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= psy1361
(1274 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 = 327 bits (839), Expect = 2e-89, Method: Compositional matrix adjust.
Identities = 193/496 (38%), Positives = 286/496 (57%), Gaps = 25/496 (5%)
Query: 550 YEVQCNQMEKIRITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQ--YXXXXX 607
Y +Q + K ++TN+ GN ++TL G R+ RNE++LLH F +++PDK+
Sbjct: 418 YRIQLLTLTK-QLTNLAGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDKEGNRSRAQK 476
Query: 608 XXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP 667
KKA Y GGLV EP+KG + ++++MDFNSLYPSIIQE+NICFTT+
Sbjct: 477 QRQNEENADAPVNSKKAKYQGGLVFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVD 536
Query: 668 VRMLQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIR 727
DI L +P +VD G+LP + LV+ RR+VK +MK +Q DIR
Sbjct: 537 ---RNKEDIDEL-PSVPPSEVDQGVLPRLLANLVDRRREVKKVMKT-ETDPHKRVQCDIR 591
Query: 728 QKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDS 787
Q+ALKLTANSMYGCLG+ NSRF+A+PLA LVT KGREIL+NT+ L E++N V+YGDTDS
Sbjct: 592 QQALKLTANSMYGCLGYVNSRFYAKPLAMLVTNKGREILMNTRQLAESMNLLVVYGDTDS 651
Query: 788 LMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXN 847
+MI ++Y KIG K N+ Y+ LE+DID V N
Sbjct: 652 VMIDTGCDNYADAIKIGLGFKRLVNERYRLLEIDIDNVFKKLLLHAKKKYAALTVNLDKN 711
Query: 848 GKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIR 907
G E+KG+D+ RR++ L+ + V++ IL +D ++ LQ ++++++ IR
Sbjct: 712 GNGTTVLEVKGLDMKRREFCPLSRDVSIHVLNTIL-----SDKDPEEALQEVYDYLEDIR 766
Query: 908 TDLDNGFVPLTLLEITKQLTKAPEEYTDRKALPHVQVALRLNNTNSKKLKQGDTISYIIC 967
++ + + +I +L+K P+ Y K +P VQVALR+ + +K G I+++I
Sbjct: 767 IKVETNNIRIDKYKINMKLSKDPKAYPGGKNMPAVQVALRMRKA-GRVVKAGSVITFVIT 825
Query: 968 E--------DGTSEAATQRAYNIEE--LKNNSKLKIDVNYYLSQQIHPVVTRLLEPIEGT 1017
+ D + + +RA+ + E +K+N+ L D YYL +QI V RLLE I+
Sbjct: 826 KQDEIDNAADTPALSVAERAHALNEVMIKSNN-LIPDPQYYLEKQIFAPVERLLERIDSF 884
Query: 1018 DAVRIAECLGLDTSLY 1033
+ VR++E LGLD+ Y
Sbjct: 885 NVVRLSEALGLDSKKY 900
Score = 95.1 bits (235), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 67/217 (30%), Positives = 112/217 (51%), Gaps = 24/217 (11%)
Query: 382 FRMFFLDAFEDIYKQPGTVYLFGKVFVKENNSHSSCCVIVQNIDRKIYLLPRSEHLKTKE 441
F+MF+LD E T+ LFGKV +K++N S+ V + + R+++ LPR + K
Sbjct: 4 FQMFWLDYCE----VNNTLILFGKVKLKDDNCVSAM-VQINGLCRELFFLPR----EGKT 54
Query: 442 PVSIAQVYSEFDQIATQYKILDFKSRKIEKKYAFNLPGVPDLSEYLEVRYSAKCP----- 496
P I + + +Y + + +++ + KY+F LP +P S+YL+V + P
Sbjct: 55 PTDIHEEIIPL--LMDKYGLDNIRAKPQKMKYSFELPDIPSESDYLKVLLPYQTPKSSRD 112
Query: 497 ALPSDLSGDTFSHVFGTKSSFLENLLLERKIKGPSWLEFPEAEKFPSR-ISWCKYEVQCN 555
+PSDLS DTF HVFG S+ E+ +++ +I GP WL+ A+ R S C EV +
Sbjct: 113 TIPSDLSSDTFYHVFGGNSNIFESFVIQNRIMGPCWLDIKGADFNSIRNASHCAVEVSVD 172
Query: 556 QMEKIRITNV-------CGNVLSRTLMGGRSERNEFL 585
+ + I T C ++ +TLM + + E +
Sbjct: 173 KPQNITPTTTKTMPNLRCLSLSIQTLMNPKENKQEIV 209
>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 = 326 bits (835), Expect = 6e-89, Method: Compositional matrix adjust.
Identities = 192/496 (38%), Positives = 286/496 (57%), Gaps = 25/496 (5%)
Query: 550 YEVQCNQMEKIRITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQ--YXXXXX 607
Y +Q + K ++TN+ GN ++TL G R+ RNE++LLH F +++PDK+
Sbjct: 418 YRIQLLTLTK-QLTNLAGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDKEGNRSRAQK 476
Query: 608 XXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP 667
KKA Y GGLV EP+KG + ++++MDFNSLYPSIIQE+NICFTT+
Sbjct: 477 QRQNEENADAPVNSKKAKYQGGLVFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVD 536
Query: 668 VRMLQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIR 727
DI L +P +VD G+LP + LV+ RR+VK +MK +Q DIR
Sbjct: 537 ---RNKEDIDEL-PSVPPSEVDQGVLPRLLANLVDRRREVKKVMKT-ETDPHKRVQCDIR 591
Query: 728 QKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDS 787
Q+ALKLTANSMYGCLG+ NSRF+A+PLA LVT KGREIL+NT+ L E++N V+YGDT+S
Sbjct: 592 QQALKLTANSMYGCLGYVNSRFYAKPLAMLVTNKGREILMNTRQLAESMNLLVVYGDTNS 651
Query: 788 LMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXN 847
+MI ++Y KIG K N+ Y+ LE+DID V N
Sbjct: 652 VMIDTGCDNYADAIKIGLGFKRLVNERYRLLEIDIDNVFKKLLLHAKKKYAALTVNLDKN 711
Query: 848 GKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIR 907
G E+KG+D+ RR++ L+ + V++ IL +D ++ LQ ++++++ IR
Sbjct: 712 GNGTTVLEVKGLDMKRREFCPLSRDVSIHVLNTIL-----SDKDPEEALQEVYDYLEDIR 766
Query: 908 TDLDNGFVPLTLLEITKQLTKAPEEYTDRKALPHVQVALRLNNTNSKKLKQGDTISYIIC 967
++ + + +I +L+K P+ Y K +P VQVALR+ + +K G I+++I
Sbjct: 767 IKVETNNIRIDKYKINMKLSKDPKAYPGGKNMPAVQVALRMRKA-GRVVKAGSVITFVIT 825
Query: 968 E--------DGTSEAATQRAYNIEE--LKNNSKLKIDVNYYLSQQIHPVVTRLLEPIEGT 1017
+ D + + +RA+ + E +K+N+ L D YYL +QI V RLLE I+
Sbjct: 826 KQDEIDNAADTPALSVAERAHALNEVMIKSNN-LIPDPQYYLEKQIFAPVERLLERIDSF 884
Query: 1018 DAVRIAECLGLDTSLY 1033
+ VR++E LGLD+ Y
Sbjct: 885 NVVRLSEALGLDSKKY 900
Score = 94.4 bits (233), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 66/217 (30%), Positives = 112/217 (51%), Gaps = 24/217 (11%)
Query: 382 FRMFFLDAFEDIYKQPGTVYLFGKVFVKENNSHSSCCVIVQNIDRKIYLLPRSEHLKTKE 441
F+MF+LD E T+ LFGKV +K++N S+ V + + R+++ LPR + K
Sbjct: 4 FQMFWLDYCE----VNNTLILFGKVKLKDDNCVSAM-VQINGLCRELFFLPR----EGKT 54
Query: 442 PVSIAQVYSEFDQIATQYKILDFKSRKIEKKYAFNLPGVPDLSEYLEVRYSAKCP----- 496
P I + + +Y + + +++ + KY+F LP +P S+YL+V + P
Sbjct: 55 PTDIHEEIIPL--LMDKYGLDNIRAKPQKMKYSFELPDIPSESDYLKVLLPYQTPKSSRD 112
Query: 497 ALPSDLSGDTFSHVFGTKSSFLENLLLERKIKGPSWLEFPEAE-KFPSRISWCKYEVQCN 555
+PSDLS DTF HVFG S+ E+ +++ +I GP WL+ A+ + S C EV +
Sbjct: 113 TIPSDLSSDTFYHVFGGNSNIFESFVIQNRIMGPCWLDIKGADFNSIAAASHCAVEVSVD 172
Query: 556 QMEKIRITNV-------CGNVLSRTLMGGRSERNEFL 585
+ + I T C ++ +TLM + + E +
Sbjct: 173 KPQNITPTTTKTMPNLRCLSLSIQTLMNPKENKQEIV 209
>pdb|4B08|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha,
Selenomethionine Protein
Length = 910
Score = 311 bits (798), Expect = 1e-84, Method: Compositional matrix adjust.
Identities = 187/495 (37%), Positives = 275/495 (55%), Gaps = 23/495 (4%)
Query: 550 YEVQCNQMEKIRITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQ--YXXXXX 607
Y +Q + K ++TN+ GN ++TL G R+ RNE++LLH F +++PDK+
Sbjct: 418 YRIQLLTLTK-QLTNLAGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDKEGNRSRAQK 476
Query: 608 XXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP 667
KKA Y GGLV EP+KG + ++++ DFNSLYPSIIQE+NICFTT+
Sbjct: 477 QRQNEENADAPVNSKKAKYQGGLVFEPEKGLHKNYVLVXDFNSLYPSIIQEFNICFTTVD 536
Query: 668 VRMLQDSDITTLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIR 727
DI L +P +VD G+LP + LV+ RR+VK + K +Q DIR
Sbjct: 537 ---RNKEDIDEL-PSVPPSEVDQGVLPRLLANLVDRRREVKKVXKT-ETDPHKRVQCDIR 591
Query: 728 QKALKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDS 787
Q+ALKLTANS YGCLG+ NSRF+A+PLA LVT KGREIL NT+ L E+ N V+YGDTDS
Sbjct: 592 QQALKLTANSXYGCLGYVNSRFYAKPLAXLVTNKGREILXNTRQLAESXNLLVVYGDTDS 651
Query: 788 LMISCNVNDYDSVFKIGNQIKSECNKLYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXN 847
+ I ++Y KIG K N+ Y+ LE+DID V N
Sbjct: 652 VXIDTGCDNYADAIKIGLGFKRLVNERYRLLEIDIDNVFKKLLLHAKKKYAALTVNLDKN 711
Query: 848 GKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIR 907
G E+KG+D RR++ L+ + V++ IL +D ++ LQ ++++++ IR
Sbjct: 712 GNGTTVLEVKGLDXKRREFCPLSRDVSIHVLNTIL-----SDKDPEEALQEVYDYLEDIR 766
Query: 908 TDLDNGFVPLTLLEITKQLTKAPEEYTDRKALPHVQVALRLNNTNSKKLKQGDTISYIIC 967
++ + + +I +L+K P+ Y K P VQVALR + +K G I+++I
Sbjct: 767 IKVETNNIRIDKYKINXKLSKDPKAYPGGKNXPAVQVALRXRKA-GRVVKAGSVITFVIT 825
Query: 968 E--------DGTSEAATQRAYNIEELK-NNSKLKIDVNYYLSQQIHPVVTRLLEPIEGTD 1018
+ D + + +RA+ + E+ ++ L D YYL +QI V RLLE I+ +
Sbjct: 826 KQDEIDNAADTPALSVAERAHALNEVXIKSNNLIPDPQYYLEKQIFAPVERLLERIDSFN 885
Query: 1019 AVRIAECLGLDTSLY 1033
VR++E LGLD+ Y
Sbjct: 886 VVRLSEALGLDSKKY 900
Score = 90.9 bits (224), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 60/185 (32%), Positives = 99/185 (53%), Gaps = 17/185 (9%)
Query: 382 FRMFFLDAFEDIYKQPGTVYLFGKVFVKENNSHSSCCVIVQNIDRKIYLLPRSEHLKTKE 441
F+ F+LD E T+ LFGKV +K++N S+ V + + R+++ LPR + K
Sbjct: 4 FQXFWLDYCE----VNNTLILFGKVKLKDDNCVSAX-VQINGLCRELFFLPR----EGKT 54
Query: 442 PVSIAQVYSEFDQIATQYKILDFKSRKIEKKYAFNLPGVPDLSEYLEVRYSAKCP----- 496
P I + + +Y + + +++ + KY+F LP +P S+YL+V + P
Sbjct: 55 PTDIHEEIIPL--LXDKYGLDNIRAKPQKXKYSFELPDIPSESDYLKVLLPYQTPKSSRD 112
Query: 497 ALPSDLSGDTFSHVFGTKSSFLENLLLERKIKGPSWLEFPEAEKFPSR-ISWCKYEVQCN 555
+PSDLS DTF HVFG S+ E+ +++ +I GP WL+ A+ R S C EV +
Sbjct: 113 TIPSDLSSDTFYHVFGGNSNIFESFVIQNRIXGPCWLDIKGADFNSIRNASHCAVEVSVD 172
Query: 556 QMEKI 560
+ + I
Sbjct: 173 KPQNI 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 = 158 bits (400), Expect = 2e-38, Method: Compositional matrix adjust.
Identities = 140/462 (30%), Positives = 221/462 (47%), Gaps = 54/462 (11%)
Query: 560 IRITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXXXXXXXXXXXXXXXX 619
I+++ + G L E+ LL +E++ V P+K
Sbjct: 331 IQLSRLIGQPLWDVSRSSTGNLVEWFLLRKAYERNEVAPNKP------------SEEEYQ 378
Query: 620 XRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDIT-- 677
R + +Y+GG V EP+KG +D I+ +DF +LYPSII +N+ T+ + ++ DI
Sbjct: 379 RRLRESYTGGFVKEPEKGLWDD-IVYLDFIALYPSIIITHNVSPDTLNLEGCKNYDIAPQ 437
Query: 678 ---TLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLT 734
C+ +P G +PS + L+E R+++K MK+ + ++ D RQKA+KL
Sbjct: 438 VGHKFCKDIP------GFIPSLLGHLLEERQKIKTKMKETQDPIEKIL-LDYRQKAIKLL 490
Query: 735 ANSMYGCLGFPNSRFFAQPLAALVTAKGRE-ILLNTKSLVENLNYEVIYGDTDSLMISCN 793
ANS YG G+ +R++ + A VTA GR+ I L K L E ++V+Y DTD L +
Sbjct: 491 ANSFYGYYGYAKARWYCKECAESVTAWGRKYIELVWKELEEKFGFKVLYIDTDGLHATIP 550
Query: 794 VNDYDSVFKIGNQIKSECN-KLYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKMIC 852
+ + + K + N KL LEL+ +G GK+I
Sbjct: 551 GGESEEIKKKALEFVKYINSKLPGLLELEYEGF----YKRGFFVTKKRYAVIDEEGKVIT 606
Query: 853 SQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDN 912
+G+++VRRDWS++A E V+ IL +++ ++ + E ++K L N
Sbjct: 607 ----RGLEIVRRDWSEIAKETQARVLETILKHG-----DVEEAVRIVKEVIQK----LAN 653
Query: 913 GFVPLTLLEITKQLTKAPEEYTDRKAL-PHVQVALRLNNTNSKKLKQGDTISYIICE-DG 970
+P L I +Q+T+ EY KA+ PHV VA +L K+K G I YI+ DG
Sbjct: 654 YEIPPEKLAIYEQITRPLHEY---KAIGPHVAVAKKL-AAKGVKIKPGMVIGYIVLRGDG 709
Query: 971 TSEAATQRAYNIEELKNNSKLKIDVNYYLSQQIHPVVTRLLE 1012
+ RA EE + K K D YY+ Q+ P V R+LE
Sbjct: 710 ---PISNRAILAEEY-DPKKHKYDAEYYIENQVLPAVLRILE 747
>pdb|2JGU|A Chain A, Crystal Structure Of Dna-directed Dna Polymerase
Length = 775
Score = 157 bits (397), Expect = 3e-38, Method: Compositional matrix adjust.
Identities = 139/462 (30%), Positives = 221/462 (47%), Gaps = 54/462 (11%)
Query: 560 IRITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXXXXXXXXXXXXXXXX 619
I+++ + G L E+ LL +E++ V P+K
Sbjct: 331 IQLSRLVGQPLWDVSRSSTGNLVEWFLLRKAYERNEVAPNKP------------SEEEYQ 378
Query: 620 XRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDIT-- 677
R + +Y+GG V EP+KG ++ I+ +D+ SLYPSII +N+ T+ + ++ DI
Sbjct: 379 RRLRESYTGGFVKEPEKGLWEN-IVYLDYKSLYPSIIITHNVSPDTLNLEGCKNYDIAPQ 437
Query: 678 ---TLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLT 734
C+ +P G +PS + L+E R+++K MK+ + ++ D RQKA+KL
Sbjct: 438 VGHKFCKDIP------GFIPSLLGHLLEERQKIKTKMKETQDPIEKIL-LDYRQKAIKLL 490
Query: 735 ANSMYGCLGFPNSRFFAQPLAALVTAKGRE-ILLNTKSLVENLNYEVIYGDTDSLMISCN 793
ANS YG G+ +R++ + A VTA GR+ I L K L E ++V+Y DTD L +
Sbjct: 491 ANSFYGYYGYAKARWYCKECAESVTAWGRKYIELVWKELEEKFGFKVLYIDTDGLYATIP 550
Query: 794 VNDYDSVFKIGNQIKSECN-KLYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKMIC 852
+ + + K + N KL LEL+ +G GK+I
Sbjct: 551 GGESEEIKKKALEFVKYINSKLPGLLELEYEGF----YKRGFFVTKKRYAVIDEEGKVIT 606
Query: 853 SQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDN 912
+G+++VRRDWS++A E V+ IL +++ ++ + E ++K L N
Sbjct: 607 ----RGLEIVRRDWSEIAKETQARVLETILKHG-----DVEEAVRIVKEVIQK----LAN 653
Query: 913 GFVPLTLLEITKQLTKAPEEYTDRKAL-PHVQVALRLNNTNSKKLKQGDTISYIICE-DG 970
+P L I +Q+T+ EY KA+ PHV VA +L K+K G I YI+ DG
Sbjct: 654 YEIPPEKLAIYEQITRPLHEY---KAIGPHVAVAKKL-AAKGVKIKPGMVIGYIVLRGDG 709
Query: 971 TSEAATQRAYNIEELKNNSKLKIDVNYYLSQQIHPVVTRLLE 1012
+ RA EE + K K D YY+ Q+ P V R+LE
Sbjct: 710 ---PISNRAILAEEY-DPKKHKYDAEYYIENQVLPAVLRILE 747
>pdb|3A2F|A Chain A, Crystal Structure Of Pyrococcus Furiosus Dna PolymerasePCNA
Monomer Mutant Complex
Length = 775
Score = 157 bits (396), Expect = 5e-38, Method: Compositional matrix adjust.
Identities = 138/462 (29%), Positives = 220/462 (47%), Gaps = 54/462 (11%)
Query: 560 IRITNVCGNVLSRTLMGGRSERNEFLLLHAFHEKSYVLPDKQYXXXXXXXXXXXXXXXXX 619
I+++ + G L E+ LL +E++ V P+K
Sbjct: 331 IQLSRLVGQPLWDVSRSSTGNLVEWFLLRKAYERNEVAPNKP------------SEEEYQ 378
Query: 620 XRKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDIT-- 677
R + +Y+GG V EP+KG ++ I+ +DF +LYPSII +N+ T+ + ++ DI
Sbjct: 379 RRLRESYTGGFVKEPEKGLWEN-IVYLDFRALYPSIIITHNVSPDTLNLEGCKNYDIAPQ 437
Query: 678 ---TLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLT 734
C+ +P G +PS + L+E R+++K K+ + ++ D RQKA+KL
Sbjct: 438 VGHKFCKDIP------GFIPSLLGHLLEERQKIKTKXKETQDPIEKIL-LDYRQKAIKLL 490
Query: 735 ANSMYGCLGFPNSRFFAQPLAALVTAKGRE-ILLNTKSLVENLNYEVIYGDTDSLMISCN 793
ANS YG G+ +R++ + A VTA GR+ I L K L E ++V+Y DTD L +
Sbjct: 491 ANSFYGYYGYAKARWYCKECAESVTAWGRKYIELVWKELEEKFGFKVLYIDTDGLYATIP 550
Query: 794 VNDYDSVFKIGNQIKSECN-KLYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKMIC 852
+ + + K + N KL LEL+ +G GK+I
Sbjct: 551 GGESEEIKKKALEFVKYINSKLPGLLELEYEGF----YKRGFFVTKKRYAVIDEEGKVIT 606
Query: 853 SQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDN 912
+G+++VRRDWS++A E V+ IL +++ ++ + E ++K L N
Sbjct: 607 ----RGLEIVRRDWSEIAKETQARVLETILKHG-----DVEEAVRIVKEVIQK----LAN 653
Query: 913 GFVPLTLLEITKQLTKAPEEYTDRKAL-PHVQVALRLNNTNSKKLKQGDTISYIICE-DG 970
+P L I +Q+T+ EY KA+ PHV VA +L K+K G I YI+ DG
Sbjct: 654 YEIPPEKLAIYEQITRPLHEY---KAIGPHVAVAKKL-AAKGVKIKPGXVIGYIVLRGDG 709
Query: 971 TSEAATQRAYNIEELKNNSKLKIDVNYYLSQQIHPVVTRLLE 1012
+ RA EE + K K D YY+ Q+ P V R+LE
Sbjct: 710 ---PISNRAILAEEY-DPKKHKYDAEYYIENQVLPAVLRILE 747
>pdb|1QHT|A Chain A, Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon
Length = 775
Score = 155 bits (391), Expect = 2e-37, Method: Compositional matrix adjust.
Identities = 123/401 (30%), Positives = 193/401 (48%), Gaps = 42/401 (10%)
Query: 621 RKKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDIT--- 677
R++ Y+GG V EP++G +D I+ +DF SLYPSII +N+ T+ ++ D+
Sbjct: 379 RRRGGYAGGYVKEPERGLWDN-IVYLDFRSLYPSIIITHNVSPDTLNREGCKEYDVAPEV 437
Query: 678 --TLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQP--NLSSDLLMQYDIRQKALKL 733
C+ P G +PS + L+E R+++K MK L LL D RQ+A+K+
Sbjct: 438 GHKFCKDFP------GFIPSLLGDLLEERQKIKRKMKATVDPLEKKLL---DYRQRAIKI 488
Query: 734 TANSMYGCLGFPNSRFFAQPLAALVTAKGRE-ILLNTKSLVENLNYEVIYGDTDSLMISC 792
ANS YG G+ +R++ + A VTA GRE I + + L E ++V+Y DTD L +
Sbjct: 489 LANSFYGYYGYAKARWYCKECAESVTAWGREYIEMVIRELEEKFGFKVLYADTDGLHATI 548
Query: 793 NVNDYDSVFKIGNQIKSECN-KLYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKMI 851
D ++V K + N KL LEL+ +G GK+
Sbjct: 549 PGADAETVKKKAKEFLKYINPKLPGLLELEYEGF----YVRGFFVTKKKYAVIDEEGKIT 604
Query: 852 CSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLD 911
+G+++VRRDWS++A E V+ IL ++ +K++ L
Sbjct: 605 T----RGLEIVRRDWSEIAKETQARVLEAILKHGD---------VEEAVRIVKEVTEKLS 651
Query: 912 NGFVPLTLLEITKQLTKAPEEYTDRKALPHVQVALRLNNTNSKKLKQGDTISYIICEDGT 971
VP L I +Q+T+ +Y + PHV VA RL K++ G ISYI+ +
Sbjct: 652 KYEVPPEKLVIHEQITRDLRDY--KATGPHVAVAKRL-AARGVKIRPGTVISYIVLKG-- 706
Query: 972 SEAATQRAYNIEELKNNSKLKIDVNYYLSQQIHPVVTRLLE 1012
S RA +E + +K + D YY+ Q+ P V R+L+
Sbjct: 707 SGRIGDRAIPADEF-DPTKHRYDAEYYIENQVLPAVERILK 746
>pdb|2VWK|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography. V93q Polymerase Variant
Length = 773
Score = 149 bits (377), Expect = 8e-36, Method: Compositional matrix adjust.
Identities = 126/438 (28%), Positives = 204/438 (46%), Gaps = 55/438 (12%)
Query: 583 EFLLLHAFHEKSYVLPDKQYXXXXXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKF 642
E+ LL +E++ + P+K R++ +Y+GG V EP++G ++
Sbjct: 354 EWFLLRKAYERNELAPNKP-------------DERELARRRESYAGGYVKEPERGLWEN- 399
Query: 643 IILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDIT-----TLCEYLPEHQVDTGILPSEI 697
I+ +DF SLYPSII +N+ T+ ++ D+ C+ P G +PS +
Sbjct: 400 IVYLDFRSLYPSIIITHNVSPDTLNREGCEEYDVAPQVGHKFCKDFP------GFIPSLL 453
Query: 698 KKLVESRRQVKALMKQP--NLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLA 755
L+E R++VK MK + LL D RQ+A+K+ ANS YG G+ +R++ + A
Sbjct: 454 GDLLEERQKVKKKMKATIDPIEKKLL---DYRQRAIKILANSFYGYYGYAKARWYCKECA 510
Query: 756 ALVTAKGREILLNT-KSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-K 813
VTA GR+ + T + + E ++V+Y DTD + D ++V K + N K
Sbjct: 511 ESVTAWGRQYIETTIREIEEKFGFKVLYADTDGFFATIPGADAETVKKKAKEFLDYINAK 570
Query: 814 LYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEA 873
L LEL+ +G +G+++VRRDWS++A E
Sbjct: 571 LPGLLELEYEGFYKRGFFVTKKKYAVIDEEDKIT--------TRGLEIVRRDWSEIAKET 622
Query: 874 GKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEEY 933
V+ IL + D R+ +K++ L VP L I +Q+T+ ++Y
Sbjct: 623 QARVLEAIL---KHGDVEEAVRI------VKEVTEKLSKYEVPPEKLVIYEQITRDLKDY 673
Query: 934 TDRKALPHVQVALRLNNTNSKKLKQGDTISYIICEDGTSEAATQRAYNIEELKNNSKLKI 993
+ PHV VA RL K++ G ISYI+ + S RA +E + +K K
Sbjct: 674 --KATGPHVAVAKRL-AARGIKIRPGTVISYIVLK--GSGRIGDRAIPFDEF-DPAKHKY 727
Query: 994 DVNYYLSQQIHPVVTRLL 1011
D YY+ Q+ P V R+L
Sbjct: 728 DAEYYIENQVLPAVERIL 745
>pdb|1TGO|A Chain A, Thermostable B Type Dna Polymerase From Thermococcus
Gorgonarius
Length = 773
Score = 149 bits (376), Expect = 9e-36, Method: Compositional matrix adjust.
Identities = 124/438 (28%), Positives = 202/438 (46%), Gaps = 55/438 (12%)
Query: 583 EFLLLHAFHEKSYVLPDKQYXXXXXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKF 642
E+ LL +E++ + P+K R++ +Y+GG V EP++G ++
Sbjct: 354 EWFLLRKAYERNELAPNKP-------------DERELARRRESYAGGYVKEPERGLWEN- 399
Query: 643 IILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDIT-----TLCEYLPEHQVDTGILPSEI 697
I+ +DF SLYPSII +N+ T+ ++ D+ C+ P G +PS +
Sbjct: 400 IVYLDFRSLYPSIIITHNVSPDTLNREGCEEYDVAPQVGHKFCKDFP------GFIPSLL 453
Query: 698 KKLVESRRQVKALMKQP--NLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLA 755
L+E R++VK MK + LL D RQ+A+K+ ANS YG G+ +R++ + A
Sbjct: 454 GDLLEERQKVKKKMKATIDPIEKKLL---DYRQRAIKILANSFYGYYGYAKARWYCKECA 510
Query: 756 ALVTAKGREILLNT-KSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-K 813
VTA GR+ + T + + E ++V+Y DTD + D ++V K + N K
Sbjct: 511 ESVTAWGRQYIETTIREIEEKFGFKVLYADTDGFFATIPGADAETVKKKAKEFLDYINAK 570
Query: 814 LYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEA 873
L LEL+ +G +G+++VRRDWS++A E
Sbjct: 571 LPGLLELEYEGFYKRGFFVTKKKYAVIDEEDKIT--------TRGLEIVRRDWSEIAKET 622
Query: 874 GKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEEY 933
V+ IL ++ +K++ L VP L I +Q+T+ ++Y
Sbjct: 623 QARVLEAILKHGD---------VEEAVRIVKEVTEKLSKYEVPPEKLVIYEQITRDLKDY 673
Query: 934 TDRKALPHVQVALRLNNTNSKKLKQGDTISYIICEDGTSEAATQRAYNIEELKNNSKLKI 993
+ PHV VA RL K++ G ISYI+ + S RA +E + +K K
Sbjct: 674 --KATGPHVAVAKRL-AARGIKIRPGTVISYIVLK--GSGRIGDRAIPFDEF-DPAKHKY 727
Query: 994 DVNYYLSQQIHPVVTRLL 1011
D YY+ Q+ P V R+L
Sbjct: 728 DAEYYIENQVLPAVERIL 745
>pdb|2XHB|A Chain A, Crystal Structure Of Dna Polymerase From Thermococcus
Gorgonarius In Complex With Hypoxanthine-Containing Dna
Length = 773
Score = 149 bits (376), Expect = 9e-36, Method: Compositional matrix adjust.
Identities = 124/438 (28%), Positives = 202/438 (46%), Gaps = 55/438 (12%)
Query: 583 EFLLLHAFHEKSYVLPDKQYXXXXXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKF 642
E+ LL +E++ + P+K R++ +Y+GG V EP++G ++
Sbjct: 354 EWFLLRKAYERNELAPNKP-------------DERELARRRESYAGGYVKEPERGLWEN- 399
Query: 643 IILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDIT-----TLCEYLPEHQVDTGILPSEI 697
I+ +DF SLYPSII +N+ T+ ++ D+ C+ P G +PS +
Sbjct: 400 IVYLDFRSLYPSIIITHNVSPDTLNREGCEEYDVAPQVGHKFCKDFP------GFIPSLL 453
Query: 698 KKLVESRRQVKALMKQP--NLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLA 755
L+E R++VK MK + LL D RQ+A+K+ ANS YG G+ +R++ + A
Sbjct: 454 GDLLEERQKVKKKMKATIDPIEKKLL---DYRQRAIKILANSFYGYYGYAKARWYCKECA 510
Query: 756 ALVTAKGREILLNT-KSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-K 813
VTA GR+ + T + + E ++V+Y DTD + D ++V K + N K
Sbjct: 511 ESVTAWGRQYIETTIREIEEKFGFKVLYADTDGFFATIPGADAETVKKKAKEFLDYINAK 570
Query: 814 LYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEA 873
L LEL+ +G +G+++VRRDWS++A E
Sbjct: 571 LPGLLELEYEGFYKRGFFVTKKKYAVIDEEDKIT--------TRGLEIVRRDWSEIAKET 622
Query: 874 GKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEEY 933
V+ IL ++ +K++ L VP L I +Q+T+ ++Y
Sbjct: 623 QARVLEAILKHGD---------VEEAVRIVKEVTEKLSKYEVPPEKLVIYEQITRDLKDY 673
Query: 934 TDRKALPHVQVALRLNNTNSKKLKQGDTISYIICEDGTSEAATQRAYNIEELKNNSKLKI 993
+ PHV VA RL K++ G ISYI+ + S RA +E + +K K
Sbjct: 674 --KATGPHVAVAKRL-AARGIKIRPGTVISYIVLK--GSGRIGDRAIPFDEF-DPAKHKY 727
Query: 994 DVNYYLSQQIHPVVTRLL 1011
D YY+ Q+ P V R+L
Sbjct: 728 DAEYYIENQVLPAVERIL 745
>pdb|2VWJ|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography
Length = 773
Score = 149 bits (376), Expect = 9e-36, Method: Compositional matrix adjust.
Identities = 124/438 (28%), Positives = 202/438 (46%), Gaps = 55/438 (12%)
Query: 583 EFLLLHAFHEKSYVLPDKQYXXXXXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKF 642
E+ LL +E++ + P+K R++ +Y+GG V EP++G ++
Sbjct: 354 EWFLLRKAYERNELAPNKP-------------DERELARRRESYAGGYVKEPERGLWEN- 399
Query: 643 IILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDIT-----TLCEYLPEHQVDTGILPSEI 697
I+ +DF SLYPSII +N+ T+ ++ D+ C+ P G +PS +
Sbjct: 400 IVYLDFRSLYPSIIITHNVSPDTLNREGCEEYDVAPQVGHKFCKDFP------GFIPSLL 453
Query: 698 KKLVESRRQVKALMKQP--NLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLA 755
L+E R++VK MK + LL D RQ+A+K+ ANS YG G+ +R++ + A
Sbjct: 454 GDLLEERQKVKKKMKATIDPIEKKLL---DYRQRAIKILANSFYGYYGYAKARWYCKECA 510
Query: 756 ALVTAKGREILLNT-KSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-K 813
VTA GR+ + T + + E ++V+Y DTD + D ++V K + N K
Sbjct: 511 ESVTAWGRQYIETTIREIEEKFGFKVLYADTDGFFATIPGADAETVKKKAKEFLDYINAK 570
Query: 814 LYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEA 873
L LEL+ +G +G+++VRRDWS++A E
Sbjct: 571 LPGLLELEYEGFYKRGFFVTKKKYAVIDEEDKIT--------TRGLEIVRRDWSEIAKET 622
Query: 874 GKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEEY 933
V+ IL ++ +K++ L VP L I +Q+T+ ++Y
Sbjct: 623 QARVLEAILKHGD---------VEEAVRIVKEVTEKLSKYEVPPEKLVIYEQITRDLKDY 673
Query: 934 TDRKALPHVQVALRLNNTNSKKLKQGDTISYIICEDGTSEAATQRAYNIEELKNNSKLKI 993
+ PHV VA RL K++ G ISYI+ + S RA +E + +K K
Sbjct: 674 --KATGPHVAVAKRL-AARGIKIRPGTVISYIVLK--GSGRIGDRAIPFDEF-DPAKHKY 727
Query: 994 DVNYYLSQQIHPVVTRLL 1011
D YY+ Q+ P V R+L
Sbjct: 728 DAEYYIENQVLPAVERIL 745
>pdb|1WN7|A Chain A, Crystal Structure Of Archaeal Family B Dna Polymerase Mutant
Length = 774
Score = 137 bits (346), Expect = 3e-32, Method: Compositional matrix adjust.
Identities = 128/438 (29%), Positives = 205/438 (46%), Gaps = 55/438 (12%)
Query: 583 EFLLLHAFHEKSYVLPDKQYXXXXXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKF 642
E+ LL +E++ + P+K R++ +Y GG V EP++G ++
Sbjct: 354 EWFLLRKAYERNELAPNKP-------------DEKELARRRQSYEGGYVKEPERGLWEN- 399
Query: 643 IILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDIT-----TLCEYLPEHQVDTGILPSEI 697
I+ +DF SLYPSII +N+ T+ ++ D+ C+ P G +PS +
Sbjct: 400 IVYLDFRSLYPSIIITHNVSPDTLNREGCKEYDVAPQVGHRFCKDFP------GFIPSLL 453
Query: 698 KKLVESRRQVKALMKQP--NLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLA 755
L+E R+++K MK + LL D RQ+A+K+ ANS YG G+ +R++ + A
Sbjct: 454 GDLLEERQKIKKKMKATIDPIERKLL---DYRQRAIKILANSYYGYYGYARARWYCKECA 510
Query: 756 ALVTAKGRE-ILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-K 813
VTA GRE I + K + E ++VIY DTD + D ++V K + N K
Sbjct: 511 ESVTAWGREYITMTIKEIEEKYGFKVIYSDTDGFFATIPGADAETVKKKAMEFLKYINAK 570
Query: 814 LYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEA 873
L LEL+ +G GK+ +G+++VRRDWS++A E
Sbjct: 571 LPGALELEYEGF----YERGFFVTKKKYAVIDEEGKITT----RGLEIVRRDWSEIAKET 622
Query: 874 GKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEEY 933
V+ +L D ++ +K++ L VP L I +Q+T+ ++Y
Sbjct: 623 QARVLEALLK---------DGDVEKAVRIVKEVTEKLSKYEVPPEKLVIHEQITRDLKDY 673
Query: 934 TDRKALPHVQVALRLNNTNSKKLKQGDTISYIICEDGTSEAATQRAYNIEELKNNSKLKI 993
+ PHV VA RL K++ G ISYI+ + S RA +E + +K K
Sbjct: 674 --KATGPHVAVAKRL-AARGVKIRPGTVISYIVLKG--SGRIGDRAIPFDEF-DPTKHKY 727
Query: 994 DVNYYLSQQIHPVVTRLL 1011
D YY+ Q+ P V R+L
Sbjct: 728 DAEYYIENQVLPAVERIL 745
>pdb|1WNS|A Chain A, Crystal Structure Of Family B Dna Polymerase From
Hyperthermophilic Archaeon Pyrococcus Kodakaraensis Kod1
Length = 774
Score = 137 bits (346), Expect = 3e-32, Method: Compositional matrix adjust.
Identities = 128/438 (29%), Positives = 205/438 (46%), Gaps = 55/438 (12%)
Query: 583 EFLLLHAFHEKSYVLPDKQYXXXXXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKF 642
E+ LL +E++ + P+K R++ +Y GG V EP++G ++
Sbjct: 354 EWFLLRKAYERNELAPNKP-------------DEKELARRRQSYEGGYVKEPERGLWEN- 399
Query: 643 IILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDIT-----TLCEYLPEHQVDTGILPSEI 697
I+ +DF SLYPSII +N+ T+ ++ D+ C+ P G +PS +
Sbjct: 400 IVYLDFRSLYPSIIITHNVSPDTLNREGCKEYDVAPQVGHRFCKDFP------GFIPSLL 453
Query: 698 KKLVESRRQVKALMKQP--NLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLA 755
L+E R+++K MK + LL D RQ+A+K+ ANS YG G+ +R++ + A
Sbjct: 454 GDLLEERQKIKKKMKATIDPIERKLL---DYRQRAIKILANSYYGYYGYARARWYCKECA 510
Query: 756 ALVTAKGRE-ILLNTKSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-K 813
VTA GRE I + K + E ++VIY DTD + D ++V K + N K
Sbjct: 511 ESVTAWGREYITMTIKEIEEKYGFKVIYSDTDGFFATIPGADAETVKKKAMEFLKYINAK 570
Query: 814 LYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEA 873
L LEL+ +G GK+ +G+++VRRDWS++A E
Sbjct: 571 LPGALELEYEGF----YKRGFFVTKKKYAVIDEEGKITT----RGLEIVRRDWSEIAKET 622
Query: 874 GKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEEY 933
V+ +L D ++ +K++ L VP L I +Q+T+ ++Y
Sbjct: 623 QARVLEALLK---------DGDVEKAVRIVKEVTEKLSKYEVPPEKLVIHEQITRDLKDY 673
Query: 934 TDRKALPHVQVALRLNNTNSKKLKQGDTISYIICEDGTSEAATQRAYNIEELKNNSKLKI 993
+ PHV VA RL K++ G ISYI+ + S RA +E + +K K
Sbjct: 674 --KATGPHVAVAKRL-AARGVKIRPGTVISYIVLKG--SGRIGDRAIPFDEF-DPTKHKY 727
Query: 994 DVNYYLSQQIHPVVTRLL 1011
D YY+ Q+ P V R+L
Sbjct: 728 DAEYYIENQVLPAVERIL 745
>pdb|4FM2|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase (Triple Mutant)
Bound To A Dsdna, In Edition Mode
Length = 793
Score = 135 bits (339), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 123/397 (30%), Positives = 197/397 (49%), Gaps = 45/397 (11%)
Query: 625 AYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITT-----L 679
+Y GG V EP+KG ++ I+ +DF SLYPSII +N+ T+ ++ D+
Sbjct: 406 SYEGGYVKEPEKGLWEG-IVSLDFRSLYPSIIITHNVSPDTLNRENCKEYDVAPQVGHRF 464
Query: 680 CEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPN--LSSDLLMQYDIRQKALKLTANS 737
C+ P G +PS + L+E R+++K MK+ + LL D RQ+A+K+ ANS
Sbjct: 465 CKDFP------GFIPSLLGNLLEERQKIKKRMKESKDPVEKKLL---DYRQRAIKILANS 515
Query: 738 MYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDY 797
YG G+ +R++ + A VTA GR+ + + +E+ ++V+Y DTD L + +
Sbjct: 516 YYGYYGYAKARWYCKECAESVTAWGRQYIDLVRRELESRGFKVLYIDTDGLYATIPGAKH 575
Query: 798 DSVFKIGNQIKSECN-KLYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEI 856
+ + + + N KL LEL+ +G GK++
Sbjct: 576 EEIKEKALKFVEYINSKLPGLLELEYEGF----YARGFFVTKKKYALIDEEGKIVT---- 627
Query: 857 KGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVP 916
+G+++VRRDWS++A E V+ IL ++D+ ++ + E +K L +P
Sbjct: 628 RGLEIVRRDWSEIAKETQAKVLEAILKHG-----NVDEAVKIVKEVTEK----LSKYEIP 678
Query: 917 LTLLEITKQLTKAPEEYTDRKAL-PHVQVALRLNNTNSKKLKQGDTISYIICE-DGTSEA 974
L I +Q+T+ EY KA+ PHV VA RL K+K G I YI+ DG
Sbjct: 679 PEKLVIYEQITRPLSEY---KAIGPHVAVAKRL-AAKGVKVKPGMVIGYIVLRGDGP--- 731
Query: 975 ATQRAYNIEELKNNSKLKIDVNYYLSQQIHPVVTRLL 1011
++RA IEE + K K D YY+ Q+ P V R+L
Sbjct: 732 ISKRAIAIEEF-DPKKHKYDAEYYIENQVLPAVERIL 767
>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 = 134 bits (338), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 123/397 (30%), Positives = 197/397 (49%), Gaps = 45/397 (11%)
Query: 625 AYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITT-----L 679
+Y GG V EP+KG ++ I+ +DF SLYPSII +N+ T+ ++ D+
Sbjct: 406 SYEGGYVKEPEKGLWEG-IVSLDFRSLYPSIIITHNVSPDTLNRENCKEYDVAPQVGHRF 464
Query: 680 CEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPN--LSSDLLMQYDIRQKALKLTANS 737
C+ P G +PS + L+E R+++K MK+ + LL D RQ+A+K+ ANS
Sbjct: 465 CKDFP------GFIPSLLGNLLEERQKIKKRMKESKDPVEKKLL---DYRQRAIKILANS 515
Query: 738 MYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISCNVNDY 797
YG G+ +R++ + A VTA GR+ + + +E+ ++V+Y DTD L + +
Sbjct: 516 YYGYYGYAKARWYCKECAESVTAWGRQYIDLVRRELESRGFKVLYIDTDGLYATIPGAKH 575
Query: 798 DSVFKIGNQIKSECN-KLYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEI 856
+ + + + N KL LEL+ +G GK++
Sbjct: 576 EEIKEKALKFVEYINSKLPGLLELEYEGF----YARGFFVTKKKYALIDEEGKIVT---- 627
Query: 857 KGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVP 916
+G+++VRRDWS++A E V+ IL ++D+ ++ + E +K L +P
Sbjct: 628 RGLEIVRRDWSEIAKETQAKVLEAILKHG-----NVDEAVKIVKEVTEK----LSKYEIP 678
Query: 917 LTLLEITKQLTKAPEEYTDRKAL-PHVQVALRLNNTNSKKLKQGDTISYIICE-DGTSEA 974
L I +Q+T+ EY KA+ PHV VA RL K+K G I YI+ DG
Sbjct: 679 PEKLVIYEQITRPLSEY---KAIGPHVAVAKRL-AAKGVKVKPGMVIGYIVLRGDG---P 731
Query: 975 ATQRAYNIEELKNNSKLKIDVNYYLSQQIHPVVTRLL 1011
++RA IEE + K K D YY+ Q+ P V R+L
Sbjct: 732 ISKRAIAIEEF-DPKKHKYDAEYYIENQVLPAVERIL 767
>pdb|3IAY|A Chain A, Ternary Complex Of Dna Polymerase Delta
Length = 919
Score = 128 bits (322), Expect = 2e-29, Method: Compositional matrix adjust.
Identities = 116/413 (28%), Positives = 196/413 (47%), Gaps = 46/413 (11%)
Query: 626 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTT---------IPVRMLQDSDI 676
Y G V+EP +G+YD I +DFNSLYPSI+ +N+C+TT + +++ +D I
Sbjct: 521 YEGATVIEPIRGYYDVPIATLDFNSLYPSIMMAHNLCYTTLCNKATVERLNLKIDEDYVI 580
Query: 677 TTLCEYLPEHQVDTGILPSEIKKLVESRRQVKALMKQPN--LSSDLLMQYDIRQKALKLT 734
T +Y + GILP + +L+ +R++ K ++ D+L + RQ ALK++
Sbjct: 581 TPNGDYFVTTKRRRGILPIILDELISARKRAKKDLRDEKDPFKRDVL---NGRQLALKIS 637
Query: 735 ANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVE---------NLNYEVIYGDT 785
ANS+YG G + +++ VTA GR ++L TK+ V+ + V+YGDT
Sbjct: 638 ANSVYGFTGATVGKLPCLAISSSVTAYGRTMILKTKTAVQEKYCIKNGYKHDAVVVYGDT 697
Query: 786 DSLMISCNVNDYDSVFKIGNQIKSECNKLYKQ-LELDIDGVXXXXXXXXXXXXXXXXXXX 844
DS+M+ D +G + + L+K + L+ +
Sbjct: 698 DSVMVKFGTTDLKEAMDLGTEAAKYVSTLFKHPINLEFE---KAYFPYLLINKKRYAGLF 754
Query: 845 XXNGKMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIHEHMK 904
N + KG+ VRRD L S V+ +IL E+ ++D L + E +
Sbjct: 755 WTNPDKFDKLDQKGLASVRRDSCSLVSIVMNKVLKKILIER-----NVDGALAFVRETIN 809
Query: 905 KIRTDLDNGFVPLTLLEITKQLTKAPEEYTDRKALPHVQVALRLNNTNSKKLKQGDTISY 964
D+ + V ++ L I+K L AP YT+ + PH +A R+ GD + Y
Sbjct: 810 ----DILHNRVDISKLIISKTL--AP-NYTNPQ--PHAVLAERMKRREGVGPNVGDRVDY 860
Query: 965 IICEDGTSEAATQRAYN-IEELKNNSKLKIDVNYYLSQQIHPVVTRLLEPIEG 1016
+I G ++ RA + + L+NN +++D YYL+ Q+ + ++ PI G
Sbjct: 861 VII--GGNDKLYNRAEDPLFVLENN--IQVDSRYYLTNQLQNPIISIVAPIIG 909
>pdb|1QQC|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase D.Tok
Length = 773
Score = 125 bits (314), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 123/438 (28%), Positives = 199/438 (45%), Gaps = 55/438 (12%)
Query: 583 EFLLLHAFHEKSYVLPDKQYXXXXXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKF 642
E+ LL +E++ V P+K R+ +Y+GG V EP+KG ++
Sbjct: 354 EWFLLRKAYERNDVAPNKP-------------DERELARRTESYAGGYVKEPEKGLWEN- 399
Query: 643 IILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITT-----LCEYLPEHQVDTGILPSEI 697
I+ +D+ SLYPSII +N+ T+ ++ D+ C+ P G +PS +
Sbjct: 400 IVYLDYKSLYPSIIITHNVSPDTLNREGCREYDVAPQVGHRFCKDFP------GFIPSLL 453
Query: 698 KKLVESRRQVKALMKQP--NLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLA 755
L+E R++VK MK + LL D RQ+A+K+ ANS YG + N+R++ + A
Sbjct: 454 GDLLEERQKVKKKMKATVDPIERKLL---DYRQRAIKILANSYYGYYAYANARWYCRECA 510
Query: 756 ALVTAKGREILLNT-KSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-K 813
VTA GR+ + T + + E ++V+Y DTD + D ++V + + N +
Sbjct: 511 ESVTAWGRQYIETTMREIEEKFGFKVLYADTDGFFATIPGADAETVKNKAKEFLNYINPR 570
Query: 814 LYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEA 873
L LEL+ +G +G+++VRRDWS++A E
Sbjct: 571 LPGLLELEYEGFYRRGFFVTKKKYAVIDEEDKIT--------TRGLEIVRRDWSEIAKET 622
Query: 874 GKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTKAPEEY 933
V+ IL ++ +K++ L VP L I +Q+T+ Y
Sbjct: 623 QARVLEAILKHGD---------VEEAVRIVKEVTEKLSRHEVPPEKLVIYEQITRDLRSY 673
Query: 934 TDRKALPHVQVALRLNNTNSKKLKQGDTISYIICEDGTSEAATQRAYNIEELKNNSKLKI 993
R PHV VA RL K++ G ISYI+ + G RA +E + +K +
Sbjct: 674 --RATGPHVAVAKRL-AARGIKIRPGTVISYIVLK-GPGRVG-DRAIPFDEF-DPAKHRY 727
Query: 994 DVNYYLSQQIHPVVTRLL 1011
D YY+ Q+ P V R+L
Sbjct: 728 DAEYYIENQVLPAVERIL 745
>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 = 110 bits (274), Expect = 6e-24, Method: Compositional matrix adjust.
Identities = 110/434 (25%), Positives = 179/434 (41%), Gaps = 79/434 (18%)
Query: 625 AYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLP 684
A GG V++ + G YD ++L D+ SLYPSII+ F PV +++ + + P
Sbjct: 401 ASPGGYVMDSRPGLYDSVLVL-DYKSLYPSIIR----TFLIDPVGLVEG-----MAQPDP 450
Query: 685 EHQVDTGI----------LPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLT 734
EH + + LP + + R + K +P LS +ALK+
Sbjct: 451 EHSTEGFLDAWFSREKHCLPEIVTNIWHGRDEAKRQGNKP-LS-----------QALKII 498
Query: 735 ANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISC-N 793
N+ YG LG RFF LA+ +T +G +I+ TK+L+E Y+VIYGDTDS +
Sbjct: 499 MNAFYGVLGTTACRFFDPRLASSITMRGHQIMRQTKALIEAQGYDVIYGDTDSTFVWLKG 558
Query: 794 VNDYDSVFKIGNQIKSECNKLYKQL--------ELDIDGVXXXXXXXXXXXXXXXXXXXX 845
+ + KIG + N + + L+++
Sbjct: 559 AHSEEEAAKIGRALVQHVNAWWAETLQKQRLTSALELEYETHFCRFLMPTIRGADTGSKK 618
Query: 846 XNGKMICSQE-----IKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRLQNIH 900
+I + KG++ VR DW+ LA + + + +I + Y +Y +
Sbjct: 619 RYAGLIQEGDKQRMVFKGLETVRTDWTPLAQQFQQELYLRIFRNEPYQEY--------VR 670
Query: 901 EHMKKIRT-DLDNGFVPLTLLEITKQLTKAPEEYTDRKALPHVQVALRLNNTNSKK---- 955
E + K+ +LD V K+L + EY R PHV+ A + N K+
Sbjct: 671 ETIDKLMAGELDARLV------YRKRLRRPLSEY-QRNVPPHVRAARLADEENQKRGRPL 723
Query: 956 -LKQGDTISYIICEDGTSEAATQRAYNIEELKNNSKLKIDVNYYLSQQIHPVVTRLLEPI 1014
+ TI Y+ +G QR+ +D +YL++Q+ PV +L I
Sbjct: 724 QYQNRGTIKYVWTTNGPEPLDYQRS------------PLDYEHYLTRQLQPVAEGILPFI 771
Query: 1015 EGTDAVRIAECLGL 1028
E A + LGL
Sbjct: 772 EDNFATLMTGQLGL 785
>pdb|1Q8I|A Chain A, Crystal Structure Of Escherichia Coli Dna Polymerase Ii
Length = 783
Score = 109 bits (273), Expect = 8e-24, Method: Compositional matrix adjust.
Identities = 113/438 (25%), Positives = 181/438 (41%), Gaps = 87/438 (19%)
Query: 625 AYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCEYLP 684
A GG V++ + G YD ++L D+ SLYPSI++ F PV +++ + + P
Sbjct: 398 ASPGGYVMDSRPGLYDSVLVL-DYKSLYPSIVR----TFLIDPVGLVEG-----MAQPDP 447
Query: 685 EHQVDTGI----------LPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKALKLT 734
EH + + LP + + R + K +P LS +ALK+
Sbjct: 448 EHSTEGFLDAWFSREKHCLPEIVTNIWHGRDEAKRQGNKP-LS-----------QALKII 495
Query: 735 ANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMISC-N 793
N+ YG LG RFF LA+ +T +G +I+ TK+L+E Y+VIYGDTDS +
Sbjct: 496 MNAFYGVLGTTACRFFDPRLASSITMRGHQIMRQTKALIEAQGYDVIYGDTDSTFVWLKG 555
Query: 794 VNDYDSVFKIGNQIKSECN----------KLYKQLELDIDG----VXXXXXXXXXXXXXX 839
+ + KIG + N +L LEL+ +
Sbjct: 556 AHSEEEAAKIGRALVQHVNAWWAETLQKQRLTSALELEYETHFCRFLMPTIRGADTGSKK 615
Query: 840 XXXXXXXNG---KMICSQEIKGVDVVRRDWSQLASEAGKFVISQILDEQSYTDYSLDDRL 896
G +M+ KG++ VR DW+ LA + + + +I + Y +Y
Sbjct: 616 RYAGLIQEGDKQRMV----FKGLETVRTDWTPLAQQFQQELYLRIFRNEPYQEY------ 665
Query: 897 QNIHEHMKKIRT-DLDNGFVPLTLLEITKQLTKAPEEYTDRKALPHVQVALRLNNTNSKK 955
+ E + K+ +LD V K+L + EY R PHV+ A + N K+
Sbjct: 666 --VRETIDKLMAGELDARLV------YRKRLRRPLSEY-QRNVPPHVRAARLADEENQKR 716
Query: 956 -----LKQGDTISYIICEDGTSEAATQRAYNIEELKNNSKLKIDVNYYLSQQIHPVVTRL 1010
+ TI Y+ +G QR+ +D +YL++Q+ PV +
Sbjct: 717 GRPLQYQNRGTIKYVWTTNGPEPLDYQRS------------PLDYEHYLTRQLQPVAEGI 764
Query: 1011 LEPIEGTDAVRIAECLGL 1028
L IE A + LGL
Sbjct: 765 LPFIEDNFATLMTGQLGL 782
>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 = 108 bits (269), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 115/441 (26%), Positives = 195/441 (44%), Gaps = 84/441 (19%)
Query: 583 EFLLLHAFHEKSYVLPDKQYXXXXXXXXXXXXXXXXXXRKKAAYSGGLVLEPKKGFYDKF 642
E+ LL +E++ V P+K R+ +Y+GG V EP+KG ++
Sbjct: 354 EWFLLRKAYERNDVAPNKP-------------DERELARRTESYAGGYVKEPEKGLWEN- 399
Query: 643 IILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITT-----LCEYLPEHQVDTGILPSEI 697
I+ +D+ SLYPSII +N+ T+ ++ D+ C+ P G +PS +
Sbjct: 400 IVYLDYKSLYPSIIITHNVSPDTLNREGCREYDVAPQVGHRFCKDFP------GFIPSLL 453
Query: 698 KKLVESRRQVKALMKQP--NLSSDLLMQYDIRQKALKLTANSMYGCLGFPNSRFFAQPLA 755
L+E R++VK MK + LL D RQ+A+K+ ANS YG + N+R++ + A
Sbjct: 454 GDLLEERQKVKKKMKATVDPIERKLL---DYRQRAIKILANSYYGYYAYANARWYCRECA 510
Query: 756 ALVTAKGREILLNT-KSLVENLNYEVIYGDTDSLMISCNVNDYDSVFKIGNQIKSECN-K 813
VTA GR+ + T + + E ++V+Y DTD + D ++V + + N +
Sbjct: 511 ESVTAWGRQYIETTMREIEEKFGFKVLYADTDGFFATIPGADAETVKNKAKEFLNYINPR 570
Query: 814 LYKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEA 873
L LEL+ +G +G+++VRRDWS++A E
Sbjct: 571 LPGLLELEYEGFYRRGFFVTKKKYAVIDEEDKIT--------TRGLEIVRRDWSEIAKET 622
Query: 874 GKFVISQILDEQSYTDYSLDDRLQNIHEHMKKIRTDLDNGFVPLTLLEITKQLTK---AP 930
V+ IL + ++ E ++ ++ E+T++L++ P
Sbjct: 623 QARVLEAIL------------KHGDVEEAVRIVK-------------EVTEKLSRHEVPP 657
Query: 931 EEYTDRKALPHVQVALRLNNTNSKKLKQGDTISYIICEDGTSEAATQRAYNIEELKNNSK 990
E+ +A PHV A ISYI+ + G RA +E + +K
Sbjct: 658 EKLVIYEAGPHVAAA-------------ATVISYIVLK-GPGRVG-DRAIPFDEF-DPAK 701
Query: 991 LKIDVNYYLSQQIHPVVTRLL 1011
+ D YY+ Q+ P V R+L
Sbjct: 702 HRYDAEYYIENQVLPAVERIL 722
>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 = 99.4 bits (246), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 96/414 (23%), Positives = 170/414 (41%), Gaps = 98/414 (23%)
Query: 622 KKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRMLQDSDITTLCE 681
+ Y G VL+P GF+ +++ DF SLYPSIIQ +N+CF+T+ +R + + +
Sbjct: 650 RHVGYQGAKVLDPTSGFHVNPVVVFDFASLYPSIIQAHNLCFSTLSLRADAVAHLEAGKD 709
Query: 682 YLP-----------EHQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKA 730
YL + V +L ++ + R+Q+++ + Q + +L+ D +Q A
Sbjct: 710 YLEIEVGGRRLFFVKAHVRESLLSILLRDWLAMRKQIRSRIPQSSPEEAVLL--DKQQAA 767
Query: 731 LKLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVEN--------------- 775
+K+ NS+YG G + +AA VT GRE+LL T+ V
Sbjct: 768 IKVVCNSVYGFTGVQHGLLPCLHVAATVTTIGREMLLATREYVHARWAAFEQLLADFPEA 827
Query: 776 --------LNYEVIYGDTDSLMISCNVNDYDSVFKIGNQ-------------IKSECNKL 814
+ +IYGDTDS+ + C + +G++ IK EC K
Sbjct: 828 ADMRAPGPYSMRIIYGDTDSIFVLCRGLTAAGLTAMGDKMASHISRALFLPPIKLECEKT 887
Query: 815 YKQLELDIDGVXXXXXXXXXXXXXXXXXXXXXNGKMICSQEIKGVDVVRRDWSQLASEAG 874
+ +L L GKM+ IKGVD+VR++ +
Sbjct: 888 FTKLLL---------------IAKKKYIGVIYGGKML----IKGVDLVRKNNCAFINRTS 928
Query: 875 KFVISQILDEQS---------------YTDYSLDDRLQ-------NIHEHMKKIRTDLDN 912
+ ++ + + + + L + LQ + H + D+ +
Sbjct: 929 RALVDLLFYDDTVSGAAAALAERPAEEWLARPLPEGLQAFGAVLVDAHRRITDPERDIQD 988
Query: 913 GFVPLTLLEITKQLTKAPEEYTDRKALPHVQVALRLNNTNSKKLKQGDTISYII 966
FV +T +L++ P YT+++ L H+ V +L ++ D I Y+I
Sbjct: 989 -FV------LTAELSRHPRAYTNKR-LAHLTVYYKLMARRAQVPSIKDRIPYVI 1034
>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: 622 KKAAYSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIPVRM------LQDSD 675
K Y G +V++P G + I ++DF SLYPSII+ +N+ + T+ ++ ++D
Sbjct: 455 KGKGYKGAVVIDPPAGIFFN-ITVLDFASLYPSIIRTWNLSYETVDIQQCKKPYEVKDET 513
Query: 676 ---ITTLCEYLPE-HQVDTGILPSEIKKLVESRRQVKALMKQPNLSSDLLMQYDIRQKAL 731
+ +C P V TG+L K+ + + K PN S + + YD+ Q+A+
Sbjct: 514 GEVLHIVCMDRPGITAVITGLLRDFRVKIYKKK------AKNPNNSEEQKLLYDVVQRAM 567
Query: 732 KLTANSMYGCLGFPNSRFFAQPLAALVTAKGREILLNTKSLVENLNYEVIYGDTDSLMI 790
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 = 60.1 bits (144), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 68/242 (28%), Positives = 93/242 (38%), Gaps = 76/242 (31%)
Query: 626 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 673
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 674 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 717
SD+ + + D G++P+EI K V R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKWVSQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 718 SDLLMQYDIR------------------------------------QKALKLTANSMYGC 741
D + D R Q ALK+T NS+YG
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQMALKVTCNSLYGA 569
Query: 742 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 791
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 792 CN 793
+
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 = 54.3 bits (129), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 65/242 (26%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 626 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 673
Y G V EP Y K++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVXSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 674 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQ--------------VKALMKQPNLS 717
SD+ + + D G++P+EI K+ R++ +K + PNLS
Sbjct: 450 PSDVYSCSPNGXXYYKDRDGVVPTEITKVFNQRKEHKGYXLAAQRNGEIIKEALHNPNLS 509
Query: 718 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 741
D + D I++K KL+A NS+YG
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEXLFRAQRTEVAGXTAQINRKLLINSLYGA 569
Query: 742 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 791
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQXALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 792 CN 793
+
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 = 53.1 bits (126), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 66/242 (27%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 626 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 673
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 674 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 717
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 718 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 741
D + D I++K KL+A NS+YG
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGA 569
Query: 742 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 791
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 792 CN 793
+
Sbjct: 629 AD 630
>pdb|3LDS|A Chain A, Crystal Structure Of Rb69 Gp43 With Dna And Datp Opposite
8-
Length = 903
Score = 53.1 bits (126), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 66/242 (27%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 626 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 673
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 674 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 717
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 718 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 741
D + D I++K KL+A NS+YG
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKALINSLYGA 569
Query: 742 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 791
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 792 CN 793
+
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 = 52.8 bits (125), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 66/242 (27%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 626 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 673
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 674 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 717
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 718 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 741
D + D I++K KL+A NS+YG
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGA 569
Query: 742 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 791
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 792 CN 793
+
Sbjct: 629 AD 630
>pdb|3SQ1|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dupcpp Opposite
Da
Length = 901
Score = 52.8 bits (125), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 66/242 (27%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 626 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 673
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 674 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 717
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 718 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 741
D + D I++K KL+A NS+YG
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGA 569
Query: 742 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 791
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 792 CN 793
+
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 = 52.8 bits (125), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 66/242 (27%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 626 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 673
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 384 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 442
Query: 674 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 717
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 443 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 502
Query: 718 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 741
D + D I++K KL+A NS+YG
Sbjct: 503 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGA 562
Query: 742 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 791
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 563 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 621
Query: 792 CN 793
+
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 = 52.8 bits (125), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 66/242 (27%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 626 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 673
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 394 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 452
Query: 674 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 717
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 453 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 512
Query: 718 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 741
D + D I++K KL+A NS+YG
Sbjct: 513 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGA 572
Query: 742 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 791
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 573 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 631
Query: 792 CN 793
+
Sbjct: 632 AD 633
>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 = 52.8 bits (125), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 66/242 (27%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 626 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 673
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 674 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 717
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 718 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 741
D + D I++K KL+A NS+YG
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGA 569
Query: 742 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 791
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 792 CN 793
+
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 = 52.8 bits (125), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 66/242 (27%), Positives = 94/242 (38%), Gaps = 76/242 (31%)
Query: 626 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 673
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 674 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 717
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 718 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 741
D + D I++K KL+A NS+YG
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGA 569
Query: 742 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 791
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 792 CN 793
+
Sbjct: 629 AD 630
>pdb|3CQ8|A Chain A, Ternary Complex Of The L415f Mutant Rb69 Exo(-)polymerase
Length = 903
Score = 51.6 bits (122), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 65/242 (26%), Positives = 93/242 (38%), Gaps = 76/242 (31%)
Query: 626 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 673
Y G V EP Y K+++ D S YPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSFYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 674 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 717
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 718 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 741
D + D I++K KL+A NS+YG
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGA 569
Query: 742 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 791
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 792 CN 793
+
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 = 49.7 bits (117), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 65/242 (26%), Positives = 93/242 (38%), Gaps = 76/242 (31%)
Query: 626 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 673
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 674 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 717
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 718 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 741
D + D I++K KL+A NS+ G
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLAGA 569
Query: 742 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 791
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 792 CN 793
+
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 = 49.7 bits (117), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 65/242 (26%), Positives = 93/242 (38%), Gaps = 76/242 (31%)
Query: 626 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 673
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 674 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 717
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 718 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 741
D + D I++K KL+A NS+ G
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLAGA 569
Query: 742 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 791
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 792 CN 793
+
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 = 49.7 bits (117), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 65/242 (26%), Positives = 93/242 (38%), Gaps = 76/242 (31%)
Query: 626 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 673
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 674 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 717
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 718 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 741
D + D I++K KL+A NS+ G
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLAGA 569
Query: 742 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 791
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 792 CN 793
+
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 = 49.7 bits (117), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 65/242 (26%), Positives = 93/242 (38%), Gaps = 76/242 (31%)
Query: 626 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 673
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 674 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 717
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 718 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 741
D + D I++K KL+A NS+ G
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLAGA 569
Query: 742 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 791
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 792 CN 793
+
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 = 49.7 bits (117), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 65/242 (26%), Positives = 93/242 (38%), Gaps = 76/242 (31%)
Query: 626 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 673
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 674 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 717
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 718 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 741
D + D I++K KL+A NS+ G
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLAGA 569
Query: 742 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 791
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 792 CN 793
+
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 = 48.1 bits (113), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 64/242 (26%), Positives = 92/242 (38%), Gaps = 76/242 (31%)
Query: 626 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 673
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 674 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 717
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 718 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 741
D + D I++K KL+A N + G
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKALINGLAGA 569
Query: 742 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 791
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 792 CN 793
+
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 = 48.1 bits (113), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 64/242 (26%), Positives = 92/242 (38%), Gaps = 76/242 (31%)
Query: 626 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 673
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 674 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 717
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 718 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 741
D + D I++K KL+A N + G
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKALINGLAGA 569
Query: 742 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 791
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 792 CN 793
+
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 = 48.1 bits (113), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 64/242 (26%), Positives = 92/242 (38%), Gaps = 76/242 (31%)
Query: 626 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 673
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 674 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 717
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 718 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 741
D + D I++K KL+A N + G
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKALINGLAGA 569
Query: 742 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 791
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 792 CN 793
+
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 = 48.1 bits (113), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 64/242 (26%), Positives = 92/242 (38%), Gaps = 76/242 (31%)
Query: 626 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 673
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 674 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 717
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 718 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 741
D + D I++K KL+A N + G
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKALINGLAGA 569
Query: 742 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 791
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 792 CN 793
+
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 = 48.1 bits (113), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 64/242 (26%), Positives = 92/242 (38%), Gaps = 76/242 (31%)
Query: 626 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 673
Y G V EP Y K+++ D SLYPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 674 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 717
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 718 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 741
D + D I++K KL+A N + G
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINGLAGA 569
Query: 742 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 791
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 792 CN 793
+
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 = 46.2 bits (108), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 63/242 (26%), Positives = 91/242 (37%), Gaps = 76/242 (31%)
Query: 626 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 673
Y G V EP Y K+++ D S YPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSAYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 674 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 717
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 718 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 741
D + D I++K KL+A N + G
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKALINGLAGA 569
Query: 742 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 791
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 792 CN 793
+
Sbjct: 629 AD 630
>pdb|3SPY|A Chain A, Rb69 Dna Polymerase(L415aL561AS565GY567A) TERNARY COMPLEX
WITH Dupcpp Opposite Da
Length = 901
Score = 46.2 bits (108), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 63/242 (26%), Positives = 91/242 (37%), Gaps = 76/242 (31%)
Query: 626 YSGGLVLEPKKGFYDKFIILMDFNSLYPSIIQEYNICFTTIP----VRMLQD-------- 673
Y G V EP Y K+++ D S YPSII++ NI TI V L D
Sbjct: 391 YPGAFVKEPIPNRY-KYVMSFDLTSAYPSIIRQVNISPETIAGTFKVAPLHDYINAVAER 449
Query: 674 -SDITTLCEYLPEHQVDT-GILPSEIKKLVESRRQVKALM--------------KQPNLS 717
SD+ + + D G++P+EI K+ R++ K M PNLS
Sbjct: 450 PSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS 509
Query: 718 SDLLMQYD--------IRQKALKLTA----------------------------NSMYGC 741
D + D I++K KL+A N + G
Sbjct: 510 VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKALINGLAGA 569
Query: 742 LGFPNSRFFAQPLAALVTAKGREIL----------LNTKSLVENLNYEVIYGDTDSLMIS 791
LG R++ A +T G+ L LN E + V+YGDTDS+ +S
Sbjct: 570 LGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAF-VLYGDTDSIYVS 628
Query: 792 CN 793
+
Sbjct: 629 AD 630
>pdb|3FLO|B Chain B, Crystal Structure Of The Carboxyl-Terminal Domain Of Yeast
Dna Polymerase Alpha In Complex With Its B Subunit
pdb|3FLO|D Chain D, Crystal Structure Of The Carboxyl-Terminal Domain Of Yeast
Dna Polymerase Alpha In Complex With Its B Subunit
pdb|3FLO|F Chain F, Crystal Structure Of The Carboxyl-Terminal Domain Of Yeast
Dna Polymerase Alpha In Complex With Its B Subunit
pdb|3FLO|H Chain H, Crystal Structure Of The Carboxyl-Terminal Domain Of Yeast
Dna Polymerase Alpha In Complex With Its B Subunit
Length = 206
Score = 46.2 bits (108), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 30/92 (32%), Positives = 47/92 (51%), Gaps = 8/92 (8%)
Query: 1102 ECKVPPYTYLP-HLINKLSQDMNKYIVKYYEGWLKCEDPGCSDLTRRCPLGLKTRL---C 1157
+CK + P L +++ + +I YY GWL+C+D C +TR+ + K L C
Sbjct: 51 QCKHCEQLFTPLQLTSQIEHSIRAHISLYYAGWLQCDDSTCGIVTRQVSVFGKRCLNDGC 110
Query: 1158 TTCHKYKLHRVYTELQLYQQLSFFHYICDITK 1189
T +YK Y++ QLY QL +F + D K
Sbjct: 111 TGVMRYK----YSDKQLYNQLLYFDSLFDCEK 138
>pdb|1N5G|A Chain A, Nmr Structures Of The Zinc Finger Domain Of Human Dna
Polymerase-Alpha
Length = 38
Score = 32.3 bits (72), Expect = 1.8, Method: Composition-based stats.
Identities = 15/36 (41%), Positives = 17/36 (47%), Gaps = 2/36 (5%)
Query: 1133 WLKCEDPGCSDLTRRCPLGLKTR--LCTTCHKYKLH 1166
WL CE+P C + TR PL LC C K L
Sbjct: 1 WLICEEPTCRNRTRHLPLQFSRTGPLCPACMKATLQ 36
>pdb|3E6J|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor (Vlr)
Rbc36 In Complex With H-Trisaccharide
Length = 229
Score = 31.2 bits (69), Expect = 3.7, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 1201 FDSETYMGYCKMKQHVERFLESSAYN-IVDLKKLFSCEEKQPKLSRGVER-EHVT 1253
FDS T + + + L S+ ++ +V LK+LF C K +L RG+ER H+T
Sbjct: 84 FDSLTQLTVLDLGTNQLTVLPSAVFDRLVHLKELFMCCNKLTELPRGIERLTHLT 138
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.316 0.133 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 33,670,640
Number of Sequences: 62578
Number of extensions: 1306063
Number of successful extensions: 3306
Number of sequences better than 100.0: 48
Number of HSP's better than 100.0 without gapping: 23
Number of HSP's successfully gapped in prelim test: 25
Number of HSP's that attempted gapping in prelim test: 3133
Number of HSP's gapped (non-prelim): 88
length of query: 1274
length of database: 14,973,337
effective HSP length: 110
effective length of query: 1164
effective length of database: 8,089,757
effective search space: 9416477148
effective search space used: 9416477148
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (26.6 bits)