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= psy5921
(1200 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IAY|A Chain A, Ternary Complex Of Dna Polymerase Delta
Length = 919
Score = 231 bits (588), Expect = 2e-60, Method: Compositional matrix adjust.
Identities = 198/710 (27%), Positives = 326/710 (45%), Gaps = 92/710 (12%)
Query: 384 LTVLAVEIHAISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRT- 442
L +++ +I R + P+P YD V I ++ I + P +R
Sbjct: 249 LRIMSFDIECAGRIGVFPEPEYDPVIQI--------------ANVVSIAGAKK-PFIRNV 293
Query: 443 ------KPIQMHFV---SNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLG 493
PI + + E+E+ S + + + DPD++IGY YLL R L
Sbjct: 294 FTLNTCSPITGSMIFSHATEEEMLSNWRNFIIKVDPDVIIGYNTTNFDIPYLLNRAKALK 353
Query: 494 LN----------LNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQS 543
+N + QE+ K +R E KN + GR+ ++L + ++ E L+S
Sbjct: 354 VNDFPYFGRLKTVKQEIKESVFSSKAYGTR-ETKNVNID--GRLQLDLLQFIQREYKLRS 410
Query: 544 YTFENIMYHVLHERIPLHSWKLLTCWW----EHRTHLYKWMTVEHYLIRVTGIIRLIEQL 599
YT + H L E+ + +++ E R L + + YL +RL+E+L
Sbjct: 411 YTLNAVSAHFLGEQKEDVHYSIISDLQNGDSETRRRLAVYCLKDAYLP-----LRLMEKL 465
Query: 600 DFIGRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPES 659
+ +EMAR+ G+ F +L+RG Q +V S + R + V P+++ +A E
Sbjct: 466 MALVNYTEMARVTGVPFSYLLARGQQIKVVSQLFR--KCLEIDTVIPNMQSQASDDQYEG 523
Query: 660 LPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGR--VEHLGVSDSFPFGCID 717
+I EP Y PI LDF SLYPS+++A+N C++T + VE L +
Sbjct: 524 ATVI-EPIRGYYDVPIATLDFNSLYPSIMMAHNLCYTTLCNKATVERLNL---------- 572
Query: 718 LNVSIRSLKKLQQKLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAA 777
K+ + I+P+G FV R GILP +L E++ R K+ +++ K +
Sbjct: 573 ---------KIDEDYVITPNGDYFVTTKRRRGILPIILDELISARKRAKKDLRDEK-DPF 622
Query: 778 LQRVLHARQLGLKLIANVTYGYTAANFSGRMPCVEVGDSVVSKGRETLQKAIETVN---- 833
+ VL+ RQL LK+ AN YG+T A G++PC+ + SV + GR + K V
Sbjct: 623 KRDVLNGRQLALKISANSVYGFTGATV-GKLPCLAISSSVTAYGRTMILKTKTAVQEKYC 681
Query: 834 --NTSKWQCRVVYGDTDSMFVLAPGKTKQEAFEIGKEIAXXXXXXXXXXXKLKFEKVYQP 891
N K VVYGDTDS+ V +EA ++G E A L+FEK Y P
Sbjct: 682 IKNGYKHDAVVVYGDTDSVMVKFGTTDLKEAMDLGTEAAKYVSTLFKHPINLEFEKAYFP 741
Query: 892 CILQTKKRYVGYMYETADQ-DKPIYEAKGIETVRRDGCPAVSKILKKSLCLLFETKDLSV 950
+L KKRY G + D+ DK + KG+ +VRRD C VS ++ K L + +++
Sbjct: 742 YLLINKKRYAGLFWTNPDKFDK--LDQKGLASVRRDSCSLVSIVMNKVLKKILIERNVDG 799
Query: 951 VKEYVEKQFSKIISGRISVQDMTFAKEYR-GQAGYKPGACVPALSLARQWVLTDPRAEPR 1009
+V + + I+ R+ + + +K +P A + R+ V P
Sbjct: 800 ALAFVRETINDILHNRVDISKLIISKTLAPNYTNPQPHAVLAERMKRREGV------GPN 853
Query: 1010 VSERVPYVIVSGAPGLPLIKLVKSPYELLQDSSLRLNSEYYITRVIIPPL 1059
V +RV YVI+ G L + P +L++ +++++S YY+T + P+
Sbjct: 854 VGDRVDYVIIGGND--KLYNRAEDPLFVLEN-NIQVDSRYYLTNQLQNPI 900
>pdb|2VWK|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography. V93q Polymerase Variant
Length = 773
Score = 147 bits (372), Expect = 3e-35, Method: Compositional matrix adjust.
Identities = 146/624 (23%), Positives = 275/624 (44%), Gaps = 64/624 (10%)
Query: 450 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKR 509
VS EKE+ F++ V++ DPD+LI Y + ++ YL +R LG+ + R
Sbjct: 184 VSTEKEMIKRFLKVVKEKDPDVLITYNGDNFAFAYLKKRSEKLGVKF---------ILGR 234
Query: 510 NSSRDEVKNT----QLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKL 565
S +++ +++ GRI +L+ ++R +NL +YT E + + + +
Sbjct: 235 EGSEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTINLPTYTLEAVYEAIFGQPKEKVYAEE 294
Query: 566 LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQ 625
+ WE L + V Y + + + + +F ++++RL G ++V +
Sbjct: 295 IAQAWETGEGLER---VARYSMEDAKVTYELGK-EFFPMEAQLSRLVGQSLWDVSRSSTG 350
Query: 626 FRVESIMLRLSRLNNFVAVS-PSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQSLY 684
VE +LR + N +A + P ++ A R + + EPE L+ + I+ LDF+SLY
Sbjct: 351 NLVEWFLLRKAYERNELAPNKPDERELARRRESYAGGYVKEPERGLWEN-IVYLDFRSLY 409
Query: 685 PSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQKLTISPSGVAFVDK 744
PS+II +N T L R GC + +V+ + K +
Sbjct: 410 PSIIITHNVSPDT-LNRE-----------GCEEYDVAPQVGHKFCKDFP----------- 446
Query: 745 SIRCGILPKMLQEILDTRLMVKQSMKEYKSNAALQRVLHARQLGLKLIANVTYGYTAANF 804
G +P +L ++L+ R VK+ MK + +++L RQ +K++AN YGY
Sbjct: 447 ----GFIPSLLGDLLEERQKVKKKMKA-TIDPIEKKLLDYRQRAIKILANSFYGYYGYA- 500
Query: 805 SGRMPCVEVGDSVVSKGRETLQKAIETVNNTSKWQCRVVYGDTDSMFVLAPGKTKQEAFE 864
R C E +SV + GR+ ++ I + K+ +V+Y DTD F PG + +
Sbjct: 501 KARWYCKECAESVTAWGRQYIETTIREIEE--KFGFKVLYADTDGFFATIPGADAETVKK 558
Query: 865 IGKEIAXXXXXXXXXXXKLKFEKVYQPCILQTKKRYVGYMYETADQDKPIYEAKGIETVR 924
KE +L++E Y+ TKK+Y D++ I +G+E VR
Sbjct: 559 KAKEFLDYINAKLPGLLELEYEGFYKRGFFVTKKKYA-----VIDEEDKI-TTRGLEIVR 612
Query: 925 RDGCPAVSKILKKSLCLLFETKDLSVVKEYVEKQFSKIISGRISVQDMTFAKEY-RGQAG 983
RD + + L + + D+ V++ K+ + + + ++ R
Sbjct: 613 RDWSEIAKETQARVLEAILKHGDVEEAVRIVKEVTEKLSKYEVPPEKLVIYEQITRDLKD 672
Query: 984 YKPGACVPALSLARQWVLTDPRAEPRVSERVPYVIVSGAPGLPLIKLVKSPYELLQDSSL 1043
YK A P +++A++ + P + Y+++ G+ + + P++ +
Sbjct: 673 YK--ATGPHVAVAKRLAARGIKIRPGTV--ISYIVLKGSGRIGDRAI---PFDEFDPAKH 725
Query: 1044 RLNSEYYITRVIIPPLERCFLLLG 1067
+ ++EYYI ++P +ER G
Sbjct: 726 KYDAEYYIENQVLPAVERILRAFG 749
>pdb|2XHB|A Chain A, Crystal Structure Of Dna Polymerase From Thermococcus
Gorgonarius In Complex With Hypoxanthine-Containing Dna
Length = 773
Score = 147 bits (371), Expect = 3e-35, Method: Compositional matrix adjust.
Identities = 146/624 (23%), Positives = 275/624 (44%), Gaps = 64/624 (10%)
Query: 450 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKR 509
VS EKE+ F++ V++ DPD+LI Y + ++ YL +R LG+ + R
Sbjct: 184 VSTEKEMIKRFLKVVKEKDPDVLITYNGDNFAFAYLKKRSEKLGVKF---------ILGR 234
Query: 510 NSSRDEVKNT----QLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKL 565
S +++ +++ GRI +L+ ++R +NL +YT E + + + +
Sbjct: 235 EGSEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTINLPTYTLEAVYEAIFGQPKEKVYAEE 294
Query: 566 LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQ 625
+ WE L + V Y + + + + +F ++++RL G ++V +
Sbjct: 295 IAQAWETGEGLER---VARYSMEDAKVTYELGK-EFFPMEAQLSRLVGQSLWDVSRSSTG 350
Query: 626 FRVESIMLRLSRLNNFVAVS-PSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQSLY 684
VE +LR + N +A + P ++ A R + + EPE L+ + I+ LDF+SLY
Sbjct: 351 NLVEWFLLRKAYERNELAPNKPDERELARRRESYAGGYVKEPERGLWEN-IVYLDFRSLY 409
Query: 685 PSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQKLTISPSGVAFVDK 744
PS+II +N T L R GC + +V+ + K +
Sbjct: 410 PSIIITHNVSPDT-LNRE-----------GCEEYDVAPQVGHKFCKDFP----------- 446
Query: 745 SIRCGILPKMLQEILDTRLMVKQSMKEYKSNAALQRVLHARQLGLKLIANVTYGYTAANF 804
G +P +L ++L+ R VK+ MK + +++L RQ +K++AN YGY
Sbjct: 447 ----GFIPSLLGDLLEERQKVKKKMKA-TIDPIEKKLLDYRQRAIKILANSFYGYYGYA- 500
Query: 805 SGRMPCVEVGDSVVSKGRETLQKAIETVNNTSKWQCRVVYGDTDSMFVLAPGKTKQEAFE 864
R C E +SV + GR+ ++ I + K+ +V+Y DTD F PG + +
Sbjct: 501 KARWYCKECAESVTAWGRQYIETTIREIEE--KFGFKVLYADTDGFFATIPGADAETVKK 558
Query: 865 IGKEIAXXXXXXXXXXXKLKFEKVYQPCILQTKKRYVGYMYETADQDKPIYEAKGIETVR 924
KE +L++E Y+ TKK+Y D++ I +G+E VR
Sbjct: 559 KAKEFLDYINAKLPGLLELEYEGFYKRGFFVTKKKYA-----VIDEEDKI-TTRGLEIVR 612
Query: 925 RDGCPAVSKILKKSLCLLFETKDLSVVKEYVEKQFSKIISGRISVQDMTFAKEY-RGQAG 983
RD + + L + + D+ V++ K+ + + + ++ R
Sbjct: 613 RDWSEIAKETQARVLEAILKHGDVEEAVRIVKEVTEKLSKYEVPPEKLVIYEQITRDLKD 672
Query: 984 YKPGACVPALSLARQWVLTDPRAEPRVSERVPYVIVSGAPGLPLIKLVKSPYELLQDSSL 1043
YK A P +++A++ + P + Y+++ G+ + + P++ +
Sbjct: 673 YK--ATGPHVAVAKRLAARGIKIRPGTV--ISYIVLKGSGRIGDRAI---PFDEFDPAKH 725
Query: 1044 RLNSEYYITRVIIPPLERCFLLLG 1067
+ ++EYYI ++P +ER G
Sbjct: 726 KYDAEYYIENQVLPAVERILRAFG 749
>pdb|2VWJ|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography
Length = 773
Score = 147 bits (370), Expect = 4e-35, Method: Compositional matrix adjust.
Identities = 146/624 (23%), Positives = 275/624 (44%), Gaps = 64/624 (10%)
Query: 450 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKR 509
VS EKE+ F++ V++ DPD+LI Y + ++ YL +R LG+ + R
Sbjct: 184 VSTEKEMIKRFLKVVKEKDPDVLITYNGDNFAFAYLKKRSEKLGVKF---------ILGR 234
Query: 510 NSSRDEVKNT----QLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKL 565
S +++ +++ GRI +L+ ++R +NL +YT E + + + +
Sbjct: 235 EGSEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTINLPTYTLEAVYEAIFGQPKEKVYAEE 294
Query: 566 LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQ 625
+ WE L + V Y + + + + +F ++++RL G ++V +
Sbjct: 295 IAQAWETGEGLER---VARYSMEDAKVTYELGK-EFFPMEAQLSRLVGQSLWDVSRSSTG 350
Query: 626 FRVESIMLRLSRLNNFVAVS-PSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQSLY 684
VE +LR + N +A + P ++ A R + + EPE L+ + I+ LDF+SLY
Sbjct: 351 NLVEWFLLRKAYERNELAPNKPDERELARRRESYAGGYVKEPERGLWEN-IVYLDFRSLY 409
Query: 685 PSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQKLTISPSGVAFVDK 744
PS+II +N T L R GC + +V+ + K +
Sbjct: 410 PSIIITHNVSPDT-LNRE-----------GCEEYDVAPQVGHKFCKDFP----------- 446
Query: 745 SIRCGILPKMLQEILDTRLMVKQSMKEYKSNAALQRVLHARQLGLKLIANVTYGYTAANF 804
G +P +L ++L+ R VK+ MK + +++L RQ +K++AN YGY
Sbjct: 447 ----GFIPSLLGDLLEERQKVKKKMKA-TIDPIEKKLLDYRQRAIKILANSFYGYYGYA- 500
Query: 805 SGRMPCVEVGDSVVSKGRETLQKAIETVNNTSKWQCRVVYGDTDSMFVLAPGKTKQEAFE 864
R C E +SV + GR+ ++ I + K+ +V+Y DTD F PG + +
Sbjct: 501 KARWYCKECAESVTAWGRQYIETTIREIEE--KFGFKVLYADTDGFFATIPGADAETVKK 558
Query: 865 IGKEIAXXXXXXXXXXXKLKFEKVYQPCILQTKKRYVGYMYETADQDKPIYEAKGIETVR 924
KE +L++E Y+ TKK+Y D++ I +G+E VR
Sbjct: 559 KAKEFLDYINAKLPGLLELEYEGFYKRGFFVTKKKYA-----VIDEEDKI-TTRGLEIVR 612
Query: 925 RDGCPAVSKILKKSLCLLFETKDLSVVKEYVEKQFSKIISGRISVQDMTFAKEY-RGQAG 983
RD + + L + + D+ V++ K+ + + + ++ R
Sbjct: 613 RDWSEIAKETQARVLEAILKHGDVEEAVRIVKEVTEKLSKYEVPPEKLVIYEQITRDLKD 672
Query: 984 YKPGACVPALSLARQWVLTDPRAEPRVSERVPYVIVSGAPGLPLIKLVKSPYELLQDSSL 1043
YK A P +++A++ + P + Y+++ G+ + + P++ +
Sbjct: 673 YK--ATGPHVAVAKRLAARGIKIRPGTV--ISYIVLKGSGRIGDRAI---PFDEFDPAKH 725
Query: 1044 RLNSEYYITRVIIPPLERCFLLLG 1067
+ ++EYYI ++P +ER G
Sbjct: 726 KYDAEYYIENQVLPAVERILRAFG 749
>pdb|1TGO|A Chain A, Thermostable B Type Dna Polymerase From Thermococcus
Gorgonarius
Length = 773
Score = 147 bits (370), Expect = 4e-35, Method: Compositional matrix adjust.
Identities = 146/624 (23%), Positives = 274/624 (43%), Gaps = 64/624 (10%)
Query: 450 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKR 509
VS EKE+ F++ V++ DPD+LI Y + + YL +R LG+ + R
Sbjct: 184 VSTEKEMIKRFLKVVKEKDPDVLITYNGDNFDFAYLKKRSEKLGVKF---------ILGR 234
Query: 510 NSSRDEVKNT----QLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKL 565
S +++ +++ GRI +L+ ++R +NL +YT E + + + +
Sbjct: 235 EGSEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTINLPTYTLEAVYEAIFGQPKEKVYAEE 294
Query: 566 LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQ 625
+ WE L + V Y + + + + +F ++++RL G ++V +
Sbjct: 295 IAQAWETGEGLER---VARYSMEDAKVTYELGK-EFFPMEAQLSRLVGQSLWDVSRSSTG 350
Query: 626 FRVESIMLRLSRLNNFVAVS-PSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQSLY 684
VE +LR + N +A + P ++ A R + + EPE L+ + I+ LDF+SLY
Sbjct: 351 NLVEWFLLRKAYERNELAPNKPDERELARRRESYAGGYVKEPERGLWEN-IVYLDFRSLY 409
Query: 685 PSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQKLTISPSGVAFVDK 744
PS+II +N T L R GC + +V+ + K +
Sbjct: 410 PSIIITHNVSPDT-LNRE-----------GCEEYDVAPQVGHKFCKDFP----------- 446
Query: 745 SIRCGILPKMLQEILDTRLMVKQSMKEYKSNAALQRVLHARQLGLKLIANVTYGYTAANF 804
G +P +L ++L+ R VK+ MK + +++L RQ +K++AN YGY
Sbjct: 447 ----GFIPSLLGDLLEERQKVKKKMKA-TIDPIEKKLLDYRQRAIKILANSFYGYYGYA- 500
Query: 805 SGRMPCVEVGDSVVSKGRETLQKAIETVNNTSKWQCRVVYGDTDSMFVLAPGKTKQEAFE 864
R C E +SV + GR+ ++ I + K+ +V+Y DTD F PG + +
Sbjct: 501 KARWYCKECAESVTAWGRQYIETTIREIEE--KFGFKVLYADTDGFFATIPGADAETVKK 558
Query: 865 IGKEIAXXXXXXXXXXXKLKFEKVYQPCILQTKKRYVGYMYETADQDKPIYEAKGIETVR 924
KE +L++E Y+ TKK+Y D++ I +G+E VR
Sbjct: 559 KAKEFLDYINAKLPGLLELEYEGFYKRGFFVTKKKYA-----VIDEEDKI-TTRGLEIVR 612
Query: 925 RDGCPAVSKILKKSLCLLFETKDLSVVKEYVEKQFSKIISGRISVQDMTFAKEY-RGQAG 983
RD + + L + + D+ V++ K+ + + + ++ R
Sbjct: 613 RDWSEIAKETQARVLEAILKHGDVEEAVRIVKEVTEKLSKYEVPPEKLVIYEQITRDLKD 672
Query: 984 YKPGACVPALSLARQWVLTDPRAEPRVSERVPYVIVSGAPGLPLIKLVKSPYELLQDSSL 1043
YK A P +++A++ + P + Y+++ G+ + + P++ +
Sbjct: 673 YK--ATGPHVAVAKRLAARGIKIRPGTV--ISYIVLKGSGRIGDRAI---PFDEFDPAKH 725
Query: 1044 RLNSEYYITRVIIPPLERCFLLLG 1067
+ ++EYYI ++P +ER G
Sbjct: 726 KYDAEYYIENQVLPAVERILRAFG 749
>pdb|1QHT|A Chain A, Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon
Length = 775
Score = 145 bits (365), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 154/623 (24%), Positives = 266/623 (42%), Gaps = 62/623 (9%)
Query: 450 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKR 509
VS EKE+ F+ VR+ DPD+LI Y + + YL +R LG+ L R K
Sbjct: 184 VSTEKEMIKRFLRVVREKDPDVLITYNGDNFDFAYLKKRCEELGIKFT--LGRDGSEPKI 241
Query: 510 NSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCW 569
D +++ GRI +L+ ++R +NL +YT E + V + + +
Sbjct: 242 QRMGDRF---AVEVKGRIHFDLYPVIRRTINLPTYTLEAVYEAVFGKPKEKVYAEEIAQA 298
Query: 570 WEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQFRVE 629
WE L + V Y + + + + +F ++++RL G ++V + VE
Sbjct: 299 WESGEGLER---VARYSMEDAKVTYELGR-EFFPMEAQLSRLIGQSLWDVSRSSTGNLVE 354
Query: 630 SIMLRLS-RLNNFVAVSPSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQSLYPSVI 688
+LR + + N P ++ A R + + EPE L+ D I+ LDF+SLYPS+I
Sbjct: 355 WFLLRKAYKRNELAPNKPDERELARRRGGYAGGYVKEPERGLW-DNIVYLDFRSLYPSII 413
Query: 689 IAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQKLTISPSGVAFVDKSIRC 748
I +N T L R GC + +V+ K +
Sbjct: 414 ITHNVSPDT-LNRE-----------GCKEYDVAPEVGHKFCKDFP--------------- 446
Query: 749 GILPKMLQEILDTRLMVKQSMKEYKSNAALQRVLHARQLGLKLIANVTYGYTAANFSGRM 808
G +P +L ++L+ R +K+ MK + +++L RQ +K++AN YGY R
Sbjct: 447 GFIPSLLGDLLEERQKIKRKMKA-TVDPLEKKLLDYRQRAIKILANSFYGYYGYA-KARW 504
Query: 809 PCVEVGDSVVSKGRETLQKAIETVNNTSKWQCRVVYGDTDSMFVLAPGKTKQEAFEIGKE 868
C E +SV + GRE ++ I + K+ +V+Y DTD + PG + + KE
Sbjct: 505 YCKECAESVTAWGREYIEMVIRELEE--KFGFKVLYADTDGLHATIPGADAETVKKKAKE 562
Query: 869 IAXXXXXXXXXXXKLKFEKVYQPCILQTKKRYVGYMYETADQDKPIYEAKGIETVRRDGC 928
+L++E Y TKK+Y D++ I +G+E VRRD
Sbjct: 563 FLKYINPKLPGLLELEYEGFYVRGFFVTKKKYA-----VIDEEGKI-TTRGLEIVRRDWS 616
Query: 929 PAVSKILKKSLCLLFETKDLS----VVKEYVEKQFSKIISGRISVQDMTFAKEYRGQAGY 984
+ + L + + D+ +VKE EK + V ++ R Y
Sbjct: 617 EIAKETQARVLEAILKHGDVEEAVRIVKEVTEKLSKYEVPPEKLVIHEQITRDLR---DY 673
Query: 985 KPGACVPALSLARQWVLTDPRAEPRVSERVPYVIVSGAPGLPLIKLVKSPYELLQDSSLR 1044
K A P +++A++ + P + Y+++ G+ + + P + + R
Sbjct: 674 K--ATGPHVAVAKRLAARGVKIRPGTV--ISYIVLKGSGRIGDRAI---PADEFDPTKHR 726
Query: 1045 LNSEYYITRVIIPPLERCFLLLG 1067
++EYYI ++P +ER G
Sbjct: 727 YDAEYYIENQVLPAVERILKAFG 749
>pdb|1WNS|A Chain A, Crystal Structure Of Family B Dna Polymerase From
Hyperthermophilic Archaeon Pyrococcus Kodakaraensis Kod1
Length = 774
Score = 140 bits (354), Expect = 3e-33, Method: Compositional matrix adjust.
Identities = 148/620 (23%), Positives = 272/620 (43%), Gaps = 56/620 (9%)
Query: 450 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKR 509
VS E+E+ F+ V++ DPD+LI Y + + YL +R LG+N L R K
Sbjct: 184 VSTEREMIKRFLRVVKEKDPDVLITYNGDNFDFAYLKKRCEKLGINFA--LGRDGSEPKI 241
Query: 510 NSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCW 569
D +++ GRI +L+ ++R +NL +YT E + V + + +T
Sbjct: 242 QRMGDRF---AVEVKGRIHFDLYPVIRRTINLPTYTLEAVYEAVFGQPKEKVYAEEITTA 298
Query: 570 WEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQFRVE 629
WE +L + V Y + + + + +F+ ++++RL G ++V + VE
Sbjct: 299 WETGENLER---VARYSMEDAKVTYELGK-EFLPMEAQLSRLIGQSLWDVSRSSTGNLVE 354
Query: 630 SIMLRLSRLNNFVAVS-PSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQSLYPSVI 688
+LR + N +A + P K+ A R + EPE L+ + I+ LDF+SLYPS+I
Sbjct: 355 WFLLRKAYERNELAPNKPDEKELARRRQSYEGGYVKEPERGLWEN-IVYLDFRSLYPSII 413
Query: 689 IAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQKLTISPSGVAFVDKSIRC 748
I +N T L R GC + +V+ + + +
Sbjct: 414 ITHNVSPDT-LNRE-----------GCKEYDVAPQVGHRFCKDFP--------------- 446
Query: 749 GILPKMLQEILDTRLMVKQSMKEYKSNAALQRVLHARQLGLKLIANVTYGYTAANFSGRM 808
G +P +L ++L+ R +K+ MK + +++L RQ +K++AN +Y R
Sbjct: 447 GFIPSLLGDLLEERQKIKKKMKA-TIDPIERKLLDYRQRAIKILAN-SYYGYYGYARARW 504
Query: 809 PCVEVGDSVVSKGRETLQKAIETVNNTSKWQCRVVYGDTDSMFVLAPGKTKQEAFEIGKE 868
C E +SV + GRE + I+ + K+ +V+Y DTD F PG + + E
Sbjct: 505 YCKECAESVTAWGREYITMTIKEIEE--KYGFKVIYSDTDGFFATIPGADAETVKKKAME 562
Query: 869 IAXXXXXXXXXXXKLKFEKVYQPCILQTKKRYVGYMYETADQDKPIYEAKGIETVRRDGC 928
+L++E Y+ TKK+Y D++ I +G+E VRRD
Sbjct: 563 FLKYINAKLPGALELEYEGFYKRGFFVTKKKYA-----VIDEEGKI-TTRGLEIVRRDWS 616
Query: 929 PAVSKILKKSLCLLFETKDLSVVKEYVEKQFSKIISGRISVQDMTFAKEY-RGQAGYKPG 987
+ + L L + D+ V++ K+ + + + ++ R YK
Sbjct: 617 EIAKETQARVLEALLKDGDVEKAVRIVKEVTEKLSKYEVPPEKLVIHEQITRDLKDYK-- 674
Query: 988 ACVPALSLARQWVLTDPRAEPRVSERVPYVIVSGAPGLPLIKLVKSPYELLQDSSLRLNS 1047
A P +++A++ + P + Y+++ G+ + + P++ + + ++
Sbjct: 675 ATGPHVAVAKRLAARGVKIRPGTV--ISYIVLKGSGRIGDRAI---PFDEFDPTKHKYDA 729
Query: 1048 EYYITRVIIPPLERCFLLLG 1067
EYYI ++P +ER G
Sbjct: 730 EYYIENQVLPAVERILRAFG 749
>pdb|1WN7|A Chain A, Crystal Structure Of Archaeal Family B Dna Polymerase Mutant
Length = 774
Score = 140 bits (354), Expect = 3e-33, Method: Compositional matrix adjust.
Identities = 148/620 (23%), Positives = 272/620 (43%), Gaps = 56/620 (9%)
Query: 450 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKR 509
VS E+E+ F+ V++ DPD+LI Y + + YL +R LG+N L R K
Sbjct: 184 VSTEREMIKRFLRVVKEKDPDVLITYNGDNFDFAYLKKRCEKLGINFA--LGRDGSEPKI 241
Query: 510 NSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCW 569
D +++ GRI +L+ ++R +NL +YT E + V + + +T
Sbjct: 242 QRMGDRF---AVEVKGRIHFDLYPVIRRTINLPTYTLEAVYEAVFGQPKEKVYAEEITTA 298
Query: 570 WEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQFRVE 629
WE +L + V Y + + + + +F+ ++++RL G ++V + VE
Sbjct: 299 WETGENLER---VARYSMEDAKVTYELGK-EFLPMEAQLSRLIGQSLWDVSRSSTGNLVE 354
Query: 630 SIMLRLSRLNNFVAVS-PSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQSLYPSVI 688
+LR + N +A + P K+ A R + EPE L+ + I+ LDF+SLYPS+I
Sbjct: 355 WFLLRKAYERNELAPNKPDEKELARRRQSYEGGYVKEPERGLWEN-IVYLDFRSLYPSII 413
Query: 689 IAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQKLTISPSGVAFVDKSIRC 748
I +N T L R GC + +V+ + + +
Sbjct: 414 ITHNVSPDT-LNRE-----------GCKEYDVAPQVGHRFCKDFP--------------- 446
Query: 749 GILPKMLQEILDTRLMVKQSMKEYKSNAALQRVLHARQLGLKLIANVTYGYTAANFSGRM 808
G +P +L ++L+ R +K+ MK + +++L RQ +K++AN +Y R
Sbjct: 447 GFIPSLLGDLLEERQKIKKKMKA-TIDPIERKLLDYRQRAIKILAN-SYYGYYGYARARW 504
Query: 809 PCVEVGDSVVSKGRETLQKAIETVNNTSKWQCRVVYGDTDSMFVLAPGKTKQEAFEIGKE 868
C E +SV + GRE + I+ + K+ +V+Y DTD F PG + + E
Sbjct: 505 YCKECAESVTAWGREYITMTIKEIEE--KYGFKVIYSDTDGFFATIPGADAETVKKKAME 562
Query: 869 IAXXXXXXXXXXXKLKFEKVYQPCILQTKKRYVGYMYETADQDKPIYEAKGIETVRRDGC 928
+L++E Y+ TKK+Y D++ I +G+E VRRD
Sbjct: 563 FLKYINAKLPGALELEYEGFYERGFFVTKKKYA-----VIDEEGKI-TTRGLEIVRRDWS 616
Query: 929 PAVSKILKKSLCLLFETKDLSVVKEYVEKQFSKIISGRISVQDMTFAKEY-RGQAGYKPG 987
+ + L L + D+ V++ K+ + + + ++ R YK
Sbjct: 617 EIAKETQARVLEALLKDGDVEKAVRIVKEVTEKLSKYEVPPEKLVIHEQITRDLKDYK-- 674
Query: 988 ACVPALSLARQWVLTDPRAEPRVSERVPYVIVSGAPGLPLIKLVKSPYELLQDSSLRLNS 1047
A P +++A++ + P + Y+++ G+ + + P++ + + ++
Sbjct: 675 ATGPHVAVAKRLAARGVKIRPGTV--ISYIVLKGSGRIGDRAI---PFDEFDPTKHKYDA 729
Query: 1048 EYYITRVIIPPLERCFLLLG 1067
EYYI ++P +ER G
Sbjct: 730 EYYIENQVLPAVERILRAFG 749
>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 = 137 bits (345), Expect = 4e-32, Method: Compositional matrix adjust.
Identities = 139/607 (22%), Positives = 255/607 (42%), Gaps = 134/607 (22%)
Query: 434 ESELPEVRTK----PIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLER- 488
ES L E+ + P+ + F S E E+ F+ V+Q+ P+ + GY I W +LL +
Sbjct: 379 ESHLNELAARGLPTPVVLEFDS-EFEMLLAFMTLVKQYGPEFVTGYNIINFDWPFLLAKL 437
Query: 489 ---------GYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEV 539
GY G + + R+ ++ + + K +++++ G + I+++ ++ ++
Sbjct: 438 TDIYKVPLDGY--GRMNGRGVFRVWDIGQSHFQ----KRSKIKVNGMVNIDMYGIITDKI 491
Query: 540 NLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGII-----R 594
L SY + VL ++ S++ + ++ T + + Y I+ + ++ +
Sbjct: 492 KLSSYKLNAVAEAVLKDKKKDLSYRDIPAYYA--TGPAQRGVIGEYCIQDSLLVGQLFFK 549
Query: 595 LIEQLDFIGRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQR--- 651
+ L+ S +ARL GI + G Q RV + +LRL+ F + P + R
Sbjct: 550 FLPHLEL----SAVARLAGINITRTIYDGQQIRVFTCLLRLADQKGF--ILPDTQGRFRG 603
Query: 652 AHMRAPESLPL--------------------------------------------ILEPE 667
A AP+ +L+P
Sbjct: 604 AGGEAPKRPAAAREDEERPEEEGEDEDEREEGGGEREPEGARETAGRHVGYQGAKVLDPT 663
Query: 668 SRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKK 727
S + +P++V DF SLYPS+I A+N CFST R + ++ L+
Sbjct: 664 SGFHVNPVVVFDFASLYPSIIQAHNLCFSTLSLRAD-----------------AVAHLEA 706
Query: 728 LQQKLTISPSG--VAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAALQRVLHAR 785
+ L I G + FV +R +L +L++ L R ++ + + A+ +L +
Sbjct: 707 GKDYLEIEVGGRRLFFVKAHVRESLLSILLRDWLAMRKQIRSRIPQSSPEEAV--LLDKQ 764
Query: 786 QLGLKLIANVTYGYTAANFSGRMPCVEVGDSVVSKGRETLQKAIETVNNTSKWQC----- 840
Q +K++ N YG+T G +PC+ V +V + GRE L E V+ ++W
Sbjct: 765 QAAIKVVCNSVYGFTGVQ-HGLLPCLHVAATVTTIGREMLLATREYVH--ARWAAFEQLL 821
Query: 841 -----------------RVVYGDTDSMFVLAPGKTKQEAFEIGKEIAXXXXXXXXX-XXK 882
R++YGDTDS+FVL G T +G ++A K
Sbjct: 822 ADFPEAADMRAPGPYSMRIIYGDTDSIFVLCRGLTAAGLTAMGDKMASHISRALFLPPIK 881
Query: 883 LKFEKVYQPCILQTKKRYVGYMYETADQDKPIYEAKGIETVRRDGCPAVSKILKKSLCLL 942
L+ EK + +L KK+Y+G +Y KG++ VR++ C +++ + + LL
Sbjct: 882 LECEKTFTKLLLIAKKKYIGVIYGGK------MLIKGVDLVRKNNCAFINRTSRALVDLL 935
Query: 943 FETKDLS 949
F +S
Sbjct: 936 FYDDTVS 942
>pdb|2JGU|A Chain A, Crystal Structure Of Dna-directed Dna Polymerase
Length = 775
Score = 134 bits (336), Expect = 4e-31, Method: Compositional matrix adjust.
Identities = 155/656 (23%), Positives = 289/656 (44%), Gaps = 64/656 (9%)
Query: 421 EEDRKVGIILI--GQESELPEVRTKPIQMHFV---SNEKELFSIFIENVRQWDPDILIGY 475
EE K II+I E+E + K I + +V S EKE+ F+ +R+ DPDI++ Y
Sbjct: 150 EEFGKGPIIMISYADENEARVITWKNIDLPYVESVSTEKEMIKRFLRIIREKDPDIIVTY 209
Query: 476 EIETLSWGYLLERGYVLGLNLNQELSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLL 535
++ + YL +R LG+ L + R K D T +++ GRI +L+ ++
Sbjct: 210 NGDSFDFPYLAKRAEKLGIKLT--IGRDGSEPKMQRIGD---MTAVEVKGRIHFDLYHVI 264
Query: 536 RHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRL 595
R +NL +YT E + + + + WE +L + V Y +
Sbjct: 265 RTTINLPTYTLEAVYEAIFGKPKEKVYADEIAKAWESGENLER---VAKYSMEDAKATYE 321
Query: 596 IEQLDFIGRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMR 655
+ + +F+ +++RL G ++V + VE +LR + N VA + ++ R
Sbjct: 322 LGK-EFLPMEIQLSRLVGQPLWDVSRSSTGNLVEWFLLRKAYERNEVAPNKPSEEEYQRR 380
Query: 656 APESLP--LILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPF 713
ES + EPE L+ + I+ LD++SLYPS+II +N T +E
Sbjct: 381 LRESYTGGFVKEPEKGLWEN-IVYLDYKSLYPSIIITHNVSPDTL--NLE---------- 427
Query: 714 GCIDLNVSIRSLKKLQQKLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYK 773
GC + +++ + K + + G +P +L +L+ R +K MKE
Sbjct: 428 GCKNYDIAPQVGHKFCKDIP---------------GFIPSLLGHLLEERQKIKTKMKE-- 470
Query: 774 SNAALQRV-LHARQLGLKLIANVTYGYTAANFSGRMPCVEVGDSVVSKGRETLQKAIETV 832
+ ++++ L RQ +KL+AN YGY R C E +SV + GR+ ++ + +
Sbjct: 471 TQDPIEKILLDYRQKAIKLLANSFYGYYGYA-KARWYCKECAESVTAWGRKYIELVWKEL 529
Query: 833 NNTSKWQCRVVYGDTDSMFVLAPGKTKQEAFEIGKEIAXXXXXXXXXXXKLKFEKVYQPC 892
K+ +V+Y DTD ++ PG +E + E +L++E Y+
Sbjct: 530 E--EKFGFKVLYIDTDGLYATIPGGESEEIKKKALEFVKYINSKLPGLLELEYEGFYKRG 587
Query: 893 ILQTKKRYVGYMYETADQDKPIYEAKGIETVRRDGCPAVSKILKKSLCLLFETKDLSVVK 952
TKKRY D++ + +G+E VRRD + + L + + D+
Sbjct: 588 FFVTKKRYA-----VIDEEGKVI-TRGLEIVRRDWSEIAKETQARVLETILKHGDVEEAV 641
Query: 953 EYVEKQFSKIISGRISVQDMTFAKEY-RGQAGYKPGACVPALSLARQWVLTDPRAEPRVS 1011
V++ K+ + I + + ++ R YK A P +++A++ + +P +
Sbjct: 642 RIVKEVIQKLANYEIPPEKLAIYEQITRPLHEYK--AIGPHVAVAKKLAAKGVKIKPGMV 699
Query: 1012 ERVPYVIVSGAPGLPLIKLVKSPYELLQDSSLRLNSEYYITRVIIPPLERCFLLLG 1067
+ Y+++ G + ++ Y+ + ++EYYI ++P + R G
Sbjct: 700 --IGYIVLRGDGPISNRAILAEEYD---PKKHKYDAEYYIENQVLPAVLRILEGFG 750
>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 = 131 bits (329), Expect = 3e-30, Method: Compositional matrix adjust.
Identities = 160/687 (23%), Positives = 301/687 (43%), Gaps = 67/687 (9%)
Query: 392 HAISRALLKPDPAYDEVKAIFYYLYTC--PPEEDRKVGIILI--GQESELPEVRTKPIQM 447
+ I + L+ P +E+K + + + T EE K II+I E+E + K I +
Sbjct: 120 YLIDKGLI-PMEGEEELKILAFAIATLYHEGEEFGKGPIIMISYADENEAKVITWKNIDL 178
Query: 448 HFV---SNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRIT 504
+V S+E+E+ F+ +R+ DPDI++ Y ++ + YL +R LG+ L + R
Sbjct: 179 PYVEVVSSEREMIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKRAEKLGIKLT--IGRDG 236
Query: 505 EVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWK 564
K D T +++ GRI +L+ ++ +NL +YT E + + +
Sbjct: 237 SEPKMQRIGD---MTAVEVKGRIHFDLYHVITRTINLPTYTLEAVYEAIFGKPKEKVYAD 293
Query: 565 LLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGS 624
+ WE +L + V Y + + + +F+ +++RL G ++V +
Sbjct: 294 EIAKAWESGENLER---VAKYSMEDAKATYELGK-EFLPMEIQLSRLIGQPLWDVSRSST 349
Query: 625 QFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLP--LILEPESRLYTDPIIVLDFQS 682
VE +LR + N VA + ++ R ES + EPE L+ D I+ LDF +
Sbjct: 350 GNLVEWFLLRKAYERNEVAPNKPSEEEYQRRLRESYTGGFVKEPEKGLWDD-IVYLDFIA 408
Query: 683 LYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQKLTISPSGVAFV 742
LYPS+II +N T +E GC + +++ + K + +
Sbjct: 409 LYPSIIITHNVSPDTL--NLE----------GCKNYDIAPQVGHKFCKDIP--------- 447
Query: 743 DKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAALQRV-LHARQLGLKLIANVTYGYTA 801
G +P +L +L+ R +K MKE + ++++ L RQ +KL+AN YGY
Sbjct: 448 ------GFIPSLLGHLLEERQKIKTKMKE--TQDPIEKILLDYRQKAIKLLANSFYGYYG 499
Query: 802 ANFSGRMPCVEVGDSVVSKGRETLQKAIETVNNTSKWQCRVVYGDTDSMFVLAPGKTKQE 861
R C E +SV + GR+ ++ + + K+ +V+Y DTD + PG +E
Sbjct: 500 YA-KARWYCKECAESVTAWGRKYIELVWKELE--EKFGFKVLYIDTDGLHATIPGGESEE 556
Query: 862 AFEIGKEIAXXXXXXXXXXXKLKFEKVYQPCILQTKKRYVGYMYETADQDKPIYEAKGIE 921
+ E +L++E Y+ TKKRY D++ + +G+E
Sbjct: 557 IKKKALEFVKYINSKLPGLLELEYEGFYKRGFFVTKKRYA-----VIDEEGKVI-TRGLE 610
Query: 922 TVRRDGCPAVSKILKKSLCLLFETKDLSVVKEYVEKQFSKIISGRISVQDMTFAKEY-RG 980
VRRD + + L + + D+ V++ K+ + I + + ++ R
Sbjct: 611 IVRRDWSEIAKETQARVLETILKHGDVEEAVRIVKEVIQKLANYEIPPEKLAIYEQITRP 670
Query: 981 QAGYKPGACVPALSLARQWVLTDPRAEPRVSERVPYVIVSGAPGLPLIKLVKSPYELLQD 1040
YK A P +++A++ + +P + + Y+++ G + ++ Y+
Sbjct: 671 LHEYK--AIGPHVAVAKKLAAKGVKIKPGMV--IGYIVLRGDGPISNRAILAEEYD---P 723
Query: 1041 SSLRLNSEYYITRVIIPPLERCFLLLG 1067
+ ++EYYI ++P + R G
Sbjct: 724 KKHKYDAEYYIENQVLPAVLRILEGFG 750
>pdb|1QQC|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase D.Tok
Length = 773
Score = 130 bits (326), Expect = 6e-30, Method: Compositional matrix adjust.
Identities = 146/624 (23%), Positives = 276/624 (44%), Gaps = 64/624 (10%)
Query: 450 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKR 509
VS EKE+ F++ +++ DPD+LI Y + + YL +R +LG+ + R
Sbjct: 184 VSTEKEMIKRFLKVIQEKDPDVLITYNGDNFDFAYLKKRSEMLGVKF---------ILGR 234
Query: 510 NSSRDEVKNT----QLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKL 565
+ S +++ +++ GRI +L+ ++R +NL +YT E + V + +
Sbjct: 235 DGSEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTINLPTYTLETVYEPVFGQPKEKVYAEE 294
Query: 566 LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQ 625
+ WE L + V Y + + + +F ++++RL G ++V +
Sbjct: 295 IARAWESGEGLER---VARYSMEDAKATYELGK-EFFPMEAQLSRLVGQSLWDVSRSSTG 350
Query: 626 FRVESIMLRLSRLNNFVAVS-PSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQSLY 684
VE +LR + N VA + P ++ A + + EPE L+ + I+ LD++SLY
Sbjct: 351 NLVEWFLLRKAYERNDVAPNKPDERELARRTESYAGGYVKEPEKGLWEN-IVYLDYKSLY 409
Query: 685 PSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQKLTISPSGVAFVDK 744
PS+II +N T L R GC + +V+ + + +
Sbjct: 410 PSIIITHNVSPDT-LNRE-----------GCREYDVAPQVGHRFCKDFP----------- 446
Query: 745 SIRCGILPKMLQEILDTRLMVKQSMKEYKSNAALQRVLHARQLGLKLIANVTYGYTAANF 804
G +P +L ++L+ R VK+ MK + +++L RQ +K++AN YGY A
Sbjct: 447 ----GFIPSLLGDLLEERQKVKKKMKA-TVDPIERKLLDYRQRAIKILANSYYGYYAYAN 501
Query: 805 SGRMPCVEVGDSVVSKGRETLQKAIETVNNTSKWQCRVVYGDTDSMFVLAPGKTKQEAFE 864
+ R C E +SV + GR+ ++ + + K+ +V+Y DTD F PG +
Sbjct: 502 A-RWYCRECAESVTAWGRQYIETTMREIEE--KFGFKVLYADTDGFFATIPGADAETVKN 558
Query: 865 IGKEIAXXXXXXXXXXXKLKFEKVYQPCILQTKKRYVGYMYETADQDKPIYEAKGIETVR 924
KE +L++E Y+ TKK+Y D++ I +G+E VR
Sbjct: 559 KAKEFLNYINPRLPGLLELEYEGFYRRGFFVTKKKYA-----VIDEEDKI-TTRGLEIVR 612
Query: 925 RDGCPAVSKILKKSLCLLFETKDLSVVKEYVEKQFSKIISGRISVQDMTFAKEY-RGQAG 983
RD + + L + + D+ V++ K+ + + + ++ R
Sbjct: 613 RDWSEIAKETQARVLEAILKHGDVEEAVRIVKEVTEKLSRHEVPPEKLVIYEQITRDLRS 672
Query: 984 YKPGACVPALSLARQWVLTDPRAEPRVSERVPYVIVSGAPGLPLIKLVKSPYELLQDSSL 1043
Y+ A P +++A++ + P + Y+++ G PG + + P++ +
Sbjct: 673 YR--ATGPHVAVAKRLAARGIKIRPGTV--ISYIVLKG-PGRVGDRAI--PFDEFDPAKH 725
Query: 1044 RLNSEYYITRVIIPPLERCFLLLG 1067
R ++EYYI ++P +ER G
Sbjct: 726 RYDAEYYIENQVLPAVERILRAFG 749
>pdb|3A2F|A Chain A, Crystal Structure Of Pyrococcus Furiosus Dna PolymerasePCNA
Monomer Mutant Complex
Length = 775
Score = 127 bits (320), Expect = 3e-29, Method: Compositional matrix adjust.
Identities = 157/690 (22%), Positives = 302/690 (43%), Gaps = 73/690 (10%)
Query: 392 HAISRALLKPDPAYDEVKAIFYYLYTC--PPEEDRKVGIILI--GQESELPEVRTKPIQM 447
+ I + L+ P +E+K + + + T EE K II I E+E + K I +
Sbjct: 120 YLIDKGLI-PXEGEEELKILAFDIETLYHEGEEFGKGPIIXISYADENEAKVITWKNIDL 178
Query: 448 HFV---SNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRIT 504
+V S+E+E F+ +R+ DPDI++ Y ++ + YL +R LG+ L + R
Sbjct: 179 PYVEVVSSEREXIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKRAEKLGIKLT--IGRDG 236
Query: 505 EVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHE-RIPLHSW 563
K D T +++ GRI +L+ ++ +NL +YT E + + + + +++
Sbjct: 237 SEPKXQRIGD---XTAVEVKGRIHFDLYHVITRTINLPTYTLEAVYEAIFGKPKEKVYAD 293
Query: 564 KLLTCW--WEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLS 621
++ W E+ + K+ + G +F+ +++RL G ++V
Sbjct: 294 EIAKAWESGENLERVAKYSXEDAKATYELG-------KEFLPXEIQLSRLVGQPLWDVSR 346
Query: 622 RGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLP--LILEPESRLYTDPIIVLD 679
+ VE +LR + N VA + ++ R ES + EPE L+ + I+ LD
Sbjct: 347 SSTGNLVEWFLLRKAYERNEVAPNKPSEEEYQRRLRESYTGGFVKEPEKGLWEN-IVYLD 405
Query: 680 FQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQKLTISPSGV 739
F++LYPS+II +N T +E GC + +++ + K + +
Sbjct: 406 FRALYPSIIITHNVSPDTL--NLE----------GCKNYDIAPQVGHKFCKDIP------ 447
Query: 740 AFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAALQRV-LHARQLGLKLIANVTYG 798
G +P +L +L+ R +K KE + ++++ L RQ +KL+AN YG
Sbjct: 448 ---------GFIPSLLGHLLEERQKIKTKXKE--TQDPIEKILLDYRQKAIKLLANSFYG 496
Query: 799 YTAANFSGRMPCVEVGDSVVSKGRETLQKAIETVNNTSKWQCRVVYGDTDSMFVLAPGKT 858
Y R C E +SV + GR+ ++ + + K+ +V+Y DTD ++ PG
Sbjct: 497 YYGYA-KARWYCKECAESVTAWGRKYIELVWKELE--EKFGFKVLYIDTDGLYATIPGGE 553
Query: 859 KQEAFEIGKEIAXXXXXXXXXXXKLKFEKVYQPCILQTKKRYVGYMYETADQDKPIYEAK 918
+E + E +L++E Y+ TKKRY D++ + +
Sbjct: 554 SEEIKKKALEFVKYINSKLPGLLELEYEGFYKRGFFVTKKRYA-----VIDEEGKVI-TR 607
Query: 919 GIETVRRDGCPAVSKILKKSLCLLFETKDLSVVKEYVEKQFSKIISGRISVQDMTFAKEY 978
G+E VRRD + + L + + D+ V++ K+ + I + + ++
Sbjct: 608 GLEIVRRDWSEIAKETQARVLETILKHGDVEEAVRIVKEVIQKLANYEIPPEKLAIYEQI 667
Query: 979 -RGQAGYKPGACVPALSLARQWVLTDPRAEPRVSERVPYVIVSGAPGLPLIKLVKSPYEL 1037
R YK A P +++A++ + +P + Y+++ G + ++ Y+
Sbjct: 668 TRPLHEYK--AIGPHVAVAKKLAAKGVKIKP--GXVIGYIVLRGDGPISNRAILAEEYD- 722
Query: 1038 LQDSSLRLNSEYYITRVIIPPLERCFLLLG 1067
+ ++EYYI ++P + R G
Sbjct: 723 --PKKHKYDAEYYIENQVLPAVLRILEGFG 750
>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 = 124 bits (310), Expect = 4e-28, Method: Compositional matrix adjust.
Identities = 143/623 (22%), Positives = 266/623 (42%), Gaps = 85/623 (13%)
Query: 450 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKR 509
VS EKE+ F++ +++ DPD+LI Y + + YL +R +LG+ + R
Sbjct: 184 VSTEKEMIKRFLKVIQEKDPDVLITYNGDNFDFAYLKKRSEMLGVKF---------ILGR 234
Query: 510 NSSRDEVKNT----QLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKL 565
+ S +++ +++ GRI +L+ ++R +NL +YT E + V + +
Sbjct: 235 DGSEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTINLPTYTLETVYEPVFGQPAEKVYAEE 294
Query: 566 LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQ 625
+ W L + V Y + + + +F ++++RL G ++V +
Sbjct: 295 IAEAWASGEGLER---VARYSMEDAKATYELGK-EFFPMEAQLSRLVGQSLWDVSRSSTG 350
Query: 626 FRVESIMLRLSRLNNFVAVS-PSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQSLY 684
VE +LR + N VA + P ++ A + + EPE L+ + I+ LD++SLY
Sbjct: 351 NLVEWFLLRKAYERNDVAPNKPDERELARRTESYAGGYVKEPEKGLWEN-IVYLDYKSLY 409
Query: 685 PSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQKLTISPSGVAFVDK 744
PS+II +N T L R GC + +V+ + + +
Sbjct: 410 PSIIITHNVSPDT-LNRE-----------GCREYDVAPQVGHRFCKDFP----------- 446
Query: 745 SIRCGILPKMLQEILDTRLMVKQSMKEYKSNAALQRVLHARQLGLKLIANVTYGYTAANF 804
G +P +L ++L+ R VK+ MK + +++L RQ +K++AN YGY A
Sbjct: 447 ----GFIPSLLGDLLEERQKVKKKMKA-TVDPIERKLLDYRQRAIKILANSYYGYYAYAN 501
Query: 805 SGRMPCVEVGDSVVSKGRETLQKAIETVNNTSKWQCRVVYGDTDSMFVLAPGKTKQEAFE 864
+ R C E +SV + GR+ ++ + + K+ +V+Y DTD F PG +
Sbjct: 502 A-RWYCRECAESVTAWGRQYIETTMREIEE--KFGFKVLYADTDGFFATIPGADAETVKN 558
Query: 865 IGKEIAXXXXXXXXXXXKLKFEKVYQPCILQTKKRYVGYMYETADQDKPIYEAKGIETVR 924
KE +L++E Y+ TKK+Y D++ I +G+E VR
Sbjct: 559 KAKEFLNYINPRLPGLLELEYEGFYRRGFFVTKKKYA-----VIDEEDKI-TTRGLEIVR 612
Query: 925 RDGCPAVSKILKKSLCLLFETKDLSVVKEYVEKQFSKIISGRISVQDMTFAKEYRGQAGY 984
RD + + L + + D+ V++ K+ + + + Y
Sbjct: 613 RDWSEIAKETQARVLEAILKHGDVEEAVRIVKEVTEKLSRHEVPPEKLVI---------Y 663
Query: 985 KPGACVPALSLARQWVLTDPRAEPRVSERVPYVIVSGAPGLPLIKLVKSPYELLQDSSLR 1044
+ G V A + + Y+++ G PG + + P++ + R
Sbjct: 664 EAGPHVAAAATV-----------------ISYIVLKG-PGRVGDRAI--PFDEFDPAKHR 703
Query: 1045 LNSEYYITRVIIPPLERCFLLLG 1067
++EYYI ++P +ER G
Sbjct: 704 YDAEYYIENQVLPAVERILRAFG 726
>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 = 119 bits (299), Expect = 8e-27, Method: Compositional matrix adjust.
Identities = 147/627 (23%), Positives = 276/627 (44%), Gaps = 64/627 (10%)
Query: 447 MHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEV 506
+ VS+E+E+ ++ +R+ DPD++I Y + ++ YLL+R LG+ L L R
Sbjct: 203 VEVVSSEREMIKRLVKVIREKDPDVIITYNGDNFAFPYLLKRAEKLGIKLP--LGRDNSE 260
Query: 507 EKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVL---HERIPLHSW 563
K D + +++ GRI +L+ ++R +NL +YT E + + E++ H
Sbjct: 261 PKMQRMGD---SLAVEIKGRIHFDLFPVIRRTINLPTYTLEAVYEAIFGKSKEKVYAHE- 316
Query: 564 KLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRG 623
+ WE L + V Y + + + + +F +++ARL G ++V
Sbjct: 317 --IAEAWETGKGLER---VAKYSMEDAKVTFELGK-EFFPMEAQLARLVGQPVWDVSRSS 370
Query: 624 SQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLP--LILEPESRLYTDPIIVLDFQ 681
+ VE +LR + N +A + ++ R ES + EPE L+ + I+ LDF+
Sbjct: 371 TGNLVEWFLLRKAYERNELAPNKPDEREYERRLRESYEGGYVKEPEKGLW-EGIVSLDFR 429
Query: 682 SLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQKLTISPSGVAF 741
SLYPS+II +N T L R C + +V+ + + +
Sbjct: 430 SLYPSIIITHNVSPDT-LNRE-----------NCKEYDVAPQVGHRFCKDFP-------- 469
Query: 742 VDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAALQRVLHARQLGLKLIANVTYGYTA 801
G +P +L +L+ R +K+ MKE K + +++L RQ +K++AN +Y
Sbjct: 470 -------GFIPSLLGNLLEERQKIKKRMKESK-DPVEKKLLDYRQRAIKILAN-SYYGYY 520
Query: 802 ANFSGRMPCVEVGDSVVSKGRETLQKAIETVNNTSKWQCRVVYGDTDSMFVLAPGKTKQE 861
R C E +SV + GR+ + + + +V+Y DTD ++ PG +E
Sbjct: 521 GYAKARWYCKECAESVTAWGRQYIDLVRRELESRG---FKVLYIDTDGLYATIPGAKHEE 577
Query: 862 AFEIGKEIAXXXXXXXXXXXKLKFEKVYQPCILQTKKRYVGYMYETADQDKPIYEAKGIE 921
E + +L++E Y TKK+Y D++ I +G+E
Sbjct: 578 IKEKALKFVEYINSKLPGLLELEYEGFYARGFFVTKKKYA-----LIDEEGKIV-TRGLE 631
Query: 922 TVRRDGCPAVSKILKKSLCLLFETKDLSVVKEYVEKQFSKIISGRISVQDMTFAKEY-RG 980
VRRD + K L + + ++ + V++ K+ I + + ++ R
Sbjct: 632 IVRRDWSEIAKETQAKVLEAILKHGNVDEAVKIVKEVTEKLSKYEIPPEKLVIYEQITRP 691
Query: 981 QAGYKPGACVPALSLARQWVLTDPRAEPRVSERVPYVIVSGAPGLPLIKLVKSPYELLQD 1040
+ YK A P +++A++ + +P + + Y+++ G P+ K + E
Sbjct: 692 LSEYK--AIGPHVAVAKRLAAKGVKVKPGMV--IGYIVLRGDG--PISKRAIA-IEEFDP 744
Query: 1041 SSLRLNSEYYITRVIIPPLERCFLLLG 1067
+ ++EYYI ++P +ER G
Sbjct: 745 KKHKYDAEYYIENQVLPAVERILRAFG 771
>pdb|4FM2|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase (Triple Mutant)
Bound To A Dsdna, In Edition Mode
Length = 793
Score = 117 bits (293), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 147/627 (23%), Positives = 274/627 (43%), Gaps = 64/627 (10%)
Query: 447 MHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEV 506
+ VS+E+E+ ++ +R+ DPD++I Y + ++ YLL+R LG+ L L R
Sbjct: 203 VEVVSSEREMIKRLVKVIREKDPDVIITYNGDNFAFPYLLKRAEKLGIKLP--LGRDNSE 260
Query: 507 EKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVL---HERIPLHSW 563
K D + + + GRI +L+ ++R +NL +YT E + + E++ H
Sbjct: 261 PKMQRMGD---SLAVAIKGRIHFDLFPVIRRTINLPTYTLEAVYEAIFGKSKEKVYAHE- 316
Query: 564 KLLTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRG 623
+ WE L + V Y + + + + +F +++ARL G + V
Sbjct: 317 --IAEAWETGKGLER---VAKYSMEDAKVTFELGK-EFFPMEAQLARLVGQPVWAVSRSS 370
Query: 624 SQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLP--LILEPESRLYTDPIIVLDFQ 681
+ VE +LR + N +A + ++ R ES + EPE L+ + I+ LDF+
Sbjct: 371 TGNLVEWFLLRKAYERNELAPNKPDEREYERRLRESYEGGYVKEPEKGLW-EGIVSLDFR 429
Query: 682 SLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQKLTISPSGVAF 741
SLYPS+II +N T L R C + +V+ + + +
Sbjct: 430 SLYPSIIITHNVSPDT-LNRE-----------NCKEYDVAPQVGHRFCKDFP-------- 469
Query: 742 VDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAALQRVLHARQLGLKLIANVTYGYTA 801
G +P +L +L+ R +K+ MKE K + +++L RQ +K++AN +Y
Sbjct: 470 -------GFIPSLLGNLLEERQKIKKRMKESK-DPVEKKLLDYRQRAIKILAN-SYYGYY 520
Query: 802 ANFSGRMPCVEVGDSVVSKGRETLQKAIETVNNTSKWQCRVVYGDTDSMFVLAPGKTKQE 861
R C E +SV + GR+ + + + +V+Y DTD ++ PG +E
Sbjct: 521 GYAKARWYCKECAESVTAWGRQYIDLVRRELESRG---FKVLYIDTDGLYATIPGAKHEE 577
Query: 862 AFEIGKEIAXXXXXXXXXXXKLKFEKVYQPCILQTKKRYVGYMYETADQDKPIYEAKGIE 921
E + +L++E Y TKK+Y D++ I +G+E
Sbjct: 578 IKEKALKFVEYINSKLPGLLELEYEGFYARGFFVTKKKYA-----LIDEEGKIV-TRGLE 631
Query: 922 TVRRDGCPAVSKILKKSLCLLFETKDLSVVKEYVEKQFSKIISGRISVQDMTFAKEY-RG 980
VRRD + K L + + ++ + V++ K+ I + + ++ R
Sbjct: 632 IVRRDWSEIAKETQAKVLEAILKHGNVDEAVKIVKEVTEKLSKYEIPPEKLVIYEQITRP 691
Query: 981 QAGYKPGACVPALSLARQWVLTDPRAEPRVSERVPYVIVSGAPGLPLIKLVKSPYELLQD 1040
+ YK A P +++A++ + +P + + Y+++ G P+ K + E
Sbjct: 692 LSEYK--AIGPHVAVAKRLAAKGVKVKPGMV--IGYIVLRGDG--PISKRAIA-IEEFDP 744
Query: 1041 SSLRLNSEYYITRVIIPPLERCFLLLG 1067
+ ++EYYI ++P +ER G
Sbjct: 745 KKHKYDAEYYIENQVLPAVERILRAFG 771
>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 = 102 bits (255), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 154/683 (22%), Positives = 280/683 (40%), Gaps = 130/683 (19%)
Query: 444 PIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGL----NLNQE 499
P ++ +NEK + S F ++ DPD++IG+ ++ + L R + L + ++ +
Sbjct: 259 PGRVRLFNNEKAMLSCFCAMLKVEDPDVIIGHRLQNVYLDVLAHRMHDLNIPTFSSIGRR 318
Query: 500 LSRI--TEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFE-NIMYHVLHE 556
L R + + NS+ + + + GR++ ++ + + + +++ + MY V
Sbjct: 319 LRRTWPEKFGRGNSNMNHFFISDI-CSGRLICDIANEMGQSLTPKCQSWDLSEMYQV--- 374
Query: 557 RIPLHSWKLLTCWWEHRTHLYKW-------------MTVEHYLIRVTGIIRLIEQLDFIG 603
TC EH+ + M ++ + + ++ +
Sbjct: 375 ----------TCEKEHKPLDIDYQNPQYQNDVNSMTMALQENITNCMISAEVSYRIQLLT 424
Query: 604 RTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAV------SPSIKQRAH---- 653
T ++ L G + + L R E I+L N F+ S + KQR +
Sbjct: 425 LTKQLTNLAGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDKEGNRSRAQKQRQNEENA 484
Query: 654 ------MRAPESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGV 707
+A L+ EPE L+ + ++V+DF SLYPS+I +N CF+T E +
Sbjct: 485 DAPVNSKKAKYQGGLVFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVDRNKEDI-- 542
Query: 708 SDSFPFGCIDLNVSIRSLKKLQQKLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQ 767
D P ++ PS + G+LP++L ++D R VK+
Sbjct: 543 -DELP--------------------SVPPS-------EVDQGVLPRLLANLVDRRREVKK 574
Query: 768 SMK-EYKSNAALQRVLHARQLGLKLIANVTY---GYTAANFSGRMPCVEVGDSVVSKGRE 823
MK E + +Q RQ LKL AN Y GY + F + P + V +KGRE
Sbjct: 575 VMKTETDPHKRVQ--CDIRQQALKLTANSMYGCLGYVNSRFYAK-PLAML---VTNKGRE 628
Query: 824 TLQKAIETVNNTSKWQCRVVYGDTDSMFVLAPGKTKQEAFEIGKEIAXXXXXXXXXXXKL 883
L + T VVYGDTDS+ + +A +IG ++
Sbjct: 629 IL---MNTRQLAESMNLLVVYGDTDSVMIDTGCDNYADAIKIGLGFK-RLVNERYRLLEI 684
Query: 884 KFEKVYQPCILQTKKRYVGYMYETADQDK-----PIYEAKGIETVRRDGCPAVSKILKKS 938
+ V++ +L KK+Y T + DK + E KG++ RR+ CP +
Sbjct: 685 DIDNVFKKLLLHAKKKYAAL---TVNLDKNGNGTTVLEVKGLDMKRREFCPLSRDVSIHV 741
Query: 939 LCLLFETKD----LSVVKEYVEKQFSKIISGRISVQ----DMTFAKEYRGQAGYKPGACV 990
L + KD L V +Y+E K+ + I + +M +K+ + G G +
Sbjct: 742 LNTILSDKDPEEALQEVYDYLEDIRIKVETNNIRIDKYKINMKLSKDPKAYPG---GKNM 798
Query: 991 PALSLARQWVLTDPRAEPRVSER---VPYVI-----VSGAPGLPLIKLVKSPYEL----L 1038
PA+ +A + R RV + + +VI + A P + + + + L +
Sbjct: 799 PAVQVALRM-----RKAGRVVKAGSVITFVITKQDEIDNAADTPALSVAERAHALNEVMI 853
Query: 1039 QDSSLRLNSEYYITRVIIPPLER 1061
+ ++L + +YY+ + I P+ER
Sbjct: 854 KSNNLIPDPQYYLEKQIFAPVER 876
>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 = 100 bits (250), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 153/683 (22%), Positives = 280/683 (40%), Gaps = 130/683 (19%)
Query: 444 PIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGL----NLNQE 499
P ++ +NEK + S F ++ DPD++IG+ ++ + L R + L + ++ +
Sbjct: 259 PGRVRLFNNEKAMLSCFCAMLKVEDPDVIIGHRLQNVYLDVLAHRMHDLNIPTFSSIGRR 318
Query: 500 LSRI--TEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFE-NIMYHVLHE 556
L R + + NS+ + + + GR++ ++ + + + +++ + MY V
Sbjct: 319 LRRTWPEKFGRGNSNMNHFFISDI-CSGRLICDIANEMGQSLTPKCQSWDLSEMYQV--- 374
Query: 557 RIPLHSWKLLTCWWEHRTHLYKW-------------MTVEHYLIRVTGIIRLIEQLDFIG 603
TC EH+ + M ++ + + ++ +
Sbjct: 375 ----------TCEKEHKPLDIDYQNPQYQNDVNSMTMALQENITNCMISAEVSYRIQLLT 424
Query: 604 RTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAV------SPSIKQRAH---- 653
T ++ L G + + L R E I+L N F+ S + KQR +
Sbjct: 425 LTKQLTNLAGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDKEGNRSRAQKQRQNEENA 484
Query: 654 ------MRAPESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGV 707
+A L+ EPE L+ + ++V+DF SLYPS+I +N CF+T E +
Sbjct: 485 DAPVNSKKAKYQGGLVFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVDRNKEDI-- 542
Query: 708 SDSFPFGCIDLNVSIRSLKKLQQKLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQ 767
D P ++ PS + G+LP++L ++D R VK+
Sbjct: 543 -DELP--------------------SVPPS-------EVDQGVLPRLLANLVDRRREVKK 574
Query: 768 SMK-EYKSNAALQRVLHARQLGLKLIANVTY---GYTAANFSGRMPCVEVGDSVVSKGRE 823
MK E + +Q RQ LKL AN Y GY + F + P + V +KGRE
Sbjct: 575 VMKTETDPHKRVQ--CDIRQQALKLTANSMYGCLGYVNSRFYAK-PLAML---VTNKGRE 628
Query: 824 TLQKAIETVNNTSKWQCRVVYGDTDSMFVLAPGKTKQEAFEIGKEIAXXXXXXXXXXXKL 883
L + T VVYGDT+S+ + +A +IG ++
Sbjct: 629 IL---MNTRQLAESMNLLVVYGDTNSVMIDTGCDNYADAIKIGLGFK-RLVNERYRLLEI 684
Query: 884 KFEKVYQPCILQTKKRYVGYMYETADQDK-----PIYEAKGIETVRRDGCPAVSKILKKS 938
+ V++ +L KK+Y T + DK + E KG++ RR+ CP +
Sbjct: 685 DIDNVFKKLLLHAKKKYAAL---TVNLDKNGNGTTVLEVKGLDMKRREFCPLSRDVSIHV 741
Query: 939 LCLLFETKD----LSVVKEYVEKQFSKIISGRISVQ----DMTFAKEYRGQAGYKPGACV 990
L + KD L V +Y+E K+ + I + +M +K+ + G G +
Sbjct: 742 LNTILSDKDPEEALQEVYDYLEDIRIKVETNNIRIDKYKINMKLSKDPKAYPG---GKNM 798
Query: 991 PALSLARQWVLTDPRAEPRVSER---VPYVI-----VSGAPGLPLIKLVKSPYEL----L 1038
PA+ +A + R RV + + +VI + A P + + + + L +
Sbjct: 799 PAVQVALRM-----RKAGRVVKAGSVITFVITKQDEIDNAADTPALSVAERAHALNEVMI 853
Query: 1039 QDSSLRLNSEYYITRVIIPPLER 1061
+ ++L + +YY+ + I P+ER
Sbjct: 854 KSNNLIPDPQYYLEKQIFAPVER 876
>pdb|4B08|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha,
Selenomethionine Protein
Length = 910
Score = 93.2 bits (230), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 153/679 (22%), Positives = 262/679 (38%), Gaps = 122/679 (17%)
Query: 444 PIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRI 503
P ++ +NEK S F ++ DPD++IG+ ++ + L R + L + + R
Sbjct: 259 PGRVRLFNNEKAXLSCFCAXLKVEDPDVIIGHRLQNVYLDVLAHRXHDLNIPTFSSIGR- 317
Query: 504 TEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIP-LHS 562
++ T + GR N ++ +I P S
Sbjct: 318 -----------RLRRTWPEKFGRGNSNXNHFFISDI-CSGRLICDIANEXGQSLTPKCQS 365
Query: 563 WKL-----LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIE-------------QLDFIGR 604
W L +TC EH+ + ++ + L E ++ +
Sbjct: 366 WDLSEXYQVTCEKEHKPLDIDYQNPQYQNDVNSXTXALQENITNCXISAEVSYRIQLLTL 425
Query: 605 TSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAV------SPSIKQRAH----- 653
T ++ L G + + L R E I+L N F+ S + KQR +
Sbjct: 426 TKQLTNLAGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDKEGNRSRAQKQRQNEENAD 485
Query: 654 -----MRAPESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVS 708
+A L+ EPE L+ + ++V DF SLYPS+I +N CF+T E +
Sbjct: 486 APVNSKKAKYQGGLVFEPEKGLHKNYVLVXDFNSLYPSIIQEFNICFTTVDRNKEDI--- 542
Query: 709 DSFPFGCIDLNVSIRSLKKLQQKLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQS 768
D P ++ PS + G+LP++L ++D R VK+
Sbjct: 543 DELP--------------------SVPPS-------EVDQGVLPRLLANLVDRRREVKKV 575
Query: 769 MK-EYKSNAALQRVLHARQLGLKLIANVTYG---YTAANFSGRMPCVEVGDSVVSKGRET 824
K E + +Q RQ LKL AN YG Y + F + P + V +KGRE
Sbjct: 576 XKTETDPHKRVQ--CDIRQQALKLTANSXYGCLGYVNSRFYAK-PLAXL---VTNKGREI 629
Query: 825 LQKAIETVNNTSKWQCRVVYGDTDSMFVLAPGKTKQEAFEIGKEIAXXXXXXXXXXXKLK 884
L + + + VVYGDTDS+ + +A +IG ++
Sbjct: 630 LXNTRQLAESXNLL---VVYGDTDSVXIDTGCDNYADAIKIGLGFK-RLVNERYRLLEID 685
Query: 885 FEKVYQPCILQTKKRYVGYMYETADQDK-----PIYEAKGIETVRRDGCPAVSKILKKSL 939
+ V++ +L KK+Y T + DK + E KG++ RR+ CP + L
Sbjct: 686 IDNVFKKLLLHAKKKYAAL---TVNLDKNGNGTTVLEVKGLDXKRREFCPLSRDVSIHVL 742
Query: 940 CLLFETKD----LSVVKEYVEKQFSKIISGRISVQDMTF-AKEYRGQAGYKPGACVPALS 994
+ KD L V +Y+E K+ + I + K + Y G PA+
Sbjct: 743 NTILSDKDPEEALQEVYDYLEDIRIKVETNNIRIDKYKINXKLSKDPKAYPGGKNXPAVQ 802
Query: 995 LARQWVLTDPRAEPRVSER---VPYVI-----VSGAPGLPLIKLVKSPYEL----LQDSS 1042
+A + R RV + + +VI + A P + + + + L ++ ++
Sbjct: 803 VALRX-----RKAGRVVKAGSVITFVITKQDEIDNAADTPALSVAERAHALNEVXIKSNN 857
Query: 1043 LRLNSEYYITRVIIPPLER 1061
L + +YY+ + I P+ER
Sbjct: 858 LIPDPQYYLEKQIFAPVER 876
>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 = 63.9 bits (154), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 134/618 (21%), Positives = 242/618 (39%), Gaps = 112/618 (18%)
Query: 394 ISRALLKPDPAY-DEVKAIFYYLYTCPPEEDRKVGIILIGQE------SELPEVRTKPIQ 446
I A LKP P Y +K + + T E +G+ GQ E + + +
Sbjct: 138 IVNARLKPHPDYRPPLKWVSIDIETTRHGELYCIGLEGCGQRIVYMLGPENGDASSLDFE 197
Query: 447 MHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERG--YVLGLNLNQELSRIT 504
+ +V++ +L +DPD++IG+ + L + Y L L L ++ S
Sbjct: 198 LEYVASRPQLLEKLNAWFANYDPDVIIGWNVVQFDLRMLQKHAERYRLPLRLGRDNS--- 254
Query: 505 EVEKRNSSRDEVKNTQL--QMPGRIVINLWRLLRHEV-NLQSYTFENIMYHVLHERIPLH 561
E+E R KN Q GR++I+ L+ N S++ E + +L E
Sbjct: 255 ELEWREHG---FKNGVFFAQAKGRLIIDGIEALKSAFWNFSSFSLETVAQELLGEG---- 307
Query: 562 SWKLLTCWWEHRTHLYKWMTVEH-----YLIR----VTGIIRLIEQLDFIGRTSEMARLF 612
K + W+ + + + Y ++ VT I E + F+ E A +
Sbjct: 308 --KSIDNPWDRMDEIDRRFAEDKPALATYNLKNCELVTQIFHKTEIMPFL---LERATVN 362
Query: 613 GIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPLILEPESRLYT 672
G+ + R L R++ V+P++ + +P +++ LY
Sbjct: 363 GLP----VDRHGGSVAAFGHLYFPRMHRAGYVAPNLGEVPPHASPGGY--VMDSRPGLY- 415
Query: 673 DPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSD--SFPFGCIDLNVSIRSLKKLQQ 730
D ++VLD++SLYPS+I + +G VE + D G +D
Sbjct: 416 DSVLVLDYKSLYPSIIRTF---LIDPVGLVEGMAQPDPEHSTEGFLD------------- 459
Query: 731 KLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAALQRVLHARQLGLK 790
A+ + C LP+++ I R K+ + S A LK
Sbjct: 460 ---------AWFSREKHC--LPEIVTNIWHGRDEAKRQGNKPLSQA------------LK 496
Query: 791 LIANVTYGYTAANFSGRMPCVEVGDSVVSKGRETLQKAIETVNNTSKWQCRVVYGDTDSM 850
+I N YG + R + S+ +G + +++ + V+YGDTDS
Sbjct: 497 IIMNAFYGVLGTT-ACRFFDPRLASSITMRGHQIMRQTKALIEAQG---YDVIYGDTDST 552
Query: 851 FVLAPG-KTKQEAFEIGKEIAXX---------XXXXXXXXXKLKFE----KVYQPCI--- 893
FV G +++EA +IG+ + +L++E + P I
Sbjct: 553 FVWLKGAHSEEEAAKIGRALVQHVNAWWAETLQKQRLTSALELEYETHFCRFLMPTIRGA 612
Query: 894 -LQTKKRYVGYMYETADQDKPIYEAKGIETVRRDGCPAVSKILKKSLCLLFETKDLSVVK 952
+KKRY G + E D+ + ++ KG+ETVR D P + ++ +F + +
Sbjct: 613 DTGSKKRYAGLIQE-GDKQRMVF--KGLETVRTDWTPLAQQFQQELYLRIFRNEP---YQ 666
Query: 953 EYVEKQFSKIISGRISVQ 970
EYV + K+++G + +
Sbjct: 667 EYVRETIDKLMAGELDAR 684
>pdb|1Q8I|A Chain A, Crystal Structure Of Escherichia Coli Dna Polymerase Ii
Length = 783
Score = 63.5 bits (153), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 133/618 (21%), Positives = 242/618 (39%), Gaps = 112/618 (18%)
Query: 394 ISRALLKPDPAY-DEVKAIFYYLYTCPPEEDRKVGIILIGQE------SELPEVRTKPIQ 446
I A LKP P Y +K + + T E +G+ GQ E + + +
Sbjct: 135 IVNARLKPHPDYRPPLKWVSIDIETTRHGELYCIGLEGCGQRIVYMLGPENGDASSLDFE 194
Query: 447 MHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERG--YVLGLNLNQELSRIT 504
+ +V++ +L +DPD++IG+ + L + Y L L L ++ S
Sbjct: 195 LEYVASRPQLLEKLNAWFANYDPDVIIGWNVVQFDLRMLQKHAERYRLPLRLGRDNS--- 251
Query: 505 EVEKRNSSRDEVKNTQL--QMPGRIVINLWRLLRHEV-NLQSYTFENIMYHVLHERIPLH 561
E+E R KN Q GR++I+ L+ N S++ E + +L E
Sbjct: 252 ELEWREHG---FKNGVFFAQAKGRLIIDGIEALKSAFWNFSSFSLETVAQELLGEG---- 304
Query: 562 SWKLLTCWWEHRTHLYKWMTVEH-----YLIR----VTGIIRLIEQLDFIGRTSEMARLF 612
K + W+ + + + Y ++ VT I E + F+ E A +
Sbjct: 305 --KSIDNPWDRMDEIDRRFAEDKPALATYNLKDCELVTQIFHKTEIMPFL---LERATVN 359
Query: 613 GIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPLILEPESRLYT 672
G+ + R L R++ V+P++ + +P +++ LY
Sbjct: 360 GLP----VDRHGGSVAAFGHLYFPRMHRAGYVAPNLGEVPPHASPGGY--VMDSRPGLY- 412
Query: 673 DPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSD--SFPFGCIDLNVSIRSLKKLQQ 730
D ++VLD++SLYPS++ + +G VE + D G +D
Sbjct: 413 DSVLVLDYKSLYPSIVRTF---LIDPVGLVEGMAQPDPEHSTEGFLD------------- 456
Query: 731 KLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAALQRVLHARQLGLK 790
A+ + C LP+++ I R K+ + S A LK
Sbjct: 457 ---------AWFSREKHC--LPEIVTNIWHGRDEAKRQGNKPLSQA------------LK 493
Query: 791 LIANVTYGYTAANFSGRMPCVEVGDSVVSKGRETLQKAIETVNNTSKWQCRVVYGDTDSM 850
+I N YG + R + S+ +G + +++ + V+YGDTDS
Sbjct: 494 IIMNAFYGVLGTT-ACRFFDPRLASSITMRGHQIMRQTKALIEAQG---YDVIYGDTDST 549
Query: 851 FVLAPG-KTKQEAFEIGKEIAXX---------XXXXXXXXXKLKFE----KVYQPCI--- 893
FV G +++EA +IG+ + +L++E + P I
Sbjct: 550 FVWLKGAHSEEEAAKIGRALVQHVNAWWAETLQKQRLTSALELEYETHFCRFLMPTIRGA 609
Query: 894 -LQTKKRYVGYMYETADQDKPIYEAKGIETVRRDGCPAVSKILKKSLCLLFETKDLSVVK 952
+KKRY G + E D+ + ++ KG+ETVR D P + ++ +F + +
Sbjct: 610 DTGSKKRYAGLIQE-GDKQRMVF--KGLETVRTDWTPLAQQFQQELYLRIFRNEP---YQ 663
Query: 953 EYVEKQFSKIISGRISVQ 970
EYV + K+++G + +
Sbjct: 664 EYVRETIDKLMAGELDAR 681
>pdb|1S5J|A Chain A, Insight In Dna Replication: The Crystal Structure Of Dna
Polymerase B1 From The Archaeon Sulfolobus Solfataricus
Length = 847
Score = 56.2 bits (134), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 59/222 (26%), Positives = 98/222 (44%), Gaps = 36/222 (16%)
Query: 642 VAVSPSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGR 701
+ S IK + + A ++++P + ++ + I VLDF SLYPS+I +N + T
Sbjct: 448 IRTSALIKGKGYKGA-----VVIDPPAGIFFN-ITVLDFASLYPSIIRTWNLSYET---- 497
Query: 702 VEHLGVSDSFPFGCIDLNVSIRSLKKLQQKLTISPSGVAFVDKSIRCGILPKMLQEILDT 761
V I+ KK ++ V + R GI + + D
Sbjct: 498 ------------------VDIQQCKK-PYEVKDETGEVLHIVCMDRPGITAVITGLLRDF 538
Query: 762 RLMVKQSMKEYKSNAALQRVLH-ARQLGLKLIANVTYG-YTAANFSGRMPCVEVGDSVVS 819
R+ + + + +N+ Q++L+ Q +K+ N TYG + A F P V +SV +
Sbjct: 539 RVKIYKKKAKNPNNSEEQKLLYDVVQRAMKVFINATYGVFGAETFPLYAP--RVAESVTA 596
Query: 820 KGRETLQKAIETVNNTSKWQCRVVYGDTDSMFVLAPGKTKQE 861
GR + TV + V+YGDTDS+F+L P K E
Sbjct: 597 LGRYVIT---STVKKAREEGLTVLYGDTDSLFLLNPPKNSLE 635
>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 = 39.7 bits (91), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 86/383 (22%), Positives = 156/383 (40%), Gaps = 48/383 (12%)
Query: 435 SELP-EVRTKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLER-GYVL 492
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+ + Y+ R +
Sbjct: 176 DEVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIF 234
Query: 493 GLNLNQELS-----RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFE 547
G + + LS R+ +E SR+ + T + I+L++ N SY+ +
Sbjct: 235 GESTAKRLSPHRKTRVKVIENMYGSREII--TLFGISVLDYIDLYKKFSF-TNQPSYSLD 291
Query: 548 NIMYHVLHERIPLHSWKL-----LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFI 602
I L+ KL ++ E Y + + +I V ++++ + FI
Sbjct: 292 YI------SEFELNVGKLKYDGPISKLRESNHQRY----ISYNIIAVYRVLQIDAKRQFI 341
Query: 603 GRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPL 662
+ +M IQ V S + ++I+ + N V P + R+H P
Sbjct: 342 NLSLDMGYYAKIQIQSVFSPIKTW--DAIIFNSLKEQN--KVIP--QGRSHPVQPYPGAF 395
Query: 663 ILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSI 722
+ EP Y ++ D SLYPS+I N T G F L+ I
Sbjct: 396 VKEPIPNRYK-YVMSFDLTSLYPSIIRQVNISPETIAGT-----------FKVAPLHDYI 443
Query: 723 RSLKKLQQKL-TISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAA-LQR 780
++ + + + SP+G+ + R G++P + ++ + R K M + N ++
Sbjct: 444 NAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKE 501
Query: 781 VLHARQLGLKLIANVTYGYTAAN 803
LH L + +V Y + ++
Sbjct: 502 ALHNPNLSVDEPLDVDYRFDFSD 524
>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 = 39.7 bits (91), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 86/383 (22%), Positives = 156/383 (40%), Gaps = 48/383 (12%)
Query: 435 SELP-EVRTKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLER-GYVL 492
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+ + Y+ R +
Sbjct: 176 DEVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIF 234
Query: 493 GLNLNQELS-----RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFE 547
G + + LS R+ +E SR+ + T + I+L++ N SY+ +
Sbjct: 235 GESTAKRLSPHRKTRVKVIENMYGSREII--TLFGISVLDYIDLYKKFSF-TNQPSYSLD 291
Query: 548 NIMYHVLHERIPLHSWKL-----LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFI 602
I L+ KL ++ E Y + + +I V ++++ + FI
Sbjct: 292 YI------SEFELNVGKLKYDGPISKLRESNHQRY----ISYNIIAVYRVLQIDAKRQFI 341
Query: 603 GRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPL 662
+ +M IQ V S + ++I+ + N V P + R+H P
Sbjct: 342 NLSLDMGYYAKIQIQSVFSPIKTW--DAIIFNSLKEQN--KVIP--QGRSHPVQPYPGAF 395
Query: 663 ILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSI 722
+ EP Y ++ D SLYPS+I N T G F L+ I
Sbjct: 396 VKEPIPNRYK-YVMSFDLTSLYPSIIRQVNISPETIAGT-----------FKVAPLHDYI 443
Query: 723 RSLKKLQQKL-TISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAA-LQR 780
++ + + + SP+G+ + R G++P + ++ + R K M + N ++
Sbjct: 444 NAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKE 501
Query: 781 VLHARQLGLKLIANVTYGYTAAN 803
LH L + +V Y + ++
Sbjct: 502 ALHNPNLSVDEPLDVDYRFDFSD 524
>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 = 39.7 bits (91), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 86/383 (22%), Positives = 156/383 (40%), Gaps = 48/383 (12%)
Query: 435 SELP-EVRTKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLER-GYVL 492
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+ + Y+ R +
Sbjct: 176 DEVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIF 234
Query: 493 GLNLNQELS-----RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFE 547
G + + LS R+ +E SR+ + T + I+L++ N SY+ +
Sbjct: 235 GESTAKRLSPHRKTRVKVIENMYGSREII--TLFGISVLDYIDLYKKFSF-TNQPSYSLD 291
Query: 548 NIMYHVLHERIPLHSWKL-----LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFI 602
I L+ KL ++ E Y + + +I V ++++ + FI
Sbjct: 292 YI------SEFELNVGKLKYDGPISKLRESNHQRY----ISYNIIAVYRVLQIDAKRQFI 341
Query: 603 GRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPL 662
+ +M IQ V S + ++I+ + N V P + R+H P
Sbjct: 342 NLSLDMGYYAKIQIQSVFSPIKTW--DAIIFNSLKEQN--KVIP--QGRSHPVQPYPGAF 395
Query: 663 ILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSI 722
+ EP Y ++ D SLYPS+I N T G F L+ I
Sbjct: 396 VKEPIPNRYK-YVMSFDLTSLYPSIIRQVNISPETIAGT-----------FKVAPLHDYI 443
Query: 723 RSLKKLQQKL-TISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAA-LQR 780
++ + + + SP+G+ + R G++P + ++ + R K M + N ++
Sbjct: 444 NAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKE 501
Query: 781 VLHARQLGLKLIANVTYGYTAAN 803
LH L + +V Y + ++
Sbjct: 502 ALHNPNLSVDEPLDVDYRFDFSD 524
>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 = 39.7 bits (91), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 86/383 (22%), Positives = 156/383 (40%), Gaps = 48/383 (12%)
Query: 435 SELP-EVRTKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLER-GYVL 492
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+ + Y+ R +
Sbjct: 176 DEVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIF 234
Query: 493 GLNLNQELS-----RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFE 547
G + + LS R+ +E SR+ + T + I+L++ N SY+ +
Sbjct: 235 GESTAKRLSPHRKTRVKVIENMYGSREII--TLFGISVLDYIDLYKKFSF-TNQPSYSLD 291
Query: 548 NIMYHVLHERIPLHSWKL-----LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFI 602
I L+ KL ++ E Y + + +I V ++++ + FI
Sbjct: 292 YI------SEFELNVGKLKYDGPISKLRESNHQRY----ISYNIIAVYRVLQIDAKRQFI 341
Query: 603 GRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPL 662
+ +M IQ V S + ++I+ + N V P + R+H P
Sbjct: 342 NLSLDMGYYAKIQIQSVFSPIKTW--DAIIFNSLKEQN--KVIP--QGRSHPVQPYPGAF 395
Query: 663 ILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSI 722
+ EP Y ++ D SLYPS+I N T G F L+ I
Sbjct: 396 VKEPIPNRYK-YVMSFDLTSLYPSIIRQVNISPETIAGT-----------FKVAPLHDYI 443
Query: 723 RSLKKLQQKL-TISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAA-LQR 780
++ + + + SP+G+ + R G++P + ++ + R K M + N ++
Sbjct: 444 NAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKE 501
Query: 781 VLHARQLGLKLIANVTYGYTAAN 803
LH L + +V Y + ++
Sbjct: 502 ALHNPNLSVDEPLDVDYRFDFSD 524
>pdb|3SUO|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dttp
Opposite 2ap (Gc Rich Sequence)
Length = 900
Score = 39.7 bits (91), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 86/383 (22%), Positives = 156/383 (40%), Gaps = 48/383 (12%)
Query: 435 SELP-EVRTKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLER-GYVL 492
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+ + Y+ R +
Sbjct: 176 DEVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIF 234
Query: 493 GLNLNQELS-----RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFE 547
G + + LS R+ +E SR+ + T + I+L++ N SY+ +
Sbjct: 235 GESTAKRLSPHRKTRVKVIENMYGSREII--TLFGISVLDYIDLYKKFSF-TNQPSYSLD 291
Query: 548 NIMYHVLHERIPLHSWKL-----LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFI 602
I L+ KL ++ E Y + + +I V ++++ + FI
Sbjct: 292 YI------SEFELNVGKLKYDGPISKLRESNHQRY----ISYNIIAVYRVLQIDAKRQFI 341
Query: 603 GRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPL 662
+ +M IQ V S + ++I+ + N V P + R+H P
Sbjct: 342 NLSLDMGYYAKIQIQSVFSPIKTW--DAIIFNSLKEQN--KVIP--QGRSHPVQPYPGAF 395
Query: 663 ILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSI 722
+ EP Y ++ D SLYPS+I N T G F L+ I
Sbjct: 396 VKEPIPNRYK-YVMSFDLTSLYPSIIRQVNISPETIAGT-----------FKVAPLHDYI 443
Query: 723 RSLKKLQQKL-TISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAA-LQR 780
++ + + + SP+G+ + R G++P + ++ + R K M + N ++
Sbjct: 444 NAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKE 501
Query: 781 VLHARQLGLKLIANVTYGYTAAN 803
LH L + +V Y + ++
Sbjct: 502 ALHNPNLSVDEPLDVDYRFDFSD 524
>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 = 39.7 bits (91), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 86/383 (22%), Positives = 156/383 (40%), Gaps = 48/383 (12%)
Query: 435 SELP-EVRTKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLER-GYVL 492
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+ + Y+ R +
Sbjct: 176 DEVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIF 234
Query: 493 GLNLNQELS-----RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFE 547
G + + LS R+ +E SR+ + T + I+L++ N SY+ +
Sbjct: 235 GESTAKRLSPHRKTRVKVIENMYGSREII--TLFGISVLDYIDLYKKFSF-TNQPSYSLD 291
Query: 548 NIMYHVLHERIPLHSWKL-----LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFI 602
I L+ KL ++ E Y + + +I V ++++ + FI
Sbjct: 292 YI------SEFELNVGKLKYDGPISKLRESNHQRY----ISYNIIAVYRVLQIDAKRQFI 341
Query: 603 GRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPL 662
+ +M IQ V S + ++I+ + N V P + R+H P
Sbjct: 342 NLSLDMGYYAKIQIQSVFSPIKTW--DAIIFNSLKEQN--KVIP--QGRSHPVQPYPGAF 395
Query: 663 ILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSI 722
+ EP Y ++ D SLYPS+I N T G F L+ I
Sbjct: 396 VKEPIPNRYK-YVMSFDLTSLYPSIIRQVNISPETIAGT-----------FKVAPLHDYI 443
Query: 723 RSLKKLQQKL-TISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAA-LQR 780
++ + + + SP+G+ + R G++P + ++ + R K M + N ++
Sbjct: 444 NAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKE 501
Query: 781 VLHARQLGLKLIANVTYGYTAAN 803
LH L + +V Y + ++
Sbjct: 502 ALHNPNLSVDEPLDVDYRFDFSD 524
>pdb|3LDS|A Chain A, Crystal Structure Of Rb69 Gp43 With Dna And Datp Opposite
8-
Length = 903
Score = 39.7 bits (91), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 86/383 (22%), Positives = 156/383 (40%), Gaps = 48/383 (12%)
Query: 435 SELP-EVRTKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLER-GYVL 492
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+ + Y+ R +
Sbjct: 176 DEVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIF 234
Query: 493 GLNLNQELS-----RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFE 547
G + + LS R+ +E SR+ + T + I+L++ N SY+ +
Sbjct: 235 GESTAKRLSPHRKTRVKVIENMYGSREII--TLFGISVLDYIDLYKKFSF-TNQPSYSLD 291
Query: 548 NIMYHVLHERIPLHSWKL-----LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFI 602
I L+ KL ++ E Y + + +I V ++++ + FI
Sbjct: 292 YI------SEFELNVGKLKYDGPISKLRESNHQRY----ISYNIIAVYRVLQIDAKRQFI 341
Query: 603 GRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPL 662
+ +M IQ V S + ++I+ + N V P + R+H P
Sbjct: 342 NLSLDMGYYAKIQIQSVFSPIKTW--DAIIFNSLKEQN--KVIP--QGRSHPVQPYPGAF 395
Query: 663 ILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSI 722
+ EP Y ++ D SLYPS+I N T G F L+ I
Sbjct: 396 VKEPIPNRYK-YVMSFDLTSLYPSIIRQVNISPETIAGT-----------FKVAPLHDYI 443
Query: 723 RSLKKLQQKL-TISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAA-LQR 780
++ + + + SP+G+ + R G++P + ++ + R K M + N ++
Sbjct: 444 NAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKE 501
Query: 781 VLHARQLGLKLIANVTYGYTAAN 803
LH L + +V Y + ++
Sbjct: 502 ALHNPNLSVDEPLDVDYRFDFSD 524
>pdb|1Q9Y|A Chain A, Crystal Structure Of Enterobacteria Phage Rb69 Gp43 Dna
Polymerase Complexed With 8-Oxoguanosine Containing Dna
Length = 906
Score = 39.7 bits (91), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 86/383 (22%), Positives = 156/383 (40%), Gaps = 48/383 (12%)
Query: 435 SELP-EVRTKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLER-GYVL 492
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+ + Y+ R +
Sbjct: 179 DEVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIF 237
Query: 493 GLNLNQELS-----RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFE 547
G + + LS R+ +E SR+ + T + I+L++ N SY+ +
Sbjct: 238 GESTAKRLSPHRKTRVKVIENMYGSREII--TLFGISVLDYIDLYKKFSF-TNQPSYSLD 294
Query: 548 NIMYHVLHERIPLHSWKL-----LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFI 602
I L+ KL ++ E Y + + +I V ++++ + FI
Sbjct: 295 YI------SEFELNVGKLKYDGPISKLRESNHQRY----ISYNIIAVYRVLQIDAKRQFI 344
Query: 603 GRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPL 662
+ +M IQ V S + ++I+ + N V P + R+H P
Sbjct: 345 NLSLDMGYYAKIQIQSVFSPIKTW--DAIIFNSLKEQN--KVIP--QGRSHPVQPYPGAF 398
Query: 663 ILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSI 722
+ EP Y ++ D SLYPS+I N T G F L+ I
Sbjct: 399 VKEPIPNRYK-YVMSFDLTSLYPSIIRQVNISPETIAGT-----------FKVAPLHDYI 446
Query: 723 RSLKKLQQKL-TISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAA-LQR 780
++ + + + SP+G+ + R G++P + ++ + R K M + N ++
Sbjct: 447 NAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKE 504
Query: 781 VLHARQLGLKLIANVTYGYTAAN 803
LH L + +V Y + ++
Sbjct: 505 ALHNPNLSVDEPLDVDYRFDFSD 527
>pdb|3SQ1|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dupcpp Opposite
Da
Length = 901
Score = 39.3 bits (90), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 86/383 (22%), Positives = 156/383 (40%), Gaps = 48/383 (12%)
Query: 435 SELP-EVRTKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLER-GYVL 492
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+ + Y+ R +
Sbjct: 176 DEVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIF 234
Query: 493 GLNLNQELS-----RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFE 547
G + + LS R+ +E SR+ + T + I+L++ N SY+ +
Sbjct: 235 GESTAKRLSPHRKTRVKVIENMYGSREII--TLFGISVLDYIDLYKKFSF-TNQPSYSLD 291
Query: 548 NIMYHVLHERIPLHSWKL-----LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFI 602
I L+ KL ++ E Y + + +I V ++++ + FI
Sbjct: 292 YI------SEFELNVGKLKYDGPISKLRESNHQRY----ISYNIIAVYRVLQIDAKRQFI 341
Query: 603 GRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPL 662
+ +M IQ V S + ++I+ + N V P + R+H P
Sbjct: 342 NLSLDMGYYAKIQIQSVFSPIKTW--DAIIFNSLKEQN--KVIP--QGRSHPVQPYPGAF 395
Query: 663 ILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSI 722
+ EP Y ++ D SLYPS+I N T G F L+ I
Sbjct: 396 VKEPIPNRYK-YVMSFDLTSLYPSIIRQVNISPETIAGT-----------FKVAPLHDYI 443
Query: 723 RSLKKLQQKL-TISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAA-LQR 780
++ + + + SP+G+ + R G++P + ++ + R K M + N ++
Sbjct: 444 NAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKE 501
Query: 781 VLHARQLGLKLIANVTYGYTAAN 803
LH L + +V Y + ++
Sbjct: 502 ALHNPNLSVDEPLDVDYRFDFSD 524
>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 = 39.3 bits (90), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 86/383 (22%), Positives = 156/383 (40%), Gaps = 48/383 (12%)
Query: 435 SELP-EVRTKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLER-GYVL 492
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+ + Y+ R +
Sbjct: 176 DEVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIF 234
Query: 493 GLNLNQELS-----RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFE 547
G + + LS R+ +E SR+ + T + I+L++ N SY+ +
Sbjct: 235 GESTAKRLSPHRKTRVKVIENMYGSREII--TLFGISVLDYIDLYKKFSF-TNQPSYSLD 291
Query: 548 NIMYHVLHERIPLHSWKL-----LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFI 602
I L+ KL ++ E Y + + +I V ++++ + FI
Sbjct: 292 YI------SEFELNVGKLKYDGPISKLRESNHQRY----ISYNIIAVYRVLQIDAKRQFI 341
Query: 603 GRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPL 662
+ +M IQ V S + ++I+ + N V P + R+H P
Sbjct: 342 NLSLDMGYYAKIQIQSVFSPIKTW--DAIIFNSLKEQN--KVIP--QGRSHPVQPYPGAF 395
Query: 663 ILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSI 722
+ EP Y ++ D SLYPS+I N T G F L+ I
Sbjct: 396 VKEPIPNRYK-YVMSFDLTSLYPSIIRQVNISPETIAGT-----------FKVAPLHDYI 443
Query: 723 RSLKKLQQKL-TISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAA-LQR 780
++ + + + SP+G+ + R G++P + ++ + R K M + N ++
Sbjct: 444 NAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKE 501
Query: 781 VLHARQLGLKLIANVTYGYTAAN 803
LH L + +V Y + ++
Sbjct: 502 ALHNPNLSVDEPLDVDYRFDFSD 524
>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 = 39.3 bits (90), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 86/383 (22%), Positives = 156/383 (40%), Gaps = 48/383 (12%)
Query: 435 SELP-EVRTKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLER-GYVL 492
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+ + Y+ R +
Sbjct: 176 DEVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIF 234
Query: 493 GLNLNQELS-----RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFE 547
G + + LS R+ +E SR+ + T + I+L++ N SY+ +
Sbjct: 235 GESTAKRLSPHRKTRVKVIENMYGSREII--TLFGISVLDYIDLYKKFSF-TNQPSYSLD 291
Query: 548 NIMYHVLHERIPLHSWKL-----LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFI 602
I L+ KL ++ E Y + + +I V ++++ + FI
Sbjct: 292 YI------SEFELNVGKLKYDGPISKLRESNHQRY----ISYNIIAVYRVLQIDAKRQFI 341
Query: 603 GRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPL 662
+ +M IQ V S + ++I+ + N V P + R+H P
Sbjct: 342 NLSLDMGYYAKIQIQSVFSPIKTW--DAIIFNSLKEQN--KVIP--QGRSHPVQPYPGAF 395
Query: 663 ILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSI 722
+ EP Y ++ D SLYPS+I N T G F L+ I
Sbjct: 396 VKEPIPNRYK-YVMSFDLTSLYPSIIRQVNISPETIAGT-----------FKVAPLHDYI 443
Query: 723 RSLKKLQQKL-TISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAA-LQR 780
++ + + + SP+G+ + R G++P + ++ + R K M + N ++
Sbjct: 444 NAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKE 501
Query: 781 VLHARQLGLKLIANVTYGYTAAN 803
LH L + +V Y + ++
Sbjct: 502 ALHNPNLSVDEPLDVDYRFDFSD 524
>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 = 39.3 bits (90), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 86/383 (22%), Positives = 156/383 (40%), Gaps = 48/383 (12%)
Query: 435 SELP-EVRTKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLER-GYVL 492
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+ + Y+ R +
Sbjct: 176 DEVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIF 234
Query: 493 GLNLNQELS-----RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFE 547
G + + LS R+ +E SR+ + T + I+L++ N SY+ +
Sbjct: 235 GESTAKRLSPHRKTRVKVIENMYGSREII--TLFGISVLDYIDLYKKFSF-TNQPSYSLD 291
Query: 548 NIMYHVLHERIPLHSWKL-----LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFI 602
I L+ KL ++ E Y + + +I V ++++ + FI
Sbjct: 292 YI------SEFELNVGKLKYDGPISKLRESNHQRY----ISYNIIAVYRVLQIDAKRQFI 341
Query: 603 GRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPL 662
+ +M IQ V S + ++I+ + N V P + R+H P
Sbjct: 342 NLSLDMGYYAKIQIQSVFSPIKTW--DAIIFNSLKEQN--KVIP--QGRSHPVQPYPGAF 395
Query: 663 ILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSI 722
+ EP Y ++ D SLYPS+I N T G F L+ I
Sbjct: 396 VKEPIPNRYK-YVMSFDLTSLYPSIIRQVNISPETIAGT-----------FKVAPLHDYI 443
Query: 723 RSLKKLQQKL-TISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAA-LQR 780
++ + + + SP+G+ + R G++P + ++ + R K M + N ++
Sbjct: 444 NAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKE 501
Query: 781 VLHARQLGLKLIANVTYGYTAAN 803
LH L + +V Y + ++
Sbjct: 502 ALHNPNLSVDEPLDVDYRFDFSD 524
>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 = 39.3 bits (90), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 86/383 (22%), Positives = 156/383 (40%), Gaps = 48/383 (12%)
Query: 435 SELP-EVRTKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLER-GYVL 492
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+ + Y+ R +
Sbjct: 176 DEVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIF 234
Query: 493 GLNLNQELS-----RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFE 547
G + + LS R+ +E SR+ + T + I+L++ N SY+ +
Sbjct: 235 GESTAKRLSPHRKTRVKVIENMYGSREII--TLFGISVLDYIDLYKKFSF-TNQPSYSLD 291
Query: 548 NIMYHVLHERIPLHSWKL-----LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFI 602
I L+ KL ++ E Y + + +I V ++++ + FI
Sbjct: 292 YI------SEFELNVGKLKYDGPISKLRESNHQRY----ISYNIIAVYRVLQIDAKRQFI 341
Query: 603 GRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPL 662
+ +M IQ V S + ++I+ + N V P + R+H P
Sbjct: 342 NLSLDMGYYAKIQIQSVFSPIKTW--DAIIFNSLKEQN--KVIP--QGRSHPVQPYPGAF 395
Query: 663 ILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSI 722
+ EP Y ++ D SLYPS+I N T G F L+ I
Sbjct: 396 VKEPIPNRYK-YVMSFDLTSLYPSIIRQVNISPETIAGT-----------FKVAPLHDYI 443
Query: 723 RSLKKLQQKL-TISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAA-LQR 780
++ + + + SP+G+ + R G++P + ++ + R K M + N ++
Sbjct: 444 NAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKE 501
Query: 781 VLHARQLGLKLIANVTYGYTAAN 803
LH L + +V Y + ++
Sbjct: 502 ALHNPNLSVDEPLDVDYRFDFSD 524
>pdb|3SUN|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dttp
Opposite 2ap (At Rich Sequence)
Length = 895
Score = 39.3 bits (90), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 86/383 (22%), Positives = 156/383 (40%), Gaps = 48/383 (12%)
Query: 435 SELP-EVRTKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLER-GYVL 492
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+ + Y+ R +
Sbjct: 176 DEVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIF 234
Query: 493 GLNLNQELS-----RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFE 547
G + + LS R+ +E SR+ + T + I+L++ N SY+ +
Sbjct: 235 GESTAKRLSPHRKTRVKVIENMYGSREII--TLFGISVLDYIDLYKKFSF-TNQPSYSLD 291
Query: 548 NIMYHVLHERIPLHSWKL-----LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFI 602
I L+ KL ++ E Y + + +I V ++++ + FI
Sbjct: 292 YI------SEFELNVGKLKYDGPISKLRESNHQRY----ISYNIIAVYRVLQIDAKRQFI 341
Query: 603 GRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPL 662
+ +M IQ V S + ++I+ + N V P + R+H P
Sbjct: 342 NLSLDMGYYAKIQIQSVFSPIKTW--DAIIFNSLKEQN--KVIP--QGRSHPVQPYPGAF 395
Query: 663 ILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSI 722
+ EP Y ++ D SLYPS+I N T G F L+ I
Sbjct: 396 VKEPIPNRYK-YVMSFDLTSLYPSIIRQVNISPETIAGT-----------FKVAPLHDYI 443
Query: 723 RSLKKLQQKL-TISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAA-LQR 780
++ + + + SP+G+ + R G++P + ++ + R K M + N ++
Sbjct: 444 NAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKE 501
Query: 781 VLHARQLGLKLIANVTYGYTAAN 803
LH L + +V Y + ++
Sbjct: 502 ALHNPNLSVDEPLDVDYRFDFSD 524
>pdb|3SUQ|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dctp
Opposite 2ap (At Rich Sequence)
Length = 897
Score = 39.3 bits (90), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 86/383 (22%), Positives = 156/383 (40%), Gaps = 48/383 (12%)
Query: 435 SELP-EVRTKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLER-GYVL 492
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+ + Y+ R +
Sbjct: 176 DEVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIF 234
Query: 493 GLNLNQELS-----RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFE 547
G + + LS R+ +E SR+ + T + I+L++ N SY+ +
Sbjct: 235 GESTAKRLSPHRKTRVKVIENMYGSREII--TLFGISVLDYIDLYKKFSF-TNQPSYSLD 291
Query: 548 NIMYHVLHERIPLHSWKL-----LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFI 602
I L+ KL ++ E Y + + +I V ++++ + FI
Sbjct: 292 YI------SEFELNVGKLKYDGPISKLRESNHQRY----ISYNIIAVYRVLQIDAKRQFI 341
Query: 603 GRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPL 662
+ +M IQ V S + ++I+ + N V P + R+H P
Sbjct: 342 NLSLDMGYYAKIQIQSVFSPIKTW--DAIIFNSLKEQN--KVIP--QGRSHPVQPYPGAF 395
Query: 663 ILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSI 722
+ EP Y ++ D SLYPS+I N T G F L+ I
Sbjct: 396 VKEPIPNRYK-YVMSFDLTSLYPSIIRQVNISPETIAGT-----------FKVAPLHDYI 443
Query: 723 RSLKKLQQKL-TISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAA-LQR 780
++ + + + SP+G+ + R G++P + ++ + R K M + N ++
Sbjct: 444 NAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKE 501
Query: 781 VLHARQLGLKLIANVTYGYTAAN 803
LH L + +V Y + ++
Sbjct: 502 ALHNPNLSVDEPLDVDYRFDFSD 524
>pdb|1WAF|A Chain A, Dna Polymerase From Bacteriophage Rb69
pdb|1WAF|B Chain B, Dna Polymerase From Bacteriophage Rb69
pdb|1CLQ|A Chain A, Crystal Structure Of A Replication Fork Dna Polymerase
Editing Complex At 2.7 A Resolution
pdb|1IH7|A Chain A, High-Resolution Structure Of Apo Rb69 Dna Polymerase
pdb|1WAJ|A Chain A, Dna Polymerase From Bacteriophage Rb69
pdb|3UIQ|A Chain A, Rb69 Dna Polymerase Ternary Complex Containing Dupnpp
Length = 903
Score = 39.3 bits (90), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 86/383 (22%), Positives = 155/383 (40%), Gaps = 48/383 (12%)
Query: 435 SELP-EVRTKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLER-GYVL 492
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+ Y+ R +
Sbjct: 176 DEVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFDIPYVYNRIKNIF 234
Query: 493 GLNLNQELS-----RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFE 547
G + + LS R+ +E SR+ + T + I+L++ N SY+ +
Sbjct: 235 GESTAKRLSPHRKTRVKVIENMYGSREII--TLFGISVLDYIDLYKKFSF-TNQPSYSLD 291
Query: 548 NIMYHVLHERIPLHSWKL-----LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFI 602
I L+ KL ++ E Y + + +I V ++++ + FI
Sbjct: 292 YI------SEFELNVGKLKYDGPISKLRESNHQRY----ISYNIIDVYRVLQIDAKRQFI 341
Query: 603 GRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPL 662
+ +M IQ V S + ++I+ + N V P + R+H P
Sbjct: 342 NLSLDMGYYAKIQIQSVFSPIKTW--DAIIFNSLKEQN--KVIP--QGRSHPVQPYPGAF 395
Query: 663 ILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSI 722
+ EP Y ++ D SLYPS+I N T G F L+ I
Sbjct: 396 VKEPIPNRYK-YVMSFDLTSLYPSIIRQVNISPETIAGT-----------FKVAPLHDYI 443
Query: 723 RSLKKLQQKL-TISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAA-LQR 780
++ + + + SP+G+ + R G++P + ++ + R K M + N ++
Sbjct: 444 NAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKE 501
Query: 781 VLHARQLGLKLIANVTYGYTAAN 803
LH L + +V Y + ++
Sbjct: 502 ALHNPNLSVDEPLDVDYRFDFSD 524
>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 = 38.9 bits (89), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 86/383 (22%), Positives = 155/383 (40%), Gaps = 48/383 (12%)
Query: 435 SELP-EVRTKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLER-GYVL 492
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+ Y+ R +
Sbjct: 176 DEVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFDIPYVYNRIKNIF 234
Query: 493 GLNLNQELS-----RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFE 547
G + + LS R+ +E SR+ + T + I+L++ N SY+ +
Sbjct: 235 GESTAKRLSPHRKTRVKVIENMYGSREII--TLFGISVLDYIDLYKKFSF-TNQPSYSLD 291
Query: 548 NIMYHVLHERIPLHSWKL-----LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFI 602
I L+ KL ++ E Y + + +I V ++++ + FI
Sbjct: 292 YI------SEFELNVGKLKYDGPISKLRESNHQRY----ISYNIIDVYRVLQIDAKRQFI 341
Query: 603 GRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPL 662
+ +M IQ V S + ++I+ + N V P + R+H P
Sbjct: 342 NLSLDMGYYAKIQIQSVFSPIKTW--DAIIFNSLKEQN--KVIP--QGRSHPVQPYPGAF 395
Query: 663 ILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSI 722
+ EP Y ++ D SLYPS+I N T G F L+ I
Sbjct: 396 VKEPIPNRYK-YVMSFDLTSLYPSIIRQVNISPETIAGT-----------FKVAPLHDYI 443
Query: 723 RSLKKLQQKL-TISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAA-LQR 780
++ + + + SP+G+ + R G++P + ++ + R K M + N ++
Sbjct: 444 NAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKE 501
Query: 781 VLHARQLGLKLIANVTYGYTAAN 803
LH L + +V Y + ++
Sbjct: 502 ALHNPNLSVDEPLDVDYRFDFSD 524
>pdb|3CQ8|A Chain A, Ternary Complex Of The L415f Mutant Rb69 Exo(-)polymerase
Length = 903
Score = 38.1 bits (87), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 85/383 (22%), Positives = 155/383 (40%), Gaps = 48/383 (12%)
Query: 435 SELP-EVRTKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLER-GYVL 492
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+ + Y+ R +
Sbjct: 176 DEVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIF 234
Query: 493 GLNLNQELS-----RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFE 547
G + + LS R+ +E SR+ + T + I+L++ N SY+ +
Sbjct: 235 GESTAKRLSPHRKTRVKVIENMYGSREII--TLFGISVLDYIDLYKKFSF-TNQPSYSLD 291
Query: 548 NIMYHVLHERIPLHSWKL-----LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFI 602
I L+ KL ++ E Y + + +I V ++++ + FI
Sbjct: 292 YI------SEFELNVGKLKYDGPISKLRESNHQRY----ISYNIIAVYRVLQIDAKRQFI 341
Query: 603 GRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPL 662
+ +M IQ V S + ++I+ + N V P + R+H P
Sbjct: 342 NLSLDMGYYAKIQIQSVFSPIKTW--DAIIFNSLKEQN--KVIP--QGRSHPVQPYPGAF 395
Query: 663 ILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSI 722
+ EP Y ++ D S YPS+I N T G F L+ I
Sbjct: 396 VKEPIPNRYK-YVMSFDLTSFYPSIIRQVNISPETIAGT-----------FKVAPLHDYI 443
Query: 723 RSLKKLQQKL-TISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAA-LQR 780
++ + + + SP+G+ + R G++P + ++ + R K M + N ++
Sbjct: 444 NAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKE 501
Query: 781 VLHARQLGLKLIANVTYGYTAAN 803
LH L + +V Y + ++
Sbjct: 502 ALHNPNLSVDEPLDVDYRFDFSD 524
>pdb|3SPZ|A Chain A, Dna Polymerase(L415aL561AS565GY567A) TERNARY COMPLEX WITH
DUPCPP Opposite Da (Ca2+)
pdb|4FJ5|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp/dt
pdb|4FJ7|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dgtp/dt
pdb|4FJ8|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp/dt
pdb|4FJ9|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp/dt
pdb|4FJG|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp/dc
pdb|4FJH|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dgtp/dc
pdb|4FJI|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp/dc
pdb|4FJJ|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp/dc
pdb|4FJK|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp/da
pdb|4FJL|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dgtp/da
pdb|4FJN|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp/da
pdb|4FJX|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp/dg
pdb|4FK0|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp/dg
pdb|4FK2|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp/dg
pdb|4FK4|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dgtp/dg
Length = 903
Score = 37.7 bits (86), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 85/383 (22%), Positives = 155/383 (40%), Gaps = 48/383 (12%)
Query: 435 SELP-EVRTKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLER-GYVL 492
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+ + Y+ R +
Sbjct: 176 DEVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIF 234
Query: 493 GLNLNQELS-----RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFE 547
G + + LS R+ +E SR+ + T + I+L++ N SY+ +
Sbjct: 235 GESTAKRLSPHRKTRVKVIENMYGSREII--TLFGISVLDYIDLYKKFSF-TNQPSYSLD 291
Query: 548 NIMYHVLHERIPLHSWKL-----LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFI 602
I L+ KL ++ E Y + + +I V ++++ + FI
Sbjct: 292 YI------SEFELNVGKLKYDGPISKLRESNHQRY----ISYNIIAVYRVLQIDAKRQFI 341
Query: 603 GRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPL 662
+ +M IQ V S + ++I+ + N V P + R+H P
Sbjct: 342 NLSLDMGYYAKIQIQSVFSPIKTW--DAIIFNSLKEQN--KVIP--QGRSHPVQPYPGAF 395
Query: 663 ILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSI 722
+ EP Y ++ D S YPS+I N T G F L+ I
Sbjct: 396 VKEPIPNRYK-YVMSFDLTSAYPSIIRQVNISPETIAGT-----------FKVAPLHDYI 443
Query: 723 RSLKKLQQKL-TISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAA-LQR 780
++ + + + SP+G+ + R G++P + ++ + R K M + N ++
Sbjct: 444 NAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKE 501
Query: 781 VLHARQLGLKLIANVTYGYTAAN 803
LH L + +V Y + ++
Sbjct: 502 ALHNPNLSVDEPLDVDYRFDFSD 524
>pdb|3KD1|E Chain E, Closed Binary Complex Of An Rb69 Gp43 Fingers Domain
Mutant Complexed With An Acyclic Gmp Terminated Primer
Template Pair.
pdb|3KD5|E Chain E, Closed Ternary Complex Of An Rb69 Gp43 Fingers Domain
Mutant Complexed With An Acyclic Gmp Terminated Primer
Template Pair And Phosphonoformic Acid
Length = 913
Score = 37.4 bits (85), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 106/489 (21%), Positives = 190/489 (38%), Gaps = 104/489 (21%)
Query: 435 SELP-EVRTKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLER-GYVL 492
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+ + Y+ R +
Sbjct: 176 DEVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIF 234
Query: 493 GLNLNQELS-----RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFE 547
G + + LS R+ +E SR+ + T + I+L++ N SY+ +
Sbjct: 235 GESTAKRLSPHRKTRVKVIENMYGSREII--TLFGISVLDYIDLYKKFSF-TNQPSYSLD 291
Query: 548 NIMYHVLHERIPLHSWKL-----LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFI 602
I L+ KL ++ E Y + + +I V ++++ + FI
Sbjct: 292 YI------SEFELNVGKLKYDGPISKLRESNHQRY----ISYNIIDVYRVLQIDAKRQFI 341
Query: 603 GRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPL 662
+ +M IQ V S + ++I+ + N V P + R+H P
Sbjct: 342 NLSLDMGYYAKIQIQSVFSPIKTW--DAIIFNSLKEQN--KVIP--QGRSHPVQPYPGAF 395
Query: 663 ILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSI 722
+ EP Y ++ D SLYPS+I N T G F L+ I
Sbjct: 396 VKEPIPNRYK-YVMSFDLTSLYPSIIRQVNISPETIAGT-----------FKVAPLHDYI 443
Query: 723 RSLKKLQQKL-TISPSGVAFVDKSIRCGILP------------------------KMLQE 757
++ + + + SP+G+ + R G++P ++++E
Sbjct: 444 NAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKWVSQRKEHKGYMLAAQRNGEIIKE 501
Query: 758 IL-------------DTRL----MVKQSMKEYKSNAALQRVLHAR---------QLGLKL 791
L D R +K+ +K+ + + + + A+ Q+ LK+
Sbjct: 502 ALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQMALKV 561
Query: 792 IANVTYGYTAANFSGRMPCVEVGDSVVSKGRETLQKAIETVNN------TSKWQCRVVYG 845
N YG N R + ++ + G+ LQ VN ++ + V+YG
Sbjct: 562 TCNSLYG-ALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFVLYG 620
Query: 846 DTDSMFVLA 854
DTDS++V A
Sbjct: 621 DTDSIYVSA 629
>pdb|3SPY|A Chain A, Rb69 Dna Polymerase(L415aL561AS565GY567A) TERNARY COMPLEX
WITH Dupcpp Opposite Da
Length = 901
Score = 37.4 bits (85), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 85/383 (22%), Positives = 155/383 (40%), Gaps = 48/383 (12%)
Query: 435 SELP-EVRTKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLER-GYVL 492
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+ + Y+ R +
Sbjct: 176 DEVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIF 234
Query: 493 GLNLNQELS-----RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFE 547
G + + LS R+ +E SR+ + T + I+L++ N SY+ +
Sbjct: 235 GESTAKRLSPHRKTRVKVIENMYGSREII--TLFGISVLDYIDLYKKFSF-TNQPSYSLD 291
Query: 548 NIMYHVLHERIPLHSWKL-----LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFI 602
I L+ KL ++ E Y + + +I V ++++ + FI
Sbjct: 292 YI------SEFELNVGKLKYDGPISKLRESNHQRY----ISYNIIAVYRVLQIDAKRQFI 341
Query: 603 GRTSEMARLFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPL 662
+ +M IQ V S + ++I+ + N V P + R+H P
Sbjct: 342 NLSLDMGYYAKIQIQSVFSPIKTW--DAIIFNSLKEQN--KVIP--QGRSHPVQPYPGAF 395
Query: 663 ILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSI 722
+ EP Y ++ D S YPS+I N T G F L+ I
Sbjct: 396 VKEPIPNRYK-YVMSFDLTSAYPSIIRQVNISPETIAGT-----------FKVAPLHDYI 443
Query: 723 RSLKKLQQKL-TISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYKSNAA-LQR 780
++ + + + SP+G+ + R G++P + ++ + R K M + N ++
Sbjct: 444 NAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKE 501
Query: 781 VLHARQLGLKLIANVTYGYTAAN 803
LH L + +V Y + ++
Sbjct: 502 ALHNPNLSVDEPLDVDYRFDFSD 524
>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
Length = 523
Score = 32.3 bits (72), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 25/121 (20%), Positives = 52/121 (42%), Gaps = 9/121 (7%)
Query: 441 RTKPIQMHFVSNEKELFSIFIENVRQWDPDILIGYEIETLS-WGYLLERGYVLGLNLNQE 499
RT I++ +++ E+ + F+E++ W+P +L E +S WG+ Y L Q
Sbjct: 112 RTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQR 171
Query: 500 LSRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIP 559
+ + ++ D + ++ L L + + S+ NI Y ++ + P
Sbjct: 172 FPTLPFMALTATADDTTRQD--------IVRLLGLNDPLIQISSFDRPNIRYMLMEKFKP 223
Query: 560 L 560
L
Sbjct: 224 L 224
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 0.135 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 32,198,766
Number of Sequences: 62578
Number of extensions: 1253911
Number of successful extensions: 2680
Number of sequences better than 100.0: 44
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 24
Number of HSP's that attempted gapping in prelim test: 2509
Number of HSP's gapped (non-prelim): 117
length of query: 1200
length of database: 14,973,337
effective HSP length: 110
effective length of query: 1090
effective length of database: 8,089,757
effective search space: 8817835130
effective search space used: 8817835130
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: 57 (26.6 bits)