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= psy16216
(129 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 100 bits (249), Expect = 2e-22, Method: Composition-based stats.
Identities = 60/137 (43%), Positives = 83/137 (60%), Gaps = 16/137 (11%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGH--IAASQLSNTFVVGF 58
YR A EV+ ++S F+ ++ERASIDEAY+DLT V ER++ + I+A L +T++ G
Sbjct: 95 YREASVEVMEIMSRFA-VIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGL 153
Query: 59 --GPDNNDEDA-----RKAGVMEWLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAV 111
GP +E RK G+ +WL + D TS D Q L + VIVEE+RAA+
Sbjct: 154 PQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTS-----PDLQ-LTVGAVIVEEMRAAI 207
Query: 112 LSKTQFHCSAGIAHNKV 128
+T F CSAGI+HNKV
Sbjct: 208 ERETGFQCSAGISHNKV 224
>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 = 100 bits (249), Expect = 2e-22, Method: Composition-based stats.
Identities = 60/137 (43%), Positives = 83/137 (60%), Gaps = 16/137 (11%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGH--IAASQLSNTFVVGF 58
YR A EV+ ++S F+ ++ERASIDEAY+DLT V ER++ + I+A L +T++ G
Sbjct: 95 YREASVEVMEIMSRFA-VIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGL 153
Query: 59 --GPDNNDEDA-----RKAGVMEWLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAV 111
GP +E RK G+ +WL + D TS D Q L + VIVEE+RAA+
Sbjct: 154 PQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTS-----PDLQ-LTVGAVIVEEMRAAI 207
Query: 112 LSKTQFHCSAGIAHNKV 128
+T F CSAGI+HNKV
Sbjct: 208 ERETGFQCSAGISHNKV 224
>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 = 47.4 bits (111), Expect = 2e-06, Method: Composition-based stats.
Identities = 34/128 (26%), Positives = 59/128 (46%), Gaps = 25/128 (19%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGP 60
YR +V +L EFS +VER DE ++DLT++V +R++ + + +LS V
Sbjct: 76 YREMSYKVTELLEEFSPVVERLGFDENFVDLTEMVEKRLQ---QLQSDELSAVTVS---- 128
Query: 61 DNNDEDARKAGVMEWLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCS 120
G VY++ +L++ L + I E+R A+ ++
Sbjct: 129 ----------------GHVYNNQSINLLDVLH--IRLLVGSQIAAEMREAMYNQLGLTGC 170
Query: 121 AGIAHNKV 128
AG+A NK+
Sbjct: 171 AGVASNKL 178
>pdb|3H40|A Chain A, Binary Complex Of Human Dna Polymerase Iota With Template
UT
Length = 389
Score = 47.4 bits (111), Expect = 2e-06, Method: Composition-based stats.
Identities = 34/128 (26%), Positives = 59/128 (46%), Gaps = 25/128 (19%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGP 60
YR +V +L EFS +VER DE ++DLT++V +R++ + + +LS V
Sbjct: 77 YREMSYKVTELLEEFSPVVERLGFDENFVDLTEMVEKRLQ---QLQSDELSAVTVS---- 129
Query: 61 DNNDEDARKAGVMEWLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCS 120
G VY++ +L++ L + I E+R A+ ++
Sbjct: 130 ----------------GHVYNNQSINLLDVLH--IRLLVGSQIAAEMREAMYNQLGLTGC 171
Query: 121 AGIAHNKV 128
AG+A NK+
Sbjct: 172 AGVASNKL 179
>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 = 47.4 bits (111), Expect = 2e-06, Method: Composition-based stats.
Identities = 34/128 (26%), Positives = 59/128 (46%), Gaps = 25/128 (19%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGP 60
YR +V +L EFS +VER DE ++DLT++V +R++ + + +LS V
Sbjct: 78 YREMSYKVTELLEEFSPVVERLGFDENFVDLTEMVEKRLQ---QLQSDELSAVTVS---- 130
Query: 61 DNNDEDARKAGVMEWLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCS 120
G VY++ +L++ L + I E+R A+ ++
Sbjct: 131 ----------------GHVYNNQSINLLDVLH--IRLLVGSQIAAEMREAMYNQLGLTGC 172
Query: 121 AGIAHNKV 128
AG+A NK+
Sbjct: 173 AGVASNKL 180
>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 = 47.0 bits (110), Expect = 3e-06, Method: Composition-based stats.
Identities = 34/128 (26%), Positives = 59/128 (46%), Gaps = 25/128 (19%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGP 60
YR +V +L EFS +VER DE ++DLT++V +R++ + + +LS V
Sbjct: 102 YREMSYKVTELLEEFSPVVERLGFDENFVDLTEMVEKRLQ---QLQSDELSAVTVS---- 154
Query: 61 DNNDEDARKAGVMEWLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCS 120
G VY++ +L++ L + I E+R A+ ++
Sbjct: 155 ----------------GHVYNNQSINLLDVLH--IRLLVGSQIAAEMREAMYNQLGLTGC 196
Query: 121 AGIAHNKV 128
AG+A NK+
Sbjct: 197 AGVASNKL 204
>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 = 44.7 bits (104), Expect = 1e-05, Method: Composition-based stats.
Identities = 34/128 (26%), Positives = 56/128 (43%), Gaps = 25/128 (19%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGP 60
YR +V +L EFS +VER DE ++DLT+ V +R++ + + +LS V
Sbjct: 102 YREXSYKVTELLEEFSPVVERLGFDENFVDLTEXVEKRLQ---QLQSDELSAVTVS---- 154
Query: 61 DNNDEDARKAGVMEWLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCS 120
G VY++ +L++ L + I E R A ++
Sbjct: 155 ----------------GHVYNNQSINLLDVLH--IRLLVGSQIAAEXREAXYNQLGLTGC 196
Query: 121 AGIAHNKV 128
AG+A NK+
Sbjct: 197 AGVASNKL 204
>pdb|2IMW|P Chain P, Mechanism Of Template-Independent Nucleotide Incorporation
Catalyzed By A Template-Dependent Dna Polymerase
Length = 348
Score = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 25/37 (67%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHE 37
Y+ ++ +L E+S +E ASIDEAY+D++D V +
Sbjct: 81 YQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRD 117
>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 = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 25/37 (67%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHE 37
Y+ ++ +L E+S +E ASIDEAY+D++D V +
Sbjct: 81 YQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRD 117
>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 = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 25/37 (67%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHE 37
Y+ ++ +L E+S +E ASIDEAY+D++D V +
Sbjct: 87 YQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRD 123
>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 = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 25/37 (67%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHE 37
Y+ ++ +L E+S +E ASIDEAY+D++D V +
Sbjct: 81 YQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRD 117
>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 = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 25/37 (67%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHE 37
Y+ ++ +L E+S +E ASIDEAY+D++D V +
Sbjct: 89 YQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRD 125
>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 = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 25/37 (67%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHE 37
Y+ ++ +L E+S +E ASIDEAY+D++D V +
Sbjct: 81 YQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRD 117
>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 = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 25/37 (67%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHE 37
Y+ ++ +L E+S +E ASIDEAY+D++D V +
Sbjct: 87 YQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRD 123
>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 = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 25/37 (67%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHE 37
Y+ ++ +L E+S +E ASIDEAY+D++D V +
Sbjct: 87 YQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRD 123
>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 = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 25/37 (67%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHE 37
Y+ ++ +L E+S +E ASIDEAY+D++D V +
Sbjct: 81 YQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRD 117
>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 = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 25/37 (67%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHE 37
Y+ ++ +L E+S +E ASIDEAY+D++D V +
Sbjct: 88 YQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRD 124
>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 = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 25/37 (67%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHE 37
Y+ ++ +L E+S +E ASIDEAY+D++D V +
Sbjct: 81 YQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRD 117
>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 = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 25/37 (67%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHE 37
Y+ ++ +L E+S +E ASIDEAY+D++D V +
Sbjct: 87 YQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRD 123
>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 = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 25/37 (67%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHE 37
Y+ ++ +L E+S +E ASIDEAY+D++D V +
Sbjct: 81 YQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRD 117
>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 = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 25/37 (67%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHE 37
Y+ ++ +L E+S +E ASIDEAY+D++D V +
Sbjct: 87 YQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRD 123
>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 = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 25/37 (67%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHE 37
Y+ ++ +L E+S +E ASIDEAY+D++D V +
Sbjct: 87 YQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRD 123
>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 = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 25/37 (67%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHE 37
Y+ ++ +L E+S +E ASIDEAY+D++D V +
Sbjct: 81 YQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRD 117
>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 = 35.0 bits (79), Expect = 0.012, Method: Composition-based stats.
Identities = 14/31 (45%), Positives = 21/31 (67%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDL 31
YR R+ +A+ ++VERASIDE ++DL
Sbjct: 138 YRRESRKALAIFKWACDLVERASIDEVFLDL 168
>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 = 35.0 bits (79), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 25/37 (67%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHE 37
Y+ ++ +L E+S +E ASIDEAY+D++D V +
Sbjct: 86 YQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRD 122
>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 = 33.9 bits (76), Expect = 0.024, Method: Composition-based stats.
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDL 31
YR R+ + + ++VERASIDE ++DL
Sbjct: 154 YRRESRKALKIFKSACDLVERASIDEVFLDL 184
>pdb|1JIH|A Chain A, Yeast Dna Polymerase Eta
pdb|1JIH|B Chain B, Yeast Dna Polymerase Eta
Length = 513
Score = 33.9 bits (76), Expect = 0.024, Method: Composition-based stats.
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDL 31
YR R+ + + ++VERASIDE ++DL
Sbjct: 131 YRRESRKALKIFKSACDLVERASIDEVFLDL 161
>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 = 33.9 bits (76), Expect = 0.024, Method: Composition-based stats.
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDL 31
YR R+ + + ++VERASIDE ++DL
Sbjct: 154 YRRESRKALKIFKSACDLVERASIDEVFLDL 184
>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 = 33.9 bits (76), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 24/37 (64%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHE 37
Y+ + +L E+S +E ASIDEAY+D++D V +
Sbjct: 81 YQQVSSRIXNLLREYSEKIEIASIDEAYLDISDKVRD 117
>pdb|1C3X|A Chain A, Purine Nucleoside Phosphorylase From Cellulomonas Sp. In
Complex With 8-Iodo-Guanine
pdb|1C3X|B Chain B, Purine Nucleoside Phosphorylase From Cellulomonas Sp. In
Complex With 8-Iodo-Guanine
pdb|1C3X|C Chain C, Purine Nucleoside Phosphorylase From Cellulomonas Sp. In
Complex With 8-Iodo-Guanine
pdb|1QE5|A Chain A, Purine Nucleoside Phosphorylase From Cellulomonas Sp. In
Complex With Phosphate
pdb|1QE5|B Chain B, Purine Nucleoside Phosphorylase From Cellulomonas Sp. In
Complex With Phosphate
pdb|1QE5|C Chain C, Purine Nucleoside Phosphorylase From Cellulomonas Sp. In
Complex With Phosphate
Length = 266
Score = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 5/74 (6%)
Query: 3 NAGREVIAVLSEFSNIVERASID-EAYIDLTDVVHERMKSIGHIAASQLSNTFVVGF-GP 60
AG V+ LS+ N+ R+ ++ ++DLTDV R++ + H L F GP
Sbjct: 128 GAGTPVL--LSDHINLTARSPLEGPTFVDLTDVYSPRLRELAHRVDPTLPEGVYAQFPGP 185
Query: 61 D-NNDEDARKAGVM 73
+ R AG++
Sbjct: 186 HYETPAEVRMAGIL 199
>pdb|1GR0|A Chain A, Myo-Inositol 1-Phosphate Synthase From Mycobacterium
Tuberculosis In Complex With Nad And Zinc
Length = 367
Score = 29.6 bits (65), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 25/101 (24%), Positives = 44/101 (43%), Gaps = 6/101 (5%)
Query: 14 EFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVM 73
+F N++ER ++ I T V +K + + VG+ D RK +
Sbjct: 235 DFLNMLERERLESKKISKTQAVTSNLKREFKTKDVHIGPSDHVGW------LDDRKWAYV 288
Query: 74 EWLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSK 114
G+ + D +L E + AGVI++ +RAA ++K
Sbjct: 289 RLEGRAFGDVPLNLEYKLEVWDSPNSAGVIIDAVRAAKIAK 329
>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 = 29.6 bits (65), Expect = 0.48, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 23/38 (60%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHER 38
YR +EV +L+++ S+DEAY+++T + ER
Sbjct: 107 YRAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEER 144
>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 = 29.6 bits (65), Expect = 0.51, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 23/38 (60%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHER 38
YR +EV +L+++ S+DEAY+++T + ER
Sbjct: 163 YRAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEER 200
>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 = 29.6 bits (65), Expect = 0.52, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 23/38 (60%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHER 38
YR +EV +L+++ S+DEAY+++T + ER
Sbjct: 156 YRAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEER 193
>pdb|1IM4|A Chain A, Crystal Structure Of A Dinb Homolog (Dbh) Lesion Bypass
Dna Polymerase Catalytic Fragment From Sulfolobus
Solfataricus
Length = 221
Score = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 24/36 (66%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVH 36
Y ++ +L++ ++ +E ASIDEAY+D+T+ V
Sbjct: 86 YEAFSNRIMNLLNKHADKIEVASIDEAYLDVTNKVE 121
>pdb|4F50|A Chain A, Y-family Dna Polymerase Chimera Dbh-dbh-dpo4
Length = 361
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 24/35 (68%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVV 35
Y ++ +L++ ++ +E ASIDEAY+D+T+ V
Sbjct: 81 YEAFSNRIMNLLNKHADKIEVASIDEAYLDVTNKV 115
>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 = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 24/36 (66%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVH 36
Y ++ +L++ ++ +E ASIDEAY+D+T+ V
Sbjct: 81 YEAFSNRIMNLLNKHADKIEVASIDEAYLDVTNKVE 116
>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 = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 24/36 (66%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVH 36
Y ++ +L++ ++ +E ASIDEAY+D+T+ V
Sbjct: 81 YEAFSNRIMNLLNKHADKIEVASIDEAYLDVTNKVE 116
>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 = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 23/29 (79%)
Query: 8 VIAVLSEFSNIVERASIDEAYIDLTDVVH 36
++ +L++ ++ +E ASIDEAY+D+T+ V
Sbjct: 88 IMNLLNKHADKIEVASIDEAYLDVTNKVE 116
>pdb|4DEZ|A Chain A, Structure Of Msdpo4
Length = 356
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 103 IVEEIRAAVLSKTQFHCSAGIAHNK 127
+ E IR V ++T CS GI+ NK
Sbjct: 124 VAERIRTVVAAETGLSCSVGISDNK 148
>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 = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 24/36 (66%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVH 36
Y ++ +L++ ++ +E ASIDEAY+D+T+ V
Sbjct: 81 YEAFSNRIMNLLNKHADKIEVASIDEAYLDVTNKVE 116
>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 = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 10/37 (27%), Positives = 23/37 (62%)
Query: 1 YRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHE 37
Y+ + + L+ +++ +E S DEA +D+T+++ E
Sbjct: 217 YKEVAQTLYETLASYTHNIEAVSCDEALVDITEILAE 253
>pdb|1A3W|A Chain A, Pyruvate Kinase From Saccharomyces Cerevisiae Complexed
With Fbp, Pg, Mn2+ And K+
pdb|1A3W|B Chain B, Pyruvate Kinase From Saccharomyces Cerevisiae Complexed
With Fbp, Pg, Mn2+ And K+
pdb|1A3X|A Chain A, Pyruvate Kinase From Saccharomyces Cerevisiae Complexed
With Pg, Mn2+ And K+
pdb|1A3X|B Chain B, Pyruvate Kinase From Saccharomyces Cerevisiae Complexed
With Pg, Mn2+ And K+
Length = 500
Score = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 5/41 (12%)
Query: 37 ERMKSIGHIAASQLSNTFVVG-FGPDNNDEDA----RKAGV 72
ER+ S+ +A S L T ++G GP N+ + RKAG+
Sbjct: 5 ERLTSLNVVAGSDLRRTSIIGTIGPKTNNPETLVALRKAGL 45
>pdb|1XS5|A Chain A, The Crystal Structure Of Lipoprotein Tp32 From Treponema
Pallidum
Length = 241
Score = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/56 (23%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 60 PDNNDEDARKAGVMEWLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKT 115
P+++ +AR ++E G + + L ED Q+ + V+++E+ +A+L +
Sbjct: 107 PNDSSNEARALRLLEAAGFIRMRAGSGLFATVEDVQQ-NVRNVVLQEVESALLPRV 161
>pdb|1B1Y|A Chain A, Sevenfold Mutant Of Barley Beta-Amylase
Length = 500
Score = 27.3 bits (59), Expect = 2.4, Method: Composition-based stats.
Identities = 14/28 (50%), Positives = 19/28 (67%), Gaps = 3/28 (10%)
Query: 78 QVYSDTDTSLMENTEDFQELAIAGVIVE 105
Q+Y+D TS EN +DF + AGVIV+
Sbjct: 146 QMYADYMTSFRENMKDFLD---AGVIVD 170
>pdb|3TSY|A Chain A, 4-Coumaroyl-Coa Ligase::stilbene Synthase Fusion Protein
Length = 979
Score = 26.9 bits (58), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 4/74 (5%)
Query: 10 AVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLS--NTFVVGFGPDNNDEDA 67
A+ +F+ I +++ I + YI LT+ + E +IG A L+ + P E A
Sbjct: 638 ALKKKFNRICDKSMIKKRYIHLTEEMLEEHPNIGAYMAPSLNIRQEIITAEVPKLGKEAA 697
Query: 68 RKAGVMEWLGQVYS 81
KA + EW GQ S
Sbjct: 698 LKA-LKEW-GQPKS 709
>pdb|4HTE|A Chain A, Crystal Structure Of The C-terminal Domain Of Nicking
Enzyme From Staphylococcus Aureus
Length = 353
Score = 26.6 bits (57), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 2/49 (4%)
Query: 6 REVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTF 54
R+V+ +E +IV+ I EA I L V+ R S+ IAA+ SN F
Sbjct: 123 RDVLPANNELEDIVKEKRIKEAQISLNTVLGNRDISLESIAAA--SNFF 169
>pdb|3P83|D Chain D, Structure Of The Pcna:rnase Hii Complex From Archaeoglobus
Fulgidus.
pdb|3P83|E Chain E, Structure Of The Pcna:rnase Hii Complex From Archaeoglobus
Fulgidus.
pdb|3P83|F Chain F, Structure Of The Pcna:rnase Hii Complex From Archaeoglobus
Fulgidus
Length = 217
Score = 26.2 bits (56), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 2 RNAGREVIAVLSE-FSNIVERASIDEAYIDLTDVVHERM 39
R A + + +L E ++ I+ R + AY+D DV+ ER+
Sbjct: 84 RMAAKTINEILKECYAEIILRLKPEIAYVDSPDVIPERL 122
>pdb|1I39|A Chain A, Rnase Hii From Archaeoglobus Fulgidus
pdb|1I3A|A Chain A, Rnase Hii From Archaeoglobus Fulgidus With Cobalt
Hexammine Chloride
Length = 225
Score = 25.8 bits (55), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 2 RNAGREVIAVLSE-FSNIVERASIDEAYIDLTDVVHERM 39
R A + + +L E ++ I+ R + AY+D DV+ ER+
Sbjct: 92 RMAAKTINEILKECYAEIILRLKPEIAYVDSPDVIPERL 130
>pdb|3ZS7|A Chain A, Crystal Structure Of Pyridoxal Kinase From Trypanosoma
Brucei
Length = 300
Score = 25.8 bits (55), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 94 FQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVK 129
F+ ++GV V ++ +A+L+ FH + G+AH +K
Sbjct: 151 FEASLLSGVTVNDLSSAILAADWFH-NCGVAHVIIK 185
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
0.316 0.131 0.362
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,513,740
Number of Sequences: 62578
Number of extensions: 133775
Number of successful extensions: 368
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 43
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 292
Number of HSP's gapped (non-prelim): 77
length of query: 129
length of database: 14,973,337
effective HSP length: 88
effective length of query: 41
effective length of database: 9,466,473
effective search space: 388125393
effective search space used: 388125393
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)