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= psy17308
(118 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1OKC|A Chain A, Structure Of Mitochondrial AdpATP CARRIER IN COMPLEX WITH
Carboxyatractyloside
pdb|2C3E|A Chain A, The Bovine Mitochondrial Adp-Atp Carrier
Length = 297
Score = 34.3 bits (77), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 28/98 (28%), Positives = 41/98 (41%), Gaps = 19/98 (19%)
Query: 23 DAFIKISRTEGILSLWSGXXXXXXXXXXXXIAYFVTYEQLRVKLKD------LFSPSLHE 76
D ++I + +G LS W G I YF T + L KD L H+
Sbjct: 55 DCVVRIPKEQGFLSFWRGNLANV-------IRYFPT-QALNFAFKDKYKQIFLGGVDRHK 106
Query: 77 QPFW----IPLISGSVARIGAVTLVSPLELVRTKMQSE 110
Q FW L SG A ++ V PL+ RT++ ++
Sbjct: 107 Q-FWRYFAGNLASGGAAGATSLCFVYPLDFARTRLAAD 143
>pdb|2LCK|A Chain A, Structure Of The Mitochondrial Uncoupling Protein 2
Determined By Nmr Molecular Fragment Replacement
Length = 303
Score = 33.9 bits (76), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 24/106 (22%), Positives = 43/106 (40%), Gaps = 4/106 (3%)
Query: 10 RPKLGKLHEASCTDAFIKISRTEGILSLWSGXXXXXXXXXXXXIAYFVTYEQLRVKLKDL 69
R G+ ++ S +A+ I+R EGI LW G A VTY+ ++ L
Sbjct: 137 RAGGGRRYQ-STVEAYKTIAREEGIRGLWKGTSPNVARNAIVNCAELVTYDLIK---DTL 192
Query: 70 FSPSLHEQPFWIPLISGSVARIGAVTLVSPLELVRTKMQSEKMSYF 115
+L S A + SP+++V+T+ + + +
Sbjct: 193 LKANLMTDDLPCHFTSAFGAGFCTTVIASPVDVVKTRYMNSALGQY 238
Score = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 29/72 (40%), Gaps = 4/72 (5%)
Query: 8 FIRPKLGKLHEASCTDAFIKISRTEGILSLWSGXXXXXXXXXXXXIAYFVTYEQLRVKLK 67
++ LG+ H A + + R EG + + G + FVTYEQL+ L
Sbjct: 230 YMNSALGQYHSAG--HCALTMLRKEGPRAFYKGFMPSFLRLGSWNVVMFVTYEQLKRALM 287
Query: 68 DLFSPSLHEQPF 79
+ E PF
Sbjct: 288 AAYQS--REAPF 297
>pdb|1K32|A Chain A, Crystal Structure Of The Tricorn Protease
pdb|1K32|B Chain B, Crystal Structure Of The Tricorn Protease
pdb|1K32|C Chain C, Crystal Structure Of The Tricorn Protease
pdb|1K32|D Chain D, Crystal Structure Of The Tricorn Protease
pdb|1K32|E Chain E, Crystal Structure Of The Tricorn Protease
pdb|1K32|F Chain F, Crystal Structure Of The Tricorn Protease
Length = 1045
Score = 28.5 bits (62), Expect = 1.1, Method: Composition-based stats.
Identities = 23/65 (35%), Positives = 30/65 (46%), Gaps = 16/65 (24%)
Query: 55 YFVTYEQL-----RVKLKDLFSPSLHEQPFWIPLISGSVARIGAVTLVSPLELVRTKMQS 109
Y+++Y L RV L FS + +PF IPLI GS +P +LV M S
Sbjct: 487 YYLSYRSLDPSPDRVVLN--FSFEVVSKPFVIPLIPGS---------PNPTKLVPRSMTS 535
Query: 110 EKMSY 114
E Y
Sbjct: 536 EAGEY 540
>pdb|1N6D|A Chain A, Tricorn Protease In Complex With Tetrapeptide Chloromethyl
Ketone Derivative
pdb|1N6D|B Chain B, Tricorn Protease In Complex With Tetrapeptide Chloromethyl
Ketone Derivative
pdb|1N6D|C Chain C, Tricorn Protease In Complex With Tetrapeptide Chloromethyl
Ketone Derivative
pdb|1N6D|D Chain D, Tricorn Protease In Complex With Tetrapeptide Chloromethyl
Ketone Derivative
pdb|1N6D|E Chain E, Tricorn Protease In Complex With Tetrapeptide Chloromethyl
Ketone Derivative
pdb|1N6D|F Chain F, Tricorn Protease In Complex With Tetrapeptide Chloromethyl
Ketone Derivative
pdb|1N6E|A Chain A, Tricorn Protease In Complex With A Tridecapeptide
Chloromethyl Ketone Derivative
pdb|1N6E|C Chain C, Tricorn Protease In Complex With A Tridecapeptide
Chloromethyl Ketone Derivative
pdb|1N6E|E Chain E, Tricorn Protease In Complex With A Tridecapeptide
Chloromethyl Ketone Derivative
pdb|1N6E|G Chain G, Tricorn Protease In Complex With A Tridecapeptide
Chloromethyl Ketone Derivative
pdb|1N6E|I Chain I, Tricorn Protease In Complex With A Tridecapeptide
Chloromethyl Ketone Derivative
pdb|1N6E|K Chain K, Tricorn Protease In Complex With A Tridecapeptide
Chloromethyl Ketone Derivative
pdb|1N6F|A Chain A, Tricorn Protease In Complex With Z-Phe-Diketo-Arg-Glu-Phe
pdb|1N6F|B Chain B, Tricorn Protease In Complex With Z-Phe-Diketo-Arg-Glu-Phe
pdb|1N6F|C Chain C, Tricorn Protease In Complex With Z-Phe-Diketo-Arg-Glu-Phe
pdb|1N6F|D Chain D, Tricorn Protease In Complex With Z-Phe-Diketo-Arg-Glu-Phe
pdb|1N6F|E Chain E, Tricorn Protease In Complex With Z-Phe-Diketo-Arg-Glu-Phe
pdb|1N6F|F Chain F, Tricorn Protease In Complex With Z-Phe-Diketo-Arg-Glu-Phe
Length = 1071
Score = 28.5 bits (62), Expect = 1.1, Method: Composition-based stats.
Identities = 23/65 (35%), Positives = 30/65 (46%), Gaps = 16/65 (24%)
Query: 55 YFVTYEQL-----RVKLKDLFSPSLHEQPFWIPLISGSVARIGAVTLVSPLELVRTKMQS 109
Y+++Y L RV L FS + +PF IPLI GS +P +LV M S
Sbjct: 513 YYLSYRSLDPSPDRVVLN--FSFEVVSKPFVIPLIPGS---------PNPTKLVPRSMTS 561
Query: 110 EKMSY 114
E Y
Sbjct: 562 EAGEY 566
>pdb|3UK6|A Chain A, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|B Chain B, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|C Chain C, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|D Chain D, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|E Chain E, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|F Chain F, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|G Chain G, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|H Chain H, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|I Chain I, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|J Chain J, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|K Chain K, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|L Chain L, Crystal Structure Of The Tip48 (Tip49b) Hexamer
Length = 368
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 9 IRPKLGKLHEASCTDAFIKISRTEGILSLWSG 40
+R K G +H S + + SRT+G L+L+SG
Sbjct: 129 VRIKAGAVHTVSLHEIDVINSRTQGFLALFSG 160
>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 = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 12/46 (26%), Positives = 24/46 (52%)
Query: 53 IAYFVTYEQLRVKLKDLFSPSLHEQPFWIPLISGSVARIGAVTLVS 98
I FV ++ +++++ +PSL +P + + SG GAV +
Sbjct: 2 IVLFVDFDYFAAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATAN 47
>pdb|2IMW|P Chain P, Mechanism Of Template-Independent Nucleotide
Incorporation Catalyzed By A Template-Dependent Dna
Polymerase
Length = 348
Score = 26.9 bits (58), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 12/46 (26%), Positives = 24/46 (52%)
Query: 53 IAYFVTYEQLRVKLKDLFSPSLHEQPFWIPLISGSVARIGAVTLVS 98
I FV ++ +++++ +PSL +P + + SG GAV +
Sbjct: 2 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATAN 47
>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 = 26.9 bits (58), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 12/46 (26%), Positives = 24/46 (52%)
Query: 53 IAYFVTYEQLRVKLKDLFSPSLHEQPFWIPLISGSVARIGAVTLVS 98
I FV ++ +++++ +PSL +P + + SG GAV +
Sbjct: 2 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATAN 47
>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 = 26.9 bits (58), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 12/46 (26%), Positives = 24/46 (52%)
Query: 53 IAYFVTYEQLRVKLKDLFSPSLHEQPFWIPLISGSVARIGAVTLVS 98
I FV ++ +++++ +PSL +P + + SG GAV +
Sbjct: 2 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATAN 47
>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 = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 12/46 (26%), Positives = 24/46 (52%)
Query: 53 IAYFVTYEQLRVKLKDLFSPSLHEQPFWIPLISGSVARIGAVTLVS 98
I FV ++ +++++ +PSL +P + + SG GAV +
Sbjct: 2 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATAN 47
>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 = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 12/46 (26%), Positives = 24/46 (52%)
Query: 53 IAYFVTYEQLRVKLKDLFSPSLHEQPFWIPLISGSVARIGAVTLVS 98
I FV ++ +++++ +PSL +P + + SG GAV +
Sbjct: 8 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATAN 53
>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 = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 12/46 (26%), Positives = 24/46 (52%)
Query: 53 IAYFVTYEQLRVKLKDLFSPSLHEQPFWIPLISGSVARIGAVTLVS 98
I FV ++ +++++ +PSL +P + + SG GAV +
Sbjct: 2 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATAN 47
>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 = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 12/46 (26%), Positives = 24/46 (52%)
Query: 53 IAYFVTYEQLRVKLKDLFSPSLHEQPFWIPLISGSVARIGAVTLVS 98
I FV ++ +++++ +PSL +P + + SG GAV +
Sbjct: 7 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATAN 52
>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 = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 12/46 (26%), Positives = 24/46 (52%)
Query: 53 IAYFVTYEQLRVKLKDLFSPSLHEQPFWIPLISGSVARIGAVTLVS 98
I FV ++ +++++ +PSL +P + + SG GAV +
Sbjct: 2 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATAN 47
>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 = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 12/46 (26%), Positives = 24/46 (52%)
Query: 53 IAYFVTYEQLRVKLKDLFSPSLHEQPFWIPLISGSVARIGAVTLVS 98
I FV ++ +++++ +PSL +P + + SG GAV +
Sbjct: 8 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATAN 53
>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 = 26.6 bits (57), Expect = 3.6, Method: Composition-based stats.
Identities = 12/42 (28%), Positives = 23/42 (54%)
Query: 53 IAYFVTYEQLRVKLKDLFSPSLHEQPFWIPLISGSVARIGAV 94
I FV ++ +++++ +PSL +P + + SG GAV
Sbjct: 2 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAV 43
>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 = 26.2 bits (56), Expect = 4.6, Method: Composition-based stats.
Identities = 12/42 (28%), Positives = 23/42 (54%)
Query: 53 IAYFVTYEQLRVKLKDLFSPSLHEQPFWIPLISGSVARIGAV 94
I FV ++ +++++ +PSL +P + + SG GAV
Sbjct: 2 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAV 43
>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 = 26.2 bits (56), Expect = 4.7, Method: Composition-based stats.
Identities = 12/42 (28%), Positives = 23/42 (54%)
Query: 53 IAYFVTYEQLRVKLKDLFSPSLHEQPFWIPLISGSVARIGAV 94
I FV ++ +++++ +PSL +P + + SG GAV
Sbjct: 8 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAV 49
>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 = 26.2 bits (56), Expect = 4.7, Method: Composition-based stats.
Identities = 12/42 (28%), Positives = 23/42 (54%)
Query: 53 IAYFVTYEQLRVKLKDLFSPSLHEQPFWIPLISGSVARIGAV 94
I FV ++ +++++ +PSL +P + + SG GAV
Sbjct: 9 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAV 50
>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 = 26.2 bits (56), Expect = 4.7, Method: Composition-based stats.
Identities = 12/42 (28%), Positives = 23/42 (54%)
Query: 53 IAYFVTYEQLRVKLKDLFSPSLHEQPFWIPLISGSVARIGAV 94
I FV ++ +++++ +PSL +P + + SG GAV
Sbjct: 8 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAV 49
>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 = 26.2 bits (56), Expect = 4.7, Method: Composition-based stats.
Identities = 12/42 (28%), Positives = 23/42 (54%)
Query: 53 IAYFVTYEQLRVKLKDLFSPSLHEQPFWIPLISGSVARIGAV 94
I FV ++ +++++ +PSL +P + + SG GAV
Sbjct: 8 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAV 49
>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 = 26.2 bits (56), Expect = 4.7, Method: Composition-based stats.
Identities = 12/42 (28%), Positives = 23/42 (54%)
Query: 53 IAYFVTYEQLRVKLKDLFSPSLHEQPFWIPLISGSVARIGAV 94
I FV ++ +++++ +PSL +P + + SG GAV
Sbjct: 8 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAV 49
>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 = 26.2 bits (56), Expect = 4.7, Method: Composition-based stats.
Identities = 12/42 (28%), Positives = 23/42 (54%)
Query: 53 IAYFVTYEQLRVKLKDLFSPSLHEQPFWIPLISGSVARIGAV 94
I FV ++ +++++ +PSL +P + + SG GAV
Sbjct: 10 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAV 51
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
0.324 0.139 0.412
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,845,173
Number of Sequences: 62578
Number of extensions: 78888
Number of successful extensions: 142
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 121
Number of HSP's gapped (non-prelim): 24
length of query: 118
length of database: 14,973,337
effective HSP length: 81
effective length of query: 37
effective length of database: 9,904,519
effective search space: 366467203
effective search space used: 366467203
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)