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= psy6283
(1030 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 277 bits (708), Expect = 3e-74, Method: Compositional matrix adjust.
Identities = 156/387 (40%), Positives = 226/387 (58%), Gaps = 15/387 (3%)
Query: 423 LNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQ--YXXXXXXXX 480
+ +L L Q+TN+ GN ++TL G R+ RNE++LLH F +++PDK+
Sbjct: 420 IQLLTLTKQLTNLAGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDKEGNRSRAQKQRQ 479
Query: 481 XXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRM 540
KKA Y GGLV EP+KG + ++++MDFNSLYPSIIQE+NICFTT+
Sbjct: 480 NEENADAPVNSKKAKYQGGLVFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVD--- 536
Query: 541 LQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKA 600
DI L +P +VD G+LP + LV+ RR+VK +MK +Q DIRQ+A
Sbjct: 537 RNKEDIDEL-PSVPPSEVDQGVLPRLLANLVDRRREVKKVMKT-ETDPHKRVQCDIRQQA 594
Query: 601 LKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMI 660
LKLTANSMYGCLG+ NSRF+A+PLA LVT KGREIL+NT+ L E++N V+YGDTDS+MI
Sbjct: 595 LKLTANSMYGCLGYVNSRFYAKPLAMLVTNKGREILMNTRQLAESMNLLVVYGDTDSVMI 654
Query: 661 SCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKM 720
++Y KIG K N+ Y+ LE+DID V NG
Sbjct: 655 DTGCDNYADAIKIGLGFKRLVNERYRLLEIDIDNVFKKLLLHAKKKYAALTVNLDKNGNG 714
Query: 721 ICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDL 780
E+KG+D+ RR++ L+ + V++ IL +D ++ LQ ++++++ IR +
Sbjct: 715 TTVLEVKGLDMKRREFCPLSRDVSIHVLNTIL-----SDKDPEEALQEVYDYLEDIRIKV 769
Query: 781 DNGFVPLTLLEITKQLTKAPE---GGK 804
+ + + +I +L+K P+ GGK
Sbjct: 770 ETNNIRIDKYKINMKLSKDPKAYPGGK 796
Score = 91.3 bits (225), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 60/186 (32%), Positives = 100/186 (53%), Gaps = 17/186 (9%)
Query: 211 VFRMFFLDAFEDIYKQPGTVYLFGKVFVKENNSHSSCCVIVQNIDRKIYLLPRSEHLKTK 270
F+MF+LD E T+ LFGKV +K++N S+ V + + R+++ LPR + K
Sbjct: 3 TFQMFWLDYCE----VNNTLILFGKVKLKDDNCVSAM-VQINGLCRELFFLPR----EGK 53
Query: 271 EPVSIAQVYSEFDQIATQYKILDFKSRKIEKKYAFNLPGVPDLSEYLEVRYSAKCP---- 326
P I + + +Y + + +++ + KY+F LP +P S+YL+V + P
Sbjct: 54 TPTDIHEEIIPL--LMDKYGLDNIRAKPQKMKYSFELPDIPSESDYLKVLLPYQTPKSSR 111
Query: 327 -ALPSDLSGDTFSHVFGTKTSFLENLLLERKIKGPSWLEFPEAEKFPSR-ISWCKYEVQC 384
+PSDLS DTF HVFG ++ E+ +++ +I GP WL+ A+ R S C EV
Sbjct: 112 DTIPSDLSSDTFYHVFGGNSNIFESFVIQNRIMGPCWLDIKGADFNSIRNASHCAVEVSV 171
Query: 385 NQMEKI 390
++ + I
Sbjct: 172 DKPQNI 177
>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 = 275 bits (703), Expect = 9e-74, Method: Compositional matrix adjust.
Identities = 155/387 (40%), Positives = 226/387 (58%), Gaps = 15/387 (3%)
Query: 423 LNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQ--YXXXXXXXX 480
+ +L L Q+TN+ GN ++TL G R+ RNE++LLH F +++PDK+
Sbjct: 420 IQLLTLTKQLTNLAGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDKEGNRSRAQKQRQ 479
Query: 481 XXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRM 540
KKA Y GGLV EP+KG + ++++MDFNSLYPSIIQE+NICFTT+
Sbjct: 480 NEENADAPVNSKKAKYQGGLVFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVD--- 536
Query: 541 LQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKA 600
DI L +P +VD G+LP + LV+ RR+VK +MK +Q DIRQ+A
Sbjct: 537 RNKEDIDEL-PSVPPSEVDQGVLPRLLANLVDRRREVKKVMKT-ETDPHKRVQCDIRQQA 594
Query: 601 LKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMI 660
LKLTANSMYGCLG+ NSRF+A+PLA LVT KGREIL+NT+ L E++N V+YGDT+S+MI
Sbjct: 595 LKLTANSMYGCLGYVNSRFYAKPLAMLVTNKGREILMNTRQLAESMNLLVVYGDTNSVMI 654
Query: 661 SCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKM 720
++Y KIG K N+ Y+ LE+DID V NG
Sbjct: 655 DTGCDNYADAIKIGLGFKRLVNERYRLLEIDIDNVFKKLLLHAKKKYAALTVNLDKNGNG 714
Query: 721 ICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDL 780
E+KG+D+ RR++ L+ + V++ IL +D ++ LQ ++++++ IR +
Sbjct: 715 TTVLEVKGLDMKRREFCPLSRDVSIHVLNTIL-----SDKDPEEALQEVYDYLEDIRIKV 769
Query: 781 DNGFVPLTLLEITKQLTKAPE---GGK 804
+ + + +I +L+K P+ GGK
Sbjct: 770 ETNNIRIDKYKINMKLSKDPKAYPGGK 796
Score = 90.5 bits (223), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 59/186 (31%), Positives = 100/186 (53%), Gaps = 17/186 (9%)
Query: 211 VFRMFFLDAFEDIYKQPGTVYLFGKVFVKENNSHSSCCVIVQNIDRKIYLLPRSEHLKTK 270
F+MF+LD E T+ LFGKV +K++N S+ V + + R+++ LPR + K
Sbjct: 3 TFQMFWLDYCE----VNNTLILFGKVKLKDDNCVSAM-VQINGLCRELFFLPR----EGK 53
Query: 271 EPVSIAQVYSEFDQIATQYKILDFKSRKIEKKYAFNLPGVPDLSEYLEVRYSAKCP---- 326
P I + + +Y + + +++ + KY+F LP +P S+YL+V + P
Sbjct: 54 TPTDIHEEIIPL--LMDKYGLDNIRAKPQKMKYSFELPDIPSESDYLKVLLPYQTPKSSR 111
Query: 327 -ALPSDLSGDTFSHVFGTKTSFLENLLLERKIKGPSWLEFPEAE-KFPSRISWCKYEVQC 384
+PSDLS DTF HVFG ++ E+ +++ +I GP WL+ A+ + S C EV
Sbjct: 112 DTIPSDLSSDTFYHVFGGNSNIFESFVIQNRIMGPCWLDIKGADFNSIAAASHCAVEVSV 171
Query: 385 NQMEKI 390
++ + I
Sbjct: 172 DKPQNI 177
>pdb|4B08|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha,
Selenomethionine Protein
Length = 910
Score = 264 bits (674), Expect = 2e-70, Method: Compositional matrix adjust.
Identities = 152/387 (39%), Positives = 219/387 (56%), Gaps = 15/387 (3%)
Query: 423 LNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQ--YXXXXXXXX 480
+ +L L Q+TN+ GN ++TL G R+ RNE++LLH F +++PDK+
Sbjct: 420 IQLLTLTKQLTNLAGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDKEGNRSRAQKQRQ 479
Query: 481 XXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRM 540
KKA Y GGLV EP+KG + ++++ DFNSLYPSIIQE+NICFTT+
Sbjct: 480 NEENADAPVNSKKAKYQGGLVFEPEKGLHKNYVLVXDFNSLYPSIIQEFNICFTTVD--- 536
Query: 541 LQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKA 600
DI L +P +VD G+LP + LV+ RR+VK + K +Q DIRQ+A
Sbjct: 537 RNKEDIDEL-PSVPPSEVDQGVLPRLLANLVDRRREVKKVXKT-ETDPHKRVQCDIRQQA 594
Query: 601 LKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMI 660
LKLTANS YGCLG+ NSRF+A+PLA LVT KGREIL NT+ L E+ N V+YGDTDS+ I
Sbjct: 595 LKLTANSXYGCLGYVNSRFYAKPLAXLVTNKGREILXNTRQLAESXNLLVVYGDTDSVXI 654
Query: 661 SCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKM 720
++Y KIG K N+ Y+ LE+DID V NG
Sbjct: 655 DTGCDNYADAIKIGLGFKRLVNERYRLLEIDIDNVFKKLLLHAKKKYAALTVNLDKNGNG 714
Query: 721 ICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDL 780
E+KG+D RR++ L+ + V++ IL +D ++ LQ ++++++ IR +
Sbjct: 715 TTVLEVKGLDXKRREFCPLSRDVSIHVLNTIL-----SDKDPEEALQEVYDYLEDIRIKV 769
Query: 781 DNGFVPLTLLEITKQLTKAPE---GGK 804
+ + + +I +L+K P+ GGK
Sbjct: 770 ETNNIRIDKYKINXKLSKDPKAYPGGK 796
Score = 88.6 bits (218), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 59/186 (31%), Positives = 99/186 (53%), Gaps = 17/186 (9%)
Query: 211 VFRMFFLDAFEDIYKQPGTVYLFGKVFVKENNSHSSCCVIVQNIDRKIYLLPRSEHLKTK 270
F+ F+LD E T+ LFGKV +K++N S+ V + + R+++ LPR + K
Sbjct: 3 TFQXFWLDYCE----VNNTLILFGKVKLKDDNCVSAX-VQINGLCRELFFLPR----EGK 53
Query: 271 EPVSIAQVYSEFDQIATQYKILDFKSRKIEKKYAFNLPGVPDLSEYLEVRYSAKCP---- 326
P I + + +Y + + +++ + KY+F LP +P S+YL+V + P
Sbjct: 54 TPTDIHEEIIPL--LXDKYGLDNIRAKPQKXKYSFELPDIPSESDYLKVLLPYQTPKSSR 111
Query: 327 -ALPSDLSGDTFSHVFGTKTSFLENLLLERKIKGPSWLEFPEAEKFPSR-ISWCKYEVQC 384
+PSDLS DTF HVFG ++ E+ +++ +I GP WL+ A+ R S C EV
Sbjct: 112 DTIPSDLSSDTFYHVFGGNSNIFESFVIQNRIXGPCWLDIKGADFNSIRNASHCAVEVSV 171
Query: 385 NQMEKI 390
++ + I
Sbjct: 172 DKPQNI 177
>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 = 134 bits (337), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 110/380 (28%), Positives = 184/380 (48%), Gaps = 44/380 (11%)
Query: 426 LPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXXXXXXXXXXXX 485
LP+ IQ++ + G L E+ LL +E++ V P+K
Sbjct: 327 LPMEIQLSRLIGQPLWDVSRSSTGNLVEWFLLRKAYERNEVAPNKP------------SE 374
Query: 486 XXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSD 545
R + +Y+GG V EP+KG +D I+ +DF +LYPSII +N+ T+ + ++ D
Sbjct: 375 EEYQRRLRESYTGGFVKEPEKGLWDD-IVYLDFIALYPSIIITHNVSPDTLNLEGCKNYD 433
Query: 546 ITT-----LCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKA 600
I C+ +P G +PS + L+E R+++K MK+ + ++ D RQKA
Sbjct: 434 IAPQVGHKFCKDIP------GFIPSLLGHLLEERQKIKTKMKETQDPIEKIL-LDYRQKA 486
Query: 601 LKLTANSMYGCLGFPNSRFFAQPLAALVTAKGRE-ILLNTKSLVENLNYEVIYGDTDSLM 659
+KL ANS YG G+ +R++ + A VTA GR+ I L K L E ++V+Y DTD L
Sbjct: 487 IKLLANSFYGYYGYAKARWYCKECAESVTAWGRKYIELVWKELEEKFGFKVLYIDTDGLH 546
Query: 660 ISCNVNDYDSVFKIGNQ-IKSECNKLYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNG 718
+ + + + K + +K +KL LEL+ +G G
Sbjct: 547 ATIPGGESEEIKKKALEFVKYINSKLPGLLELEYEGF----YKRGFFVTKKRYAVIDEEG 602
Query: 719 KMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRT 778
K+I +G+++VRRDWS++A E V+ IL +++ ++ + E ++K
Sbjct: 603 KVIT----RGLEIVRRDWSEIAKETQARVLETILKHG-----DVEEAVRIVKEVIQK--- 650
Query: 779 DLDNGFVPLTLLEITKQLTK 798
L N +P L I +Q+T+
Sbjct: 651 -LANYEIPPEKLAIYEQITR 669
>pdb|2JGU|A Chain A, Crystal Structure Of Dna-directed Dna Polymerase
Length = 775
Score = 134 bits (337), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 109/380 (28%), Positives = 184/380 (48%), Gaps = 44/380 (11%)
Query: 426 LPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXXXXXXXXXXXX 485
LP+ IQ++ + G L E+ LL +E++ V P+K
Sbjct: 327 LPMEIQLSRLVGQPLWDVSRSSTGNLVEWFLLRKAYERNEVAPNKP------------SE 374
Query: 486 XXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSD 545
R + +Y+GG V EP+KG ++ I+ +D+ SLYPSII +N+ T+ + ++ D
Sbjct: 375 EEYQRRLRESYTGGFVKEPEKGLWEN-IVYLDYKSLYPSIIITHNVSPDTLNLEGCKNYD 433
Query: 546 IT-----TLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKA 600
I C+ +P G +PS + L+E R+++K MK+ + ++ D RQKA
Sbjct: 434 IAPQVGHKFCKDIP------GFIPSLLGHLLEERQKIKTKMKETQDPIEKIL-LDYRQKA 486
Query: 601 LKLTANSMYGCLGFPNSRFFAQPLAALVTAKGRE-ILLNTKSLVENLNYEVIYGDTDSLM 659
+KL ANS YG G+ +R++ + A VTA GR+ I L K L E ++V+Y DTD L
Sbjct: 487 IKLLANSFYGYYGYAKARWYCKECAESVTAWGRKYIELVWKELEEKFGFKVLYIDTDGLY 546
Query: 660 ISCNVNDYDSVFKIGNQ-IKSECNKLYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNG 718
+ + + + K + +K +KL LEL+ +G G
Sbjct: 547 ATIPGGESEEIKKKALEFVKYINSKLPGLLELEYEGF----YKRGFFVTKKRYAVIDEEG 602
Query: 719 KMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRT 778
K+I +G+++VRRDWS++A E V+ IL +++ ++ + E ++K
Sbjct: 603 KVIT----RGLEIVRRDWSEIAKETQARVLETILKHG-----DVEEAVRIVKEVIQK--- 650
Query: 779 DLDNGFVPLTLLEITKQLTK 798
L N +P L I +Q+T+
Sbjct: 651 -LANYEIPPEKLAIYEQITR 669
>pdb|3A2F|A Chain A, Crystal Structure Of Pyrococcus Furiosus Dna
PolymerasePCNA Monomer Mutant Complex
Length = 775
Score = 131 bits (329), Expect = 2e-30, Method: Compositional matrix adjust.
Identities = 108/380 (28%), Positives = 182/380 (47%), Gaps = 44/380 (11%)
Query: 426 LPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXXXXXXXXXXXX 485
LP IQ++ + G L E+ LL +E++ V P+K
Sbjct: 327 LPXEIQLSRLVGQPLWDVSRSSTGNLVEWFLLRKAYERNEVAPNKP------------SE 374
Query: 486 XXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSD 545
R + +Y+GG V EP+KG ++ I+ +DF +LYPSII +N+ T+ + ++ D
Sbjct: 375 EEYQRRLRESYTGGFVKEPEKGLWEN-IVYLDFRALYPSIIITHNVSPDTLNLEGCKNYD 433
Query: 546 ITT-----LCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKA 600
I C+ +P G +PS + L+E R+++K K+ + ++ D RQKA
Sbjct: 434 IAPQVGHKFCKDIP------GFIPSLLGHLLEERQKIKTKXKETQDPIEKIL-LDYRQKA 486
Query: 601 LKLTANSMYGCLGFPNSRFFAQPLAALVTAKGRE-ILLNTKSLVENLNYEVIYGDTDSLM 659
+KL ANS YG G+ +R++ + A VTA GR+ I L K L E ++V+Y DTD L
Sbjct: 487 IKLLANSFYGYYGYAKARWYCKECAESVTAWGRKYIELVWKELEEKFGFKVLYIDTDGLY 546
Query: 660 ISCNVNDYDSVFKIGNQ-IKSECNKLYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNG 718
+ + + + K + +K +KL LEL+ +G G
Sbjct: 547 ATIPGGESEEIKKKALEFVKYINSKLPGLLELEYEGF----YKRGFFVTKKRYAVIDEEG 602
Query: 719 KMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRT 778
K+I +G+++VRRDWS++A E V+ IL +++ ++ + E ++K
Sbjct: 603 KVIT----RGLEIVRRDWSEIAKETQARVLETILKHG-----DVEEAVRIVKEVIQK--- 650
Query: 779 DLDNGFVPLTLLEITKQLTK 798
L N +P L I +Q+T+
Sbjct: 651 -LANYEIPPEKLAIYEQITR 669
>pdb|1QHT|A Chain A, Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon
Length = 775
Score = 129 bits (323), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 100/346 (28%), Positives = 160/346 (46%), Gaps = 42/346 (12%)
Query: 418 KIMCELN--VLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXX 475
K+ EL P+ Q++ + G L E+ LL ++++ + P+K
Sbjct: 317 KVTYELGREFFPMEAQLSRLIGQSLWDVSRSSTGNLVEWFLLRKAYKRNELAPNKP---- 372
Query: 476 XXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTT 535
R++ Y+GG V EP++G +D I+ +DF SLYPSII +N+ T
Sbjct: 373 ---------DERELARRRGGYAGGYVKEPERGLWDN-IVYLDFRSLYPSIIITHNVSPDT 422
Query: 536 IPVRMLQDSDIT-----TLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQP--NLSS 588
+ ++ D+ C+ P G +PS + L+E R+++K MK L
Sbjct: 423 LNREGCKEYDVAPEVGHKFCKDFP------GFIPSLLGDLLEERQKIKRKMKATVDPLEK 476
Query: 589 DLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGRE-ILLNTKSLVENLN 647
LL D RQ+A+K+ ANS YG G+ +R++ + A VTA GRE I + + L E
Sbjct: 477 KLL---DYRQRAIKILANSFYGYYGYAKARWYCKECAESVTAWGREYIEMVIRELEEKFG 533
Query: 648 YEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-KLYKQLELDIDGVXXXXXXXXXXX 706
++V+Y DTD L + D ++V K + N KL LEL+ +G
Sbjct: 534 FKVLYADTDGLHATIPGADAETVKKKAKEFLKYINPKLPGLLELEYEGF----YVRGFFV 589
Query: 707 XXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQIL 752
GK+ +G+++VRRDWS++A E V+ IL
Sbjct: 590 TKKKYAVIDEEGKITT----RGLEIVRRDWSEIAKETQARVLEAIL 631
>pdb|2VWJ|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography
Length = 773
Score = 125 bits (313), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 95/346 (27%), Positives = 157/346 (45%), Gaps = 42/346 (12%)
Query: 418 KIMCELN--VLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXX 475
K+ EL P+ Q++ + G L E+ LL +E++ + P+K
Sbjct: 317 KVTYELGKEFFPMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKP---- 372
Query: 476 XXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTT 535
R++ +Y+GG V EP++G ++ I+ +DF SLYPSII +N+ T
Sbjct: 373 ---------DERELARRRESYAGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVSPDT 422
Query: 536 IPVRMLQDSDIT-----TLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQP--NLSS 588
+ ++ D+ C+ P G +PS + L+E R++VK MK +
Sbjct: 423 LNREGCEEYDVAPQVGHKFCKDFP------GFIPSLLGDLLEERQKVKKKMKATIDPIEK 476
Query: 589 DLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNT-KSLVENLN 647
LL D RQ+A+K+ ANS YG G+ +R++ + A VTA GR+ + T + + E
Sbjct: 477 KLL---DYRQRAIKILANSFYGYYGYAKARWYCKECAESVTAWGRQYIETTIREIEEKFG 533
Query: 648 YEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-KLYKQLELDIDGVXXXXXXXXXXX 706
++V+Y DTD + D ++V K + N KL LEL+ +G
Sbjct: 534 FKVLYADTDGFFATIPGADAETVKKKAKEFLDYINAKLPGLLELEYEGFYKRGFFVTKKK 593
Query: 707 XXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQIL 752
+G+++VRRDWS++A E V+ IL
Sbjct: 594 YAVIDEEDKIT--------TRGLEIVRRDWSEIAKETQARVLEAIL 631
>pdb|2VWK|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography. V93q Polymerase Variant
Length = 773
Score = 124 bits (312), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 95/346 (27%), Positives = 157/346 (45%), Gaps = 42/346 (12%)
Query: 418 KIMCELN--VLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXX 475
K+ EL P+ Q++ + G L E+ LL +E++ + P+K
Sbjct: 317 KVTYELGKEFFPMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKP---- 372
Query: 476 XXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTT 535
R++ +Y+GG V EP++G ++ I+ +DF SLYPSII +N+ T
Sbjct: 373 ---------DERELARRRESYAGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVSPDT 422
Query: 536 IPVRMLQDSDIT-----TLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQP--NLSS 588
+ ++ D+ C+ P G +PS + L+E R++VK MK +
Sbjct: 423 LNREGCEEYDVAPQVGHKFCKDFP------GFIPSLLGDLLEERQKVKKKMKATIDPIEK 476
Query: 589 DLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNT-KSLVENLN 647
LL D RQ+A+K+ ANS YG G+ +R++ + A VTA GR+ + T + + E
Sbjct: 477 KLL---DYRQRAIKILANSFYGYYGYAKARWYCKECAESVTAWGRQYIETTIREIEEKFG 533
Query: 648 YEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-KLYKQLELDIDGVXXXXXXXXXXX 706
++V+Y DTD + D ++V K + N KL LEL+ +G
Sbjct: 534 FKVLYADTDGFFATIPGADAETVKKKAKEFLDYINAKLPGLLELEYEGFYKRGFFVTKKK 593
Query: 707 XXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQIL 752
+G+++VRRDWS++A E V+ IL
Sbjct: 594 YAVIDEEDKIT--------TRGLEIVRRDWSEIAKETQARVLEAIL 631
>pdb|2XHB|A Chain A, Crystal Structure Of Dna Polymerase From Thermococcus
Gorgonarius In Complex With Hypoxanthine-Containing Dna
Length = 773
Score = 124 bits (312), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 95/346 (27%), Positives = 157/346 (45%), Gaps = 42/346 (12%)
Query: 418 KIMCELN--VLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXX 475
K+ EL P+ Q++ + G L E+ LL +E++ + P+K
Sbjct: 317 KVTYELGKEFFPMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKP---- 372
Query: 476 XXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTT 535
R++ +Y+GG V EP++G ++ I+ +DF SLYPSII +N+ T
Sbjct: 373 ---------DERELARRRESYAGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVSPDT 422
Query: 536 IPVRMLQDSDIT-----TLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQP--NLSS 588
+ ++ D+ C+ P G +PS + L+E R++VK MK +
Sbjct: 423 LNREGCEEYDVAPQVGHKFCKDFP------GFIPSLLGDLLEERQKVKKKMKATIDPIEK 476
Query: 589 DLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNT-KSLVENLN 647
LL D RQ+A+K+ ANS YG G+ +R++ + A VTA GR+ + T + + E
Sbjct: 477 KLL---DYRQRAIKILANSFYGYYGYAKARWYCKECAESVTAWGRQYIETTIREIEEKFG 533
Query: 648 YEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-KLYKQLELDIDGVXXXXXXXXXXX 706
++V+Y DTD + D ++V K + N KL LEL+ +G
Sbjct: 534 FKVLYADTDGFFATIPGADAETVKKKAKEFLDYINAKLPGLLELEYEGFYKRGFFVTKKK 593
Query: 707 XXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQIL 752
+G+++VRRDWS++A E V+ IL
Sbjct: 594 YAVIDEEDKIT--------TRGLEIVRRDWSEIAKETQARVLEAIL 631
>pdb|1TGO|A Chain A, Thermostable B Type Dna Polymerase From Thermococcus
Gorgonarius
Length = 773
Score = 124 bits (312), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 95/346 (27%), Positives = 157/346 (45%), Gaps = 42/346 (12%)
Query: 418 KIMCELN--VLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXX 475
K+ EL P+ Q++ + G L E+ LL +E++ + P+K
Sbjct: 317 KVTYELGKEFFPMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKP---- 372
Query: 476 XXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTT 535
R++ +Y+GG V EP++G ++ I+ +DF SLYPSII +N+ T
Sbjct: 373 ---------DERELARRRESYAGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVSPDT 422
Query: 536 IPVRMLQDSDIT-----TLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQP--NLSS 588
+ ++ D+ C+ P G +PS + L+E R++VK MK +
Sbjct: 423 LNREGCEEYDVAPQVGHKFCKDFP------GFIPSLLGDLLEERQKVKKKMKATIDPIEK 476
Query: 589 DLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNT-KSLVENLN 647
LL D RQ+A+K+ ANS YG G+ +R++ + A VTA GR+ + T + + E
Sbjct: 477 KLL---DYRQRAIKILANSFYGYYGYAKARWYCKECAESVTAWGRQYIETTIREIEEKFG 533
Query: 648 YEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-KLYKQLELDIDGVXXXXXXXXXXX 706
++V+Y DTD + D ++V K + N KL LEL+ +G
Sbjct: 534 FKVLYADTDGFFATIPGADAETVKKKAKEFLDYINAKLPGLLELEYEGFYKRGFFVTKKK 593
Query: 707 XXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQIL 752
+G+++VRRDWS++A E V+ IL
Sbjct: 594 YAVIDEEDKIT--------TRGLEIVRRDWSEIAKETQARVLEAIL 631
>pdb|1WN7|A Chain A, Crystal Structure Of Archaeal Family B Dna Polymerase
Mutant
Length = 774
Score = 114 bits (284), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 108/392 (27%), Positives = 177/392 (45%), Gaps = 51/392 (13%)
Query: 418 KIMCELN--VLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXX 475
K+ EL LP+ Q++ + G L E+ LL +E++ + P+K
Sbjct: 317 KVTYELGKEFLPMEAQLSRLIGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKP---- 372
Query: 476 XXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTT 535
R++ +Y GG V EP++G ++ I+ +DF SLYPSII +N+ T
Sbjct: 373 ---------DEKELARRRQSYEGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVSPDT 422
Query: 536 IPVRMLQDSDITT-----LCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQP--NLSS 588
+ ++ D+ C+ P G +PS + L+E R+++K MK +
Sbjct: 423 LNREGCKEYDVAPQVGHRFCKDFP------GFIPSLLGDLLEERQKIKKKMKATIDPIER 476
Query: 589 DLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGRE-ILLNTKSLVENLN 647
LL D RQ+A+K+ ANS YG G+ +R++ + A VTA GRE I + K + E
Sbjct: 477 KLL---DYRQRAIKILANSYYGYYGYARARWYCKECAESVTAWGREYITMTIKEIEEKYG 533
Query: 648 YEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-KLYKQLELDIDGVXXXXXXXXXXX 706
++VIY DTD + D ++V K + N KL LEL+ +G
Sbjct: 534 FKVIYSDTDGFFATIPGADAETVKKKAMEFLKYINAKLPGALELEYEGF----YERGFFV 589
Query: 707 XXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRL 766
GK+ +G+++VRRDWS++A E V+ +L D +
Sbjct: 590 TKKKYAVIDEEGKITT----RGLEIVRRDWSEIAKETQARVLEALLK---------DGDV 636
Query: 767 QNIHEHMKKIRTDLDNGFVPLTLLEITKQLTK 798
+ +K++ L VP L I +Q+T+
Sbjct: 637 EKAVRIVKEVTEKLSKYEVPPEKLVIHEQITR 668
>pdb|1WNS|A Chain A, Crystal Structure Of Family B Dna Polymerase From
Hyperthermophilic Archaeon Pyrococcus Kodakaraensis Kod1
Length = 774
Score = 114 bits (284), Expect = 4e-25, Method: Compositional matrix adjust.
Identities = 108/392 (27%), Positives = 177/392 (45%), Gaps = 51/392 (13%)
Query: 418 KIMCELN--VLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXX 475
K+ EL LP+ Q++ + G L E+ LL +E++ + P+K
Sbjct: 317 KVTYELGKEFLPMEAQLSRLIGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKP---- 372
Query: 476 XXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTT 535
R++ +Y GG V EP++G ++ I+ +DF SLYPSII +N+ T
Sbjct: 373 ---------DEKELARRRQSYEGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVSPDT 422
Query: 536 IPVRMLQDSDITT-----LCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQP--NLSS 588
+ ++ D+ C+ P G +PS + L+E R+++K MK +
Sbjct: 423 LNREGCKEYDVAPQVGHRFCKDFP------GFIPSLLGDLLEERQKIKKKMKATIDPIER 476
Query: 589 DLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGRE-ILLNTKSLVENLN 647
LL D RQ+A+K+ ANS YG G+ +R++ + A VTA GRE I + K + E
Sbjct: 477 KLL---DYRQRAIKILANSYYGYYGYARARWYCKECAESVTAWGREYITMTIKEIEEKYG 533
Query: 648 YEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-KLYKQLELDIDGVXXXXXXXXXXX 706
++VIY DTD + D ++V K + N KL LEL+ +G
Sbjct: 534 FKVIYSDTDGFFATIPGADAETVKKKAMEFLKYINAKLPGALELEYEGF----YKRGFFV 589
Query: 707 XXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRL 766
GK+ +G+++VRRDWS++A E V+ +L D +
Sbjct: 590 TKKKYAVIDEEGKITT----RGLEIVRRDWSEIAKETQARVLEALLK---------DGDV 636
Query: 767 QNIHEHMKKIRTDLDNGFVPLTLLEITKQLTK 798
+ +K++ L VP L I +Q+T+
Sbjct: 637 EKAVRIVKEVTEKLSKYEVPPEKLVIHEQITR 668
>pdb|3IAY|A Chain A, Ternary Complex Of Dna Polymerase Delta
Length = 919
Score = 106 bits (265), Expect = 5e-23, Method: Compositional matrix adjust.
Identities = 67/212 (31%), Positives = 111/212 (52%), Gaps = 23/212 (10%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTT---------IPVRMLQDSDI 546
Y G V+EP +G+YD I +DFNSLYPSI+ +N+C+TT + +++ +D I
Sbjct: 521 YEGATVIEPIRGYYDVPIATLDFNSLYPSIMMAHNLCYTTLCNKATVERLNLKIDEDYVI 580
Query: 547 TTLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPN--LSSDLLMQYDIRQKALKLT 604
T +Y + GILP + +L+ +R++ K ++ D+L + RQ ALK++
Sbjct: 581 TPNGDYFVTTKRRRGILPIILDELISARKRAKKDLRDEKDPFKRDVL---NGRQLALKIS 637
Query: 605 ANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVE---------NLNYEVIYGDT 655
ANS+YG G + +++ VTA GR ++L TK+ V+ + V+YGDT
Sbjct: 638 ANSVYGFTGATVGKLPCLAISSSVTAYGRTMILKTKTAVQEKYCIKNGYKHDAVVVYGDT 697
Query: 656 DSLMISCNVNDYDSVFKIGNQIKSECNKLYKQ 687
DS+M+ D +G + + L+K
Sbjct: 698 DSVMVKFGTTDLKEAMDLGTEAAKYVSTLFKH 729
>pdb|4FM2|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase (Triple Mutant)
Bound To A Dsdna, In Edition Mode
Length = 793
Score = 103 bits (257), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 103/406 (25%), Positives = 185/406 (45%), Gaps = 49/406 (12%)
Query: 401 GIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAF 460
G+ K++M + ++ E P+ Q+ + G + E+ LL
Sbjct: 326 GLERVAKYSMEDAKVTFELGKEF--FPMEAQLARLVGQPVWAVSRSSTGNLVEWFLLRKA 383
Query: 461 HEKSYVLPDKQYXXXXXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNS 520
+E++ + P+K R + +Y GG V EP+KG ++ I+ +DF S
Sbjct: 384 YERNELAPNKP------------DEREYERRLRESYEGGYVKEPEKGLWEG-IVSLDFRS 430
Query: 521 LYPSIIQEYNICFTTIPVRMLQDSDITT-----LCEYLPEHQVDTGILPSEIKKLVESRR 575
LYPSII +N+ T+ ++ D+ C+ P G +PS + L+E R+
Sbjct: 431 LYPSIIITHNVSPDTLNRENCKEYDVAPQVGHRFCKDFP------GFIPSLLGNLLEERQ 484
Query: 576 QVKALMKQPN--LSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGR 633
++K MK+ + LL D RQ+A+K+ ANS YG G+ +R++ + A VTA GR
Sbjct: 485 KIKKRMKESKDPVEKKLL---DYRQRAIKILANSYYGYYGYAKARWYCKECAESVTAWGR 541
Query: 634 EILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-KLYKQLELDI 692
+ + + +E+ ++V+Y DTD L + ++ + + + N KL LEL+
Sbjct: 542 QYIDLVRRELESRGFKVLYIDTDGLYATIPGAKHEEIKEKALKFVEYINSKLPGLLELEY 601
Query: 693 DGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQIL 752
+G GK++ +G+++VRRDWS++A E V+ IL
Sbjct: 602 EGF----YARGFFVTKKKYALIDEEGKIVT----RGLEIVRRDWSEIAKETQAKVLEAIL 653
Query: 753 DEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTK 798
++D+ ++ + E +K L +P L I +Q+T+
Sbjct: 654 KHG-----NVDEAVKIVKEVTEK----LSKYEIPPEKLVIYEQITR 690
>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 = 103 bits (257), Expect = 5e-22, Method: Compositional matrix adjust.
Identities = 103/406 (25%), Positives = 185/406 (45%), Gaps = 49/406 (12%)
Query: 401 GIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAF 460
G+ K++M + ++ E P+ Q+ + G + E+ LL
Sbjct: 326 GLERVAKYSMEDAKVTFELGKEF--FPMEAQLARLVGQPVWDVSRSSTGNLVEWFLLRKA 383
Query: 461 HEKSYVLPDKQYXXXXXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNS 520
+E++ + P+K R + +Y GG V EP+KG ++ I+ +DF S
Sbjct: 384 YERNELAPNKP------------DEREYERRLRESYEGGYVKEPEKGLWEG-IVSLDFRS 430
Query: 521 LYPSIIQEYNICFTTIPVRMLQDSDITT-----LCEYLPEHQVDTGILPSEIKKLVESRR 575
LYPSII +N+ T+ ++ D+ C+ P G +PS + L+E R+
Sbjct: 431 LYPSIIITHNVSPDTLNRENCKEYDVAPQVGHRFCKDFP------GFIPSLLGNLLEERQ 484
Query: 576 QVKALMKQPN--LSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGR 633
++K MK+ + LL D RQ+A+K+ ANS YG G+ +R++ + A VTA GR
Sbjct: 485 KIKKRMKESKDPVEKKLL---DYRQRAIKILANSYYGYYGYAKARWYCKECAESVTAWGR 541
Query: 634 EILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-KLYKQLELDI 692
+ + + +E+ ++V+Y DTD L + ++ + + + N KL LEL+
Sbjct: 542 QYIDLVRRELESRGFKVLYIDTDGLYATIPGAKHEEIKEKALKFVEYINSKLPGLLELEY 601
Query: 693 DGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQIL 752
+G GK++ +G+++VRRDWS++A E V+ IL
Sbjct: 602 EGF----YARGFFVTKKKYALIDEEGKIVT----RGLEIVRRDWSEIAKETQAKVLEAIL 653
Query: 753 DEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTK 798
++D+ ++ + E +K L +P L I +Q+T+
Sbjct: 654 KHG-----NVDEAVKIVKEVTEK----LSKYEIPPEKLVIYEQITR 690
>pdb|1QQC|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
D.Tok
Length = 773
Score = 101 bits (251), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 104/407 (25%), Positives = 180/407 (44%), Gaps = 51/407 (12%)
Query: 401 GIVEFIKFTMLHSSYIIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAF 460
G+ +++M + ++ E P+ Q++ + G L E+ LL
Sbjct: 304 GLERVARYSMEDAKATYELGKEF--FPMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKA 361
Query: 461 HEKSYVLPDKQYXXXXXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNS 520
+E++ V P+K R+ +Y+GG V EP+KG ++ I+ +D+ S
Sbjct: 362 YERNDVAPNKP-------------DERELARRTESYAGGYVKEPEKGLWEN-IVYLDYKS 407
Query: 521 LYPSIIQEYNICFTTIPVRMLQDSDITT-----LCEYLPEHQVDTGILPSEIKKLVESRR 575
LYPSII +N+ T+ ++ D+ C+ P G +PS + L+E R+
Sbjct: 408 LYPSIIITHNVSPDTLNREGCREYDVAPQVGHRFCKDFP------GFIPSLLGDLLEERQ 461
Query: 576 QVKALMKQP--NLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGR 633
+VK MK + LL D RQ+A+K+ ANS YG + N+R++ + A VTA GR
Sbjct: 462 KVKKKMKATVDPIERKLL---DYRQRAIKILANSYYGYYAYANARWYCRECAESVTAWGR 518
Query: 634 EILLNT-KSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-KLYKQLELD 691
+ + T + + E ++V+Y DTD + D ++V + + N +L LEL+
Sbjct: 519 QYIETTMREIEEKFGFKVLYADTDGFFATIPGADAETVKNKAKEFLNYINPRLPGLLELE 578
Query: 692 IDGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQI 751
+G +G+++VRRDWS++A E V+ I
Sbjct: 579 YEGFYRRGFFVTKKKYAVIDEEDKIT--------TRGLEIVRRDWSEIAKETQARVLEAI 630
Query: 752 LDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTK 798
L + D R+ +K++ L VP L I +Q+T+
Sbjct: 631 L---KHGDVEEAVRI------VKEVTEKLSRHEVPPEKLVIYEQITR 668
>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 = 100 bits (249), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 91/336 (27%), Positives = 152/336 (45%), Gaps = 40/336 (11%)
Query: 426 LPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXXXXXXXXXXXX 485
P+ Q++ + G L E+ LL +E++ V P+K
Sbjct: 327 FPMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKAYERNDVAPNKP-------------D 373
Query: 486 XXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSD 545
R+ +Y+GG V EP+KG ++ I+ +D+ SLYPSII +N+ T+ ++ D
Sbjct: 374 ERELARRTESYAGGYVKEPEKGLWEN-IVYLDYKSLYPSIIITHNVSPDTLNREGCREYD 432
Query: 546 ITT-----LCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQP--NLSSDLLMQYDIRQ 598
+ C+ P G +PS + L+E R++VK MK + LL D RQ
Sbjct: 433 VAPQVGHRFCKDFP------GFIPSLLGDLLEERQKVKKKMKATVDPIERKLL---DYRQ 483
Query: 599 KALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNT-KSLVENLNYEVIYGDTDS 657
+A+K+ ANS YG + N+R++ + A VTA GR+ + T + + E ++V+Y DTD
Sbjct: 484 RAIKILANSYYGYYAYANARWYCRECAESVTAWGRQYIETTMREIEEKFGFKVLYADTDG 543
Query: 658 LMISCNVNDYDSVFKIGNQIKSECN-KLYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXX 716
+ D ++V + + N +L LEL+ +G
Sbjct: 544 FFATIPGADAETVKNKAKEFLNYINPRLPGLLELEYEGFYRRGFFVTKKKYAVIDEEDKI 603
Query: 717 NGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQIL 752
+G+++VRRDWS++A E V+ IL
Sbjct: 604 T--------TRGLEIVRRDWSEIAKETQARVLEAIL 631
>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 = 94.7 bits (234), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 76/291 (26%), Positives = 125/291 (42%), Gaps = 68/291 (23%)
Query: 492 KKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCE 551
+ Y G VL+P GF+ +++ DF SLYPSIIQ +N+CF+T+ +R + + +
Sbjct: 650 RHVGYQGAKVLDPTSGFHVNPVVVFDFASLYPSIIQAHNLCFSTLSLRADAVAHLEAGKD 709
Query: 552 YLP-----------EHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKA 600
YL + V +L ++ + R+Q+++ + Q + +L+ D +Q A
Sbjct: 710 YLEIEVGGRRLFFVKAHVRESLLSILLRDWLAMRKQIRSRIPQSSPEEAVLL--DKQQAA 767
Query: 601 LKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVEN--------------- 645
+K+ NS+YG G + +AA VT GRE+LL T+ V
Sbjct: 768 IKVVCNSVYGFTGVQHGLLPCLHVAATVTTIGREMLLATREYVHARWAAFEQLLADFPEA 827
Query: 646 --------LNYEVIYGDTDSLMISCNVNDYDSVFKIGNQ-------------IKSECNKL 684
+ +IYGDTDS+ + C + +G++ IK EC K
Sbjct: 828 ADMRAPGPYSMRIIYGDTDSIFVLCRGLTAAGLTAMGDKMASHISRALFLPPIKLECEKT 887
Query: 685 YKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRD 735
+ +L L GKM+ IKGVD+VR++
Sbjct: 888 FTKLLL---------------IAKKKYIGVIYGGKML----IKGVDLVRKN 919
>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 = 91.3 bits (225), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 90/373 (24%), Positives = 146/373 (39%), Gaps = 74/373 (19%)
Query: 416 IIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXX 475
+ +I + ++P ++ V G + R GG L H YV P+
Sbjct: 342 VTQIFHKTEIMPFLLERATVNGLPVDR--HGGSVAAFGHLYFPRMHRAGYVAPN------ 393
Query: 476 XXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTT 535
A GG V++ + G YD ++L D+ SLYPSII+ F
Sbjct: 394 ------------LGEVPPHASPGGYVMDSRPGLYDSVLVL-DYKSLYPSIIR----TFLI 436
Query: 536 IPVRMLQDSDITTLCEYLPEHQVDTGI----------LPSEIKKLVESRRQVKALMKQPN 585
PV +++ + + PEH + + LP + + R + K +P
Sbjct: 437 DPVGLVEG-----MAQPDPEHSTEGFLDAWFSREKHCLPEIVTNIWHGRDEAKRQGNKP- 490
Query: 586 LSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVEN 645
LS +ALK+ N+ YG LG RFF LA+ +T +G +I+ TK+L+E
Sbjct: 491 LS-----------QALKIIMNAFYGVLGTTACRFFDPRLASSITMRGHQIMRQTKALIEA 539
Query: 646 LNYEVIYGDTDSLMISC-NVNDYDSVFKIGNQIKSECN----------KLYKQLELDIDG 694
Y+VIYGDTDS + + + KIG + N +L LEL+ +
Sbjct: 540 QGYDVIYGDTDSTFVWLKGAHSEEEAAKIGRALVQHVNAWWAETLQKQRLTSALELEYET 599
Query: 695 -------VXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFV 747
+M+ KG++ VR DW+ LA + + +
Sbjct: 600 HFCRFLMPTIRGADTGSKKRYAGLIQEGDKQRMV----FKGLETVRTDWTPLAQQFQQEL 655
Query: 748 ISQILDEQSYTDY 760
+I + Y +Y
Sbjct: 656 YLRIFRNEPYQEY 668
>pdb|1Q8I|A Chain A, Crystal Structure Of Escherichia Coli Dna Polymerase Ii
Length = 783
Score = 90.5 bits (223), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 89/373 (23%), Positives = 146/373 (39%), Gaps = 74/373 (19%)
Query: 416 IIKIMCELNVLPLAIQITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXX 475
+ +I + ++P ++ V G + R GG L H YV P+
Sbjct: 339 VTQIFHKTEIMPFLLERATVNGLPVDR--HGGSVAAFGHLYFPRMHRAGYVAPN------ 390
Query: 476 XXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTT 535
A GG V++ + G YD ++L D+ SLYPSI++ F
Sbjct: 391 ------------LGEVPPHASPGGYVMDSRPGLYDSVLVL-DYKSLYPSIVR----TFLI 433
Query: 536 IPVRMLQDSDITTLCEYLPEHQVDTGI----------LPSEIKKLVESRRQVKALMKQPN 585
PV +++ + + PEH + + LP + + R + K +P
Sbjct: 434 DPVGLVEG-----MAQPDPEHSTEGFLDAWFSREKHCLPEIVTNIWHGRDEAKRQGNKP- 487
Query: 586 LSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVEN 645
LS +ALK+ N+ YG LG RFF LA+ +T +G +I+ TK+L+E
Sbjct: 488 LS-----------QALKIIMNAFYGVLGTTACRFFDPRLASSITMRGHQIMRQTKALIEA 536
Query: 646 LNYEVIYGDTDSLMISC-NVNDYDSVFKIGNQIKSECN----------KLYKQLELDIDG 694
Y+VIYGDTDS + + + KIG + N +L LEL+ +
Sbjct: 537 QGYDVIYGDTDSTFVWLKGAHSEEEAAKIGRALVQHVNAWWAETLQKQRLTSALELEYET 596
Query: 695 -------VXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAGKFV 747
+M+ KG++ VR DW+ LA + + +
Sbjct: 597 HFCRFLMPTIRGADTGSKKRYAGLIQEGDKQRMV----FKGLETVRTDWTPLAQQFQQEL 652
Query: 748 ISQILDEQSYTDY 760
+I + Y +Y
Sbjct: 653 YLRIFRNEPYQEY 665
>pdb|1S5J|A Chain A, Insight In Dna Replication: The Crystal Structure Of Dna
Polymerase B1 From The Archaeon Sulfolobus Solfataricus
Length = 847
Score = 79.3 bits (194), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 55/179 (30%), Positives = 90/179 (50%), Gaps = 17/179 (9%)
Query: 492 KKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRM------LQDSD 545
K Y G +V++P G + I ++DF SLYPSII+ +N+ + T+ ++ ++D
Sbjct: 455 KGKGYKGAVVIDPPAGIFFN-ITVLDFASLYPSIIRTWNLSYETVDIQQCKKPYEVKDET 513
Query: 546 ---ITTLCEYLPE-HQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKAL 601
+ +C P V TG+L K+ + + K PN S + + YD+ Q+A+
Sbjct: 514 GEVLHIVCMDRPGITAVITGLLRDFRVKIYKKK------AKNPNNSEEQKLLYDVVQRAM 567
Query: 602 KLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMI 660
K+ N+ YG G +A +A VTA GR ++ +T V+YGDTDSL +
Sbjct: 568 KVFINATYGVFGAETFPLYAPRVAESVTALGRYVITSTVKKAREEGLTVLYGDTDSLFL 626
>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 = 60.8 bits (146), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 68/242 (28%), Positives = 93/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
SD+ + + D G++P+EI K V R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKWVSQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYDIR------------------------------------QKALKLTANSMYGC 611
D + D R Q ALK+T NS+YG
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQMALKVTCNSLYGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
+
Sbjct: 629 AD 630
>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 = 55.1 bits (131), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 65/242 (26%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
Y G V EP Y K++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVXSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQ--------------VKALMKQPNLS 587
SD+ + + D G++P+EI K+ R++ +K + PNLS
Sbjct: 450 PSDVYSCSPNGXXYYKDRDGVVPTEITKVFNQRKEHKGYXLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
D + D I++K KL+A NS+YG
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEXLFRAQRTEVAGXTAQINRKLLINSLYGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQXALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
+
Sbjct: 629 AD 630
>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 = 53.5 bits (127), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 66/242 (27%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
D + D I++K KL+A NS+YG
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
+
Sbjct: 629 AD 630
>pdb|3LDS|A Chain A, Crystal Structure Of Rb69 Gp43 With Dna And Datp Opposite
8-
Length = 903
Score = 53.5 bits (127), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 66/242 (27%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
D + D I++K KL+A NS+YG
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKALINSLYGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
+
Sbjct: 629 AD 630
>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 = 53.5 bits (127), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 66/242 (27%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
D + D I++K KL+A NS+YG
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
+
Sbjct: 629 AD 630
>pdb|3SQ1|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dupcpp Opposite
Da
Length = 901
Score = 53.5 bits (127), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 66/242 (27%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
D + D I++K KL+A NS+YG
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
+
Sbjct: 629 AD 630
>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 = 53.5 bits (127), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 66/242 (27%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
D + D I++K KL+A NS+YG
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
+
Sbjct: 629 AD 630
>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 = 53.5 bits (127), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 66/242 (27%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
D + D I++K KL+A NS+YG
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
+
Sbjct: 629 AD 630
>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 = 53.5 bits (127), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 66/242 (27%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 384 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 442
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 443 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 502
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
D + D I++K KL+A NS+YG
Sbjct: 503 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGA 562
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 563 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 621
Query: 662 CN 663
+
Sbjct: 622 AD 623
>pdb|1Q9Y|A Chain A, Crystal Structure Of Enterobacteria Phage Rb69 Gp43 Dna
Polymerase Complexed With 8-Oxoguanosine Containing Dna
Length = 906
Score = 53.5 bits (127), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 66/242 (27%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 394 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 452
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 453 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 512
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
D + D I++K KL+A NS+YG
Sbjct: 513 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGA 572
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 573 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 631
Query: 662 CN 663
+
Sbjct: 632 AD 633
>pdb|3CQ8|A Chain A, Ternary Complex Of The L415f Mutant Rb69 Exo(-)polymerase
Length = 903
Score = 52.0 bits (123), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 65/242 (26%), Positives = 93/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
Y G V EP Y K+++ D S YPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSFYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
D + D I++K KL+A NS+YG
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
+
Sbjct: 629 AD 630
>pdb|3SUQ|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dctp
Opposite 2ap (At Rich Sequence)
Length = 897
Score = 50.4 bits (119), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 65/242 (26%), Positives = 93/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
D + D I++K KL+A NS+ G
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLAGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
+
Sbjct: 629 AD 630
>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 = 50.1 bits (118), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 65/242 (26%), Positives = 93/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
D + D I++K KL+A NS+ G
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLAGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
+
Sbjct: 629 AD 630
>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 = 50.1 bits (118), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 65/242 (26%), Positives = 93/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
D + D I++K KL+A NS+ G
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLAGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
+
Sbjct: 629 AD 630
>pdb|3SUO|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dttp
Opposite 2ap (Gc Rich Sequence)
Length = 900
Score = 50.1 bits (118), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 65/242 (26%), Positives = 93/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
D + D I++K KL+A NS+ G
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLAGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
+
Sbjct: 629 AD 630
>pdb|3SUN|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dttp
Opposite 2ap (At Rich Sequence)
Length = 895
Score = 50.1 bits (118), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 65/242 (26%), Positives = 93/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
D + D I++K KL+A NS+ G
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLAGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
+
Sbjct: 629 AD 630
>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 = 48.5 bits (114), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 64/242 (26%), Positives = 92/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
D + D I++K KL+A N + G
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKALINGLAGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
+
Sbjct: 629 AD 630
>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 = 48.5 bits (114), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 64/242 (26%), Positives = 92/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
D + D I++K KL+A N + G
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKALINGLAGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
+
Sbjct: 629 AD 630
>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 = 48.5 bits (114), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 64/242 (26%), Positives = 92/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
D + D I++K KL+A N + G
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKALINGLAGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
+
Sbjct: 629 AD 630
>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 = 48.5 bits (114), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 64/242 (26%), Positives = 92/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
D + D I++K KL+A N + G
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINGLAGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
+
Sbjct: 629 AD 630
>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 = 48.5 bits (114), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 64/242 (26%), Positives = 92/242 (38%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
D + D I++K KL+A N + G
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKALINGLAGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
+
Sbjct: 629 AD 630
>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 = 47.0 bits (110), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 63/242 (26%), Positives = 91/242 (37%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
Y G V EP Y K+++ D S YPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSAYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
D + D I++K KL+A N + G
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKALINGLAGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
+
Sbjct: 629 AD 630
>pdb|3SPY|A Chain A, Rb69 Dna Polymerase(L415aL561AS565GY567A) TERNARY COMPLEX
WITH Dupcpp Opposite Da
Length = 901
Score = 46.6 bits (109), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 63/242 (26%), Positives = 91/242 (37%), Gaps = 76/242 (31%)
Query: 496 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 543
Y G V EP Y K+++ D S YPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSAYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 544 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 587
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 588 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 611
D + D I++K KL+A N + G
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKALINGLAGA 569
Query: 612 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 661
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 662 CN 663
+
Sbjct: 629 AD 630
>pdb|1A0R|P Chain P, Heterotrimeric Complex Of PhosducinTRANSDUCIN BETA-Gamma
Length = 245
Score = 29.6 bits (65), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 22/42 (52%)
Query: 618 RFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLM 659
RF + L L+ KG E+L N S+ E L E GD +S +
Sbjct: 180 RFSSDVLPTLLVYKGGELLSNFISVTEQLAEEFFTGDVESFL 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
0.320 0.138 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,267,729
Number of Sequences: 62578
Number of extensions: 885463
Number of successful extensions: 2060
Number of sequences better than 100.0: 46
Number of HSP's better than 100.0 without gapping: 42
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1888
Number of HSP's gapped (non-prelim): 85
length of query: 1030
length of database: 14,973,337
effective HSP length: 109
effective length of query: 921
effective length of database: 8,152,335
effective search space: 7508300535
effective search space used: 7508300535
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: 56 (26.2 bits)