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= psy12447
(551 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IAY|A Chain A, Ternary Complex Of Dna Polymerase Delta
Length = 919
Score = 289 bits (740), Expect = 3e-78, Method: Compositional matrix adjust.
Identities = 186/533 (34%), Positives = 250/533 (46%), Gaps = 149/533 (27%)
Query: 15 PPELNPKEDKIVFQQISIEHYTGEPIPGMPGSQLKPVPIVRMFGVTMEGNSVCCHVHGFS 74
P + +P I FQQI E I S +VR FGVT EG+SV C+V GF
Sbjct: 37 PTDFDPSLYDISFQQIDAEQSVLNGIKDENTST-----VVRFFGVTSEGHSVLCNVTGFK 91
Query: 75 PYLYVSAPKEFNSTHCRAFKEALNRAIIADMRGNKDEIQEAVLMVEIVQKQTVFGFWGEE 134
YLYV AP ++ +E +N+ + + A+ +E+V KQ+++G+ G+
Sbjct: 92 NYLYVPAPNSSDAND----QEQINKFV----HYLNETFDHAIDSIEVVSKQSIWGYSGDT 143
Query: 135 LENFLKITESVFPTFPTHTYKAFE-----------------SNIDFDIRFMVDNDIVGCN 177
F KI + +P AFE NI + +R MVD IVG +
Sbjct: 144 KLPFWKIYVT-YPHMVNKLRTAFERGHLSFNSWFSNGTTTYDNIAYTLRLMVDCGIVGMS 202
Query: 178 WIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHAPEEIDVSTDDIVSHAPE 237
WI +P GK+ + NR VS CQLE+ ++ ++++H E
Sbjct: 203 WITLPKGKYSM-----IEPNNR--VSSCQLEVSINYRNLIAHPAE--------------- 240
Query: 238 GEWSKVAPLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTC 297
G+WS APLRI+SFDIECAGR G+FP+P +DP+IQIAN+ GA +
Sbjct: 241 GDWSHTAPLRIMSFDIECAGRIGVFPEPEYDPVIQIANVVSIAGAKKP------------ 288
Query: 298 APIVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKT 357
F++NVFTLNTC+PI GS + T
Sbjct: 289 ------------------------------------FIRNVFTLNTCSPITGSMIFSHAT 312
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDIRSVIKD 417
E E+L W FI ++DPD+ GYN NFD PYL+NRAK L V +F + GR+K ++ IK+
Sbjct: 313 EEEMLSNWRNFIIKVDPDVIIGYNTTNFDIPYLLNRAKALKVNDFPYFGRLKTVKQEIKE 372
Query: 418 SFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRE 477
S SK G RE K +N +G
Sbjct: 373 SVFSSKAYGTRETKNVNIDG---------------------------------------- 392
Query: 478 NKTINFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSIISDLQ 530
R+ DLL + REYKLRSYTLN+VS HFL EQKEDV +SIISDLQ
Sbjct: 393 --------RLQLDLLQFIQREYKLRSYTLNAVSAHFLGEQKEDVHYSIISDLQ 437
>pdb|2GV9|A Chain A, Crystal Structure Of The Herpes Simplex Virus Type 1 Dna
Polymerase
pdb|2GV9|B Chain B, Crystal Structure Of The Herpes Simplex Virus Type 1 Dna
Polymerase
Length = 1193
Score = 77.0 bits (188), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 110/495 (22%), Positives = 193/495 (38%), Gaps = 136/495 (27%)
Query: 53 IVRMFGVTMEGNSVCCHVHGFSPYLYVSAPKEFNSTHCRAFKE-------ALNRAIIADM 105
++ + G+T EG+ V HV+G Y Y++ + CRA ++ AL + A
Sbjct: 139 VITLLGLTPEGHRVAVHVYGTRQYFYMNKEEVDRHLQCRAPRDLCERMAAALRESPGASF 198
Query: 106 RGNKDEIQEAVLMVEIVQKQTVFGFWGEELENFLKI---TESVFPTFPTH---TYKAFES 159
RG + EA E+V++ V+ ++ F ++ + V + K +E
Sbjct: 199 RGISADHFEA----EVVERTDVY-YYETRPALFYRVYVRSGRVLSYLCDNFCPAIKKYEG 253
Query: 160 NIDFDIRFMVDN-DIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVS 218
+D RF++DN V W + PG+ N R + S+D
Sbjct: 254 GVDATTRFILDNPGFVTFGWYRLKPGR-----------NNTLAQPRAPMAFGTSSD---- 298
Query: 219 HAPEEIDVSTDDIVSHAPEGEWSKVAPLRILSFDIEC-AGRKG--IFPDPNH--DPIIQI 273
E + + D++ A EG S + +++ FDIEC AG + FP H D +IQI
Sbjct: 299 ---VEFNCTADNL---AIEGGMSDLPAYKLMCFDIECKAGGEDELAFPVAGHPEDLVIQI 352
Query: 274 ANMC--ISQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASE 331
+ + +S A E++ +F+L +C + +
Sbjct: 353 SCLLYDLSTTALEHVL---LFSLGSC--------------------------DLPESHLN 383
Query: 332 NIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLI 391
+ + + T P+ V+ +E E+L + +++ P+ TGYNI NFD+P+L
Sbjct: 384 ELAARGLPT-----PV----VLEFDSEFEMLLAFMTLVKQYGPEFVTGYNIINFDWPFL- 433
Query: 392 NRAKHLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFT 451
L ++ DI V D +
Sbjct: 434 -------------LAKLTDIYKVPLDGY-------------------------------- 448
Query: 452 FLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGRVCFDLLFVLLREYKLRSYTLNSVSY 511
GR+ R V + I KR +N G V D+ ++ + KL SY LN+V+
Sbjct: 449 --GRMNG-RGVFRVWDIGQSHFQKRSKIKVN--GMVNIDMYGIITDKIKLSSYKLNAVAE 503
Query: 512 HFLQEQKEDVQHSII 526
L+++K+D+ + I
Sbjct: 504 AVLKDKKKDLSYRDI 518
>pdb|2JGU|A Chain A, Crystal Structure Of Dna-directed Dna Polymerase
Length = 775
Score = 52.4 bits (124), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 24/49 (48%), Positives = 31/49 (63%)
Query: 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVK 400
V TE E++ ++ IRE DPDI YN +FDFPYL RA+ LG+K
Sbjct: 181 VESVSTEKEMIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKRAEKLGIK 229
>pdb|4AHC|A Chain A, Crystal Structure Of An Evolved Replicating Dna Polymerase
pdb|4AHC|B Chain B, Crystal Structure Of An Evolved Replicating Dna Polymerase
pdb|4AIL|C Chain C, Crystal Structure Of An Evolved Replicating Dna Polymerase
Length = 775
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/49 (46%), Positives = 31/49 (63%)
Query: 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVK 400
V +E E++ ++ IRE DPDI YN +FDFPYL RA+ LG+K
Sbjct: 181 VEVVSSEREMIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKRAEKLGIK 229
>pdb|4FLT|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FLU|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FLV|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FLW|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FLX|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FLY|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FLZ|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FM0|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FM1|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
Length = 793
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 40/78 (51%), Gaps = 11/78 (14%)
Query: 334 FVKNVFTLNTCAPIVGSQVICCKT-----------ETELLDKWSAFIRELDPDIFTGYNI 382
F K + + A G++VI K+ E E++ + IRE DPD+ YN
Sbjct: 174 FGKGPIIMISYADEEGAKVITWKSIDLPYVEVVSSEREMIKRLVKVIREKDPDVIITYNG 233
Query: 383 QNFDFPYLINRAKHLGVK 400
NF FPYL+ RA+ LG+K
Sbjct: 234 DNFAFPYLLKRAEKLGIK 251
>pdb|4FM2|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase (Triple Mutant)
Bound To A Dsdna, In Edition Mode
Length = 793
Score = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 40/78 (51%), Gaps = 11/78 (14%)
Query: 334 FVKNVFTLNTCAPIVGSQVICCKT-----------ETELLDKWSAFIRELDPDIFTGYNI 382
F K + + A G++VI K+ E E++ + IRE DPD+ YN
Sbjct: 174 FGKGPIIMISYADEEGAKVITWKSIDLPYVEVVSSEREMIKRLVKVIREKDPDVIITYNG 233
Query: 383 QNFDFPYLINRAKHLGVK 400
NF FPYL+ RA+ LG+K
Sbjct: 234 DNFAFPYLLKRAEKLGIK 251
>pdb|3A2F|A Chain A, Crystal Structure Of Pyrococcus Furiosus Dna
PolymerasePCNA Monomer Mutant Complex
Length = 775
Score = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 42/170 (24%), Positives = 62/170 (36%), Gaps = 60/170 (35%)
Query: 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDI 411
V +E E + ++ IRE DPDI YN +FDFPYL RA+ LG+K
Sbjct: 181 VEVVSSEREXIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKRAEKLGIKL---------- 230
Query: 412 RSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSK 471
TI +G+ + + +G
Sbjct: 231 --------------------TIGRDGSEPKXQRIG------------------------- 245
Query: 472 QMGKRENKTINFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDV 521
+ + +GR+ FDL V+ R L +YTL +V + KE V
Sbjct: 246 -----DXTAVEVKGRIHFDLYHVITRTINLPTYTLEAVYEAIFGKPKEKV 290
>pdb|1QHT|A Chain A, Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon
Length = 775
Score = 48.9 bits (115), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 26/56 (46%), Positives = 34/56 (60%), Gaps = 2/56 (3%)
Query: 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGR 407
V TE E++ ++ +RE DPD+ YN NFDF YL R + LG+K FT LGR
Sbjct: 181 VDVVSTEKEMIKRFLRVVREKDPDVLITYNGDNFDFAYLKKRCEELGIK-FT-LGR 234
>pdb|1TGO|A Chain A, Thermostable B Type Dna Polymerase From Thermococcus
Gorgonarius
Length = 773
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/56 (42%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGR 407
V TE E++ ++ ++E DPD+ YN NFDF YL R++ LGVK LGR
Sbjct: 181 VDVVSTEKEMIKRFLKVVKEKDPDVLITYNGDNFDFAYLKKRSEKLGVK--FILGR 234
>pdb|1QQC|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
D.Tok
Length = 773
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/56 (44%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGR 407
V TE E++ ++ I+E DPD+ YN NFDF YL R++ LGVK LGR
Sbjct: 181 VESVSTEKEMIKRFLKVIQEKDPDVLITYNGDNFDFAYLKKRSEMLGVK--FILGR 234
>pdb|1D5A|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
D.Tok. Deposition Of Second Native Structure At 2.4
Angstrom
Length = 733
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/56 (44%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGR 407
V TE E++ ++ I+E DPD+ YN NFDF YL R++ LGVK LGR
Sbjct: 181 VESVSTEKEMIKRFLKVIQEKDPDVLITYNGDNFDFAYLKKRSEMLGVK--FILGR 234
>pdb|1WNS|A Chain A, Crystal Structure Of Family B Dna Polymerase From
Hyperthermophilic Archaeon Pyrococcus Kodakaraensis Kod1
Length = 774
Score = 46.2 bits (108), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/56 (42%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGR 407
V TE E++ ++ ++E DPD+ YN NFDF YL R + LG+ NF LGR
Sbjct: 181 VDVVSTEREMIKRFLRVVKEKDPDVLITYNGDNFDFAYLKKRCEKLGI-NFA-LGR 234
>pdb|1WN7|A Chain A, Crystal Structure Of Archaeal Family B Dna Polymerase
Mutant
Length = 774
Score = 46.2 bits (108), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/56 (42%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGR 407
V TE E++ ++ ++E DPD+ YN NFDF YL R + LG+ NF LGR
Sbjct: 181 VDVVSTEREMIKRFLRVVKEKDPDVLITYNGDNFDFAYLKKRCEKLGI-NFA-LGR 234
>pdb|2XHB|A Chain A, Crystal Structure Of Dna Polymerase From Thermococcus
Gorgonarius In Complex With Hypoxanthine-Containing Dna
Length = 773
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/56 (41%), Positives = 32/56 (57%), Gaps = 2/56 (3%)
Query: 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGR 407
V TE E++ ++ ++E DPD+ YN NF F YL R++ LGVK LGR
Sbjct: 181 VDVVSTEKEMIKRFLKVVKEKDPDVLITYNGDNFAFAYLKKRSEKLGVK--FILGR 234
>pdb|2VWJ|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography
Length = 773
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/56 (41%), Positives = 32/56 (57%), Gaps = 2/56 (3%)
Query: 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGR 407
V TE E++ ++ ++E DPD+ YN NF F YL R++ LGVK LGR
Sbjct: 181 VDVVSTEKEMIKRFLKVVKEKDPDVLITYNGDNFAFAYLKKRSEKLGVK--FILGR 234
>pdb|2VWK|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography. V93q Polymerase Variant
Length = 773
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/56 (41%), Positives = 32/56 (57%), Gaps = 2/56 (3%)
Query: 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGR 407
V TE E++ ++ ++E DPD+ YN NF F YL R++ LGVK LGR
Sbjct: 181 VDVVSTEKEMIKRFLKVVKEKDPDVLITYNGDNFAFAYLKKRSEKLGVK--FILGR 234
>pdb|1NOZ|A Chain A, T4 Dna Polymerase Fragment (Residues 1-388) At 110k
pdb|1NOZ|B Chain B, T4 Dna Polymerase Fragment (Residues 1-388) At 110k
pdb|1NOY|A Chain A, Dna Polymerase (e.c.2.7.7.7)/dna Complex
pdb|1NOY|B Chain B, Dna Polymerase (e.c.2.7.7.7)/dna Complex
Length = 388
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 35/57 (61%), Gaps = 4/57 (7%)
Query: 357 TETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL----GVKNFTFLGRVK 409
E ++L ++ + P IFTG+NI+ FD PY++NR K + +K F+ +GRVK
Sbjct: 190 NERDMLMEYINLWEQKRPAIFTGWNIEGFDVPYIMNRVKMILGERSMKRFSPIGRVK 246
>pdb|3CFO|A Chain A, Triple Mutant Apo Structure
pdb|3CFP|A Chain A, Structure Of The Replicating Complex Of A Pol Alpha Family
Dna Polymerase, Ternary Complex 1
pdb|3CFR|A Chain A, Structure Of The Replicating Complex Of A Pol Alpha Family
Dna Polymerase, Ternary Complex 2
Length = 909
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/40 (42%), Positives = 28/40 (70%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397
E ELL ++ F ++ P I TG+N+++FD PY+ NR K++
Sbjct: 194 EKELLMEYLNFWQQKTPVILTGWNVESFDIPYVYNRIKNI 233
>pdb|1WAF|A Chain A, Dna Polymerase From Bacteriophage Rb69
pdb|1WAF|B Chain B, Dna Polymerase From Bacteriophage Rb69
pdb|1CLQ|A Chain A, Crystal Structure Of A Replication Fork Dna Polymerase
Editing Complex At 2.7 A Resolution
pdb|1IH7|A Chain A, High-Resolution Structure Of Apo Rb69 Dna Polymerase
pdb|1WAJ|A Chain A, Dna Polymerase From Bacteriophage Rb69
pdb|3UIQ|A Chain A, Rb69 Dna Polymerase Ternary Complex Containing Dupnpp
Length = 903
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/40 (42%), Positives = 28/40 (70%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397
E ELL ++ F ++ P I TG+N+++FD PY+ NR K++
Sbjct: 194 EKELLMEYLNFWQQKTPVILTGWNVESFDIPYVYNRIKNI 233
>pdb|2DY4|A Chain A, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing Thymine Glycol
pdb|2DY4|B Chain B, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing Thymine Glycol
pdb|2DY4|C Chain C, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing Thymine Glycol
pdb|2DY4|D Chain D, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing Thymine Glycol
pdb|2P5O|A Chain A, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing An Abasic Site Analog
pdb|2P5O|B Chain B, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing An Abasic Site Analog
pdb|2P5O|C Chain C, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing An Abasic Site Analog
pdb|2P5O|D Chain D, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing An Abasic Site Analog
pdb|2P5G|A Chain A, Crystal Structure Of Rb69 Gp43 In Complex With Dna With
Damp Opposite An Abasic Site Analog In A 21mer Template
pdb|2P5G|B Chain B, Crystal Structure Of Rb69 Gp43 In Complex With Dna With
Damp Opposite An Abasic Site Analog In A 21mer Template
pdb|2P5G|C Chain C, Crystal Structure Of Rb69 Gp43 In Complex With Dna With
Damp Opposite An Abasic Site Analog In A 21mer Template
pdb|2P5G|D Chain D, Crystal Structure Of Rb69 Gp43 In Complex With Dna With
Damp Opposite An Abasic Site Analog In A 21mer Template
Length = 903
Score = 37.4 bits (85), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 27/40 (67%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397
E ELL ++ F ++ P I TG+N+++F PY+ NR K++
Sbjct: 194 EKELLXEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNI 233
>pdb|3SUN|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dttp
Opposite 2ap (At Rich Sequence)
Length = 895
Score = 37.0 bits (84), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 27/40 (67%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397
E ELL ++ F ++ P I TG+N+++F PY+ NR K++
Sbjct: 194 EKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNI 233
>pdb|3SUQ|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dctp
Opposite 2ap (At Rich Sequence)
Length = 897
Score = 37.0 bits (84), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 27/40 (67%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397
E ELL ++ F ++ P I TG+N+++F PY+ NR K++
Sbjct: 194 EKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNI 233
>pdb|3SCX|A Chain A, Rb69 Dna Polymerase Triple Mutant(L561aS565GY567A) TERNARY
COMPLEX With Dupnpp And A Deoxy-Terminated Primer In The
Presence Of Ca2+
pdb|3SI6|A Chain A, Rb69 Dna Polymerase Triple Mutant (L561aS565GY567A)
TERNARY COMPLEX With Dupnpp And A Deoxy-Terminated
Primer In The Presence Of Mg2+
pdb|3SJJ|A Chain A, Rb69 Dna Polymerase Triple Mutant (L561aS565GY567A)
TERNARY COMPLEX With Dupnpp And A Deoxy-Terminated
Primer In The Presence Of Mn2+
pdb|3SNN|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DCTP Opposite Dg In The Presence Of Mg2+
Length = 903
Score = 37.0 bits (84), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 27/40 (67%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397
E ELL ++ F ++ P I TG+N+++F PY+ NR K++
Sbjct: 194 EKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNI 233
>pdb|3KD1|E Chain E, Closed Binary Complex Of An Rb69 Gp43 Fingers Domain
Mutant Complexed With An Acyclic Gmp Terminated Primer
Template Pair.
pdb|3KD5|E Chain E, Closed Ternary Complex Of An Rb69 Gp43 Fingers Domain
Mutant Complexed With An Acyclic Gmp Terminated Primer
Template Pair And Phosphonoformic Acid
Length = 913
Score = 37.0 bits (84), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 27/40 (67%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397
E ELL ++ F ++ P I TG+N+++F PY+ NR K++
Sbjct: 194 EKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNI 233
>pdb|4DTJ|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp Opposite An
Abasic Site And DdtDA AS THE PENULTIMATE BASE-Pair
pdb|4DTM|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp Opposite An
Abasic Site And DdgDC AS THE PENULTIMATE BASE-Pair
Length = 901
Score = 37.0 bits (84), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 27/40 (67%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397
E ELL ++ F ++ P I TG+N+++F PY+ NR K++
Sbjct: 194 EKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNI 233
>pdb|3SPY|A Chain A, Rb69 Dna Polymerase(L415aL561AS565GY567A) TERNARY COMPLEX
WITH Dupcpp Opposite Da
Length = 901
Score = 37.0 bits (84), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 27/40 (67%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397
E ELL ++ F ++ P I TG+N+++F PY+ NR K++
Sbjct: 194 EKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNI 233
>pdb|3SUO|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dttp
Opposite 2ap (Gc Rich Sequence)
Length = 900
Score = 37.0 bits (84), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 27/40 (67%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397
E ELL ++ F ++ P I TG+N+++F PY+ NR K++
Sbjct: 194 EKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNI 233
>pdb|3RWU|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Datp
Opposite Difluorotoluene Nucleoside
pdb|3QNN|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dgt
Opposite 3tco
pdb|3QNO|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Datp
Opposite 3tco
Length = 901
Score = 37.0 bits (84), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 27/40 (67%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397
E ELL ++ F ++ P I TG+N+++F PY+ NR K++
Sbjct: 194 EKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNI 233
>pdb|3SQ1|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dupcpp Opposite
Da
Length = 901
Score = 37.0 bits (84), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 27/40 (67%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397
E ELL ++ F ++ P I TG+N+++F PY+ NR K++
Sbjct: 194 EKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNI 233
>pdb|3SPZ|A Chain A, Dna Polymerase(L415aL561AS565GY567A) TERNARY COMPLEX WITH
DUPCPP Opposite Da (Ca2+)
pdb|4FJ5|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp/dt
pdb|4FJ7|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dgtp/dt
pdb|4FJ8|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp/dt
pdb|4FJ9|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp/dt
pdb|4FJG|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp/dc
pdb|4FJH|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dgtp/dc
pdb|4FJI|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp/dc
pdb|4FJJ|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp/dc
pdb|4FJK|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp/da
pdb|4FJL|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dgtp/da
pdb|4FJN|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp/da
pdb|4FJX|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp/dg
pdb|4FK0|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp/dg
pdb|4FK2|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp/dg
pdb|4FK4|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dgtp/dg
Length = 903
Score = 37.0 bits (84), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 27/40 (67%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397
E ELL ++ F ++ P I TG+N+++F PY+ NR K++
Sbjct: 194 EKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNI 233
>pdb|3QEP|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DTTP Opposite Difluorotoluene Nucleoside
pdb|3S9H|A Chain A, Rb69 Dna Polymerase Triple Mutant(L561aS565GY567A) TERNARY
COMPLEX With Dupnpp And A Dideoxy-Terminated Primer In
The Presence Of Ca2+
pdb|3SQ0|A Chain A, Dna Polymerase(L561aS565GY567A) TERNARY COMPLEX WITH
DUPNPP OPPOSITE Da (Mn2+)
pdb|3QEI|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DCTP Opposite Difluorotoluene Nucleoside
pdb|3QER|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DATP Opposite Difluorotoluene Nucleoside
pdb|3QES|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DGTP Opposite Difluorotoluene Nucleoside
pdb|3QET|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DTTP Opposite Dt
pdb|3QEV|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DCTP Opposite Dt
pdb|3QEW|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DDTP Opposite Dt
pdb|3QEX|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DGTP Opposite Dt
pdb|4E3S|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dqtp Opposite Dt
pdb|4DTN|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp Opposite An
Abasic Site And DdaDT AS THE PENULTIMATE BASE-Pair
pdb|4DTO|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp Opposite An
Abasic Site And DdaDT AS THE PENULTIMATE BASE-Pair
pdb|4DTP|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dgtp Opposite An
Abasic Site And DdaDT AS THE PENULTIMATE BASE-Pair
pdb|4DTR|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp Opposite An
Abasic Site And DdcDG AS THE PENULTIMATE BASE-Pair
pdb|4DTS|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp Opposite An
Abasic Site And DdcDG AS THE PENULTIMATE BASE-Pair
pdb|4DTU|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dgtp Opposite An
Abasic Site And DdcDG AS THE PENULTIMATE BASE-Pair
pdb|4DTX|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp Opposite An
Abasic Site And DdcDG AS THE PENULTIMATE BASE-Pair
pdb|4FJM|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp/da
Length = 903
Score = 37.0 bits (84), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 27/40 (67%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397
E ELL ++ F ++ P I TG+N+++F PY+ NR K++
Sbjct: 194 EKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNI 233
>pdb|3SQ2|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp Opposite 2ap
(At Rich Sequence)
pdb|3SQ4|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp Opposite 2ap
(Gc Rich Sequence)
Length = 902
Score = 37.0 bits (84), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 27/40 (67%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397
E ELL ++ F ++ P I TG+N+++F PY+ NR K++
Sbjct: 194 EKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNI 233
>pdb|3LZI|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Datp
Opposite 7,8- Dihydro-8-Oxoguanine
pdb|3LZJ|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dctp
Opposite 7,8- Dihydro-8-Oxoguanine
pdb|3NAE|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Datp
Opposite Guanidinohydantoin
pdb|3NDK|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dctp
Opposite Dg
pdb|3NGI|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dttp
Opposite Dg
pdb|3SUP|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dctp
Opposite 2ap (Gc Rich Sequence)
Length = 903
Score = 37.0 bits (84), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 27/40 (67%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397
E ELL ++ F ++ P I TG+N+++F PY+ NR K++
Sbjct: 194 EKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNI 233
>pdb|3LDS|A Chain A, Crystal Structure Of Rb69 Gp43 With Dna And Datp Opposite
8-
Length = 903
Score = 37.0 bits (84), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 27/40 (67%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397
E ELL ++ F ++ P I TG+N+++F PY+ NR K++
Sbjct: 194 EKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNI 233
>pdb|2DTU|A Chain A, Crystal Structure Of The Beta Hairpin Loop Deletion
Variant Of Rb69 Gp43 In Complex With Dna Containing An
Abasic Site Analog
pdb|2DTU|B Chain B, Crystal Structure Of The Beta Hairpin Loop Deletion
Variant Of Rb69 Gp43 In Complex With Dna Containing An
Abasic Site Analog
pdb|2DTU|C Chain C, Crystal Structure Of The Beta Hairpin Loop Deletion
Variant Of Rb69 Gp43 In Complex With Dna Containing An
Abasic Site Analog
pdb|2DTU|D Chain D, Crystal Structure Of The Beta Hairpin Loop Deletion
Variant Of Rb69 Gp43 In Complex With Dna Containing An
Abasic Site Analog
Length = 896
Score = 37.0 bits (84), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 27/40 (67%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397
E ELL ++ F ++ P I TG+N+++F PY+ NR K++
Sbjct: 194 EKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNI 233
>pdb|3NE6|A Chain A, Rb69 Dna Polymerase (S565gY567A) TERNARY COMPLEX WITH DCTP
OPPOSITE Dg
pdb|3NHG|A Chain A, Rb69 Dna Polymerase (S565gY567A) TERNARY COMPLEX WITH DTTP
OPPOSITE Dg
Length = 903
Score = 37.0 bits (84), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 27/40 (67%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397
E ELL ++ F ++ P I TG+N+++F PY+ NR K++
Sbjct: 194 EKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNI 233
>pdb|1Q9Y|A Chain A, Crystal Structure Of Enterobacteria Phage Rb69 Gp43 Dna
Polymerase Complexed With 8-Oxoguanosine Containing Dna
Length = 906
Score = 36.6 bits (83), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 27/40 (67%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397
E ELL ++ F ++ P I TG+N+++F PY+ NR K++
Sbjct: 197 EKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNI 236
>pdb|1IG9|A Chain A, Structure Of The Replicating Complex Of A Pol Alpha Family
Dna Polymerase
pdb|1Q9X|A Chain A, Crystal Structure Of Enterobacteria Phage Rb69 Gp43 Dna
Polymerase Complexed With Tetrahydrofuran Containing Dna
pdb|1Q9X|B Chain B, Crystal Structure Of Enterobacteria Phage Rb69 Gp43 Dna
Polymerase Complexed With Tetrahydrofuran Containing Dna
pdb|1Q9X|C Chain C, Crystal Structure Of Enterobacteria Phage Rb69 Gp43 Dna
Polymerase Complexed With Tetrahydrofuran Containing Dna
pdb|1Q9X|D Chain D, Crystal Structure Of Enterobacteria Phage Rb69 Gp43 Dna
Polymerase Complexed With Tetrahydrofuran Containing Dna
pdb|2ATQ|A Chain A, Rb69 Single-Stranded Dna Binding Protein-Dna Polymerase
Fusion
pdb|2OYQ|A Chain A, Crystal Structure Of Rb69 Gp43 In Complex With Dna With 5-
Nimp Opposite An Abasic Site Analog
pdb|2OYQ|B Chain B, Crystal Structure Of Rb69 Gp43 In Complex With Dna With 5-
Nimp Opposite An Abasic Site Analog
pdb|2OYQ|C Chain C, Crystal Structure Of Rb69 Gp43 In Complex With Dna With 5-
Nimp Opposite An Abasic Site Analog
pdb|2OYQ|D Chain D, Crystal Structure Of Rb69 Gp43 In Complex With Dna With 5-
Nimp Opposite An Abasic Site Analog
pdb|2OZM|A Chain A, Crystal Structure Of Rb69 Gp43 In Complex With Dna With 5-
Nitp Opposite An Abasic Site Analog
pdb|2OZS|A Chain A, Crystal Structure Of Rb69 Gp43 In Complex With Dna With
Datp Opposite Dtmp
pdb|3NCI|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp Opposite Dg
At 1.8 Angstrom Resolution
pdb|4DU1|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp Opposite Dt
pdb|4DU3|A Chain A, Rb69 Dna Polymerase Ternary Complex With Ddtp Opposite Dt
With 3- Deaza-Adenine At The N-1 Position Of Template
Strand
pdb|4DU4|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp Opposite Dt
With 3- Deaza-Adenine At The N-3 Position Of Primer
Strand
Length = 903
Score = 36.6 bits (83), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 27/40 (67%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397
E ELL ++ F ++ P I TG+N+++F PY+ NR K++
Sbjct: 194 EKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNI 233
>pdb|3CQ8|A Chain A, Ternary Complex Of The L415f Mutant Rb69 Exo(-)polymerase
Length = 903
Score = 36.6 bits (83), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 27/40 (67%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397
E ELL ++ F ++ P I TG+N+++F PY+ NR K++
Sbjct: 194 EKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNI 233
>pdb|3L8B|A Chain A, Crystal Structure Of A Replicative Dna Polymerase Bound To
The Oxidized Guanine Lesion Guanidinohydantoin
pdb|3L8B|B Chain B, Crystal Structure Of A Replicative Dna Polymerase Bound To
The Oxidized Guanine Lesion Guanidinohydantoin
pdb|3RMA|A Chain A, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMA|B Chain B, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMA|C Chain C, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMA|D Chain D, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMB|A Chain A, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMB|B Chain B, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMB|C Chain C, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMB|D Chain D, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMC|A Chain A, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMC|B Chain B, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMC|C Chain C, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMC|D Chain D, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMD|A Chain A, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMD|B Chain B, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMD|C Chain C, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3RMD|D Chain D, Crystal Structure Of A Replicative Dna Polymerase Bound To
Dna Containing Thymine Glycol
pdb|3TAB|A Chain A, 5-Hydroxycytosine Paired With Dgmp In Rb69 Gp43
pdb|3TAB|B Chain B, 5-Hydroxycytosine Paired With Dgmp In Rb69 Gp43
pdb|3TAB|C Chain C, 5-Hydroxycytosine Paired With Dgmp In Rb69 Gp43
pdb|3TAB|D Chain D, 5-Hydroxycytosine Paired With Dgmp In Rb69 Gp43
pdb|3TAE|A Chain A, 5-Hydroxycytosine Paired With Damp In Rb69 Gp43
pdb|3TAE|B Chain B, 5-Hydroxycytosine Paired With Damp In Rb69 Gp43
pdb|3TAE|C Chain C, 5-Hydroxycytosine Paired With Damp In Rb69 Gp43
pdb|3TAE|D Chain D, 5-Hydroxycytosine Paired With Damp In Rb69 Gp43
pdb|3TAF|A Chain A, 5-Fluorocytosine Paired With Ddgmp In Rb69 Gp43
pdb|3TAF|B Chain B, 5-Fluorocytosine Paired With Ddgmp In Rb69 Gp43
pdb|3TAF|C Chain C, 5-Fluorocytosine Paired With Ddgmp In Rb69 Gp43
pdb|3TAF|D Chain D, 5-Fluorocytosine Paired With Ddgmp In Rb69 Gp43
pdb|3TAG|A Chain A, 5-Fluorocytosine Paired With Damp In Rb69 Gp43
pdb|3TAG|B Chain B, 5-Fluorocytosine Paired With Damp In Rb69 Gp43
pdb|3TAG|C Chain C, 5-Fluorocytosine Paired With Damp In Rb69 Gp43
pdb|3TAG|D Chain D, 5-Fluorocytosine Paired With Damp In Rb69 Gp43
Length = 906
Score = 36.6 bits (83), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 27/40 (67%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397
E ELL ++ F ++ P I TG+N+++F PY+ NR K++
Sbjct: 194 EKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNI 233
>pdb|4FYD|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To
Dna/rna And Dgtp
pdb|4FYD|B Chain B, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To
Dna/rna And Dgtp
Length = 910
Score = 34.3 bits (77), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 26/50 (52%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGR 407
E +L + A ++ DPD+ G+ +QN L +R L + F+ +GR
Sbjct: 268 EKAMLSCFCAMLKVEDPDVIIGHRLQNVYLDVLAHRMHDLNIPTFSSIGR 317
>pdb|4FVM|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha
pdb|4FXD|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To
Dna/rna
pdb|4FXD|B Chain B, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To
Dna/rna
Length = 910
Score = 34.3 bits (77), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 26/50 (52%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGR 407
E +L + A ++ DPD+ G+ +QN L +R L + F+ +GR
Sbjct: 268 EKAMLSCFCAMLKVEDPDVIIGHRLQNVYLDVLAHRMHDLNIPTFSSIGR 317
>pdb|4B08|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha,
Selenomethionine Protein
Length = 910
Score = 32.0 bits (71), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 25/50 (50%)
Query: 358 ETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGR 407
E L + A ++ DPD+ G+ +QN L +R L + F+ +GR
Sbjct: 268 EKAXLSCFCAXLKVEDPDVIIGHRLQNVYLDVLAHRXHDLNIPTFSSIGR 317
>pdb|3K5L|A Chain A, Crystal Structure Of E.Coli Pol Ii-Abasic Dna-Datp Lt(0,
3) Ternary Complex
pdb|3K5M|A Chain A, Crystal Structure Of E.Coli Pol Ii-Abasic Dna-Ddgtp Lt(-2,
2) Ternary Complex
pdb|3K5N|A Chain A, Crystal Structure Of E.Coli Pol Ii-Abasic Dna Binary
Complex
pdb|3K5N|B Chain B, Crystal Structure Of E.Coli Pol Ii-Abasic Dna Binary
Complex
pdb|3K5O|A Chain A, Crystal Structure Of E.Coli Pol Ii
pdb|3K5O|B Chain B, Crystal Structure Of E.Coli Pol Ii
pdb|3K57|A Chain A, Crystal Structure Of E.Coli Pol Ii-Normal Dna-Datp Ternary
Complex
pdb|3K58|A Chain A, Crystal Structure Of E.Coli Pol Ii-Normal Dna-Dttp Ternary
Complex
pdb|3K59|A Chain A, Crystal Structure Of E.Coli Pol Ii-Normal Dna-Dctp Ternary
Complex
pdb|3MAQ|A Chain A, Crystal Structure Of E.coli Pol Ii-normal Dna-dgtp Ternary
Complex
Length = 786
Score = 31.2 bits (69), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 360 ELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAK 395
+LL+K +A+ DPD+ G+N+ FD L A+
Sbjct: 206 QLLEKLNAWFANYDPDVIIGWNVVQFDLRMLQKHAE 241
>pdb|1Q8I|A Chain A, Crystal Structure Of Escherichia Coli Dna Polymerase Ii
Length = 783
Score = 31.2 bits (69), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 360 ELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAK 395
+LL+K +A+ DPD+ G+N+ FD L A+
Sbjct: 203 QLLEKLNAWFANYDPDVIIGWNVVQFDLRMLQKHAE 238
>pdb|3HWD|A Chain A, Crystal Structure Of Siderocalin (Ngal, Lipocalin 2)
K125a-K Mutant Complexed With Ferric Enterobactin
pdb|3HWD|B Chain B, Crystal Structure Of Siderocalin (Ngal, Lipocalin 2)
K125a-K Mutant Complexed With Ferric Enterobactin
pdb|3HWD|C Chain C, Crystal Structure Of Siderocalin (Ngal, Lipocalin 2)
K125a-K Mutant Complexed With Ferric Enterobactin
Length = 198
Score = 30.0 bits (66), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 30/54 (55%), Gaps = 4/54 (7%)
Query: 429 ENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQ-SKQMGKRENKTI 481
++ + F+ S RE + T GR K++ S +K++FI+ SK +G EN +
Sbjct: 137 QHAMVFFKAVSQNREYFAI---TLYGRTKELTSELKENFIRFSKSLGLPENHIV 187
>pdb|3DTQ|A Chain A, Engineered Human Lipocalin 2 With Specificity For Y-Dtpa,
Apo-Form
pdb|3DTQ|B Chain B, Engineered Human Lipocalin 2 With Specificity For Y-Dtpa,
Apo-Form
pdb|3DTQ|C Chain C, Engineered Human Lipocalin 2 With Specificity For Y-Dtpa,
Apo-Form
Length = 186
Score = 29.6 bits (65), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 31/54 (57%), Gaps = 4/54 (7%)
Query: 429 ENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQ-SKQMGKRENKTI 481
++ + F+ S RE + T LGR K++ S +K++FI+ SK +G EN +
Sbjct: 117 QHAMVFFKKVSQNREYFSI---TLLGRTKELASELKENFIRFSKSLGLPENHIV 167
>pdb|3DSZ|A Chain A, Engineered Human Lipocalin 2 In Complex With Y-Dtpa
pdb|3DSZ|B Chain B, Engineered Human Lipocalin 2 In Complex With Y-Dtpa
Length = 186
Score = 29.6 bits (65), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 31/54 (57%), Gaps = 4/54 (7%)
Query: 429 ENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQ-SKQMGKRENKTI 481
++ + F+ S RE + T LGR K++ S +K++FI+ SK +G EN +
Sbjct: 117 QHAMVFFKKVSQNREYFSI---TLLGRTKELASELKENFIRFSKSLGLPENHIV 167
>pdb|3I0A|A Chain A, Crystal Structure Of Siderocalin (Ngal, Lipocalin 2) K134a
M Complexed With Ferric Enterobactin
pdb|3I0A|B Chain B, Crystal Structure Of Siderocalin (Ngal, Lipocalin 2) K134a
M Complexed With Ferric Enterobactin
pdb|3I0A|C Chain C, Crystal Structure Of Siderocalin (Ngal, Lipocalin 2) K134a
M Complexed With Ferric Enterobactin
Length = 198
Score = 28.9 bits (63), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 30/54 (55%), Gaps = 4/54 (7%)
Query: 429 ENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQ-SKQMGKRENKTI 481
++ + F+ S RE + T GR K++ S +K++FI+ SK +G EN +
Sbjct: 137 QHAMVFFKKVSQNREYFAI---TLYGRTKELTSELKENFIRFSKSLGLPENHIV 187
>pdb|3CMP|A Chain A, Crystal Structure Of Siderocalin (Ngal, Lipocalin 2) K125a
Mutant Complexed With Ferric Enterobactin
pdb|3CMP|B Chain B, Crystal Structure Of Siderocalin (Ngal, Lipocalin 2) K125a
Mutant Complexed With Ferric Enterobactin
pdb|3CMP|C Chain C, Crystal Structure Of Siderocalin (Ngal, Lipocalin 2) K125a
Mutant Complexed With Ferric Enterobactin
Length = 198
Score = 28.9 bits (63), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 30/54 (55%), Gaps = 4/54 (7%)
Query: 429 ENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQ-SKQMGKRENKTI 481
++ + F+ S RE + T GR K++ S +K++FI+ SK +G EN +
Sbjct: 137 QHAMVFFKAVSQNREYFKI---TLYGRTKELTSELKENFIRFSKSLGLPENHIV 187
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
0.321 0.137 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,705,594
Number of Sequences: 62578
Number of extensions: 706735
Number of successful extensions: 1488
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 45
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1413
Number of HSP's gapped (non-prelim): 77
length of query: 551
length of database: 14,973,337
effective HSP length: 104
effective length of query: 447
effective length of database: 8,465,225
effective search space: 3783955575
effective search space used: 3783955575
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)