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= psy4416
(290 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 29.3 bits (64), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 47/168 (27%), Positives = 67/168 (39%), Gaps = 38/168 (22%)
Query: 98 VYDYKNRLSHYNLLSAIKNNPLFEEFNKLTLGFSFNKLTSNSKTQDTLILNTLKTSKAEP 157
V DY+ YNL IKN L +E +T+G S NK + + A+P
Sbjct: 115 VRDYR---EAYNLGLEIKNKILEKEKITVTVGISKNK-----------VFAKIAADMAKP 160
Query: 158 NG------------IHKYYADDIVGILNIIEENLKWSNYKTELNILSRKQCESDLLNSIV 205
NG I + D+ GI NI E LK ++ LS E D L ++
Sbjct: 161 NGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLS---IEFDKLKGMI 217
Query: 206 ELGETNLSVSDTIMKERLQEKCPLPDPEVAIVIGRKLSSYGLLPWNIR 253
GE ++ ++ E P+ V IGR L+ LP+N R
Sbjct: 218 --GEAKAKYLISLARDEYNE--PIR-TRVRKSIGRYLT----LPYNTR 256
>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 = 28.9 bits (63), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 39/96 (40%), Gaps = 28/96 (29%)
Query: 98 VYDYKNRLSHYNLLSAIKNNPLFEEFNKLTLGFSFNKLTSNSKTQDTLILNTLKTSKAEP 157
V DY+ YNL IKN L +E +T+G S NK + + A+P
Sbjct: 115 VRDYRE---AYNLGLEIKNKILEKEKITVTVGISKNK-----------VFAKIAADXAKP 160
Query: 158 NGIHKYYAD-------------DIVGILNIIEENLK 180
NGI K D D+ GI NI E LK
Sbjct: 161 NGI-KVIDDEEVKRLIRELDIADVPGIGNITAEKLK 195
>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 = 28.9 bits (63), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 39/96 (40%), Gaps = 28/96 (29%)
Query: 98 VYDYKNRLSHYNLLSAIKNNPLFEEFNKLTLGFSFNKLTSNSKTQDTLILNTLKTSKAEP 157
V DY+ YNL IKN L +E +T+G S NK + + A+P
Sbjct: 115 VRDYRE---AYNLGLEIKNKILEKEKITVTVGISKNK-----------VFAKIAADMAKP 160
Query: 158 NGIHKYYAD-------------DIVGILNIIEENLK 180
NGI K D D+ GI NI E LK
Sbjct: 161 NGI-KVIDDEEVKRLIRELDIADVPGIGNITAEKLK 195
>pdb|2IMW|P Chain P, Mechanism Of Template-Independent Nucleotide Incorporation
Catalyzed By A Template-Dependent Dna Polymerase
Length = 348
Score = 28.9 bits (63), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 39/96 (40%), Gaps = 28/96 (29%)
Query: 98 VYDYKNRLSHYNLLSAIKNNPLFEEFNKLTLGFSFNKLTSNSKTQDTLILNTLKTSKAEP 157
V DY+ YNL IKN L +E +T+G S NK + + A+P
Sbjct: 115 VRDYRE---AYNLGLEIKNKILEKEKITVTVGISKNK-----------VFAKIAADMAKP 160
Query: 158 NGIHKYYAD-------------DIVGILNIIEENLK 180
NGI K D D+ GI NI E LK
Sbjct: 161 NGI-KVIDDEEVKRLIRELDIADVPGIGNITAEKLK 195
>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 = 28.5 bits (62), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 39/96 (40%), Gaps = 28/96 (29%)
Query: 98 VYDYKNRLSHYNLLSAIKNNPLFEEFNKLTLGFSFNKLTSNSKTQDTLILNTLKTSKAEP 157
V DY+ YNL IKN L +E +T+G S NK + + A+P
Sbjct: 115 VRDYRE---AYNLGLEIKNKILEKEKITVTVGISKNK-----------VFAKIAADMAKP 160
Query: 158 NGIHKYYAD-------------DIVGILNIIEENLK 180
NGI K D D+ GI NI E LK
Sbjct: 161 NGI-KVIDDEEVKRLIRELDIADVPGIGNITAEKLK 195
>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 = 28.5 bits (62), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 39/96 (40%), Gaps = 28/96 (29%)
Query: 98 VYDYKNRLSHYNLLSAIKNNPLFEEFNKLTLGFSFNKLTSNSKTQDTLILNTLKTSKAEP 157
V DY+ YNL IKN L +E +T+G S NK + + A+P
Sbjct: 121 VRDYRE---AYNLGLEIKNKILEKEKITVTVGISKNK-----------VFAKIAADMAKP 166
Query: 158 NGIHKYYAD-------------DIVGILNIIEENLK 180
NGI K D D+ GI NI E LK
Sbjct: 167 NGI-KVIDDEEVKRLIRELDIADVPGIGNITAEKLK 201
>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 = 28.5 bits (62), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 39/96 (40%), Gaps = 28/96 (29%)
Query: 98 VYDYKNRLSHYNLLSAIKNNPLFEEFNKLTLGFSFNKLTSNSKTQDTLILNTLKTSKAEP 157
V DY+ YNL IKN L +E +T+G S NK + + A+P
Sbjct: 115 VRDYRE---AYNLGLEIKNKILEKEKITVTVGISKNK-----------VFAKIAADMAKP 160
Query: 158 NGIHKYYAD-------------DIVGILNIIEENLK 180
NGI K D D+ GI NI E LK
Sbjct: 161 NGI-KVIDDEEVKRLIRELDIADVPGIGNITAEKLK 195
>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 = 28.5 bits (62), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 39/96 (40%), Gaps = 28/96 (29%)
Query: 98 VYDYKNRLSHYNLLSAIKNNPLFEEFNKLTLGFSFNKLTSNSKTQDTLILNTLKTSKAEP 157
V DY+ YNL IKN L +E +T+G S NK + + A+P
Sbjct: 115 VRDYRE---AYNLGLEIKNKILEKEKITVTVGISKNK-----------VFAKIAADMAKP 160
Query: 158 NGIHKYYAD-------------DIVGILNIIEENLK 180
NGI K D D+ GI NI E LK
Sbjct: 161 NGI-KVIDDEEVKRLIRELDIADVPGIGNITAEKLK 195
>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 = 28.5 bits (62), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 39/96 (40%), Gaps = 28/96 (29%)
Query: 98 VYDYKNRLSHYNLLSAIKNNPLFEEFNKLTLGFSFNKLTSNSKTQDTLILNTLKTSKAEP 157
V DY+ YNL IKN L +E +T+G S NK + + A+P
Sbjct: 121 VRDYRE---AYNLGLEIKNKILEKEKITVTVGISKNK-----------VFAKIAADMAKP 166
Query: 158 NGIHKYYAD-------------DIVGILNIIEENLK 180
NGI K D D+ GI NI E LK
Sbjct: 167 NGI-KVIDDEEVKRLIRELDIADVPGIGNITAEKLK 201
>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 = 28.5 bits (62), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 39/96 (40%), Gaps = 28/96 (29%)
Query: 98 VYDYKNRLSHYNLLSAIKNNPLFEEFNKLTLGFSFNKLTSNSKTQDTLILNTLKTSKAEP 157
V DY+ YNL IKN L +E +T+G S NK + + A+P
Sbjct: 121 VRDYRE---AYNLGLEIKNKILEKEKITVTVGISKNK-----------VFAKIAADMAKP 166
Query: 158 NGIHKYYAD-------------DIVGILNIIEENLK 180
NGI K D D+ GI NI E LK
Sbjct: 167 NGI-KVIDDEEVKRLIRELDIADVPGIGNITAEKLK 201
>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 = 28.5 bits (62), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 39/96 (40%), Gaps = 28/96 (29%)
Query: 98 VYDYKNRLSHYNLLSAIKNNPLFEEFNKLTLGFSFNKLTSNSKTQDTLILNTLKTSKAEP 157
V DY+ YNL IKN L +E +T+G S NK + + A+P
Sbjct: 121 VRDYRE---AYNLGLEIKNKILEKEKITVTVGISKNK-----------VFAKIAADMAKP 166
Query: 158 NGIHKYYAD-------------DIVGILNIIEENLK 180
NGI K D D+ GI NI E LK
Sbjct: 167 NGI-KVIDDEEVKRLIRELDIADVPGIGNITAEKLK 201
>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 = 28.5 bits (62), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 39/96 (40%), Gaps = 28/96 (29%)
Query: 98 VYDYKNRLSHYNLLSAIKNNPLFEEFNKLTLGFSFNKLTSNSKTQDTLILNTLKTSKAEP 157
V DY+ YNL IKN L +E +T+G S NK + + A+P
Sbjct: 115 VRDYRE---AYNLGLEIKNKILEKEKITVTVGISKNK-----------VFAKIAADMAKP 160
Query: 158 NGIHKYYAD-------------DIVGILNIIEENLK 180
NGI K D D+ GI NI E LK
Sbjct: 161 NGI-KVIDDEEVKRLIRELDIADVPGIGNITAEKLK 195
>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 = 28.5 bits (62), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 39/96 (40%), Gaps = 28/96 (29%)
Query: 98 VYDYKNRLSHYNLLSAIKNNPLFEEFNKLTLGFSFNKLTSNSKTQDTLILNTLKTSKAEP 157
V DY+ YNL IKN L +E +T+G S NK + + A+P
Sbjct: 122 VRDYRE---AYNLGLEIKNKILEKEKITVTVGISKNK-----------VFAKIAADMAKP 167
Query: 158 NGIHKYYAD-------------DIVGILNIIEENLK 180
NGI K D D+ GI NI E LK
Sbjct: 168 NGI-KVIDDEEVKRLIRELDIADVPGIGNITAEKLK 202
>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 = 28.5 bits (62), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 39/96 (40%), Gaps = 28/96 (29%)
Query: 98 VYDYKNRLSHYNLLSAIKNNPLFEEFNKLTLGFSFNKLTSNSKTQDTLILNTLKTSKAEP 157
V DY+ YNL IKN L +E +T+G S NK + + A+P
Sbjct: 121 VRDYRE---AYNLGLEIKNKILEKEKITVTVGISKNK-----------VFAKIAADMAKP 166
Query: 158 NGIHKYYAD-------------DIVGILNIIEENLK 180
NGI K D D+ GI NI E LK
Sbjct: 167 NGI-KVIDDEEVKRLIRELDIADVPGIGNITAEKLK 201
>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 = 28.5 bits (62), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 39/96 (40%), Gaps = 28/96 (29%)
Query: 98 VYDYKNRLSHYNLLSAIKNNPLFEEFNKLTLGFSFNKLTSNSKTQDTLILNTLKTSKAEP 157
V DY+ YNL IKN L +E +T+G S NK + + A+P
Sbjct: 115 VRDYRE---AYNLGLEIKNKILEKEKITVTVGISKNK-----------VFAKIAADMAKP 160
Query: 158 NGIHKYYAD-------------DIVGILNIIEENLK 180
NGI K D D+ GI NI E LK
Sbjct: 161 NGI-KVIDDEEVKRLIRELDIADVPGIGNITAEKLK 195
>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 = 28.5 bits (62), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 39/96 (40%), Gaps = 28/96 (29%)
Query: 98 VYDYKNRLSHYNLLSAIKNNPLFEEFNKLTLGFSFNKLTSNSKTQDTLILNTLKTSKAEP 157
V DY+ YNL IKN L +E +T+G S NK + + A+P
Sbjct: 121 VRDYRE---AYNLGLEIKNKILEKEKITVTVGISKNK-----------VFAKIAADMAKP 166
Query: 158 NGIHKYYAD-------------DIVGILNIIEENLK 180
NGI K D D+ GI NI E LK
Sbjct: 167 NGI-KVIDDEEVKRLIRELDIADVPGIGNITAEKLK 201
>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 = 28.5 bits (62), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 39/96 (40%), Gaps = 28/96 (29%)
Query: 98 VYDYKNRLSHYNLLSAIKNNPLFEEFNKLTLGFSFNKLTSNSKTQDTLILNTLKTSKAEP 157
V DY+ YNL IKN L +E +T+G S NK + + A+P
Sbjct: 123 VRDYRE---AYNLGLEIKNKILEKEKITVTVGISKNK-----------VFAKIAADMAKP 168
Query: 158 NGIHKYYAD-------------DIVGILNIIEENLK 180
NGI K D D+ GI NI E LK
Sbjct: 169 NGI-KVIDDEEVKRLIRELDIADVPGIGNITAEKLK 203
>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 = 28.5 bits (62), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 39/96 (40%), Gaps = 28/96 (29%)
Query: 98 VYDYKNRLSHYNLLSAIKNNPLFEEFNKLTLGFSFNKLTSNSKTQDTLILNTLKTSKAEP 157
V DY+ YNL IKN L +E +T+G S NK + + A+P
Sbjct: 120 VRDYRE---AYNLGLEIKNKILEKEKITVTVGISKNK-----------VFAKIAADMAKP 165
Query: 158 NGIHKYYAD-------------DIVGILNIIEENLK 180
NGI K D D+ GI NI E LK
Sbjct: 166 NGI-KVIDDEEVKRLIRELDIADVPGIGNITAEKLK 200
>pdb|4GIR|A Chain A, Crystal Structure Of An Enolase Family Member From Vibrio
Harveyi (Efi-Target 501692) With Homology To Mannonate
Dehydratase, With Mg, Ethylene Glycol And Sulfate Bound
(Ordered Loops, Space Group P41212)
pdb|4GIR|B Chain B, Crystal Structure Of An Enolase Family Member From Vibrio
Harveyi (Efi-Target 501692) With Homology To Mannonate
Dehydratase, With Mg, Ethylene Glycol And Sulfate Bound
(Ordered Loops, Space Group P41212)
pdb|4GIR|C Chain C, Crystal Structure Of An Enolase Family Member From Vibrio
Harveyi (Efi-Target 501692) With Homology To Mannonate
Dehydratase, With Mg, Ethylene Glycol And Sulfate Bound
(Ordered Loops, Space Group P41212)
pdb|4GIR|D Chain D, Crystal Structure Of An Enolase Family Member From Vibrio
Harveyi (Efi-Target 501692) With Homology To Mannonate
Dehydratase, With Mg, Ethylene Glycol And Sulfate Bound
(Ordered Loops, Space Group P41212)
pdb|4GIS|A Chain A, Crystal Structure Of An Enolase Family Member From Vibrio
Harveyi (Efi-Target 501692) With Homology To Mannonate
Dehydratase, With Mg, Glycerol And Dicarboxylates Bound
(Mixed Loops, Space Group I4122)
pdb|4GIS|B Chain B, Crystal Structure Of An Enolase Family Member From Vibrio
Harveyi (Efi-Target 501692) With Homology To Mannonate
Dehydratase, With Mg, Glycerol And Dicarboxylates Bound
(Mixed Loops, Space Group I4122)
pdb|4GGH|A Chain A, Crystal Structure Of An Enolase Family Member From Vibrio
Harveyi (Efi-Target 501692) With Homology To Mannonate
Dehydratase, With Mg, Hepes, And Ethylene Glycol Bound
(Ordered Loops, Space Group C2221)
pdb|4GGH|B Chain B, Crystal Structure Of An Enolase Family Member From Vibrio
Harveyi (Efi-Target 501692) With Homology To Mannonate
Dehydratase, With Mg, Hepes, And Ethylene Glycol Bound
(Ordered Loops, Space Group C2221)
pdb|4GGH|C Chain C, Crystal Structure Of An Enolase Family Member From Vibrio
Harveyi (Efi-Target 501692) With Homology To Mannonate
Dehydratase, With Mg, Hepes, And Ethylene Glycol Bound
(Ordered Loops, Space Group C2221)
pdb|4GGH|D Chain D, Crystal Structure Of An Enolase Family Member From Vibrio
Harveyi (Efi-Target 501692) With Homology To Mannonate
Dehydratase, With Mg, Hepes, And Ethylene Glycol Bound
(Ordered Loops, Space Group C2221)
Length = 422
Score = 27.3 bits (59), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 6/46 (13%)
Query: 241 KLSSYGLLPWNIRLTE------FFQFDNYYDISASKFKNILRKYSK 280
+L YG +P NI+ + ++ D Y + + FKN+ KY K
Sbjct: 176 QLGFYGGVPENIQTAQNPTQGSYYDQDQYIENTVEMFKNLREKYGK 221
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
0.322 0.138 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,238,326
Number of Sequences: 62578
Number of extensions: 311950
Number of successful extensions: 737
Number of sequences better than 100.0: 40
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 37
Number of HSP's that attempted gapping in prelim test: 734
Number of HSP's gapped (non-prelim): 40
length of query: 290
length of database: 14,973,337
effective HSP length: 98
effective length of query: 192
effective length of database: 8,840,693
effective search space: 1697413056
effective search space used: 1697413056
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)