2V4Q|A Chain A, Post-Insertion Complex Of The Y-Family Dna Polymerase Dpo4
With M1dg Containing Template Dna
pdb|2V4R|A Chain A, Non-Productive Complex Of The Y-Family Dna Polymerase Dpo4
With Dgtp Skipping The M1dg Adduct To Pair With The Next
Template Cytosine
pdb|2XC9|A Chain A, Binary Complex Of Sulfolobus Solfataricus Dpo4 Dna
Polymerase And 1,N2-Ethenoguanine Modified Dna,
Magnesium Form
pdb|2XCA|A Chain A, Ternary Complex Of Sulfolobus Solfataricus Dpo4 Dna
Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna
And Dgtp - Magnesium Form
pdb|2XCP|A Chain A, Ternary Complex Of Sulfolobus Solfataricus Dpo4 Dna
Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna
And Dctp - Magnesium Form
pdb|2XCP|B Chain B, Ternary Complex Of Sulfolobus Solfataricus Dpo4 Dna
Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna
And Dctp - Magnesium Form
pdb|4GC6|A Chain A, Crystal Structure Of Dpo4 In Complex With N-mc-damp
Opposite Dt
Length = 358
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 37/145 (25%), Positives = 69/145 (47%), Gaps = 4/145 (2%)
Query: 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKL 61
++L++ + T + GI+ NK+ AK+A+ M KP + VK L+ L I + +G
Sbjct: 137 KILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNIT 196
Query: 62 GTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSG 121
L+ +LG+ + D L DKL+ G +L ++AR E ++ R+ G
Sbjct: 197 AEKLK-KLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRV---RKSIG 252
Query: 122 KSFPGPRALKTVASVQHWLNQLCEE 146
+ R + + ++ +L + EE
Sbjct: 253 RIVTMKRNSRNLEEIKPYLFRAIEE 277
>pdb|1JXL|A Chain A, Crystal Structure Of A Y-Family Dna Polymerase In A
Ternary Complex With Dna Substrates And An Incoming
Nucleotide
pdb|1N48|A Chain A, Y-Family Dna Polymerase Dpo4 In Complex With Dna
Containing Abasic Lesion
pdb|1N56|A Chain A, Y-Family Dna Polymerase Dpo4 In Complex With Dna
Containing Abasic Lesion
pdb|1N56|B Chain B, Y-Family Dna Polymerase Dpo4 In Complex With Dna
Containing Abasic Lesion
pdb|1RYR|A Chain A, Replication Of A Cis-Syn Thymine Dimer At Atomic
Resolution
pdb|1RYS|A Chain A, Replication Of A Cis-Syn Thymine Dimer At Atomic
Resolution
pdb|1RYS|B Chain B, Replication Of A Cis-Syn Thymine Dimer At Atomic
Resolution
pdb|1S0M|A Chain A, Crystal Structure Of A Benzo[a]pyrene Diol Epoxide Adduct
In A Ternary Complex With A Dna Polymerase
pdb|1S0M|B Chain B, Crystal Structure Of A Benzo[a]pyrene Diol Epoxide Adduct
In A Ternary Complex With A Dna Polymerase
pdb|1S0N|A Chain A, Snapshots Of Replication Through An Abasic Lesion:
Structural Basis For Base Substitution And Frameshift
pdb|1S0O|A Chain A, Snapshots Of Replication Through An Abasic Lesion:
Structural Basis For Base Substitution And Frameshift
pdb|1S0O|B Chain B, Snapshots Of Replication Through An Abasic Lesion:
Structural Basis For Base Substitution And Frameshift
pdb|1S10|A Chain A, Snapshots Of Replication Through An Abasic Lesion:
Structural Basis For Base Substitution And Frameshift
pdb|1S97|A Chain A, Dpo4 With Gt Mismatch
pdb|1S97|B Chain B, Dpo4 With Gt Mismatch
pdb|1S97|C Chain C, Dpo4 With Gt Mismatch
pdb|1S97|D Chain D, Dpo4 With Gt Mismatch
pdb|1S9F|A Chain A, Dpo With At Matched
pdb|1S9F|B Chain B, Dpo With At Matched
pdb|1S9F|C Chain C, Dpo With At Matched
pdb|1S9F|D Chain D, Dpo With At Matched
pdb|2IA6|A Chain A, Bypass Of Major Benzopyrene-Dg Adduct By Y-Family Dna
Polymerase With Unique Structural Gap
pdb|2IA6|B Chain B, Bypass Of Major Benzopyrene-Dg Adduct By Y-Family Dna
Polymerase With Unique Structural Gap
pdb|2IBK|A Chain A, Bypass Of Major Benzopyrene-Dg Adduct By Y-Family Dna
Polymerase With Unique Structural Gap
pdb|2RDJ|A Chain A, Snapshots Of A Y-family Dna Polymerase In Replication:
Dpo4 In Apo And Binary/ternary Complex Forms
pdb|2RDJ|B Chain B, Snapshots Of A Y-family Dna Polymerase In Replication:
Dpo4 In Apo And Binary/ternary Complex Forms
pdb|2R8G|A Chain A, Selectivity Of Nucleoside Triphosphate Incorporation
Opposite 1,N2-Propanodeoxyguanosine (Pdg) By The
Sulfolobus Solfataricus Dna Polymerase Dpo4 Polymerase
pdb|2R8H|A Chain A, Selectivity Of Nucleoside Triphosphate Incorporation
Opposite 1,N2- Propanodeoxyguanosine (Pdg) By The
Sulfolobus Solfataricus Dna Polymerase Dpo4 Polymerase
pdb|2R8I|A Chain A, Selectivity Of Nucleoside Triphosphate Incorporation
Opposite 1,N2-Propanodeoxyguanosine (Pdg) By The
Sulfolobus Solfataricus Dna Polymerase Dpo4 Polymerase
pdb|3FDS|A Chain A, Structural Insight Into Recruitment Of Translesion Dna
Polymerase Dpo4 To Sliding Clamp Pcna
pdb|3M9M|B Chain B, Crystal Structure Of Dpo4 In Complex With Dna Containing
The Major Cisplatin Lesion
pdb|3M9N|B Chain B, Crystal Structure Of Dpo4 In Complex With Dna Containing
The Major Cisplatin Lesion
pdb|3M9O|B Chain B, Crystal Structure Of Dpo4 In Complex With Dna Containing
The Major Cisplatin Lesion
Length = 352
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 37/145 (25%), Positives = 69/145 (47%), Gaps = 4/145 (2%)
Query: 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKL 61
++L++ + T + GI+ NK+ AK+A+ M KP + VK L+ L I + +G
Sbjct: 131 KILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNIT 190
Query: 62 GTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSG 121
L+ +LG+ + D L DKL+ G +L ++AR E ++ R+ G
Sbjct: 191 AEKLK-KLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRV---RKSIG 246
Query: 122 KSFPGPRALKTVASVQHWLNQLCEE 146
+ R + + ++ +L + EE
Sbjct: 247 RIVTMKRNSRNLEEIKPYLFRAIEE 271
>pdb|4GC7|A Chain A, Crystal Structure Of Dpo4 In Complex With S-mc-dadp
Opposite Dt
pdb|4GC7|B Chain B, Crystal Structure Of Dpo4 In Complex With S-mc-dadp
Opposite Dt
Length = 359
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 37/145 (25%), Positives = 69/145 (47%), Gaps = 4/145 (2%)
Query: 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKL 61
++L++ + T + GI+ NK+ AK+A+ M KP + VK L+ L I + +G
Sbjct: 138 KILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNIT 197
Query: 62 GTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSG 121
L+ +LG+ + D L DKL+ G +L ++AR E ++ R+ G
Sbjct: 198 AEKLK-KLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRV---RKSIG 253
Query: 122 KSFPGPRALKTVASVQHWLNQLCEE 146
+ R + + ++ +L + EE
Sbjct: 254 RIVTMKRNSRNLEEIKPYLFRAIEE 278
>pdb|2W9B|A Chain A, Binary Complex Of Dpo4 Bound To N2,N2-Dimethyl-
Deoxyguanosine Modified Dna
pdb|2W9C|A Chain A, Ternary Complex Of Dpo4 Bound To N2,N2-Dimethyl-
Deoxyguanosine Modified Dna With Incoming Dttp
Length = 358
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 37/145 (25%), Positives = 69/145 (47%), Gaps = 4/145 (2%)
Query: 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKL 61
++L++ + T + GI+ NK+ AK+A+ M KP + VK L+ L I + +G
Sbjct: 137 KILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNIT 196
Query: 62 GTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSG 121
L+ +LG+ + D L DKL+ G +L ++AR E ++ R+ G
Sbjct: 197 AEKLK-KLGINKLVDTLSIEFDKLKGMIGEAKARYLISLARDEYNEPIRTRV---RKSIG 252
Query: 122 KSFPGPRALKTVASVQHWLNQLCEE 146
+ R + + ++ +L + EE
Sbjct: 253 RIVTMKRNSRNLEEIKPYLFRAIEE 277
>pdb|2ASD|A Chain A, Oxog-Modified Insertion Ternary Complex
pdb|2ASD|B Chain B, Oxog-Modified Insertion Ternary Complex
pdb|2ASJ|A Chain A, Oxog-Modified Preinsertion Binary Complex
pdb|2ASJ|B Chain B, Oxog-Modified Preinsertion Binary Complex
pdb|2ASL|A Chain A, Oxog-Modified Postinsertion Binary Complex
pdb|2ASL|B Chain B, Oxog-Modified Postinsertion Binary Complex
pdb|2ATL|A Chain A, Unmodified Insertion Ternary Complex
pdb|2ATL|B Chain B, Unmodified Insertion Ternary Complex
pdb|2AU0|A Chain A, Unmodified Preinsertion Binary Complex
pdb|2AU0|B Chain B, Unmodified Preinsertion Binary Complex
Length = 360
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 37/145 (25%), Positives = 69/145 (47%), Gaps = 4/145 (2%)
Query: 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKL 61
++L++ + T + GI+ NK+ AK+A+ M KP + VK L+ L I + +G
Sbjct: 139 KILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNIT 198
Query: 62 GTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSG 121
L+ +LG+ + D L DKL+ G +L ++AR E ++ R+ G
Sbjct: 199 AEKLK-KLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRV---RKSIG 254
Query: 122 KSFPGPRALKTVASVQHWLNQLCEE 146
+ R + + ++ +L + EE
Sbjct: 255 RIVTMKRNSRNLEEIKPYLFRAIEE 279
>pdb|2UVR|A Chain A, Crystal Structures Of Mutant Dpo4 Dna Polymerases With 8-
Oxog Containing Dna Template-Primer Constructs
pdb|2UVU|A Chain A, Crystal Structures Of Mutant Dpo4 Dna Polymerases With 8-
Oxog Containing Dna Template-Primer Constructs
Length = 358
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 37/145 (25%), Positives = 69/145 (47%), Gaps = 4/145 (2%)
Query: 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKL 61
++L++ + T + GI+ NK+ AK+A+ M KP + VK L+ L I + +G
Sbjct: 137 KILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNIT 196
Query: 62 GTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSG 121
L+ +LG+ + D L DKL+ G +L ++AR E ++ R+ G
Sbjct: 197 AEKLK-KLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRV---RKSIG 252
Query: 122 KSFPGPRALKTVASVQHWLNQLCEE 146
+ R + + ++ +L + EE
Sbjct: 253 RIVTMKRNSRNLEEIKPYLFRAIEE 277
>pdb|3GII|A Chain A, Dpo4 Extension Ternary Complex With Disordered A Opposite
An Oxog In Anti Conformation
pdb|3GIJ|A Chain A, Dpo4 Extension Ternary Complex With Oxog(Syn)-A(Anti) And
Oxog(Anti)- A(Syn) Pairs
pdb|3GIJ|B Chain B, Dpo4 Extension Ternary Complex With Oxog(Syn)-A(Anti) And
Oxog(Anti)- A(Syn) Pairs
pdb|3GIK|A Chain A, Dpo4 Extension Ternary Complex With The Oxog(Anti)-C(Anti)
Pair
pdb|3GIL|A Chain A, Dpo4 Extension Ternary Complex With Oxog(Anti)-T(Anti)
Pair
pdb|3GIL|B Chain B, Dpo4 Extension Ternary Complex With Oxog(Anti)-T(Anti)
Pair
pdb|3GIM|A Chain A, Dpo4 Extension Ternary Complex With Oxog(Anti)-G(Syn) Pair
pdb|3KHG|A Chain A, Dpo4 Extension Ternary Complex With Misinserted A Opposite
The 2- Aminofluorene-Guanine [af]g Lesion
pdb|3KHG|B Chain B, Dpo4 Extension Ternary Complex With Misinserted A Opposite
The 2- Aminofluorene-Guanine [af]g Lesion
pdb|3KHH|A Chain A, Dpo4 Extension Ternary Complex With A C Base Opposite The
2- Aminofluorene-Guanine [af]g Lesion
pdb|3KHH|B Chain B, Dpo4 Extension Ternary Complex With A C Base Opposite The
2- Aminofluorene-Guanine [af]g Lesion
pdb|3KHL|A Chain A, Dpo4 Post-Extension Ternary Complex With Misinserted A
Opposite The 2- Aminofluorene-Guanine [af]g Lesion
pdb|3KHL|B Chain B, Dpo4 Post-Extension Ternary Complex With Misinserted A
Opposite The 2- Aminofluorene-Guanine [af]g Lesion
pdb|3KHR|A Chain A, Dpo4 Post-Extension Ternary Complex With The Correct C
Opposite The 2- Aminofluorene-Guanine [af]g Lesion
pdb|3KHR|B Chain B, Dpo4 Post-Extension Ternary Complex With The Correct C
Opposite The 2- Aminofluorene-Guanine [af]g Lesion
pdb|3RAQ|A Chain A, Dpo4 Extension Ternary Complex With 3'-Terminal Primer C
Base Opposite The 1-Methylguanine (Mg1) Lesion
pdb|3RAQ|B Chain B, Dpo4 Extension Ternary Complex With 3'-Terminal Primer C
Base Opposite The 1-Methylguanine (Mg1) Lesion
pdb|3RAX|A Chain A, Dpo4 Extension Ternary Complex With 3'-Terminal Primer T
Base Opposite The 1-Methylguanine (M1g) Lesion
pdb|3RAX|B Chain B, Dpo4 Extension Ternary Complex With 3'-Terminal Primer T
Base Opposite The 1-Methylguanine (M1g) Lesion
pdb|3RB0|A Chain A, Dpo4 Extension Ternary Complex With 3'-Terminal Primer G
Base Opposite The 1-Methylguanine (M1g) Lesion
pdb|3RB0|B Chain B, Dpo4 Extension Ternary Complex With 3'-Terminal Primer G
Base Opposite The 1-Methylguanine (M1g) Lesion
pdb|3RB3|A Chain A, Dpo4 Extension Ternary Complex With 3'-Terminal Primer A
Base Opposite The 1-Methylguanine (M1g) Lesion
pdb|3RB4|A Chain A, Dpo4 Extension Ternary Complex With 3'-Terminal Primer G
Base Opposite The 3-Methylcytosine (M3c) Lesion
pdb|3RB4|B Chain B, Dpo4 Extension Ternary Complex With 3'-Terminal Primer G
Base Opposite The 3-Methylcytosine (M3c) Lesion
pdb|3RB6|A Chain A, Dpo4 Extension Ternary Complex With 3'-Terminal Primer A
Base Opposite The 3-Methylcytosine (M3c) Lesion
pdb|3RB6|B Chain B, Dpo4 Extension Ternary Complex With 3'-Terminal Primer A
Base Opposite The 3-Methylcytosine (M3c) Lesion
pdb|3RBD|A Chain A, Dpo4 Extension Ternary Complex With 3'-Terminal Primer C
Base Opposite The 3-Methylcytosine (M3c) Lesion
pdb|3RBD|B Chain B, Dpo4 Extension Ternary Complex With 3'-Terminal Primer C
Base Opposite The 3-Methylcytosine (M3c) Lesion
pdb|3RBE|A Chain A, Dpo4 Extension Ternary Complex With 3'-Terminal Primer T
Base Opposite The 3-Methylcytosine (M3c) Lesion
pdb|3RBE|B Chain B, Dpo4 Extension Ternary Complex With 3'-Terminal Primer T
Base Opposite The 3-Methylcytosine (M3c) Lesion
Length = 341
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 37/145 (25%), Positives = 69/145 (47%), Gaps = 4/145 (2%)
Query: 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKL 61
++L++ + T + GI+ NK+ AK+A+ M KP + VK L+ L I + +G
Sbjct: 131 KILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNIT 190
Query: 62 GTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSG 121
L+ +LG+ + D L DKL+ G +L ++AR E ++ R+ G
Sbjct: 191 AEKLK-KLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRV---RKSIG 246
Query: 122 KSFPGPRALKTVASVQHWLNQLCEE 146
+ R + + ++ +L + EE
Sbjct: 247 RIVTMKRNSRNLEEIKPYLFRAIEE 271
>pdb|4F4Z|B Chain B, Y-family Dna Polymerase Chimera Dpo4-dpo4-dbh
pdb|4F4Z|A Chain A, Y-family Dna Polymerase Chimera Dpo4-dpo4-dbh
Length = 361
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 37/145 (25%), Positives = 67/145 (46%), Gaps = 4/145 (2%)
Query: 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKL 61
++L++ + T + GI+ NK+ AK+A+ M KP + VK L+ L I + +G
Sbjct: 131 KILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNIT 190
Query: 62 GTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSG 121
L+ +LG+ + D L DKL+ G +L ++AR E ++ R+ G
Sbjct: 191 AEKLK-KLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRV---RKSIG 246
Query: 122 KSFPGPRALKTVASVQHWLNQLCEE 146
+ P + V + +L + E
Sbjct: 247 RYLTLPYNTRDVKVILPYLKKAINE 271
>pdb|3QZ7|A Chain A, T-3 Ternary Complex Of Dpo4
pdb|3QZ8|A Chain A, Tt-4 Ternary Complex Of Dpo4
Length = 360
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 37/145 (25%), Positives = 69/145 (47%), Gaps = 4/145 (2%)
Query: 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKL 61
++L++ + T + GI+ NK+ AK+A+ M KP + VK L+ L I + +G
Sbjct: 131 KILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNIT 190
Query: 62 GTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSG 121
L+ +LG+ + D L DKL+ G +L ++AR E ++ R+ G
Sbjct: 191 AEKLK-KLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRV---RKSIG 246
Query: 122 KSFPGPRALKTVASVQHWLNQLCEE 146
+ R + + ++ +L + EE
Sbjct: 247 RIVTMKRNSRNLEEIKPYLFRAIEE 271
>pdb|4F4Y|A Chain A, Y-family Dna Polymerase Chimera Dbh-dpo4-dbh
pdb|4F4Y|B Chain B, Y-family Dna Polymerase Chimera Dbh-dpo4-dbh
Length = 362
Score = 52.4 bits (124), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 35/145 (24%), Positives = 72/145 (49%), Gaps = 4/145 (2%)
Query: 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKL 61
++L++ + T + G+A NK+LAK+ + +KP + + V+ L+ L I ++ +G L
Sbjct: 132 EILEKEKITVTVGVAPNKILAKIIADKSKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVL 191
Query: 62 GTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSG 121
L NELG+ + D+L + ++L++ G +L +A+ E ++ R+ G
Sbjct: 192 ARRL-NELGIQKLRDILSKNYNELEKITGKAKALYLLKLAQDEYNEPIRTRV---RKSIG 247
Query: 122 KSFPGPRALKTVASVQHWLNQLCEE 146
+ P + V + +L + E
Sbjct: 248 RYLTLPYNTRDVKVILPYLKKAINE 272
>pdb|4F4W|A Chain A, Y-family Dna Polymerase Chimera Dbh-dpo4-dpo4 #1
pdb|4F4W|B Chain B, Y-family Dna Polymerase Chimera Dbh-dpo4-dpo4 #1
pdb|4F4X|A Chain A, Y-family Dna Polymerase Chimera Dbh-dpo4-dpo4 #2
Length = 361
Score = 52.0 bits (123), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 35/145 (24%), Positives = 74/145 (51%), Gaps = 4/145 (2%)
Query: 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKL 61
++L++ + T + G+A NK+LAK+ + +KP + + V+ L+ L I ++ +G L
Sbjct: 132 EILEKEKITVTVGVAPNKILAKIIADKSKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVL 191
Query: 62 GTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSG 121
L NELG+ + D+L + ++L++ G +L +A+ E ++ R+ G
Sbjct: 192 ARRL-NELGIQKLRDILSKNYNELEKITGKAKALYLLKLAQDEYNEPIRTRV---RKSIG 247
Query: 122 KSFPGPRALKTVASVQHWLNQLCEE 146
+ R + + ++ +L + EE
Sbjct: 248 RIVTMKRNSRNLEEIKPYLFRAIEE 272
>pdb|1JX4|A Chain A, Crystal Structure Of A Y-Family Dna Polymerase In A
Ternary Complex With Dna Substrates And An Incoming
Nucleotide
Length = 352
Score = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 36/145 (24%), Positives = 68/145 (46%), Gaps = 4/145 (2%)
Query: 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKL 61
++L++ + T + GI+ NK+ AK+A+ KP + VK L+ L I + +G
Sbjct: 131 KILEKEKITVTVGISKNKVFAKIAADXAKPNGIKVIDDEEVKRLIRELDIADVPGIGNIT 190
Query: 62 GTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSG 121
L+ +LG+ + D L DKL+ G +L ++AR E ++ R+ G
Sbjct: 191 AEKLK-KLGINKLVDTLSIEFDKLKGXIGEAKAKYLISLARDEYNEPIRTRV---RKSIG 246
Query: 122 KSFPGPRALKTVASVQHWLNQLCEE 146
+ R + + ++ +L + EE
Sbjct: 247 RIVTXKRNSRNLEEIKPYLFRAIEE 271
>pdb|1JIH|A Chain A, Yeast Dna Polymerase Eta
pdb|1JIH|B Chain B, Yeast Dna Polymerase Eta
Length = 513
Score = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 50/177 (28%), Positives = 76/177 (42%), Gaps = 30/177 (16%)
Query: 9 FTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDS--LPIKKMKQLGGKLGTSLQ 66
+T S G++ K + KLAS KP QT V + LD I LGG LG L
Sbjct: 258 YTTSCGLSSTKNVCKLASNYKKPDAQTIVKNDCLLDFLDCGKFEITSFWTLGGVLGKELI 317
Query: 67 NELGV--------------TTVGDLLKFSEDKLQES-YGFNTGTW-----------LWNI 100
+ L + G L +F + K+++S Y +T L+ +
Sbjct: 318 DVLDLPHENSIKHIRETWPDNAGQLKEFLDAKVKQSDYDRSTSNIDPLKTADLAEKLFKL 377
Query: 101 ARGISGEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQ 157
+RG G + +R + KS S K+ G ++ ++ WL C EL+ R+ DLEQ
Sbjct: 378 SRGRYGLPLSSRPVVKSMMSNKNLRG-KSCNSIVDCISWLEVFCAELTSRI-QDLEQ 432
>pdb|3MFH|A Chain A, Dna Polymerase Eta In Complex With Undamaged Dna
pdb|3MFI|A Chain A, Dna Polymerase Eta In Complex With A Cis-Syn Thymidine
Dimer
pdb|3OHA|A Chain A, Yeast Dna Polymerase Eta Inserting Dctp Opposite An 8oxog
Lesion
pdb|3OHB|A Chain A, Yeast Dna Polymerase Eta Extending From An 8-Oxog Lesion
Length = 520
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 50/177 (28%), Positives = 76/177 (42%), Gaps = 30/177 (16%)
Query: 9 FTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDS--LPIKKMKQLGGKLGTSLQ 66
+T S G++ K + KLAS KP QT V + LD I LGG LG L
Sbjct: 265 YTTSCGLSSTKNVCKLASNYKKPDAQTIVKNDCLLDFLDCGKFEITSFWTLGGVLGKELI 324
Query: 67 NELGV--------------TTVGDLLKFSEDKLQES-YGFNTGTW-----------LWNI 100
+ L + G L +F + K+++S Y +T L+ +
Sbjct: 325 DVLDLPHENSIKHIRETWPDNAGQLKEFLDAKVKQSDYDRSTSNIDPLKTADLAEKLFKL 384
Query: 101 ARGISGEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQ 157
+RG G + +R + KS S K+ G ++ ++ WL C EL+ R+ DLEQ
Sbjct: 385 SRGRYGLPLSSRPVVKSMMSNKNLRG-KSCNSIVDCISWLEVFCAELTSRI-QDLEQ 439
>pdb|2WTF|A Chain A, Dna Polymerase Eta In Complex With The
Cis-Diammineplatinum (Ii) 1,3-Gtg Intrastrand Cross-Link
pdb|2WTF|B Chain B, Dna Polymerase Eta In Complex With The
Cis-Diammineplatinum (Ii) 1,3-Gtg Intrastrand Cross-Link
pdb|2XGP|A Chain A, Yeast Dna Polymerase Eta In Complex With C8-2-
Acetylaminofluorene Containing Dna
pdb|2XGP|B Chain B, Yeast Dna Polymerase Eta In Complex With C8-2-
Acetylaminofluorene Containing Dna
pdb|2XGQ|A Chain A, Structure Of Yeast Dna Polymerase Eta In Complex With
C8-N- Acetyl-2-Aminoanthracene Containing Dna
pdb|2XGQ|B Chain B, Structure Of Yeast Dna Polymerase Eta In Complex With
C8-N- Acetyl-2-Aminoanthracene Containing Dna
Length = 536
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 50/177 (28%), Positives = 76/177 (42%), Gaps = 30/177 (16%)
Query: 9 FTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDS--LPIKKMKQLGGKLGTSLQ 66
+T S G++ K + KLAS KP QT V + LD I LGG LG L
Sbjct: 281 YTTSCGLSSTKNVCKLASNYKKPDAQTIVKNDCLLDFLDCGKFEITSFWTLGGVLGKELI 340
Query: 67 NELGV--------------TTVGDLLKFSEDKLQES-YGFNTGTW-----------LWNI 100
+ L + G L +F + K+++S Y +T L+ +
Sbjct: 341 DVLDLPHENSIKHIRETWPDNAGQLKEFLDAKVKQSDYDRSTSNIDPLKTADLAEKLFKL 400
Query: 101 ARGISGEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQ 157
+RG G + +R + KS S K+ G ++ ++ WL C EL+ R+ DLEQ
Sbjct: 401 SRGRYGLPLSSRPVVKSMMSNKNLRG-KSCNSIVDCISWLEVFCAELTSRI-QDLEQ 455
>pdb|2R8J|A Chain A, Structure Of The Eukaryotic Dna Polymerase Eta In Complex
With 1,2- D(gpg)-cisplatin Containing Dna
pdb|2R8J|B Chain B, Structure Of The Eukaryotic Dna Polymerase Eta In Complex
With 1,2- D(gpg)-cisplatin Containing Dna
pdb|2R8K|A Chain A, Structure Of The Eukaryotic Dna Polymerase Eta In Complex
With 1,2- D(gpg)-cisplatin Containing Dna
pdb|2R8K|B Chain B, Structure Of The Eukaryotic Dna Polymerase Eta In Complex
With 1,2- D(gpg)-cisplatin Containing Dna
Length = 554
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 50/177 (28%), Positives = 76/177 (42%), Gaps = 30/177 (16%)
Query: 9 FTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDS--LPIKKMKQLGGKLGTSLQ 66
+T S G++ K + KLAS KP QT V + LD I LGG LG L
Sbjct: 281 YTTSCGLSSTKNVCKLASNYKKPDAQTIVKNDCLLDFLDCGKFEITSFWTLGGVLGKELI 340
Query: 67 NELGV--------------TTVGDLLKFSEDKLQES-YGFNTGTW-----------LWNI 100
+ L + G L +F + K+++S Y +T L+ +
Sbjct: 341 DVLDLPHENSIKHIRETWPDNAGQLKEFLDAKVKQSDYDRSTSNIDPLKTADLAEKLFKL 400
Query: 101 ARGISGEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQ 157
+RG G + +R + KS S K+ G ++ ++ WL C EL+ R+ DLEQ
Sbjct: 401 SRGRYGLPLSSRPVVKSMMSNKNLRG-KSCNSIVDCISWLEVFCAELTSRI-QDLEQ 455
>pdb|3BQ0|A Chain A, Pre-insertion Binary Complex Of Dbh Dna Polymerase
pdb|3BQ1|A Chain A, Insertion Ternary Complex Of Dbh Dna Polymerase
pdb|3BQ2|A Chain A, Post-Insertion Binary Complex Of Dbh Dna Polymerase
pdb|4HYK|A Chain A, Dbh Ternary Complex (substrates Partially Disordered)
Length = 354
Score = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 34/125 (27%), Positives = 67/125 (53%), Gaps = 4/125 (3%)
Query: 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKL 61
++L++ + T + G+A NK+LAK+ + +KP + + V+ L+ L I ++ +G L
Sbjct: 132 EILEKEKITVTVGVAPNKILAKIIADKSKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVL 191
Query: 62 GTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQAR-LLPKSHGS 120
L NELG+ + D+L + ++L++ G +L +A+ E V+ + +P HG
Sbjct: 192 ARRL-NELGIQKLRDILSKNYNELEKITGKAKALYLLKLAQNKYSEPVENKSKIP--HGR 248
Query: 121 GKSFP 125
+ P
Sbjct: 249 YLTLP 253
>pdb|1K1Q|A Chain A, Crystal Structure Of A Dinb Family Error Prone Dna
Polymerase From Sulfolobus Solfataricus
pdb|1K1Q|B Chain B, Crystal Structure Of A Dinb Family Error Prone Dna
Polymerase From Sulfolobus Solfataricus
pdb|1K1S|A Chain A, Crystal Structure Of Dinb From Sulfolobus Solfataricus
Length = 354
Score = 49.7 bits (117), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 34/125 (27%), Positives = 67/125 (53%), Gaps = 4/125 (3%)
Query: 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKL 61
++L++ + T + G+A NK+LAK+ + +KP + + V+ L+ L I ++ +G L
Sbjct: 132 EILEKEKITVTVGVAPNKILAKIIADKSKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVL 191
Query: 62 GTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQAR-LLPKSHGS 120
L NELG+ + D+L + ++L++ G +L +A+ E V+ + +P HG
Sbjct: 192 ARRL-NELGIQKLRDILSKNYNELEKITGKAKALYLLKLAQNKYSEPVENKSKIP--HGR 248
Query: 121 GKSFP 125
+ P
Sbjct: 249 YLTLP 253
>pdb|4F50|A Chain A, Y-family Dna Polymerase Chimera Dbh-dbh-dpo4
Length = 361
Score = 49.7 bits (117), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 30/109 (27%), Positives = 60/109 (55%), Gaps = 1/109 (0%)
Query: 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKL 61
++L++ + T + G+A NK+LAK+ + +KP + + V+ L+ L I ++ +G L
Sbjct: 132 EILEKEKITVTVGVAPNKILAKIIADKSKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVL 191
Query: 62 GTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQ 110
L NELG+ + D+L + ++L++ G +L +A+ E V+
Sbjct: 192 ARRL-NELGIQKLRDILSKNYNELEKITGKAKALYLLKLAQNKYSEPVE 239
>pdb|1IM4|A Chain A, Crystal Structure Of A Dinb Homolog (Dbh) Lesion Bypass
Dna Polymerase Catalytic Fragment From Sulfolobus
Solfataricus
Length = 221
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 51/86 (59%), Gaps = 1/86 (1%)
Query: 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKL 61
++L++ + T + G+A NK+LAK+ + +KP + + V+ L+ L I ++ +G L
Sbjct: 137 EILEKEKITVTVGVAPNKILAKIIADKSKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVL 196
Query: 62 GTSLQNELGVTTVGDLLKFSEDKLQE 87
L NELG+ + D+L + ++L++
Sbjct: 197 ARRL-NELGIQKLRDILSKNYNELEK 221
>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
Length = 715
Score = 30.8 bits (68), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 5/56 (8%)
Query: 24 LASGMNKPAQQTTV----PFSS-VKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTV 74
LA+G+N PA+ + F+ + G D +PI + KQ+ G+ G +++G + V
Sbjct: 348 LAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMSGRAGRPGFDQIGESIV 403
>pdb|3KFU|E Chain E, Crystal Structure Of The Transamidosome
pdb|3KFU|H Chain H, Crystal Structure Of The Transamidosome
Length = 471
Score = 30.4 bits (67), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 5/73 (6%)
Query: 212 FLGSFGVKTQGSHYSGWRITALSVSASKIVPV---LSGTCSIMKYFNGPDKFGSTSEQLP 268
F G +G+K S + + A + S +I P+ + +M GPD +TS LP
Sbjct: 172 FCGVYGLKPTYGRVSRFGLIAYASSLDQIGPMARSVRDLALLMDAAAGPDPLDATSLDLP 231
Query: 269 DNFIDA--APLSP 279
F +A PL P
Sbjct: 232 PRFQEALEGPLPP 244
>pdb|2FFK|A Chain A, Solution Structure Of The Complex Between Poxvirus-Encoded
Cc Chemokine Inhibitor Vcci And Human Mip-1beta,
Minimized Average Structure
pdb|2FIN|A Chain A, Solution Structure Of The Complex Between Poxvirus-Encoded
Cc Chemokine Inhibitor Vcci And Human Mip-1beta,
Ensemble Structure
Length = 242
Score = 30.0 bits (66), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 5/77 (6%)
Query: 85 LQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLC 144
L+ ++GF + +I+ G V ARL S G GK P + +A ++ C
Sbjct: 88 LRMNFGFTKCPQIKSISESADGNTVNARLSSVSPGQGKDSPAITHEEALAMIKD-----C 142
Query: 145 EELSERLCSDLEQNKRI 161
E + CS+ E++ I
Sbjct: 143 EVSIDIRCSEEEKDSDI 159
>pdb|2X1I|A Chain A, Glycoside Hydrolase Family 77 4-Alpha-Glucanotransferase
From Thermus Brockianus
Length = 500
Score = 30.0 bits (66), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 28/63 (44%)
Query: 60 KLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHG 119
+LG + + L V V D+L + G +G W W + G EE RLL +
Sbjct: 437 RLGMASRARLAVYPVQDVLALGSEARMNYPGRPSGNWAWRLRPGEIKEEHGERLLSLAEA 496
Query: 120 SGK 122
+G+
Sbjct: 497 TGR 499
>pdb|3AI4|A Chain A, Crystal Structure Of Yeast Enhanced Green Fluorescent
Protein - Mouse Polymerase Iota Ubiquitin Binding Motif
Fusion Protein
Length = 283
Score = 29.6 bits (65), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 17/34 (50%), Positives = 22/34 (64%), Gaps = 4/34 (11%)
Query: 481 EIDPSVIDELPKEIQDEIQA-WLRP-SKRP--HR 510
+IDP V ELP+E+Q E+ A W R + RP HR
Sbjct: 250 DIDPQVFYELPEEVQKELMAEWERAGAARPSAHR 283
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
0.312 0.129 0.376
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,902,709
Number of Sequences: 62578
Number of extensions: 586745
Number of successful extensions: 1094
Number of sequences better than 100.0: 49
Number of HSP's better than 100.0 without gapping: 43
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1023
Number of HSP's gapped (non-prelim): 54
length of query: 527
length of database: 14,973,337
effective HSP length: 103
effective length of query: 424
effective length of database: 8,527,803
effective search space: 3615788472
effective search space used: 3615788472
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 54 (25.4 bits)