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= 000430
(1517 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4FVM|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha
pdb|4FXD|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To
Dna/rna
pdb|4FXD|B Chain B, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To
Dna/rna
Length = 910
Score = 456 bits (1172), Expect = e-128, Method: Compositional matrix adjust.
Identities = 306/880 (34%), Positives = 480/880 (54%), Gaps = 74/880 (8%)
Query: 435 VSNYIVSPVKRRYAFGQAEIPAGENYVLKINYPFKDP-----PLPADLKGENFCSLLGTH 489
+ N P K +Y+F +IP+ +Y LK+ P++ P +P+DL + F + G +
Sbjct: 72 LDNIRAKPQKMKYSFELPDIPSESDY-LKVLLPYQTPKSSRDTIPSDLSSDTFYHVFGGN 130
Query: 490 SSALELFLVKRKVKGPSWLSISKFSSCPAPQRVSWCKYEITVDSPKDIRVSSSSKHVAEV 549
S+ E F+++ ++ GP WL I K + + + S C E++VD P++I +++ +
Sbjct: 131 SNIFESFVIQNRIMGPCWLDI-KGADFNSIRNASHCAVEVSVDKPQNITPTTTKT----M 185
Query: 550 PPVTVTAINLKTVFNKRQDVNEIVSASVVCCHKAKIDTPMLASEWKKPGMLSHFTVVRKL 609
P + +++++T+ N +++ EIVS ++ +D+P+ E KP L T+VR
Sbjct: 186 PNLRCLSLSIQTLMNPKENKQEIVSITLSAYRNISLDSPI--PENIKPDDLC--TLVRPP 241
Query: 610 DGGIFPMGFNKEATDRNSKAGSNVLCCESSERALLNRLMIELYKLDSDVLVGHNISGFDL 669
FP+G A + G L ++E+A+L+ L D DV++GH + L
Sbjct: 242 QSTSFPLGL--AALAKQKLPGRVRLF--NNEKAMLSCFCAMLKVEDPDVIIGHRLQNVYL 297
Query: 670 DVLLHRAQVCRVPSSMWSKIGRLKRSEMPKLRKGRTIFGSGASPG----IMSCIAGRLLC 725
DVL HR +P+ +S IGR R P+ FG G S I +GRL+C
Sbjct: 298 DVLAHRMHDLNIPT--FSSIGRRLRRTWPEK------FGRGNSNMNHFFISDICSGRLIC 349
Query: 726 DTFLCSRDLLREV-----SYSLTQLAKTQLNKDRKEVGPHDVLKMFQT-LESLMELIEYG 779
D + ++ + + S+ L+++ + K+ K + +Q + S+ ++
Sbjct: 350 DI---ANEMGQSLTPKCQSWDLSEMYQVTCEKEHKPLDIDYQNPQYQNDVNSMTMALQEN 406
Query: 780 ETDAWLSMELMFHLSVLPLTRQLTNISGNLWGKTLQGARAQRVEYLLLHAFRAKKYIVPD 839
T+ +S E+ + + +L LT+QLTN++GN W +TL G RA R EY+LLH F +IVPD
Sbjct: 407 ITNCMISAEVSYRIQLLTLTKQLTNLAGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPD 466
Query: 840 KFTYVKETKMAKQRSNHGVEDRNVEELTNEDANFDNDTSHNDHRKGKRGPAYAGGLVLEP 899
K ++ KQR N EE N DA ++ +K K Y GGLV EP
Sbjct: 467 KEG--NRSRAQKQRQN--------EE--NADAPVNS-------KKAK----YQGGLVFEP 503
Query: 900 KKGLYDKYILLLDFNSLYPSIIQEYNICFTTVERSPDGL--VPHLPSSKT-TGVLPELLK 956
+KGL+ Y+L++DFNSLYPSIIQE+NICFTTV+R+ + + +P +P S+ GVLP LL
Sbjct: 504 EKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVDRNKEDIDELPSVPPSEVDQGVLPRLLA 563
Query: 957 NLVQRRRMVKTWMKTASG-LKIQQLDIQQQALKLTANSMYGCLGFSNSRFYAKPLAELIT 1015
NLV RRR VK MKT + K Q DI+QQALKLTANSMYGCLG+ NSRFYAKPLA L+T
Sbjct: 564 NLVDRRREVKKVMKTETDPHKRVQCDIRQQALKLTANSMYGCLGYVNSRFYAKPLAMLVT 623
Query: 1016 QQGREILRSTVDLVQNNLNLEVIYGDTDSIMIHSXXXXXXXXXXXXXXVIQEVNKKYKCL 1075
+GREIL +T L + ++NL V+YGDTDS+MI + + VN++Y+ L
Sbjct: 624 NKGREILMNTRQLAE-SMNLLVVYGDTDSVMIDTGCDNYADAIKIGLGFKRLVNERYRLL 682
Query: 1076 EIDLDGXXXXXXXXXXXXXXXXXXQF-KDGMPYEVIERKGLDMVRRDWSLLSKEVGDFCL 1134
EID+D K+G V+E KGLDM RR++ LS++V L
Sbjct: 683 EIDIDNVFKKLLLHAKKKYAALTVNLDKNGNGTTVLEVKGLDMKRREFCPLSRDVSIHVL 742
Query: 1135 SQILSERSCEDVVESIHNSLMKVQEDMRSGQVALEKYVITKTLTKPPEAYPDAKNQPHVQ 1194
+ ILS++ E+ ++ +++ L ++ + + + ++KY I L+K P+AYP KN P VQ
Sbjct: 743 NTILSDKDPEEALQEVYDYLEDIRIKVETNNIRIDKYKINMKLSKDPKAYPGGKNMPAVQ 802
Query: 1195 VALRLKQSGYSTGCSAGDTVPYIICCEQGTSSGS---SVGIAQRARHPDELKKGDGKWMI 1251
VALR++++G AG + ++I + + + ++ +A+RA +E+ +
Sbjct: 803 VALRMRKAGRVV--KAGSVITFVITKQDEIDNAADTPALSVAERAHALNEVMIKSNNLIP 860
Query: 1252 DIDYYASQQIHPVVSRLCASIEGTSPERLADCLGLDPSKF 1291
D YY +QI V RL I+ + RL++ LGLD K+
Sbjct: 861 DPQYYLEKQIFAPVERLLERIDSFNVVRLSEALGLDSKKY 900
>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 = 455 bits (1170), Expect = e-127, Method: Compositional matrix adjust.
Identities = 307/882 (34%), Positives = 481/882 (54%), Gaps = 78/882 (8%)
Query: 435 VSNYIVSPVKRRYAFGQAEIPAGENYVLKINYPFKDP-----PLPADLKGENFCSLLGTH 489
+ N P K +Y+F +IP+ +Y LK+ P++ P +P+DL + F + G +
Sbjct: 72 LDNIRAKPQKMKYSFELPDIPSESDY-LKVLLPYQTPKSSRDTIPSDLSSDTFYHVFGGN 130
Query: 490 SSALELFLVKRKVKGPSWLSI--SKFSSCPAPQRVSWCKYEITVDSPKDIRVSSSSKHVA 547
S+ E F+++ ++ GP WL I + F+S A S C E++VD P++I +++
Sbjct: 131 SNIFESFVIQNRIMGPCWLDIKGADFNSIAA---ASHCAVEVSVDKPQNITPTTTKT--- 184
Query: 548 EVPPVTVTAINLKTVFNKRQDVNEIVSASVVCCHKAKIDTPMLASEWKKPGMLSHFTVVR 607
+P + +++++T+ N +++ EIVS ++ +D+P+ E KP L T+VR
Sbjct: 185 -MPNLRCLSLSIQTLMNPKENKQEIVSITLSAYRNISLDSPI--PENIKPDDLC--TLVR 239
Query: 608 KLDGGIFPMGFNKEATDRNSKAGSNVLCCESSERALLNRLMIELYKLDSDVLVGHNISGF 667
FP+G A + G L ++E+A+L+ L D DV++GH +
Sbjct: 240 PPQSTSFPLGL--AALAKQKLPGRVRLF--NNEKAMLSCFCAMLKVEDPDVIIGHRLQNV 295
Query: 668 DLDVLLHRAQVCRVPSSMWSKIGRLKRSEMPKLRKGRTIFGSGASPG----IMSCIAGRL 723
LDVL HR +P+ +S IGR R P+ FG G S I +GRL
Sbjct: 296 YLDVLAHRMHDLNIPT--FSSIGRRLRRTWPEK------FGRGNSNMNHFFISDICSGRL 347
Query: 724 LCDTFLCSRDLLREV-----SYSLTQLAKTQLNKDRKEVGPHDVLKMFQT-LESLMELIE 777
+CD + ++ + + S+ L+++ + K+ K + +Q + S+ ++
Sbjct: 348 ICDI---ANEMGQSLTPKCQSWDLSEMYQVTCEKEHKPLDIDYQNPQYQNDVNSMTMALQ 404
Query: 778 YGETDAWLSMELMFHLSVLPLTRQLTNISGNLWGKTLQGARAQRVEYLLLHAFRAKKYIV 837
T+ +S E+ + + +L LT+QLTN++GN W +TL G RA R EY+LLH F +IV
Sbjct: 405 ENITNCMISAEVSYRIQLLTLTKQLTNLAGNAWAQTLGGTRAGRNEYILLHEFSRNGFIV 464
Query: 838 PDKFTYVKETKMAKQRSNHGVEDRNVEELTNEDANFDNDTSHNDHRKGKRGPAYAGGLVL 897
PDK ++ KQR N EE N DA ++ +K K Y GGLV
Sbjct: 465 PDKEG--NRSRAQKQRQN--------EE--NADAPVNS-------KKAK----YQGGLVF 501
Query: 898 EPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTVERSPDGL--VPHLPSSKT-TGVLPEL 954
EP+KGL+ Y+L++DFNSLYPSIIQE+NICFTTV+R+ + + +P +P S+ GVLP L
Sbjct: 502 EPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVDRNKEDIDELPSVPPSEVDQGVLPRL 561
Query: 955 LKNLVQRRRMVKTWMKTASG-LKIQQLDIQQQALKLTANSMYGCLGFSNSRFYAKPLAEL 1013
L NLV RRR VK MKT + K Q DI+QQALKLTANSMYGCLG+ NSRFYAKPLA L
Sbjct: 562 LANLVDRRREVKKVMKTETDPHKRVQCDIRQQALKLTANSMYGCLGYVNSRFYAKPLAML 621
Query: 1014 ITQQGREILRSTVDLVQNNLNLEVIYGDTDSIMIHSXXXXXXXXXXXXXXVIQEVNKKYK 1073
+T +GREIL +T L + ++NL V+YGDT+S+MI + + VN++Y+
Sbjct: 622 VTNKGREILMNTRQLAE-SMNLLVVYGDTNSVMIDTGCDNYADAIKIGLGFKRLVNERYR 680
Query: 1074 CLEIDLDGXXXXXXXXXXXXXXXXXXQF-KDGMPYEVIERKGLDMVRRDWSLLSKEVGDF 1132
LEID+D K+G V+E KGLDM RR++ LS++V
Sbjct: 681 LLEIDIDNVFKKLLLHAKKKYAALTVNLDKNGNGTTVLEVKGLDMKRREFCPLSRDVSIH 740
Query: 1133 CLSQILSERSCEDVVESIHNSLMKVQEDMRSGQVALEKYVITKTLTKPPEAYPDAKNQPH 1192
L+ ILS++ E+ ++ +++ L ++ + + + ++KY I L+K P+AYP KN P
Sbjct: 741 VLNTILSDKDPEEALQEVYDYLEDIRIKVETNNIRIDKYKINMKLSKDPKAYPGGKNMPA 800
Query: 1193 VQVALRLKQSGYSTGCSAGDTVPYIICCEQGTSSGS---SVGIAQRARHPDELKKGDGKW 1249
VQVALR++++G AG + ++I + + + ++ +A+RA +E+
Sbjct: 801 VQVALRMRKAGRVV--KAGSVITFVITKQDEIDNAADTPALSVAERAHALNEVMIKSNNL 858
Query: 1250 MIDIDYYASQQIHPVVSRLCASIEGTSPERLADCLGLDPSKF 1291
+ D YY +QI V RL I+ + RL++ LGLD K+
Sbjct: 859 IPDPQYYLEKQIFAPVERLLERIDSFNVVRLSEALGLDSKKY 900
>pdb|4B08|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha,
Selenomethionine Protein
Length = 910
Score = 434 bits (1117), Expect = e-121, Method: Compositional matrix adjust.
Identities = 300/877 (34%), Positives = 463/877 (52%), Gaps = 68/877 (7%)
Query: 435 VSNYIVSPVKRRYAFGQAEIPAGENYVLKINYPFKDP-----PLPADLKGENFCSLLGTH 489
+ N P K +Y+F +IP+ +Y LK+ P++ P +P+DL + F + G +
Sbjct: 72 LDNIRAKPQKXKYSFELPDIPSESDY-LKVLLPYQTPKSSRDTIPSDLSSDTFYHVFGGN 130
Query: 490 SSALELFLVKRKVKGPSWLSISKFSSCPAPQRVSWCKYEITVDSPKDIRVSSSSKHVAEV 549
S+ E F+++ ++ GP WL I K + + + S C E++VD P++I +++
Sbjct: 131 SNIFESFVIQNRIXGPCWLDI-KGADFNSIRNASHCAVEVSVDKPQNITPTTTKTXPN-- 187
Query: 550 PPVTVTAINLKTVFNKRQDVNEIVSASVVCCHKAKIDTPMLASEWKKPGMLSHFTVVRKL 609
+ +++++T+ N +++ EIVS ++ +D+P+ E KP L T+VR
Sbjct: 188 --LRCLSLSIQTLXNPKENKQEIVSITLSAYRNISLDSPI--PENIKPDDLC--TLVRPP 241
Query: 610 DGGIFPMGFNKEATDRNSKAGSNVLCCESSERALLNRLMIELYKLDSDVLVGHNISGFDL 669
FP+G A + G L ++E+A L+ L D DV++GH + L
Sbjct: 242 QSTSFPLGL--AALAKQKLPGRVRLF--NNEKAXLSCFCAXLKVEDPDVIIGHRLQNVYL 297
Query: 670 DVLLHRAQVCRVPSSMWSKIGRLKRSEMPKLRKGRTIFGSGASPG----IMSCIAGRLLC 725
DVL HR +P+ +S IGR R P+ FG G S I +GRL+C
Sbjct: 298 DVLAHRXHDLNIPT--FSSIGRRLRRTWPEK------FGRGNSNXNHFFISDICSGRLIC 349
Query: 726 DTFLCSRDLL--REVSYSLTQLAKTQLNKDRKEVGPHDVLKMFQT-LESLMELIEYGETD 782
D L + S+ L++ + K+ K + +Q + S ++ T+
Sbjct: 350 DIANEXGQSLTPKCQSWDLSEXYQVTCEKEHKPLDIDYQNPQYQNDVNSXTXALQENITN 409
Query: 783 AWLSMELMFHLSVLPLTRQLTNISGNLWGKTLQGARAQRVEYLLLHAFRAKKYIVPDKFT 842
+S E+ + + +L LT+QLTN++GN W +TL G RA R EY+LLH F +IVPDK
Sbjct: 410 CXISAEVSYRIQLLTLTKQLTNLAGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDKEG 469
Query: 843 YVKETKMAKQRSNHGVEDRNVEELTNEDANFDNDTSHNDHRKGKRGPAYAGGLVLEPKKG 902
++ KQR N N DA ++ +K K Y GGLV EP+KG
Sbjct: 470 --NRSRAQKQRQNE----------ENADAPVNS-------KKAK----YQGGLVFEPEKG 506
Query: 903 LYDKYILLLDFNSLYPSIIQEYNICFTTVERSPDGL--VPHLPSSKT-TGVLPELLKNLV 959
L+ Y+L+ DFNSLYPSIIQE+NICFTTV+R+ + + +P +P S+ GVLP LL NLV
Sbjct: 507 LHKNYVLVXDFNSLYPSIIQEFNICFTTVDRNKEDIDELPSVPPSEVDQGVLPRLLANLV 566
Query: 960 QRRRMVKTWMKTASG-LKIQQLDIQQQALKLTANSMYGCLGFSNSRFYAKPLAELITQQG 1018
RRR VK KT + K Q DI+QQALKLTANS YGCLG+ NSRFYAKPLA L+T +G
Sbjct: 567 DRRREVKKVXKTETDPHKRVQCDIRQQALKLTANSXYGCLGYVNSRFYAKPLAXLVTNKG 626
Query: 1019 REILRSTVDLVQNNLNLEVIYGDTDSIMIHSXXXXXXXXXXXXXXVIQEVNKKYKCLEID 1078
REIL +T L + + NL V+YGDTDS+ I + + VN++Y+ LEID
Sbjct: 627 REILXNTRQLAE-SXNLLVVYGDTDSVXIDTGCDNYADAIKIGLGFKRLVNERYRLLEID 685
Query: 1079 LDGXXXXXXXXXXXXXXXXXXQF-KDGMPYEVIERKGLDMVRRDWSLLSKEVGDFCLSQI 1137
+D K+G V+E KGLD RR++ LS++V L+ I
Sbjct: 686 IDNVFKKLLLHAKKKYAALTVNLDKNGNGTTVLEVKGLDXKRREFCPLSRDVSIHVLNTI 745
Query: 1138 LSERSCEDVVESIHNSLMKVQEDMRSGQVALEKYVITKTLTKPPEAYPDAKNQPHVQVAL 1197
LS++ E+ ++ +++ L ++ + + + ++KY I L+K P+AYP KN P VQVAL
Sbjct: 746 LSDKDPEEALQEVYDYLEDIRIKVETNNIRIDKYKINXKLSKDPKAYPGGKNXPAVQVAL 805
Query: 1198 RLKQSGYSTGCSAGDTVPYIICCEQGTSSGS---SVGIAQRARHPDELKKGDGKWMIDID 1254
R +++G AG + ++I + + + ++ +A+RA +E+ + D
Sbjct: 806 RXRKAGRVV--KAGSVITFVITKQDEIDNAADTPALSVAERAHALNEVXIKSNNLIPDPQ 863
Query: 1255 YYASQQIHPVVSRLCASIEGTSPERLADCLGLDPSKF 1291
YY +QI V RL I+ + RL++ LGLD K+
Sbjct: 864 YYLEKQIFAPVERLLERIDSFNVVRLSEALGLDSKKY 900
>pdb|1TGO|A Chain A, Thermostable B Type Dna Polymerase From Thermococcus
Gorgonarius
Length = 773
Score = 179 bits (454), Expect = 1e-44, Method: Compositional matrix adjust.
Identities = 166/646 (25%), Positives = 278/646 (43%), Gaps = 93/646 (14%)
Query: 638 SSERALLNRLMIELYKLDSDVLVGHNISGFDLDVLLHRAQVCRVPSSMWSKIGRLKRSEM 697
S+E+ ++ R + + + D DVL+ +N FD L R++ V + GR
Sbjct: 185 STEKEMIKRFLKVVKEKDPDVLITYNGDNFDFAYLKKRSEKLGVKFIL----GR--EGSE 238
Query: 698 PKLRKGRTIFGSGASPGIMSCIAGRLLCDTFLCSRDLLREVSYSLTQLAKTQLNKDRKEV 757
PK+++ F + GR+ D + R + +Y+L + + + +++V
Sbjct: 239 PKIQRMGDRFAVE--------VKGRIHFDLYPVIRRTINLPTYTLEAVYEAIFGQPKEKV 290
Query: 758 GPHDVLKMFQTLESLMELIEYGETDAWLSMELMFHLSVLPLTRQLTNISG-NLWGKTLQG 816
++ + ++T E L + Y DA ++ EL P+ QL+ + G +LW + +
Sbjct: 291 YAEEIAQAWETGEGLERVARYSMEDAKVTYEL--GKEFFPMEAQLSRLVGQSLWDVS-RS 347
Query: 817 ARAQRVEYLLLHAFRAKKYIVPDKFTYVKETKMAKQRSNHGVEDRNVEELTNEDANFDND 876
+ VE+ LL + + P+K E ++A++R
Sbjct: 348 STGNLVEWFLLRKAYERNELAPNK---PDERELARRRE---------------------- 382
Query: 877 TSHNDHRKGKRGPAYAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTVER--- 933
+YAGG V EP++GL++ I+ LDF SLYPSII +N+ T+ R
Sbjct: 383 -------------SYAGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVSPDTLNREGC 428
Query: 934 -----SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMK-TASGLKIQQLDIQQQAL 987
+P V H G +P LL +L++ R+ VK MK T ++ + LD +Q+A+
Sbjct: 429 EEYDVAPQ--VGHKFCKDFPGFIPSLLGDLLEERQKVKKKMKATIDPIEKKLLDYRQRAI 486
Query: 988 KLTANSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLNLEVIYGDTDSIMI 1047
K+ ANS YG G++ +R+Y K AE +T GR+ + +T+ ++ +V+Y DTD
Sbjct: 487 KILANSFYGYYGYAKARWYCKECAESVTAWGRQYIETTIREIEEKFGFKVLYADTDGFFA 546
Query: 1048 HSXXXXXXXXXXXXXXVIQEVNKKYK-CLEIDLDGXXXXXXXXXXXXXXXXXXQFKDGMP 1106
+ +N K LE++ +G + K
Sbjct: 547 TIPGADAETVKKKAKEFLDYINAKLPGLLELEYEGFYKRGFFVTKKKYAVIDEEDK---- 602
Query: 1107 YEVIERKGLDMVRRDWSLLSKEVGDFCLSQILSERSCEDVVESIHNSLMKVQEDMRSGQV 1166
I +GL++VRRDWS ++KE L IL E+ V + +V E + +V
Sbjct: 603 ---ITTRGLEIVRRDWSEIAKETQARVLEAILKHGDVEEAVRIVK----EVTEKLSKYEV 655
Query: 1167 ALEKYVITKTLTKPPEAYPDAKNQPHVQVALRLKQSGYSTGCSAGDTVPYIICCEQGTSS 1226
EK VI + +T+ + Y PHV VA RL G G + YI+ G
Sbjct: 656 PPEKLVIYEQITRDLKDY--KATGPHVAVAKRLAARG--IKIRPGTVISYIVLKGSGR-- 709
Query: 1227 GSSVGIAQRARHPDELKKGDGKWMIDIDYYASQQIHPVVSRLCASI 1272
I RA DE K+ D +YY Q+ P V R+ +
Sbjct: 710 -----IGDRAIPFDEFDPAKHKY--DAEYYIENQVLPAVERILRAF 748
>pdb|1QHT|A Chain A, Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon
Length = 775
Score = 178 bits (452), Expect = 2e-44, Method: Compositional matrix adjust.
Identities = 165/646 (25%), Positives = 277/646 (42%), Gaps = 93/646 (14%)
Query: 638 SSERALLNRLMIELYKLDSDVLVGHNISGFDLDVLLHRAQVCRVPSSMWSKIGRLKRSEM 697
S+E+ ++ R + + + D DVL+ +N FD L R + + ++ GR
Sbjct: 185 STEKEMIKRFLRVVREKDPDVLITYNGDNFDFAYLKKRCEELGIKFTL----GR--DGSE 238
Query: 698 PKLRKGRTIFGSGASPGIMSCIAGRLLCDTFLCSRDLLREVSYSLTQLAKTQLNKDRKEV 757
PK+++ F + GR+ D + R + +Y+L + + K +++V
Sbjct: 239 PKIQRMGDRFAVE--------VKGRIHFDLYPVIRRTINLPTYTLEAVYEAVFGKPKEKV 290
Query: 758 GPHDVLKMFQTLESLMELIEYGETDAWLSMELMFHLSVLPLTRQLTNISG-NLWGKTLQG 816
++ + +++ E L + Y DA ++ EL P+ QL+ + G +LW + +
Sbjct: 291 YAEEIAQAWESGEGLERVARYSMEDAKVTYEL--GREFFPMEAQLSRLIGQSLWDVS-RS 347
Query: 817 ARAQRVEYLLLHAFRAKKYIVPDKFTYVKETKMAKQRSNHGVEDRNVEELTNEDANFDND 876
+ VE+ LL + + P+K E ++A++R
Sbjct: 348 STGNLVEWFLLRKAYKRNELAPNK---PDERELARRRG---------------------- 382
Query: 877 TSHNDHRKGKRGPAYAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTVER--- 933
YAGG V EP++GL+D I+ LDF SLYPSII +N+ T+ R
Sbjct: 383 -------------GYAGGYVKEPERGLWDN-IVYLDFRSLYPSIIITHNVSPDTLNREGC 428
Query: 934 -----SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMK-TASGLKIQQLDIQQQAL 987
+P+ V H G +P LL +L++ R+ +K MK T L+ + LD +Q+A+
Sbjct: 429 KEYDVAPE--VGHKFCKDFPGFIPSLLGDLLEERQKIKRKMKATVDPLEKKLLDYRQRAI 486
Query: 988 KLTANSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLNLEVIYGDTDSIMI 1047
K+ ANS YG G++ +R+Y K AE +T GRE + + ++ +V+Y DTD +
Sbjct: 487 KILANSFYGYYGYAKARWYCKECAESVTAWGREYIEMVIRELEEKFGFKVLYADTDGLHA 546
Query: 1048 HSXXXXXXXXXXXXXXVIQEVNKKYK-CLEIDLDGXXXXXXXXXXXXXXXXXXQFKDGMP 1106
++ +N K LE++ +G + K
Sbjct: 547 TIPGADAETVKKKAKEFLKYINPKLPGLLELEYEGFYVRGFFVTKKKYAVIDEEGK---- 602
Query: 1107 YEVIERKGLDMVRRDWSLLSKEVGDFCLSQILSERSCEDVVESIHNSLMKVQEDMRSGQV 1166
I +GL++VRRDWS ++KE L IL E+ V + +V E + +V
Sbjct: 603 ---ITTRGLEIVRRDWSEIAKETQARVLEAILKHGDVEEAVRIVK----EVTEKLSKYEV 655
Query: 1167 ALEKYVITKTLTKPPEAYPDAKNQPHVQVALRLKQSGYSTGCSAGDTVPYIICCEQGTSS 1226
EK VI + +T+ Y PHV VA RL G G + YI+ G
Sbjct: 656 PPEKLVIHEQITRDLRDY--KATGPHVAVAKRLAARG--VKIRPGTVISYIVLKGSGR-- 709
Query: 1227 GSSVGIAQRARHPDELKKGDGKWMIDIDYYASQQIHPVVSRLCASI 1272
I RA DE ++ D +YY Q+ P V R+ +
Sbjct: 710 -----IGDRAIPADEFDPTKHRY--DAEYYIENQVLPAVERILKAF 748
>pdb|2XHB|A Chain A, Crystal Structure Of Dna Polymerase From Thermococcus
Gorgonarius In Complex With Hypoxanthine-Containing Dna
Length = 773
Score = 176 bits (446), Expect = 8e-44, Method: Compositional matrix adjust.
Identities = 165/646 (25%), Positives = 277/646 (42%), Gaps = 93/646 (14%)
Query: 638 SSERALLNRLMIELYKLDSDVLVGHNISGFDLDVLLHRAQVCRVPSSMWSKIGRLKRSEM 697
S+E+ ++ R + + + D DVL+ +N F L R++ V + GR
Sbjct: 185 STEKEMIKRFLKVVKEKDPDVLITYNGDNFAFAYLKKRSEKLGVKFIL----GR--EGSE 238
Query: 698 PKLRKGRTIFGSGASPGIMSCIAGRLLCDTFLCSRDLLREVSYSLTQLAKTQLNKDRKEV 757
PK+++ F + GR+ D + R + +Y+L + + + +++V
Sbjct: 239 PKIQRMGDRFAVE--------VKGRIHFDLYPVIRRTINLPTYTLEAVYEAIFGQPKEKV 290
Query: 758 GPHDVLKMFQTLESLMELIEYGETDAWLSMELMFHLSVLPLTRQLTNISG-NLWGKTLQG 816
++ + ++T E L + Y DA ++ EL P+ QL+ + G +LW + +
Sbjct: 291 YAEEIAQAWETGEGLERVARYSMEDAKVTYEL--GKEFFPMEAQLSRLVGQSLWDVS-RS 347
Query: 817 ARAQRVEYLLLHAFRAKKYIVPDKFTYVKETKMAKQRSNHGVEDRNVEELTNEDANFDND 876
+ VE+ LL + + P+K E ++A++R
Sbjct: 348 STGNLVEWFLLRKAYERNELAPNK---PDERELARRRE---------------------- 382
Query: 877 TSHNDHRKGKRGPAYAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTVER--- 933
+YAGG V EP++GL++ I+ LDF SLYPSII +N+ T+ R
Sbjct: 383 -------------SYAGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVSPDTLNREGC 428
Query: 934 -----SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMK-TASGLKIQQLDIQQQAL 987
+P V H G +P LL +L++ R+ VK MK T ++ + LD +Q+A+
Sbjct: 429 EEYDVAPQ--VGHKFCKDFPGFIPSLLGDLLEERQKVKKKMKATIDPIEKKLLDYRQRAI 486
Query: 988 KLTANSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLNLEVIYGDTDSIMI 1047
K+ ANS YG G++ +R+Y K AE +T GR+ + +T+ ++ +V+Y DTD
Sbjct: 487 KILANSFYGYYGYAKARWYCKECAESVTAWGRQYIETTIREIEEKFGFKVLYADTDGFFA 546
Query: 1048 HSXXXXXXXXXXXXXXVIQEVNKKYK-CLEIDLDGXXXXXXXXXXXXXXXXXXQFKDGMP 1106
+ +N K LE++ +G + K
Sbjct: 547 TIPGADAETVKKKAKEFLDYINAKLPGLLELEYEGFYKRGFFVTKKKYAVIDEEDK---- 602
Query: 1107 YEVIERKGLDMVRRDWSLLSKEVGDFCLSQILSERSCEDVVESIHNSLMKVQEDMRSGQV 1166
I +GL++VRRDWS ++KE L IL E+ V + +V E + +V
Sbjct: 603 ---ITTRGLEIVRRDWSEIAKETQARVLEAILKHGDVEEAVRIVK----EVTEKLSKYEV 655
Query: 1167 ALEKYVITKTLTKPPEAYPDAKNQPHVQVALRLKQSGYSTGCSAGDTVPYIICCEQGTSS 1226
EK VI + +T+ + Y PHV VA RL G G + YI+ G
Sbjct: 656 PPEKLVIYEQITRDLKDY--KATGPHVAVAKRLAARG--IKIRPGTVISYIVLKGSGR-- 709
Query: 1227 GSSVGIAQRARHPDELKKGDGKWMIDIDYYASQQIHPVVSRLCASI 1272
I RA DE K+ D +YY Q+ P V R+ +
Sbjct: 710 -----IGDRAIPFDEFDPAKHKY--DAEYYIENQVLPAVERILRAF 748
>pdb|2VWJ|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography
Length = 773
Score = 176 bits (446), Expect = 9e-44, Method: Compositional matrix adjust.
Identities = 165/646 (25%), Positives = 277/646 (42%), Gaps = 93/646 (14%)
Query: 638 SSERALLNRLMIELYKLDSDVLVGHNISGFDLDVLLHRAQVCRVPSSMWSKIGRLKRSEM 697
S+E+ ++ R + + + D DVL+ +N F L R++ V + GR
Sbjct: 185 STEKEMIKRFLKVVKEKDPDVLITYNGDNFAFAYLKKRSEKLGVKFIL----GR--EGSE 238
Query: 698 PKLRKGRTIFGSGASPGIMSCIAGRLLCDTFLCSRDLLREVSYSLTQLAKTQLNKDRKEV 757
PK+++ F + GR+ D + R + +Y+L + + + +++V
Sbjct: 239 PKIQRMGDRFAVE--------VKGRIHFDLYPVIRRTINLPTYTLEAVYEAIFGQPKEKV 290
Query: 758 GPHDVLKMFQTLESLMELIEYGETDAWLSMELMFHLSVLPLTRQLTNISG-NLWGKTLQG 816
++ + ++T E L + Y DA ++ EL P+ QL+ + G +LW + +
Sbjct: 291 YAEEIAQAWETGEGLERVARYSMEDAKVTYEL--GKEFFPMEAQLSRLVGQSLWDVS-RS 347
Query: 817 ARAQRVEYLLLHAFRAKKYIVPDKFTYVKETKMAKQRSNHGVEDRNVEELTNEDANFDND 876
+ VE+ LL + + P+K E ++A++R
Sbjct: 348 STGNLVEWFLLRKAYERNELAPNK---PDERELARRRE---------------------- 382
Query: 877 TSHNDHRKGKRGPAYAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTVER--- 933
+YAGG V EP++GL++ I+ LDF SLYPSII +N+ T+ R
Sbjct: 383 -------------SYAGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVSPDTLNREGC 428
Query: 934 -----SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMK-TASGLKIQQLDIQQQAL 987
+P V H G +P LL +L++ R+ VK MK T ++ + LD +Q+A+
Sbjct: 429 EEYDVAPQ--VGHKFCKDFPGFIPSLLGDLLEERQKVKKKMKATIDPIEKKLLDYRQRAI 486
Query: 988 KLTANSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLNLEVIYGDTDSIMI 1047
K+ ANS YG G++ +R+Y K AE +T GR+ + +T+ ++ +V+Y DTD
Sbjct: 487 KILANSFYGYYGYAKARWYCKECAESVTAWGRQYIETTIREIEEKFGFKVLYADTDGFFA 546
Query: 1048 HSXXXXXXXXXXXXXXVIQEVNKKYK-CLEIDLDGXXXXXXXXXXXXXXXXXXQFKDGMP 1106
+ +N K LE++ +G + K
Sbjct: 547 TIPGADAETVKKKAKEFLDYINAKLPGLLELEYEGFYKRGFFVTKKKYAVIDEEDK---- 602
Query: 1107 YEVIERKGLDMVRRDWSLLSKEVGDFCLSQILSERSCEDVVESIHNSLMKVQEDMRSGQV 1166
I +GL++VRRDWS ++KE L IL E+ V + +V E + +V
Sbjct: 603 ---ITTRGLEIVRRDWSEIAKETQARVLEAILKHGDVEEAVRIVK----EVTEKLSKYEV 655
Query: 1167 ALEKYVITKTLTKPPEAYPDAKNQPHVQVALRLKQSGYSTGCSAGDTVPYIICCEQGTSS 1226
EK VI + +T+ + Y PHV VA RL G G + YI+ G
Sbjct: 656 PPEKLVIYEQITRDLKDY--KATGPHVAVAKRLAARG--IKIRPGTVISYIVLKGSGR-- 709
Query: 1227 GSSVGIAQRARHPDELKKGDGKWMIDIDYYASQQIHPVVSRLCASI 1272
I RA DE K+ D +YY Q+ P V R+ +
Sbjct: 710 -----IGDRAIPFDEFDPAKHKY--DAEYYIENQVLPAVERILRAF 748
>pdb|2VWK|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography. V93q Polymerase Variant
Length = 773
Score = 176 bits (445), Expect = 1e-43, Method: Compositional matrix adjust.
Identities = 165/646 (25%), Positives = 277/646 (42%), Gaps = 93/646 (14%)
Query: 638 SSERALLNRLMIELYKLDSDVLVGHNISGFDLDVLLHRAQVCRVPSSMWSKIGRLKRSEM 697
S+E+ ++ R + + + D DVL+ +N F L R++ V + GR
Sbjct: 185 STEKEMIKRFLKVVKEKDPDVLITYNGDNFAFAYLKKRSEKLGVKFIL----GR--EGSE 238
Query: 698 PKLRKGRTIFGSGASPGIMSCIAGRLLCDTFLCSRDLLREVSYSLTQLAKTQLNKDRKEV 757
PK+++ F + GR+ D + R + +Y+L + + + +++V
Sbjct: 239 PKIQRMGDRFAVE--------VKGRIHFDLYPVIRRTINLPTYTLEAVYEAIFGQPKEKV 290
Query: 758 GPHDVLKMFQTLESLMELIEYGETDAWLSMELMFHLSVLPLTRQLTNISG-NLWGKTLQG 816
++ + ++T E L + Y DA ++ EL P+ QL+ + G +LW + +
Sbjct: 291 YAEEIAQAWETGEGLERVARYSMEDAKVTYEL--GKEFFPMEAQLSRLVGQSLWDVS-RS 347
Query: 817 ARAQRVEYLLLHAFRAKKYIVPDKFTYVKETKMAKQRSNHGVEDRNVEELTNEDANFDND 876
+ VE+ LL + + P+K E ++A++R
Sbjct: 348 STGNLVEWFLLRKAYERNELAPNK---PDERELARRRE---------------------- 382
Query: 877 TSHNDHRKGKRGPAYAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTVER--- 933
+YAGG V EP++GL++ I+ LDF SLYPSII +N+ T+ R
Sbjct: 383 -------------SYAGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVSPDTLNREGC 428
Query: 934 -----SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMK-TASGLKIQQLDIQQQAL 987
+P V H G +P LL +L++ R+ VK MK T ++ + LD +Q+A+
Sbjct: 429 EEYDVAPQ--VGHKFCKDFPGFIPSLLGDLLEERQKVKKKMKATIDPIEKKLLDYRQRAI 486
Query: 988 KLTANSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLNLEVIYGDTDSIMI 1047
K+ ANS YG G++ +R+Y K AE +T GR+ + +T+ ++ +V+Y DTD
Sbjct: 487 KILANSFYGYYGYAKARWYCKECAESVTAWGRQYIETTIREIEEKFGFKVLYADTDGFFA 546
Query: 1048 HSXXXXXXXXXXXXXXVIQEVNKKYK-CLEIDLDGXXXXXXXXXXXXXXXXXXQFKDGMP 1106
+ +N K LE++ +G + K
Sbjct: 547 TIPGADAETVKKKAKEFLDYINAKLPGLLELEYEGFYKRGFFVTKKKYAVIDEEDK---- 602
Query: 1107 YEVIERKGLDMVRRDWSLLSKEVGDFCLSQILSERSCEDVVESIHNSLMKVQEDMRSGQV 1166
I +GL++VRRDWS ++KE L IL E+ V + +V E + +V
Sbjct: 603 ---ITTRGLEIVRRDWSEIAKETQARVLEAILKHGDVEEAVRIVK----EVTEKLSKYEV 655
Query: 1167 ALEKYVITKTLTKPPEAYPDAKNQPHVQVALRLKQSGYSTGCSAGDTVPYIICCEQGTSS 1226
EK VI + +T+ + Y PHV VA RL G G + YI+ G
Sbjct: 656 PPEKLVIYEQITRDLKDY--KATGPHVAVAKRLAARG--IKIRPGTVISYIVLKGSGR-- 709
Query: 1227 GSSVGIAQRARHPDELKKGDGKWMIDIDYYASQQIHPVVSRLCASI 1272
I RA DE K+ D +YY Q+ P V R+ +
Sbjct: 710 -----IGDRAIPFDEFDPAKHKY--DAEYYIENQVLPAVERILRAF 748
>pdb|2JGU|A Chain A, Crystal Structure Of Dna-directed Dna Polymerase
Length = 775
Score = 165 bits (417), Expect = 2e-40, Method: Compositional matrix adjust.
Identities = 166/650 (25%), Positives = 277/650 (42%), Gaps = 106/650 (16%)
Query: 638 SSERALLNRLMIELYKLDSDVLVGHNISGFDLDVLLHRAQVCRVPSSMWSKIGRLKRSEM 697
S+E+ ++ R + + + D D++V +N FD L RA+ + + IGR
Sbjct: 185 STEKEMIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKRAEKLGIKLT----IGR--DGSE 238
Query: 698 PKLRKGRTIFGSGASPGIMSCI--AGRLLCDTFLCSRDLLREVSYSLTQLAKTQLNKDRK 755
PK+++ G M+ + GR+ D + R + +Y+L + + K ++
Sbjct: 239 PKMQR----------IGDMTAVEVKGRIHFDLYHVIRTTINLPTYTLEAVYEAIFGKPKE 288
Query: 756 EVGPHDVLKMFQTLESLMELIEYGETDAWLSMELMFHLSVLPLTRQLTNISGN-LWGKTL 814
+V ++ K +++ E+L + +Y DA + EL LP+ QL+ + G LW +
Sbjct: 289 KVYADEIAKAWESGENLERVAKYSMEDAKATYEL--GKEFLPMEIQLSRLVGQPLWDVS- 345
Query: 815 QGARAQRVEYLLLHAFRAKKYIVPDKFTYVKETKMAKQRSNHGVEDRNVEELTNEDANFD 874
+ + VE+ LL + + P
Sbjct: 346 RSSTGNLVEWFLLRKAYERNEVAP------------------------------------ 369
Query: 875 NDTSHNDHRKGKRGPAYAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTVERS 934
N S ++++ R +Y GG V EP+KGL++ I+ LD+ SLYPSII +N+ S
Sbjct: 370 NKPSEEEYQRRLR-ESYTGGFVKEPEKGLWEN-IVYLDYKSLYPSIIITHNV-------S 420
Query: 935 PDGL-------------VPHLPSSKTTGVLPELLKNLVQRRRMVKTWMK-TASGLKIQQL 980
PD L V H G +P LL +L++ R+ +KT MK T ++ L
Sbjct: 421 PDTLNLEGCKNYDIAPQVGHKFCKDIPGFIPSLLGHLLEERQKIKTKMKETQDPIEKILL 480
Query: 981 DIQQQALKLTANSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLNLEVIYG 1040
D +Q+A+KL ANS YG G++ +R+Y K AE +T GR+ + ++ +V+Y
Sbjct: 481 DYRQKAIKLLANSFYGYYGYAKARWYCKECAESVTAWGRKYIELVWKELEEKFGFKVLYI 540
Query: 1041 DTDSIMIHSXXXXXXXXXXXXXXVIQEVNKKYK-CLEIDLDGXXXXXXXXXXXXXXXXXX 1099
DTD + ++ +N K LE++ +G
Sbjct: 541 DTDGLYATIPGGESEEIKKKALEFVKYINSKLPGLLELEYEGFYKRGFFVTKKRYAVIDE 600
Query: 1100 QFKDGMPYEVIERKGLDMVRRDWSLLSKEVGDFCLSQILSERSCEDVVESIHNSLMKVQE 1159
+ K VI R GL++VRRDWS ++KE L IL E+ V + + K
Sbjct: 601 EGK------VITR-GLEIVRRDWSEIAKETQARVLETILKHGDVEEAVRIVKEVIQK--- 650
Query: 1160 DMRSGQVALEKYVITKTLTKPPEAYPDAKNQPHVQVALRLKQSGYSTGCSAGDTVPYIIC 1219
+ + ++ EK I + +T+P Y PHV VA +L G G + YI+
Sbjct: 651 -LANYEIPPEKLAIYEQITRPLHEYKAI--GPHVAVAKKLAAKG--VKIKPGMVIGYIVL 705
Query: 1220 CEQGTSSGSSVGIAQRARHPDELKKGDGKWMIDIDYYASQQIHPVVSRLC 1269
G I+ RA +E K+ D +YY Q+ P V R+
Sbjct: 706 RGDGP-------ISNRAILAEEYDPKKHKY--DAEYYIENQVLPAVLRIL 746
>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 = 164 bits (415), Expect = 3e-40, Method: Compositional matrix adjust.
Identities = 168/650 (25%), Positives = 276/650 (42%), Gaps = 106/650 (16%)
Query: 638 SSERALLNRLMIELYKLDSDVLVGHNISGFDLDVLLHRAQVCRVPSSMWSKIGRLKRSEM 697
SSER ++ R + + + D D++V +N FD L RA+ + + IGR
Sbjct: 185 SSEREMIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKRAEKLGIKLT----IGR--DGSE 238
Query: 698 PKLRKGRTIFGSGASPGIMSCI--AGRLLCDTFLCSRDLLREVSYSLTQLAKTQLNKDRK 755
PK+++ G M+ + GR+ D + + +Y+L + + K ++
Sbjct: 239 PKMQR----------IGDMTAVEVKGRIHFDLYHVITRTINLPTYTLEAVYEAIFGKPKE 288
Query: 756 EVGPHDVLKMFQTLESLMELIEYGETDAWLSMELMFHLSVLPLTRQLTNISGN-LWGKTL 814
+V ++ K +++ E+L + +Y DA + EL LP+ QL+ + G LW +
Sbjct: 289 KVYADEIAKAWESGENLERVAKYSMEDAKATYEL--GKEFLPMEIQLSRLIGQPLWDVS- 345
Query: 815 QGARAQRVEYLLLHAFRAKKYIVPDKFTYVKETKMAKQRSNHGVEDRNVEELTNEDANFD 874
+ + VE+ LL + + P
Sbjct: 346 RSSTGNLVEWFLLRKAYERNEVAP------------------------------------ 369
Query: 875 NDTSHNDHRKGKRGPAYAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTVERS 934
N S ++++ R +Y GG V EP+KGL+D I+ LDF +LYPSII +N+ S
Sbjct: 370 NKPSEEEYQRRLR-ESYTGGFVKEPEKGLWDD-IVYLDFIALYPSIIITHNV-------S 420
Query: 935 PDGL-------------VPHLPSSKTTGVLPELLKNLVQRRRMVKTWMK-TASGLKIQQL 980
PD L V H G +P LL +L++ R+ +KT MK T ++ L
Sbjct: 421 PDTLNLEGCKNYDIAPQVGHKFCKDIPGFIPSLLGHLLEERQKIKTKMKETQDPIEKILL 480
Query: 981 DIQQQALKLTANSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLNLEVIYG 1040
D +Q+A+KL ANS YG G++ +R+Y K AE +T GR+ + ++ +V+Y
Sbjct: 481 DYRQKAIKLLANSFYGYYGYAKARWYCKECAESVTAWGRKYIELVWKELEEKFGFKVLYI 540
Query: 1041 DTDSIMIHSXXXXXXXXXXXXXXVIQEVNKKYK-CLEIDLDGXXXXXXXXXXXXXXXXXX 1099
DTD + ++ +N K LE++ +G
Sbjct: 541 DTDGLHATIPGGESEEIKKKALEFVKYINSKLPGLLELEYEGFYKRGFFVTKKRYAVIDE 600
Query: 1100 QFKDGMPYEVIERKGLDMVRRDWSLLSKEVGDFCLSQILSERSCEDVVESIHNSLMKVQE 1159
+ K VI R GL++VRRDWS ++KE L IL E+ V + + K
Sbjct: 601 EGK------VITR-GLEIVRRDWSEIAKETQARVLETILKHGDVEEAVRIVKEVIQK--- 650
Query: 1160 DMRSGQVALEKYVITKTLTKPPEAYPDAKNQPHVQVALRLKQSGYSTGCSAGDTVPYIIC 1219
+ + ++ EK I + +T+P Y PHV VA +L G G + YI+
Sbjct: 651 -LANYEIPPEKLAIYEQITRPLHEYKAI--GPHVAVAKKLAAKG--VKIKPGMVIGYIVL 705
Query: 1220 CEQGTSSGSSVGIAQRARHPDELKKGDGKWMIDIDYYASQQIHPVVSRLC 1269
G I+ RA +E K+ D +YY Q+ P V R+
Sbjct: 706 RGDGP-------ISNRAILAEEYDPKKHKY--DAEYYIENQVLPAVLRIL 746
>pdb|1WNS|A Chain A, Crystal Structure Of Family B Dna Polymerase From
Hyperthermophilic Archaeon Pyrococcus Kodakaraensis Kod1
Length = 774
Score = 160 bits (404), Expect = 6e-39, Method: Compositional matrix adjust.
Identities = 166/646 (25%), Positives = 278/646 (43%), Gaps = 93/646 (14%)
Query: 638 SSERALLNRLMIELYKLDSDVLVGHNISGFDLDVLLHRAQVCRVPSSMWSKIGRLKRSEM 697
S+ER ++ R + + + D DVL+ +N FD L R + + ++ GR
Sbjct: 185 STEREMIKRFLRVVKEKDPDVLITYNGDNFDFAYLKKRCEKLGINFAL----GR--DGSE 238
Query: 698 PKLRKGRTIFGSGASPGIMSCIAGRLLCDTFLCSRDLLREVSYSLTQLAKTQLNKDRKEV 757
PK+++ F + GR+ D + R + +Y+L + + + +++V
Sbjct: 239 PKIQRMGDRFAVE--------VKGRIHFDLYPVIRRTINLPTYTLEAVYEAVFGQPKEKV 290
Query: 758 GPHDVLKMFQTLESLMELIEYGETDAWLSMELMFHLSVLPLTRQLTNISG-NLWGKTLQG 816
++ ++T E+L + Y DA ++ EL LP+ QL+ + G +LW + +
Sbjct: 291 YAEEITTAWETGENLERVARYSMEDAKVTYEL--GKEFLPMEAQLSRLIGQSLWDVS-RS 347
Query: 817 ARAQRVEYLLLHAFRAKKYIVPDKFTYVKETKMAKQRSNHGVEDRNVEELTNEDANFDND 876
+ VE+ LL + + P+K E ++A++R
Sbjct: 348 STGNLVEWFLLRKAYERNELAPNK---PDEKELARRRQ---------------------- 382
Query: 877 TSHNDHRKGKRGPAYAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTVER--- 933
+Y GG V EP++GL++ I+ LDF SLYPSII +N+ T+ R
Sbjct: 383 -------------SYEGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVSPDTLNREGC 428
Query: 934 -----SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMK-TASGLKIQQLDIQQQAL 987
+P V H G +P LL +L++ R+ +K MK T ++ + LD +Q+A+
Sbjct: 429 KEYDVAPQ--VGHRFCKDFPGFIPSLLGDLLEERQKIKKKMKATIDPIERKLLDYRQRAI 486
Query: 988 KLTANSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLNLEVIYGDTDSIMI 1047
K+ ANS YG G++ +R+Y K AE +T GRE + T+ ++ +VIY DTD
Sbjct: 487 KILANSYYGYYGYARARWYCKECAESVTAWGREYITMTIKEIEEKYGFKVIYSDTDGFFA 546
Query: 1048 HSXXXXXXXXXXXXXXVIQEVNKKYK-CLEIDLDGXXXXXXXXXXXXXXXXXXQFKDGMP 1106
++ +N K LE++ +G + K
Sbjct: 547 TIPGADAETVKKKAMEFLKYINAKLPGALELEYEGFYKRGFFVTKKKYAVIDEEGK---- 602
Query: 1107 YEVIERKGLDMVRRDWSLLSKEVGDFCLSQILSERSCEDVVESIHNSLMKVQEDMRSGQV 1166
I +GL++VRRDWS ++KE L +L + E V + +V E + +V
Sbjct: 603 ---ITTRGLEIVRRDWSEIAKETQARVLEALLKDGDVEKAVRIVK----EVTEKLSKYEV 655
Query: 1167 ALEKYVITKTLTKPPEAYPDAKNQPHVQVALRLKQSGYSTGCSAGDTVPYIICCEQGTSS 1226
EK VI + +T+ + Y PHV VA RL G G + YI+ G
Sbjct: 656 PPEKLVIHEQITRDLKDY--KATGPHVAVAKRLAARG--VKIRPGTVISYIVLKGSGR-- 709
Query: 1227 GSSVGIAQRARHPDELKKGDGKWMIDIDYYASQQIHPVVSRLCASI 1272
I RA DE K+ D +YY Q+ P V R+ +
Sbjct: 710 -----IGDRAIPFDEFDPTKHKY--DAEYYIENQVLPAVERILRAF 748
>pdb|1WN7|A Chain A, Crystal Structure Of Archaeal Family B Dna Polymerase Mutant
Length = 774
Score = 160 bits (404), Expect = 6e-39, Method: Compositional matrix adjust.
Identities = 166/646 (25%), Positives = 278/646 (43%), Gaps = 93/646 (14%)
Query: 638 SSERALLNRLMIELYKLDSDVLVGHNISGFDLDVLLHRAQVCRVPSSMWSKIGRLKRSEM 697
S+ER ++ R + + + D DVL+ +N FD L R + + ++ GR
Sbjct: 185 STEREMIKRFLRVVKEKDPDVLITYNGDNFDFAYLKKRCEKLGINFAL----GR--DGSE 238
Query: 698 PKLRKGRTIFGSGASPGIMSCIAGRLLCDTFLCSRDLLREVSYSLTQLAKTQLNKDRKEV 757
PK+++ F + GR+ D + R + +Y+L + + + +++V
Sbjct: 239 PKIQRMGDRFAVE--------VKGRIHFDLYPVIRRTINLPTYTLEAVYEAVFGQPKEKV 290
Query: 758 GPHDVLKMFQTLESLMELIEYGETDAWLSMELMFHLSVLPLTRQLTNISG-NLWGKTLQG 816
++ ++T E+L + Y DA ++ EL LP+ QL+ + G +LW + +
Sbjct: 291 YAEEITTAWETGENLERVARYSMEDAKVTYEL--GKEFLPMEAQLSRLIGQSLWDVS-RS 347
Query: 817 ARAQRVEYLLLHAFRAKKYIVPDKFTYVKETKMAKQRSNHGVEDRNVEELTNEDANFDND 876
+ VE+ LL + + P+K E ++A++R
Sbjct: 348 STGNLVEWFLLRKAYERNELAPNK---PDEKELARRRQ---------------------- 382
Query: 877 TSHNDHRKGKRGPAYAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTVER--- 933
+Y GG V EP++GL++ I+ LDF SLYPSII +N+ T+ R
Sbjct: 383 -------------SYEGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVSPDTLNREGC 428
Query: 934 -----SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMK-TASGLKIQQLDIQQQAL 987
+P V H G +P LL +L++ R+ +K MK T ++ + LD +Q+A+
Sbjct: 429 KEYDVAPQ--VGHRFCKDFPGFIPSLLGDLLEERQKIKKKMKATIDPIERKLLDYRQRAI 486
Query: 988 KLTANSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLNLEVIYGDTDSIMI 1047
K+ ANS YG G++ +R+Y K AE +T GRE + T+ ++ +VIY DTD
Sbjct: 487 KILANSYYGYYGYARARWYCKECAESVTAWGREYITMTIKEIEEKYGFKVIYSDTDGFFA 546
Query: 1048 HSXXXXXXXXXXXXXXVIQEVNKKYK-CLEIDLDGXXXXXXXXXXXXXXXXXXQFKDGMP 1106
++ +N K LE++ +G + K
Sbjct: 547 TIPGADAETVKKKAMEFLKYINAKLPGALELEYEGFYERGFFVTKKKYAVIDEEGK---- 602
Query: 1107 YEVIERKGLDMVRRDWSLLSKEVGDFCLSQILSERSCEDVVESIHNSLMKVQEDMRSGQV 1166
I +GL++VRRDWS ++KE L +L + E V + +V E + +V
Sbjct: 603 ---ITTRGLEIVRRDWSEIAKETQARVLEALLKDGDVEKAVRIVK----EVTEKLSKYEV 655
Query: 1167 ALEKYVITKTLTKPPEAYPDAKNQPHVQVALRLKQSGYSTGCSAGDTVPYIICCEQGTSS 1226
EK VI + +T+ + Y PHV VA RL G G + YI+ G
Sbjct: 656 PPEKLVIHEQITRDLKDY--KATGPHVAVAKRLAARG--VKIRPGTVISYIVLKGSGR-- 709
Query: 1227 GSSVGIAQRARHPDELKKGDGKWMIDIDYYASQQIHPVVSRLCASI 1272
I RA DE K+ D +YY Q+ P V R+ +
Sbjct: 710 -----IGDRAIPFDEFDPTKHKY--DAEYYIENQVLPAVERILRAF 748
>pdb|4FM2|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase (Triple Mutant)
Bound To A Dsdna, In Edition Mode
Length = 793
Score = 159 bits (402), Expect = 1e-38, Method: Compositional matrix adjust.
Identities = 163/648 (25%), Positives = 276/648 (42%), Gaps = 97/648 (14%)
Query: 638 SSERALLNRLMIELYKLDSDVLVGHNISGFDLDVLLHRAQVCRVPSSMWSKIGRLKRSEM 697
SSER ++ RL+ + + D DV++ +N F LL RA+ + K+ + +
Sbjct: 207 SSEREMIKRLVKVIREKDPDVIITYNGDNFAFPYLLKRAEKLGI------KLPLGRDNSE 260
Query: 698 PKLRKGRTIFGSGASPGIMSCIAGRLLCDTFLCSRDLLREVSYSLTQLAKTQLNKDRKEV 757
PK+++ + I GR+ D F R + +Y+L + + K +++V
Sbjct: 261 PKMQR--------MGDSLAVAIKGRIHFDLFPVIRRTINLPTYTLEAVYEAIFGKSKEKV 312
Query: 758 GPHDVLKMFQTLESLMELIEYGETDAWLSMELMFHLSVLPLTRQLTNISGNLWGKTLQGA 817
H++ + ++T + L + +Y DA ++ EL P+ QL + G + +
Sbjct: 313 YAHEIAEAWETGKGLERVAKYSMEDAKVTFEL--GKEFFPMEAQLARLVGQPVWAVSRSS 370
Query: 818 RAQRVEYLLLHAFRAKKYIVPDKFTYVKETKMAKQRSNHGVEDRNVEELTNEDANFDNDT 877
VE+ LL + + P+K
Sbjct: 371 TGNLVEWFLLRKAYERNELAPNK------------------------------------- 393
Query: 878 SHNDHRKGKRGPAYAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTVER---- 933
+ + +Y GG V EP+KGL++ I+ LDF SLYPSII +N+ T+ R
Sbjct: 394 PDEREYERRLRESYEGGYVKEPEKGLWEG-IVSLDFRSLYPSIIITHNVSPDTLNRENCK 452
Query: 934 ----SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMKTASG-LKIQQLDIQQQALK 988
+P V H G +P LL NL++ R+ +K MK + ++ + LD +Q+A+K
Sbjct: 453 EYDVAPQ--VGHRFCKDFPGFIPSLLGNLLEERQKIKKRMKESKDPVEKKLLDYRQRAIK 510
Query: 989 LTANSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNL---NLEVIYGDTDSI 1045
+ ANS YG G++ +R+Y K AE +T GR+ +DLV+ L +V+Y DTD +
Sbjct: 511 ILANSYYGYYGYAKARWYCKECAESVTAWGRQ----YIDLVRRELESRGFKVLYIDTDGL 566
Query: 1046 MIHSXXXXXXXXXXXXXXVIQEVNKKYK-CLEIDLDGXXXXXXXXXXXXXXXXXXQFKDG 1104
++ +N K LE++ +G + K
Sbjct: 567 YATIPGAKHEEIKEKALKFVEYINSKLPGLLELEYEGFYARGFFVTKKKYALIDEEGK-- 624
Query: 1105 MPYEVIERKGLDMVRRDWSLLSKEVGDFCLSQILSERSCEDVVESIHNSLMKVQEDMRSG 1164
I +GL++VRRDWS ++KE L IL + ++ V+ + +V E +
Sbjct: 625 -----IVTRGLEIVRRDWSEIAKETQAKVLEAILKHGNVDEAVKIVK----EVTEKLSKY 675
Query: 1165 QVALEKYVITKTLTKPPEAYPDAKNQPHVQVALRLKQSGYSTGCSAGDTVPYIICCEQGT 1224
++ EK VI + +T+P Y PHV VA RL G G + YI+ G
Sbjct: 676 EIPPEKLVIYEQITRPLSEYKAI--GPHVAVAKRLAAKG--VKVKPGMVIGYIVLRGDGP 731
Query: 1225 SSGSSVGIAQRARHPDELKKGDGKWMIDIDYYASQQIHPVVSRLCASI 1272
S ++ I +E K+ D +YY Q+ P V R+ +
Sbjct: 732 ISKRAIAI-------EEFDPKKHKY--DAEYYIENQVLPAVERILRAF 770
>pdb|3A2F|A Chain A, Crystal Structure Of Pyrococcus Furiosus Dna PolymerasePCNA
Monomer Mutant Complex
Length = 775
Score = 158 bits (400), Expect = 2e-38, Method: Compositional matrix adjust.
Identities = 165/648 (25%), Positives = 271/648 (41%), Gaps = 102/648 (15%)
Query: 638 SSERALLNRLMIELYKLDSDVLVGHNISGFDLDVLLHRAQVCRVPSSMWSKIGRLKRSEM 697
SSER + R + + + D D++V +N FD L RA+ + + IGR
Sbjct: 185 SSEREXIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKRAEKLGIKLT----IGR--DGSE 238
Query: 698 PKLRKGRTIFGSGASPGIMSCIAGRLLCDTFLCSRDLLREVSYSLTQLAKTQLNKDRKEV 757
PK ++ G + + GR+ D + + +Y+L + + K +++V
Sbjct: 239 PKXQR----IGDXTA----VEVKGRIHFDLYHVITRTINLPTYTLEAVYEAIFGKPKEKV 290
Query: 758 GPHDVLKMFQTLESLMELIEYGETDAWLSMELMFHLSVLPLTRQLTNISGN-LWGKTLQG 816
++ K +++ E+L + +Y DA + EL LP QL+ + G LW + +
Sbjct: 291 YADEIAKAWESGENLERVAKYSXEDAKATYELGKEF--LPXEIQLSRLVGQPLWDVS-RS 347
Query: 817 ARAQRVEYLLLHAFRAKKYIVPDKFTYVKETKMAKQRSNHGVEDRNVEELTNEDANFDND 876
+ VE+ LL + + P N
Sbjct: 348 STGNLVEWFLLRKAYERNEVAP------------------------------------NK 371
Query: 877 TSHNDHRKGKRGPAYAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTVERSPD 936
S ++++ R +Y GG V EP+KGL++ I+ LDF +LYPSII +N+ SPD
Sbjct: 372 PSEEEYQRRLR-ESYTGGFVKEPEKGLWEN-IVYLDFRALYPSIIITHNV-------SPD 422
Query: 937 GL-------------VPHLPSSKTTGVLPELLKNLVQRRRMVKTWMK-TASGLKIQQLDI 982
L V H G +P LL +L++ R+ +KT K T ++ LD
Sbjct: 423 TLNLEGCKNYDIAPQVGHKFCKDIPGFIPSLLGHLLEERQKIKTKXKETQDPIEKILLDY 482
Query: 983 QQQALKLTANSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLNLEVIYGDT 1042
+Q+A+KL ANS YG G++ +R+Y K AE +T GR+ + ++ +V+Y DT
Sbjct: 483 RQKAIKLLANSFYGYYGYAKARWYCKECAESVTAWGRKYIELVWKELEEKFGFKVLYIDT 542
Query: 1043 DSIMIHSXXXXXXXXXXXXXXVIQEVNKKYK-CLEIDLDGXXXXXXXXXXXXXXXXXXQF 1101
D + ++ +N K LE++ +G +
Sbjct: 543 DGLYATIPGGESEEIKKKALEFVKYINSKLPGLLELEYEGFYKRGFFVTKKRYAVIDEEG 602
Query: 1102 KDGMPYEVIERKGLDMVRRDWSLLSKEVGDFCLSQILSERSCEDVVESIHNSLMKVQEDM 1161
K VI R GL++VRRDWS ++KE L IL E+ V + + K +
Sbjct: 603 K------VITR-GLEIVRRDWSEIAKETQARVLETILKHGDVEEAVRIVKEVIQK----L 651
Query: 1162 RSGQVALEKYVITKTLTKPPEAYPDAKNQPHVQVALRLKQSGYSTGCSAGDTVPYIICCE 1221
+ ++ EK I + +T+P Y PHV VA +L G G + YI+
Sbjct: 652 ANYEIPPEKLAIYEQITRPLHEYKAI--GPHVAVAKKLAAKG--VKIKPGXVIGYIVLRG 707
Query: 1222 QGTSSGSSVGIAQRARHPDELKKGDGKWMIDIDYYASQQIHPVVSRLC 1269
G I+ RA +E K+ D +YY Q+ P V R+
Sbjct: 708 DGP-------ISNRAILAEEYDPKKHKY--DAEYYIENQVLPAVLRIL 746
>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 = 157 bits (398), Expect = 3e-38, Method: Compositional matrix adjust.
Identities = 165/648 (25%), Positives = 278/648 (42%), Gaps = 97/648 (14%)
Query: 638 SSERALLNRLMIELYKLDSDVLVGHNISGFDLDVLLHRAQVCRVPSSMWSKIGRLKRSEM 697
SSER ++ RL+ + + D DV++ +N F LL RA+ + K+ + +
Sbjct: 207 SSEREMIKRLVKVIREKDPDVIITYNGDNFAFPYLLKRAEKLGI------KLPLGRDNSE 260
Query: 698 PKLRKGRTIFGSGASPGIMSCIAGRLLCDTFLCSRDLLREVSYSLTQLAKTQLNKDRKEV 757
PK+++ G S + I GR+ D F R + +Y+L + + K +++V
Sbjct: 261 PKMQR------MGDSLAVE--IKGRIHFDLFPVIRRTINLPTYTLEAVYEAIFGKSKEKV 312
Query: 758 GPHDVLKMFQTLESLMELIEYGETDAWLSMELMFHLSVLPLTRQLTNISGNLWGKTLQGA 817
H++ + ++T + L + +Y DA ++ EL P+ QL + G + +
Sbjct: 313 YAHEIAEAWETGKGLERVAKYSMEDAKVTFEL--GKEFFPMEAQLARLVGQPVWDVSRSS 370
Query: 818 RAQRVEYLLLHAFRAKKYIVPDKFTYVKETKMAKQRSNHGVEDRNVEELTNEDANFDNDT 877
VE+ LL + + P+K
Sbjct: 371 TGNLVEWFLLRKAYERNELAPNK------------------------------------- 393
Query: 878 SHNDHRKGKRGPAYAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTVER---- 933
+ + +Y GG V EP+KGL++ I+ LDF SLYPSII +N+ T+ R
Sbjct: 394 PDEREYERRLRESYEGGYVKEPEKGLWEG-IVSLDFRSLYPSIIITHNVSPDTLNRENCK 452
Query: 934 ----SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMKTASG-LKIQQLDIQQQALK 988
+P V H G +P LL NL++ R+ +K MK + ++ + LD +Q+A+K
Sbjct: 453 EYDVAPQ--VGHRFCKDFPGFIPSLLGNLLEERQKIKKRMKESKDPVEKKLLDYRQRAIK 510
Query: 989 LTANSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNL---NLEVIYGDTDSI 1045
+ ANS YG G++ +R+Y K AE +T GR+ +DLV+ L +V+Y DTD +
Sbjct: 511 ILANSYYGYYGYAKARWYCKECAESVTAWGRQ----YIDLVRRELESRGFKVLYIDTDGL 566
Query: 1046 MIHSXXXXXXXXXXXXXXVIQEVNKKYK-CLEIDLDGXXXXXXXXXXXXXXXXXXQFKDG 1104
++ +N K LE++ +G + K
Sbjct: 567 YATIPGAKHEEIKEKALKFVEYINSKLPGLLELEYEGFYARGFFVTKKKYALIDEEGK-- 624
Query: 1105 MPYEVIERKGLDMVRRDWSLLSKEVGDFCLSQILSERSCEDVVESIHNSLMKVQEDMRSG 1164
I +GL++VRRDWS ++KE L IL + ++ V+ + +V E +
Sbjct: 625 -----IVTRGLEIVRRDWSEIAKETQAKVLEAILKHGNVDEAVKIVK----EVTEKLSKY 675
Query: 1165 QVALEKYVITKTLTKPPEAYPDAKNQPHVQVALRLKQSGYSTGCSAGDTVPYIICCEQGT 1224
++ EK VI + +T+P Y PHV VA RL G G + YI+ G
Sbjct: 676 EIPPEKLVIYEQITRPLSEYKAI--GPHVAVAKRLAAKG--VKVKPGMVIGYIVLRGDGP 731
Query: 1225 SSGSSVGIAQRARHPDELKKGDGKWMIDIDYYASQQIHPVVSRLCASI 1272
S ++ I +E K+ D +YY Q+ P V R+ +
Sbjct: 732 ISKRAIAI-------EEFDPKKHKY--DAEYYIENQVLPAVERILRAF 770
>pdb|1QQC|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase D.Tok
Length = 773
Score = 152 bits (385), Expect = 1e-36, Method: Compositional matrix adjust.
Identities = 160/653 (24%), Positives = 273/653 (41%), Gaps = 107/653 (16%)
Query: 638 SSERALLNRLMIELYKLDSDVLVGHNISGFDLDVLLHRAQVCRVPSSMWSKIGRLKRSEM 697
S+E+ ++ R + + + D DVL+ +N FD L R+++ V
Sbjct: 185 STEKEMIKRFLKVIQEKDPDVLITYNGDNFDFAYLKKRSEMLGV---------------- 228
Query: 698 PKLRKGRTIFGSGASPGIMSC-------IAGRLLCDTFLCSRDLLREVSYSLTQLAKTQL 750
K GR G+ P I + GR+ D + R + +Y+L + +
Sbjct: 229 -KFILGR----DGSEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTINLPTYTLETVYEPVF 283
Query: 751 NKDRKEVGPHDVLKMFQTLESLMELIEYGETDAWLSMELMFHLSVLPLTRQLTNISG-NL 809
+ +++V ++ + +++ E L + Y DA + EL P+ QL+ + G +L
Sbjct: 284 GQPKEKVYAEEIARAWESGEGLERVARYSMEDAKATYEL--GKEFFPMEAQLSRLVGQSL 341
Query: 810 WGKTLQGARAQRVEYLLLHAFRAKKYIVPDKFTYVKETKMAKQRSNHGVEDRNVEELTNE 869
W + + + VE+ LL + + P+K
Sbjct: 342 WDVS-RSSTGNLVEWFLLRKAYERNDVAPNK----------------------------- 371
Query: 870 DANFDNDTSHNDHRKGKRGPAYAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFT 929
++ +R +YAGG V EP+KGL++ I+ LD+ SLYPSII +N+
Sbjct: 372 ---------PDERELARRTESYAGGYVKEPEKGLWEN-IVYLDYKSLYPSIIITHNVSPD 421
Query: 930 TVER--------SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMK-TASGLKIQQL 980
T+ R +P V H G +P LL +L++ R+ VK MK T ++ + L
Sbjct: 422 TLNREGCREYDVAPQ--VGHRFCKDFPGFIPSLLGDLLEERQKVKKKMKATVDPIERKLL 479
Query: 981 DIQQQALKLTANSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLNLEVIYG 1040
D +Q+A+K+ ANS YG ++N+R+Y + AE +T GR+ + +T+ ++ +V+Y
Sbjct: 480 DYRQRAIKILANSYYGYYAYANARWYCRECAESVTAWGRQYIETTMREIEEKFGFKVLYA 539
Query: 1041 DTDSIMIHSXXXXXXXXXXXXXXVIQEVNKKYK-CLEIDLDGXXXXXXXXXXXXXXXXXX 1099
DTD + +N + LE++ +G
Sbjct: 540 DTDGFFATIPGADAETVKNKAKEFLNYINPRLPGLLELEYEGFYRRGFFVTKKKYAVIDE 599
Query: 1100 QFKDGMPYEVIERKGLDMVRRDWSLLSKEVGDFCLSQILSERSCEDVVESIHNSLMKVQE 1159
+ K I +GL++VRRDWS ++KE L IL E+ V + +V E
Sbjct: 600 EDK-------ITTRGLEIVRRDWSEIAKETQARVLEAILKHGDVEEAVRIVK----EVTE 648
Query: 1160 DMRSGQVALEKYVITKTLTKPPEAYPDAKNQPHVQVALRLKQSGYSTGCSAGDTVPYIIC 1219
+ +V EK VI + +T+ +Y PHV VA RL G G + YI+
Sbjct: 649 KLSRHEVPPEKLVIYEQITRDLRSY--RATGPHVAVAKRLAARG--IKIRPGTVISYIVL 704
Query: 1220 CEQGTSSGSSVGIAQRARHPDELKKGDGKWMIDIDYYASQQIHPVVSRLCASI 1272
G + RA DE ++ D +YY Q+ P V R+ +
Sbjct: 705 KGPGR-------VGDRAIPFDEFDPAKHRY--DAEYYIENQVLPAVERILRAF 748
>pdb|3IAY|A Chain A, Ternary Complex Of Dna Polymerase Delta
Length = 919
Score = 149 bits (375), Expect = 1e-35, Method: Compositional matrix adjust.
Identities = 190/811 (23%), Positives = 341/811 (42%), Gaps = 137/811 (16%)
Query: 502 VKGPSWLSI--SKFSSCPAPQRVSWCKYEITVDSPKDIRVSSSSKHVAEVPPVTVTAINL 559
+ G SW+++ K+S RVS C+ E++++ +++ + + P+ + + ++
Sbjct: 198 IVGMSWITLPKGKYSMIEPNNRVSSCQLEVSINY-RNLIAHPAEGDWSHTAPLRIMSFDI 256
Query: 560 K-----TVFNKRQDVNEIVSASVVCCHKAKIDTPMLASEWKKPGMLSHFTVVRKLDGGIF 614
+ VF + + I A+VV AK KP + + FT+
Sbjct: 257 ECAGRIGVFPEPEYDPVIQIANVVSIAGAK-----------KPFIRNVFTL--------- 296
Query: 615 PMGFNKEATDRNSKAGSNVLCCESSERALLNRLMIELYKLDSDVLVGHNISGFDLDVLLH 674
+ S +++ ++E +L+ + K+D DV++G+N + FD+ LL+
Sbjct: 297 ---------NTCSPITGSMIFSHATEEEMLSNWRNFIIKVDPDVIIGYNTTNFDIPYLLN 347
Query: 675 RAQVCRVPSSMWSKIGRLK--RSEMPKLRKGRTIFGSGASPGIMSCIAGRLLCDTFLCSR 732
RA+ +V + GRLK + E+ + +G+ + + I GRL D +
Sbjct: 348 RAKALKVND--FPYFGRLKTVKQEIKESVFSSKAYGTRETKNV--NIDGRLQLDLLQFIQ 403
Query: 733 DLLREVSYSLTQLAKTQLNKDRKEVGPHDVLKMFQT--LESLMELIEYGETDAWLSMELM 790
+ SY+L ++ L + +++V + ++ Q E+ L Y DA+L + LM
Sbjct: 404 REYKLRSYTLNAVSAHFLGEQKEDVH-YSIISDLQNGDSETRRRLAVYCLKDAYLPLRLM 462
Query: 791 FHLSVLPLTRQLTNISGNLWGKTLQGARAQRVEYLLLHAFRAKKYIVPDKFTYVKETKMA 850
L L ++ ++G + L AR Q+++ +V F
Sbjct: 463 EKLMALVNYTEMARVTGVPFSYLL--ARGQQIK------------VVSQLF--------- 499
Query: 851 KQRSNHGVEDRNVEELTNEDANFDNDTSHNDHRKGKRGPAYAGGLVLEPKKGLYDKYILL 910
R E+ N + S + Y G V+EP +G YD I
Sbjct: 500 ----------RKCLEIDTVIPNMQSQASDDQ---------YEGATVIEPIRGYYDVPIAT 540
Query: 911 LDFNSLYPSIIQEYNICFT------TVER-----------SPDGLVPHLPSSKTTGVLPE 953
LDFNSLYPSI+ +N+C+T TVER +P+G + + + G+LP
Sbjct: 541 LDFNSLYPSIMMAHNLCYTTLCNKATVERLNLKIDEDYVITPNGDY-FVTTKRRRGILPI 599
Query: 954 LLKNLVQ-RRRMVKTWMKTASGLKIQQLDIQQQALKLTANSMYGCLGFSNSRFYAKPLAE 1012
+L L+ R+R K K L+ +Q ALK++ANS+YG G + + ++
Sbjct: 600 ILDELISARKRAKKDLRDEKDPFKRDVLNGRQLALKISANSVYGFTGATVGKLPCLAISS 659
Query: 1013 LITQQGREILRSTVDLVQNNLNLE--------VIYGDTDSIMIHSXXXXXXXXXXXXXXV 1064
+T GR ++ T VQ ++ V+YGDTDS+M+
Sbjct: 660 SVTAYGRTMILKTKTAVQEKYCIKNGYKHDAVVVYGDTDSVMVKFGTTDLKEAMDLGTEA 719
Query: 1065 IQEVNKKYKCLEIDLDGXXXXXXXXXXXXXXXXXXQFKDGMPYEVIERKGLDMVRRDWSL 1124
+ V+ +K I+L+ + + ++ +++KGL VRRD
Sbjct: 720 AKYVSTLFKH-PINLEFEKAYFPYLLINKKRYAGLFWTNPDKFDKLDQKGLASVRRDSCS 778
Query: 1125 LSKEVGDFCLSQILSERSCEDVVESIHNSLMKVQEDMRSGQVALEKYVITKTLTKPPEAY 1184
L V + L +IL ER+ + + + ++ D+ +V + K +I+KTL
Sbjct: 779 LVSIVMNKVLKKILIERNVDGALAFVRETI----NDILHNRVDISKLIISKTLA------ 828
Query: 1185 PDAKN-QPHVQVALRLKQSGYSTGCSAGDTVPYIICCEQGTSSGSSVGIAQRARHPDELK 1243
P+ N QPH +A R+K+ G + GD V Y+I G + + RA P L
Sbjct: 829 PNYTNPQPHAVLAERMKRRE-GVGPNVGDRVDYVII-------GGNDKLYNRAEDP--LF 878
Query: 1244 KGDGKWMIDIDYYASQQIHPVVSRLCASIEG 1274
+ +D YY + Q+ + + A I G
Sbjct: 879 VLENNIQVDSRYYLTNQLQNPIISIVAPIIG 909
>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 = 132 bits (332), Expect = 1e-30, Method: Compositional matrix adjust.
Identities = 153/653 (23%), Positives = 262/653 (40%), Gaps = 130/653 (19%)
Query: 638 SSERALLNRLMIELYKLDSDVLVGHNISGFDLDVLLHRAQVCRVPSSMWSKIGRLKRSEM 697
S+E+ ++ R + + + D DVL+ +N FD L R+++ V
Sbjct: 185 STEKEMIKRFLKVIQEKDPDVLITYNGDNFDFAYLKKRSEMLGV---------------- 228
Query: 698 PKLRKGRTIFGSGASPGIMSC-------IAGRLLCDTFLCSRDLLREVSYSLTQLAKTQL 750
K GR G+ P I + GR+ D + R + +Y+L + +
Sbjct: 229 -KFILGR----DGSEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTINLPTYTLETVYEPVF 283
Query: 751 NKDRKEVGPHDVLKMFQTLESLMELIEYGETDAWLSMELMFHLSVLPLTRQLTNISG-NL 809
+ ++V ++ + + + E L + Y DA + EL P+ QL+ + G +L
Sbjct: 284 GQPAEKVYAEEIAEAWASGEGLERVARYSMEDAKATYEL--GKEFFPMEAQLSRLVGQSL 341
Query: 810 WGKTLQGARAQRVEYLLLHAFRAKKYIVPDKFTYVKETKMAKQRSNHGVEDRNVEELTNE 869
W + + + VE+ LL + + P+K
Sbjct: 342 WDVS-RSSTGNLVEWFLLRKAYERNDVAPNK----------------------------- 371
Query: 870 DANFDNDTSHNDHRKGKRGPAYAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFT 929
++ +R +YAGG V EP+KGL++ I+ LD+ SLYPSII +N+
Sbjct: 372 ---------PDERELARRTESYAGGYVKEPEKGLWEN-IVYLDYKSLYPSIIITHNVSPD 421
Query: 930 TVER--------SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMK-TASGLKIQQL 980
T+ R +P V H G +P LL +L++ R+ VK MK T ++ + L
Sbjct: 422 TLNREGCREYDVAPQ--VGHRFCKDFPGFIPSLLGDLLEERQKVKKKMKATVDPIERKLL 479
Query: 981 DIQQQALKLTANSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLNLEVIYG 1040
D +Q+A+K+ ANS YG ++N+R+Y + AE +T GR+ + +T+ ++ +V+Y
Sbjct: 480 DYRQRAIKILANSYYGYYAYANARWYCRECAESVTAWGRQYIETTMREIEEKFGFKVLYA 539
Query: 1041 DTDSIMIHSXXXXXXXXXXXXXXVIQEVNKKYK-CLEIDLDGXXXXXXXXXXXXXXXXXX 1099
DTD + +N + LE++ +G
Sbjct: 540 DTDGFFATIPGADAETVKNKAKEFLNYINPRLPGLLELEYEGFYRRGFFVTKKKYAVIDE 599
Query: 1100 QFKDGMPYEVIERKGLDMVRRDWSLLSKEVGDFCLSQILSERSCEDVVESIHNSLMKVQE 1159
+ K I +GL++VRRDWS ++KE L IL E+ V + +V E
Sbjct: 600 EDK-------ITTRGLEIVRRDWSEIAKETQARVLEAILKHGDVEEAVRIVK----EVTE 648
Query: 1160 DMRSGQVALEKYVITKTLTKPPEAYPDAKNQPHVQVALRLKQSGYSTGCSAGDTVPYIIC 1219
+ +V EK VI + PHV +A + YI+
Sbjct: 649 KLSRHEVPPEKLVIYEA-------------GPHV--------------AAAATVISYIVL 681
Query: 1220 CEQGTSSGSSVGIAQRARHPDELKKGDGKWMIDIDYYASQQIHPVVSRLCASI 1272
G + RA DE ++ D +YY Q+ P V R+ +
Sbjct: 682 KGPGR-------VGDRAIPFDEFDPAKHRY--DAEYYIENQVLPAVERILRAF 725
>pdb|1Q8I|A Chain A, Crystal Structure Of Escherichia Coli Dna Polymerase Ii
Length = 783
Score = 99.0 bits (245), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 156/687 (22%), Positives = 249/687 (36%), Gaps = 141/687 (20%)
Query: 638 SSERALLNRLMIELYKLDSDVLVGHNISGFDLDVLLHRAQVCRVPSSMWSKIGRLKRSEM 697
+S LL +L D DV++G N+ FDL +L A+ R+P ++GR SE+
Sbjct: 199 ASRPQLLEKLNAWFANYDPDVIIGWNVVQFDLRMLQKHAERYRLP----LRLGR-DNSEL 253
Query: 698 PKLRKGRTIFGSGASPGIMSCIAGRLLCDTFLCSRDLLREV-SYSLTQLAKTQLNKDRKE 756
G F +G + GRL+ D + S+SL +A+ L + +
Sbjct: 254 EWREHG---FKNGV---FFAQAKGRLIIDGIEALKSAFWNFSSFSLETVAQELLGEGKSI 307
Query: 757 VGPHDVLKMF--QTLESLMELIEYGETDAWLSMELMFHLSVLPLTRQLTNISGNLWGKTL 814
P D + + E L Y D L ++ ++P + ++G +
Sbjct: 308 DNPWDRMDEIDRRFAEDKPALATYNLKDCELVTQIFHKTEIMPFLLERATVNGLPVDR-- 365
Query: 815 QGARAQRVEYLLLHAFRAKKYIVPDKFTYVKETKMAKQRSNHGVEDRNVEELTNEDANFD 874
G +L Y+ P N
Sbjct: 366 HGGSVAAFGHLYFPRMHRAGYVAP---------------------------------NLG 392
Query: 875 NDTSHNDHRKGKRGPAYAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTVERS 934
H A GG V++ + GLYD +L+LD+ SLYPSI++ + I
Sbjct: 393 EVPPH----------ASPGGYVMDSRPGLYDS-VLVLDYKSLYPSIVRTFLI-------D 434
Query: 935 PDGLVPHL----PSSKTTGV-----------LPELLKNLVQRRRMVKTWMKTASGLKIQQ 979
P GLV + P T G LPE++ N+ R K Q
Sbjct: 435 PVGLVEGMAQPDPEHSTEGFLDAWFSREKHCLPEIVTNIWHGRDEAKR----------QG 484
Query: 980 LDIQQQALKLTANSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLNLEVIY 1039
QALK+ N+ YG LG + RF+ LA IT +G +I+R T L++ +VIY
Sbjct: 485 NKPLSQALKIIMNAFYGVLGTTACRFFDPRLASSITMRGHQIMRQTKALIEAQ-GYDVIY 543
Query: 1040 GDTDSIMIH-SXXXXXXXXXXXXXXVIQEVNKKY----------KCLEIDLDGXXXXXXX 1088
GDTDS + ++Q VN + LE++ +
Sbjct: 544 GDTDSTFVWLKGAHSEEEAAKIGRALVQHVNAWWAETLQKQRLTSALELEYETHFCRFLM 603
Query: 1089 XXXXXXXXXXXQFKDGMPYEVIER----KGLDMVRRDWSLLSKEVGDFCLSQILSERSCE 1144
+ G+ E ++ KGL+ VR DW+ L+++ +I +
Sbjct: 604 PTIRGADTGSKKRYAGLIQEGDKQRMVFKGLETVRTDWTPLAQQFQQELYLRIFRNEPYQ 663
Query: 1145 DVVESIHNSLMKVQEDMRSGQVALEKYVITKTLTKPPEAYPDAKNQPHVQVALRL----- 1199
+ V + LM + D R V K L +P Y PHV+ A RL
Sbjct: 664 EYVRETIDKLMAGELDAR--------LVYRKRLRRPLSEY-QRNVPPHVRAA-RLADEEN 713
Query: 1200 KQSGYSTGCSAGDTVPYIICCEQGTSSGSSVGIAQRARHPDELKKGDGKWMIDIDYYASQ 1259
++ G T+ Y+ T++G QR+ +D ++Y ++
Sbjct: 714 QKRGRPLQYQNRGTIKYVW-----TTNGPEPLDYQRS-------------PLDYEHYLTR 755
Query: 1260 QIHPVVSRLCASIEGTSPERLADCLGL 1286
Q+ PV + IE + LGL
Sbjct: 756 QLQPVAEGILPFIEDNFATLMTGQLGL 782
>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 = 97.8 bits (242), Expect = 4e-20, Method: Compositional matrix adjust.
Identities = 156/687 (22%), Positives = 249/687 (36%), Gaps = 141/687 (20%)
Query: 638 SSERALLNRLMIELYKLDSDVLVGHNISGFDLDVLLHRAQVCRVPSSMWSKIGRLKRSEM 697
+S LL +L D DV++G N+ FDL +L A+ R+P ++GR SE+
Sbjct: 202 ASRPQLLEKLNAWFANYDPDVIIGWNVVQFDLRMLQKHAERYRLP----LRLGR-DNSEL 256
Query: 698 PKLRKGRTIFGSGASPGIMSCIAGRLLCDTFLCSRDLLREV-SYSLTQLAKTQLNKDRKE 756
G F +G + GRL+ D + S+SL +A+ L + +
Sbjct: 257 EWREHG---FKNGV---FFAQAKGRLIIDGIEALKSAFWNFSSFSLETVAQELLGEGKSI 310
Query: 757 VGPHDVLKMF--QTLESLMELIEYGETDAWLSMELMFHLSVLPLTRQLTNISGNLWGKTL 814
P D + + E L Y + L ++ ++P + ++G +
Sbjct: 311 DNPWDRMDEIDRRFAEDKPALATYNLKNCELVTQIFHKTEIMPFLLERATVNGLPVDR-- 368
Query: 815 QGARAQRVEYLLLHAFRAKKYIVPDKFTYVKETKMAKQRSNHGVEDRNVEELTNEDANFD 874
G +L Y+ P N
Sbjct: 369 HGGSVAAFGHLYFPRMHRAGYVAP---------------------------------NLG 395
Query: 875 NDTSHNDHRKGKRGPAYAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTVERS 934
H A GG V++ + GLYD +L+LD+ SLYPSII+ + I
Sbjct: 396 EVPPH----------ASPGGYVMDSRPGLYDS-VLVLDYKSLYPSIIRTFLI-------D 437
Query: 935 PDGLVPHL----PSSKTTGV-----------LPELLKNLVQRRRMVKTWMKTASGLKIQQ 979
P GLV + P T G LPE++ N+ R K Q
Sbjct: 438 PVGLVEGMAQPDPEHSTEGFLDAWFSREKHCLPEIVTNIWHGRDEAKR----------QG 487
Query: 980 LDIQQQALKLTANSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLNLEVIY 1039
QALK+ N+ YG LG + RF+ LA IT +G +I+R T L++ +VIY
Sbjct: 488 NKPLSQALKIIMNAFYGVLGTTACRFFDPRLASSITMRGHQIMRQTKALIEAQ-GYDVIY 546
Query: 1040 GDTDSIMIH-SXXXXXXXXXXXXXXVIQEVNKKY----------KCLEIDLDGXXXXXXX 1088
GDTDS + ++Q VN + LE++ +
Sbjct: 547 GDTDSTFVWLKGAHSEEEAAKIGRALVQHVNAWWAETLQKQRLTSALELEYETHFCRFLM 606
Query: 1089 XXXXXXXXXXXQFKDGMPYEVIER----KGLDMVRRDWSLLSKEVGDFCLSQILSERSCE 1144
+ G+ E ++ KGL+ VR DW+ L+++ +I +
Sbjct: 607 PTIRGADTGSKKRYAGLIQEGDKQRMVFKGLETVRTDWTPLAQQFQQELYLRIFRNEPYQ 666
Query: 1145 DVVESIHNSLMKVQEDMRSGQVALEKYVITKTLTKPPEAYPDAKNQPHVQVALRL----- 1199
+ V + LM + D R V K L +P Y PHV+ A RL
Sbjct: 667 EYVRETIDKLMAGELDAR--------LVYRKRLRRPLSEY-QRNVPPHVRAA-RLADEEN 716
Query: 1200 KQSGYSTGCSAGDTVPYIICCEQGTSSGSSVGIAQRARHPDELKKGDGKWMIDIDYYASQ 1259
++ G T+ Y+ T++G QR+ +D ++Y ++
Sbjct: 717 QKRGRPLQYQNRGTIKYVW-----TTNGPEPLDYQRS-------------PLDYEHYLTR 758
Query: 1260 QIHPVVSRLCASIEGTSPERLADCLGL 1286
Q+ PV + IE + LGL
Sbjct: 759 QLQPVAEGILPFIEDNFATLMTGQLGL 785
>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 = 93.6 bits (231), Expect = 8e-19, Method: Compositional matrix adjust.
Identities = 108/462 (23%), Positives = 188/462 (40%), Gaps = 64/462 (13%)
Query: 639 SERALLNRLMIELYKLDSDVLVGHNISGFDLDVLLHR-AQVCRVPSSMWSKIGRLKRSEM 697
SE +L M + + + + G+NI FD LL + + +VP + ++ R
Sbjct: 400 SEFEMLLAFMTLVKQYGPEFVTGYNIINFDWPFLLAKLTDIYKVPLDGYGRMN--GRGVF 457
Query: 698 PKLRKGRTIFGSGASPGIMSCIAGRLLCDTFLCSRDLLREVSYSLTQLAKTQLNKDRKEV 757
G++ F + + G + D + D ++ SY L +A+ L +K++
Sbjct: 458 RVWDIGQSHFQKRSK----IKVNGMVNIDMYGIITDKIKLSSYKLNAVAEAVLKDKKKDL 513
Query: 758 GPHDVLKMFQTLESLMELI-EYGETDAWLSMELMF----HLSVLPLTRQLTNISGNLWGK 812
D+ + T + +I EY D+ L +L F HL + + R ++G +
Sbjct: 514 SYRDIPAYYATGPAQRGVIGEYCIQDSLLVGQLFFKFLPHLELSAVAR----LAGINITR 569
Query: 813 TLQGARAQRVEYLLLHAFRAKKYIVPDKFTYVKET------KMAKQRSNHGVEDRNVEEL 866
T+ + RV LL K +I+PD + + A R + + E+
Sbjct: 570 TIYDGQQIRVFTCLLRLADQKGFILPDTQGRFRGAGGEAPKRPAAAREDEERPEEEGEDE 629
Query: 867 TNEDANFDNDTSHNDHRKGKRGPAYAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNI 926
+ R Y G VL+P G + +++ DF SLYPSIIQ +N+
Sbjct: 630 DEREEGGGEREPEGARETAGRHVGYQGAKVLDPTSGFHVNPVVVFDFASLYPSIIQAHNL 689
Query: 927 CFTTVERSPDGLVPHLPSSK-------------------TTGVLPELLKNLVQRRRMVKT 967
CF+T+ D V HL + K +L LL++ + R+ +++
Sbjct: 690 CFSTLSLRADA-VAHLEAGKDYLEIEVGGRRLFFVKAHVRESLLSILLRDWLAMRKQIRS 748
Query: 968 WMKTASGLKIQQLDIQQQALKLTANSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVD 1027
+ +S + LD QQ A+K+ NS+YG G + +A +T GRE+L +T +
Sbjct: 749 RIPQSSPEEAVLLDKQQAAIKVVCNSVYGFTGVQHGLLPCLHVAATVTTIGREMLLATRE 808
Query: 1028 LVQNN----------------------LNLEVIYGDTDSIMI 1047
V ++ +IYGDTDSI +
Sbjct: 809 YVHARWAAFEQLLADFPEAADMRAPGPYSMRIIYGDTDSIFV 850
>pdb|1S5J|A Chain A, Insight In Dna Replication: The Crystal Structure Of Dna
Polymerase B1 From The Archaeon Sulfolobus Solfataricus
Length = 847
Score = 91.7 bits (226), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 91/336 (27%), Positives = 156/336 (46%), Gaps = 38/336 (11%)
Query: 887 RGPAYAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTVE----------RSPD 936
+G Y G +V++P G++ I +LDF SLYPSII+ +N+ + TV+ +
Sbjct: 455 KGKGYKGAVVIDPPAGIFFN-ITVLDFASLYPSIIRTWNLSYETVDIQQCKKPYEVKDET 513
Query: 937 GLVPH---LPSSKTTGVLPELLKNLVQRRRMVKTWMKTASGLKIQQL--DIQQQALKLTA 991
G V H + T V+ LL++ R ++ K K + + Q+L D+ Q+A+K+
Sbjct: 514 GEVLHIVCMDRPGITAVITGLLRDF--RVKIYKKKAKNPNNSEEQKLLYDVVQRAMKVFI 571
Query: 992 NSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLNLEVIYGDTDSIMIHSXX 1051
N+ YG G YA +AE +T GR ++ STV + L V+YGDTDS+ + +
Sbjct: 572 NATYGVFGAETFPLYAPRVAESVTALGRYVITSTVKKAREE-GLTVLYGDTDSLFLLN-- 628
Query: 1052 XXXXXXXXXXXXVIQEVNKKYKCLEIDLDGXXXXXXXXXXXXXXXXXXQFKDGMPYEVIE 1111
+I+ V + +DL+ ++DG ++
Sbjct: 629 ----PPKNSLENIIKWVKTTF---NLDLEVDKTYKFVAFSGLKKNYFGVYQDGK----VD 677
Query: 1112 RKGLDMVRRDWSLLSKEVGDFCLSQILSERSCEDVVE---SIHNSLMKVQEDMRSGQVAL 1168
KG+ + +R+ K+V + ++S S DV E I + + E +++ L
Sbjct: 678 IKGMLVKKRNTPEFVKKVFNEVKELMISINSPNDVKEIKRKIVDVVKGSYEKLKNKGYNL 737
Query: 1169 EKYVITKTLTKPPEAYPDAKNQP-HVQVALRLKQSG 1203
++ L+KP +AY KN P HV+ AL+L+ G
Sbjct: 738 DELAFKVMLSKPLDAY--KKNTPQHVKAALQLRPFG 771
>pdb|3FLO|B Chain B, Crystal Structure Of The Carboxyl-Terminal Domain Of Yeast
Dna Polymerase Alpha In Complex With Its B Subunit
pdb|3FLO|D Chain D, Crystal Structure Of The Carboxyl-Terminal Domain Of Yeast
Dna Polymerase Alpha In Complex With Its B Subunit
pdb|3FLO|F Chain F, Crystal Structure Of The Carboxyl-Terminal Domain Of Yeast
Dna Polymerase Alpha In Complex With Its B Subunit
pdb|3FLO|H Chain H, Crystal Structure Of The Carboxyl-Terminal Domain Of Yeast
Dna Polymerase Alpha In Complex With Its B Subunit
Length = 206
Score = 65.1 bits (157), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 54/193 (27%), Positives = 86/193 (44%), Gaps = 29/193 (15%)
Query: 1310 AVGDEERYRGCEPLILSCPSCSSTFDCPAVCSSICMSVSEKPSKPETEYNFWRTLRCPKC 1369
+ D ER++ L LSCPSC F + SS VS + L+C C
Sbjct: 8 TITDVERFKDTVTLELSCPSCDKRFPFGGIVSSNYYRVS------------YNGLQCKHC 55
Query: 1370 PEEVEAGRISPGMIANQVKRQADGFVSMYYKGLMMCDDETCKYTTCSLNLRLIGDAERGT 1429
+ +P + +Q++ +S+YY G + CDD TC T +++ G
Sbjct: 56 EQ-----LFTPLQLTSQIEHSIRAHISLYYAGWLQCDDSTCGIVTRQVSV-------FGK 103
Query: 1430 VCPNYPRCNGRLVRKYTEADLYKQLTYFCHLLDTQRGIEKMEISAKIPLEKELNKIRPVV 1489
C N C G + KY++ LY QL YF L D ++ +K E+ I L +L+ P
Sbjct: 104 RCLN-DGCTGVMRYKYSDKQLYNQLLYFDSLFDCEKN-KKQELKP-IYLPDDLD--YPKE 158
Query: 1490 ALAASTVQRIRER 1502
L S+++ + E+
Sbjct: 159 QLTESSIKALTEQ 171
>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 = 52.4 bits (124), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 67/252 (26%), Positives = 95/252 (37%), Gaps = 90/252 (35%)
Query: 884 KGKRGPA--YAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTV---------- 931
+G+ P Y G V EP Y KY++ D SLYPSII++ NI T+
Sbjct: 382 QGRSHPVQPYPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLH 440
Query: 932 -------ER-------SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMKTA--SGL 975
ER SP+G++ + GV+P + V +R+ K +M A +G
Sbjct: 441 DYINAVAERPSDVYSCSPNGMMYY---KDRDGVVPTEITKWVSQRKEHKGYMLAAQRNGE 497
Query: 976 KIQQ------------LDIQ--------------------------------------QQ 985
I++ LD+ Q
Sbjct: 498 IIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQM 557
Query: 986 ALKLTANSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLN--------LEV 1037
ALK+T NS+YG LG R+Y A IT G+ L+ V LN V
Sbjct: 558 ALKVTCNSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFV 617
Query: 1038 IYGDTDSIMIHS 1049
+YGDTDSI + +
Sbjct: 618 LYGDTDSIYVSA 629
>pdb|1Q9Y|A Chain A, Crystal Structure Of Enterobacteria Phage Rb69 Gp43 Dna
Polymerase Complexed With 8-Oxoguanosine Containing Dna
Length = 906
Score = 44.7 bits (104), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 63/252 (25%), Positives = 95/252 (37%), Gaps = 90/252 (35%)
Query: 884 KGKRGPA--YAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTV---------- 931
+G+ P Y G V EP Y KY++ D SLYPSII++ NI T+
Sbjct: 385 QGRSHPVQPYPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLH 443
Query: 932 -------ER-------SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMKTA--SGL 975
ER SP+G++ + GV+P + + +R+ K +M A +G
Sbjct: 444 DYINAVAERPSDVYSCSPNGMMYY---KDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGE 500
Query: 976 KIQQL----------------------DIQQQALKLTA---------------------- 991
I++ +I+++ KL+A
Sbjct: 501 IIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQI 560
Query: 992 ------NSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLN--------LEV 1037
NS+YG LG R+Y A IT G+ L+ V LN V
Sbjct: 561 NRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFV 620
Query: 1038 IYGDTDSIMIHS 1049
+YGDTDSI + +
Sbjct: 621 LYGDTDSIYVSA 632
>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 = 44.7 bits (104), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 63/252 (25%), Positives = 95/252 (37%), Gaps = 90/252 (35%)
Query: 884 KGKRGPA--YAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTV---------- 931
+G+ P Y G V EP Y KY++ D SLYPSII++ NI T+
Sbjct: 382 QGRSHPVQPYPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLH 440
Query: 932 -------ER-------SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMKTA--SGL 975
ER SP+G++ + GV+P + + +R+ K +M A +G
Sbjct: 441 DYINAVAERPSDVYSCSPNGMMYY---KDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGE 497
Query: 976 KIQQL----------------------DIQQQALKLTA---------------------- 991
I++ +I+++ KL+A
Sbjct: 498 IIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQI 557
Query: 992 ------NSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLN--------LEV 1037
NS+YG LG R+Y A IT G+ L+ V LN V
Sbjct: 558 NRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFV 617
Query: 1038 IYGDTDSIMIHS 1049
+YGDTDSI + +
Sbjct: 618 LYGDTDSIYVSA 629
>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 = 44.7 bits (104), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 63/252 (25%), Positives = 95/252 (37%), Gaps = 90/252 (35%)
Query: 884 KGKRGPA--YAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTV---------- 931
+G+ P Y G V EP Y KY++ D SLYPSII++ NI T+
Sbjct: 382 QGRSHPVQPYPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLH 440
Query: 932 -------ER-------SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMKTA--SGL 975
ER SP+G++ + GV+P + + +R+ K +M A +G
Sbjct: 441 DYINAVAERPSDVYSCSPNGMMYY---KDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGE 497
Query: 976 KIQQL----------------------DIQQQALKLTA---------------------- 991
I++ +I+++ KL+A
Sbjct: 498 IIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQI 557
Query: 992 ------NSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLN--------LEV 1037
NS+YG LG R+Y A IT G+ L+ V LN V
Sbjct: 558 NRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFV 617
Query: 1038 IYGDTDSIMIHS 1049
+YGDTDSI + +
Sbjct: 618 LYGDTDSIYVSA 629
>pdb|3LDS|A Chain A, Crystal Structure Of Rb69 Gp43 With Dna And Datp Opposite 8-
Length = 903
Score = 44.7 bits (104), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 63/252 (25%), Positives = 95/252 (37%), Gaps = 90/252 (35%)
Query: 884 KGKRGPA--YAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTV---------- 931
+G+ P Y G V EP Y KY++ D SLYPSII++ NI T+
Sbjct: 382 QGRSHPVQPYPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLH 440
Query: 932 -------ER-------SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMKTA--SGL 975
ER SP+G++ + GV+P + + +R+ K +M A +G
Sbjct: 441 DYINAVAERPSDVYSCSPNGMMYY---KDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGE 497
Query: 976 KIQQL----------------------DIQQQALKLTA---------------------- 991
I++ +I+++ KL+A
Sbjct: 498 IIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQI 557
Query: 992 ------NSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLN--------LEV 1037
NS+YG LG R+Y A IT G+ L+ V LN V
Sbjct: 558 NRKALINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFV 617
Query: 1038 IYGDTDSIMIHS 1049
+YGDTDSI + +
Sbjct: 618 LYGDTDSIYVSA 629
>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 = 44.7 bits (104), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 63/250 (25%), Positives = 94/250 (37%), Gaps = 90/250 (36%)
Query: 884 KGKRGPA--YAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTV---------- 931
+G+ P Y G V EP Y KY++ D SLYPSII++ NI T+
Sbjct: 382 QGRSHPVQPYPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLH 440
Query: 932 -------ER-------SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMKTA--SGL 975
ER SP+G++ + GV+P + + +R+ K +M A +G
Sbjct: 441 DYINAVAERPSDVYSCSPNGMMYY---KDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGE 497
Query: 976 KIQQL----------------------DIQQQALKLTA---------------------- 991
I++ +I+++ KL+A
Sbjct: 498 IIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQI 557
Query: 992 ------NSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLN--------LEV 1037
NS+YG LG R+Y A IT G+ L+ V LN V
Sbjct: 558 NRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFV 617
Query: 1038 IYGDTDSIMI 1047
+YGDTDSI +
Sbjct: 618 LYGDTDSIYV 627
>pdb|3SQ1|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dupcpp Opposite Da
Length = 901
Score = 44.7 bits (104), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 63/252 (25%), Positives = 95/252 (37%), Gaps = 90/252 (35%)
Query: 884 KGKRGPA--YAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTV---------- 931
+G+ P Y G V EP Y KY++ D SLYPSII++ NI T+
Sbjct: 382 QGRSHPVQPYPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLH 440
Query: 932 -------ER-------SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMKTA--SGL 975
ER SP+G++ + GV+P + + +R+ K +M A +G
Sbjct: 441 DYINAVAERPSDVYSCSPNGMMYY---KDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGE 497
Query: 976 KIQQL----------------------DIQQQALKLTA---------------------- 991
I++ +I+++ KL+A
Sbjct: 498 IIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQI 557
Query: 992 ------NSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLN--------LEV 1037
NS+YG LG R+Y A IT G+ L+ V LN V
Sbjct: 558 NRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFV 617
Query: 1038 IYGDTDSIMIHS 1049
+YGDTDSI + +
Sbjct: 618 LYGDTDSIYVSA 629
>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 = 44.7 bits (104), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 63/252 (25%), Positives = 95/252 (37%), Gaps = 90/252 (35%)
Query: 884 KGKRGPA--YAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTV---------- 931
+G+ P Y G V EP Y KY++ D SLYPSII++ NI T+
Sbjct: 382 QGRSHPVQPYPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLH 440
Query: 932 -------ER-------SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMKTA--SGL 975
ER SP+G++ + GV+P + + +R+ K +M A +G
Sbjct: 441 DYINAVAERPSDVYSCSPNGMMYY---KDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGE 497
Query: 976 KIQQL----------------------DIQQQALKLTA---------------------- 991
I++ +I+++ KL+A
Sbjct: 498 IIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQI 557
Query: 992 ------NSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLN--------LEV 1037
NS+YG LG R+Y A IT G+ L+ V LN V
Sbjct: 558 NRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFV 617
Query: 1038 IYGDTDSIMIHS 1049
+YGDTDSI + +
Sbjct: 618 LYGDTDSIYVSA 629
>pdb|2DTU|A Chain A, Crystal Structure Of The Beta Hairpin Loop Deletion Variant
Of Rb69 Gp43 In Complex With Dna Containing An Abasic
Site Analog
pdb|2DTU|B Chain B, Crystal Structure Of The Beta Hairpin Loop Deletion Variant
Of Rb69 Gp43 In Complex With Dna Containing An Abasic
Site Analog
pdb|2DTU|C Chain C, Crystal Structure Of The Beta Hairpin Loop Deletion Variant
Of Rb69 Gp43 In Complex With Dna Containing An Abasic
Site Analog
pdb|2DTU|D Chain D, Crystal Structure Of The Beta Hairpin Loop Deletion Variant
Of Rb69 Gp43 In Complex With Dna Containing An Abasic
Site Analog
Length = 896
Score = 44.7 bits (104), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 63/252 (25%), Positives = 95/252 (37%), Gaps = 90/252 (35%)
Query: 884 KGKRGPA--YAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTV---------- 931
+G+ P Y G V EP Y KY++ D SLYPSII++ NI T+
Sbjct: 375 QGRSHPVQPYPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLH 433
Query: 932 -------ER-------SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMKTA--SGL 975
ER SP+G++ + GV+P + + +R+ K +M A +G
Sbjct: 434 DYINAVAERPSDVYSCSPNGMMYY---KDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGE 490
Query: 976 KIQQL----------------------DIQQQALKLTA---------------------- 991
I++ +I+++ KL+A
Sbjct: 491 IIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQI 550
Query: 992 ------NSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLN--------LEV 1037
NS+YG LG R+Y A IT G+ L+ V LN V
Sbjct: 551 NRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFV 610
Query: 1038 IYGDTDSIMIHS 1049
+YGDTDSI + +
Sbjct: 611 LYGDTDSIYVSA 622
>pdb|3CQ8|A Chain A, Ternary Complex Of The L415f Mutant Rb69 Exo(-)polymerase
Length = 903
Score = 43.5 bits (101), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 62/252 (24%), Positives = 94/252 (37%), Gaps = 90/252 (35%)
Query: 884 KGKRGPA--YAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTV---------- 931
+G+ P Y G V EP Y KY++ D S YPSII++ NI T+
Sbjct: 382 QGRSHPVQPYPGAFVKEPIPNRY-KYVMSFDLTSFYPSIIRQVNISPETIAGTFKVAPLH 440
Query: 932 -------ER-------SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMKTA--SGL 975
ER SP+G++ + GV+P + + +R+ K +M A +G
Sbjct: 441 DYINAVAERPSDVYSCSPNGMMYY---KDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGE 497
Query: 976 KIQQL----------------------DIQQQALKLTA---------------------- 991
I++ +I+++ KL+A
Sbjct: 498 IIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQI 557
Query: 992 ------NSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLN--------LEV 1037
NS+YG LG R+Y A IT G+ L+ V LN V
Sbjct: 558 NRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFV 617
Query: 1038 IYGDTDSIMIHS 1049
+YGDTDSI + +
Sbjct: 618 LYGDTDSIYVSA 629
>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 = 41.2 bits (95), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 62/252 (24%), Positives = 94/252 (37%), Gaps = 90/252 (35%)
Query: 884 KGKRGPA--YAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTV---------- 931
+G+ P Y G V EP Y KY++ D SLYPSII++ NI T+
Sbjct: 382 QGRSHPVQPYPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLH 440
Query: 932 -------ER-------SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMKTA--SGL 975
ER SP+G++ + GV+P + + +R+ K +M A +G
Sbjct: 441 DYINAVAERPSDVYSCSPNGMMYY---KDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGE 497
Query: 976 KIQQL----------------------DIQQQALKLTA---------------------- 991
I++ +I+++ KL+A
Sbjct: 498 IIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQI 557
Query: 992 ------NSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLN--------LEV 1037
NS+ G LG R+Y A IT G+ L+ V LN V
Sbjct: 558 NRKLLINSLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFV 617
Query: 1038 IYGDTDSIMIHS 1049
+YGDTDSI + +
Sbjct: 618 LYGDTDSIYVSA 629
>pdb|3SUO|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dttp
Opposite 2ap (Gc Rich Sequence)
Length = 900
Score = 41.2 bits (95), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 62/252 (24%), Positives = 94/252 (37%), Gaps = 90/252 (35%)
Query: 884 KGKRGPA--YAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTV---------- 931
+G+ P Y G V EP Y KY++ D SLYPSII++ NI T+
Sbjct: 382 QGRSHPVQPYPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLH 440
Query: 932 -------ER-------SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMKTA--SGL 975
ER SP+G++ + GV+P + + +R+ K +M A +G
Sbjct: 441 DYINAVAERPSDVYSCSPNGMMYY---KDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGE 497
Query: 976 KIQQL----------------------DIQQQALKLTA---------------------- 991
I++ +I+++ KL+A
Sbjct: 498 IIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQI 557
Query: 992 ------NSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLN--------LEV 1037
NS+ G LG R+Y A IT G+ L+ V LN V
Sbjct: 558 NRKLLINSLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFV 617
Query: 1038 IYGDTDSIMIHS 1049
+YGDTDSI + +
Sbjct: 618 LYGDTDSIYVSA 629
>pdb|3SUN|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dttp
Opposite 2ap (At Rich Sequence)
Length = 895
Score = 41.2 bits (95), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 62/252 (24%), Positives = 94/252 (37%), Gaps = 90/252 (35%)
Query: 884 KGKRGPA--YAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTV---------- 931
+G+ P Y G V EP Y KY++ D SLYPSII++ NI T+
Sbjct: 382 QGRSHPVQPYPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLH 440
Query: 932 -------ER-------SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMKTA--SGL 975
ER SP+G++ + GV+P + + +R+ K +M A +G
Sbjct: 441 DYINAVAERPSDVYSCSPNGMMYY---KDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGE 497
Query: 976 KIQQL----------------------DIQQQALKLTA---------------------- 991
I++ +I+++ KL+A
Sbjct: 498 IIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQI 557
Query: 992 ------NSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLN--------LEV 1037
NS+ G LG R+Y A IT G+ L+ V LN V
Sbjct: 558 NRKLLINSLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFV 617
Query: 1038 IYGDTDSIMIHS 1049
+YGDTDSI + +
Sbjct: 618 LYGDTDSIYVSA 629
>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 = 41.2 bits (95), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 62/252 (24%), Positives = 94/252 (37%), Gaps = 90/252 (35%)
Query: 884 KGKRGPA--YAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTV---------- 931
+G+ P Y G V EP Y KY++ D SLYPSII++ NI T+
Sbjct: 382 QGRSHPVQPYPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLH 440
Query: 932 -------ER-------SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMKTA--SGL 975
ER SP+G++ + GV+P + + +R+ K +M A +G
Sbjct: 441 DYINAVAERPSDVYSCSPNGMMYY---KDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGE 497
Query: 976 KIQQL----------------------DIQQQALKLTA---------------------- 991
I++ +I+++ KL+A
Sbjct: 498 IIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQI 557
Query: 992 ------NSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLN--------LEV 1037
NS+ G LG R+Y A IT G+ L+ V LN V
Sbjct: 558 NRKLLINSLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFV 617
Query: 1038 IYGDTDSIMIHS 1049
+YGDTDSI + +
Sbjct: 618 LYGDTDSIYVSA 629
>pdb|3SUQ|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dctp
Opposite 2ap (At Rich Sequence)
Length = 897
Score = 41.2 bits (95), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 62/252 (24%), Positives = 94/252 (37%), Gaps = 90/252 (35%)
Query: 884 KGKRGPA--YAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTV---------- 931
+G+ P Y G V EP Y KY++ D SLYPSII++ NI T+
Sbjct: 382 QGRSHPVQPYPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLH 440
Query: 932 -------ER-------SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMKTA--SGL 975
ER SP+G++ + GV+P + + +R+ K +M A +G
Sbjct: 441 DYINAVAERPSDVYSCSPNGMMYY---KDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGE 497
Query: 976 KIQQL----------------------DIQQQALKLTA---------------------- 991
I++ +I+++ KL+A
Sbjct: 498 IIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQI 557
Query: 992 ------NSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLN--------LEV 1037
NS+ G LG R+Y A IT G+ L+ V LN V
Sbjct: 558 NRKLLINSLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFV 617
Query: 1038 IYGDTDSIMIHS 1049
+YGDTDSI + +
Sbjct: 618 LYGDTDSIYVSA 629
>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 = 39.7 bits (91), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 61/252 (24%), Positives = 93/252 (36%), Gaps = 90/252 (35%)
Query: 884 KGKRGPA--YAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTV---------- 931
+G+ P Y G V EP Y KY++ D SLYPSII++ NI T+
Sbjct: 382 QGRSHPVQPYPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLH 440
Query: 932 -------ER-------SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMKTA--SGL 975
ER SP+G++ + GV+P + + +R+ K +M A +G
Sbjct: 441 DYINAVAERPSDVYSCSPNGMMYY---KDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGE 497
Query: 976 KIQQL----------------------DIQQQALKLTA---------------------- 991
I++ +I+++ KL+A
Sbjct: 498 IIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQI 557
Query: 992 ------NSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLN--------LEV 1037
N + G LG R+Y A IT G+ L+ V LN V
Sbjct: 558 NRKALINGLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFV 617
Query: 1038 IYGDTDSIMIHS 1049
+YGDTDSI + +
Sbjct: 618 LYGDTDSIYVSA 629
>pdb|3CFO|A Chain A, Triple Mutant Apo Structure
pdb|3CFP|A Chain A, Structure Of The Replicating Complex Of A Pol Alpha Family
Dna Polymerase, Ternary Complex 1
pdb|3CFR|A Chain A, Structure Of The Replicating Complex Of A Pol Alpha Family
Dna Polymerase, Ternary Complex 2
Length = 909
Score = 39.7 bits (91), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 61/252 (24%), Positives = 93/252 (36%), Gaps = 90/252 (35%)
Query: 884 KGKRGPA--YAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTV---------- 931
+G+ P Y G V EP Y KY++ D SLYPSII++ NI T+
Sbjct: 382 QGRSHPVQPYPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLH 440
Query: 932 -------ER-------SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMKTA--SGL 975
ER SP+G++ + GV+P + + +R+ K +M A +G
Sbjct: 441 DYINAVAERPSDVYSCSPNGMMYY---KDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGE 497
Query: 976 KIQQL----------------------DIQQQALKLTA---------------------- 991
I++ +I+++ KL+A
Sbjct: 498 IIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQI 557
Query: 992 ------NSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLN--------LEV 1037
N + G LG R+Y A IT G+ L+ V LN V
Sbjct: 558 NRKALINGLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFV 617
Query: 1038 IYGDTDSIMIHS 1049
+YGDTDSI + +
Sbjct: 618 LYGDTDSIYVSA 629
>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 = 39.7 bits (91), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 61/252 (24%), Positives = 93/252 (36%), Gaps = 90/252 (35%)
Query: 884 KGKRGPA--YAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTV---------- 931
+G+ P Y G V EP Y KY++ D SLYPSII++ NI T+
Sbjct: 382 QGRSHPVQPYPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLH 440
Query: 932 -------ER-------SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMKTA--SGL 975
ER SP+G++ + GV+P + + +R+ K +M A +G
Sbjct: 441 DYINAVAERPSDVYSCSPNGMMYY---KDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGE 497
Query: 976 KIQQL----------------------DIQQQALKLTA---------------------- 991
I++ +I+++ KL+A
Sbjct: 498 IIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQI 557
Query: 992 ------NSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLN--------LEV 1037
N + G LG R+Y A IT G+ L+ V LN V
Sbjct: 558 NRKALINGLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFV 617
Query: 1038 IYGDTDSIMIHS 1049
+YGDTDSI + +
Sbjct: 618 LYGDTDSIYVSA 629
>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 = 39.7 bits (91), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 61/252 (24%), Positives = 93/252 (36%), Gaps = 90/252 (35%)
Query: 884 KGKRGPA--YAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTV---------- 931
+G+ P Y G V EP Y KY++ D SLYPSII++ NI T+
Sbjct: 382 QGRSHPVQPYPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLH 440
Query: 932 -------ER-------SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMKTA--SGL 975
ER SP+G++ + GV+P + + +R+ K +M A +G
Sbjct: 441 DYINAVAERPSDVYSCSPNGMMYY---KDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGE 497
Query: 976 KIQQL----------------------DIQQQALKLTA---------------------- 991
I++ +I+++ KL+A
Sbjct: 498 IIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQI 557
Query: 992 ------NSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLN--------LEV 1037
N + G LG R+Y A IT G+ L+ V LN V
Sbjct: 558 NRKALINGLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFV 617
Query: 1038 IYGDTDSIMIHS 1049
+YGDTDSI + +
Sbjct: 618 LYGDTDSIYVSA 629
>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 = 39.7 bits (91), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 61/252 (24%), Positives = 93/252 (36%), Gaps = 90/252 (35%)
Query: 884 KGKRGPA--YAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTV---------- 931
+G+ P Y G V EP Y KY++ D SLYPSII++ NI T+
Sbjct: 382 QGRSHPVQPYPGAFVKEPIPNRY-KYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLH 440
Query: 932 -------ER-------SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMKTA--SGL 975
ER SP+G++ + GV+P + + +R+ K +M A +G
Sbjct: 441 DYINAVAERPSDVYSCSPNGMMYY---KDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGE 497
Query: 976 KIQQL----------------------DIQQQALKLTA---------------------- 991
I++ +I+++ KL+A
Sbjct: 498 IIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQI 557
Query: 992 ------NSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLN--------LEV 1037
N + G LG R+Y A IT G+ L+ V LN V
Sbjct: 558 NRKLLINGLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFV 617
Query: 1038 IYGDTDSIMIHS 1049
+YGDTDSI + +
Sbjct: 618 LYGDTDSIYVSA 629
>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 = 0.056, Method: Compositional matrix adjust.
Identities = 60/252 (23%), Positives = 92/252 (36%), Gaps = 90/252 (35%)
Query: 884 KGKRGPA--YAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTV---------- 931
+G+ P Y G V EP Y KY++ D S YPSII++ NI T+
Sbjct: 382 QGRSHPVQPYPGAFVKEPIPNRY-KYVMSFDLTSAYPSIIRQVNISPETIAGTFKVAPLH 440
Query: 932 -------ER-------SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMKTA--SGL 975
ER SP+G++ + GV+P + + +R+ K +M A +G
Sbjct: 441 DYINAVAERPSDVYSCSPNGMMYY---KDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGE 497
Query: 976 KIQQL----------------------DIQQQALKLTA---------------------- 991
I++ +I+++ KL+A
Sbjct: 498 IIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQI 557
Query: 992 ------NSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLN--------LEV 1037
N + G LG R+Y A IT G+ L+ V LN V
Sbjct: 558 NRKALINGLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFV 617
Query: 1038 IYGDTDSIMIHS 1049
+YGDTDSI + +
Sbjct: 618 LYGDTDSIYVSA 629
>pdb|2DY4|A Chain A, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing Thymine Glycol
pdb|2DY4|B Chain B, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing Thymine Glycol
pdb|2DY4|C Chain C, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing Thymine Glycol
pdb|2DY4|D Chain D, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing Thymine Glycol
pdb|2P5O|A Chain A, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing An Abasic Site Analog
pdb|2P5O|B Chain B, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing An Abasic Site Analog
pdb|2P5O|C Chain C, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing An Abasic Site Analog
pdb|2P5O|D Chain D, Crystal Structure Of Rb69 Gp43 In Complex With Dna
Containing An Abasic Site Analog
pdb|2P5G|A Chain A, Crystal Structure Of Rb69 Gp43 In Complex With Dna With Damp
Opposite An Abasic Site Analog In A 21mer Template
pdb|2P5G|B Chain B, Crystal Structure Of Rb69 Gp43 In Complex With Dna With Damp
Opposite An Abasic Site Analog In A 21mer Template
pdb|2P5G|C Chain C, Crystal Structure Of Rb69 Gp43 In Complex With Dna With Damp
Opposite An Abasic Site Analog In A 21mer Template
pdb|2P5G|D Chain D, Crystal Structure Of Rb69 Gp43 In Complex With Dna With Damp
Opposite An Abasic Site Analog In A 21mer Template
Length = 903
Score = 37.4 bits (85), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 61/252 (24%), Positives = 90/252 (35%), Gaps = 90/252 (35%)
Query: 884 KGKRGPA--YAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTV---------- 931
+G+ P Y G V EP Y KY+ D SLYPSII++ NI T+
Sbjct: 382 QGRSHPVQPYPGAFVKEPIPNRY-KYVXSFDLTSLYPSIIRQVNISPETIAGTFKVAPLH 440
Query: 932 -------ER-------SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMKTA--SGL 975
ER SP+G + GV+P + + +R+ K + A +G
Sbjct: 441 DYINAVAERPSDVYSCSPNGXXYY---KDRDGVVPTEITKVFNQRKEHKGYXLAAQRNGE 497
Query: 976 KIQQL----------------------DIQQQALKLTANS-------------------- 993
I++ +I+++ KL+A S
Sbjct: 498 IIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEXLFRAQRTEVAGXTAQI 557
Query: 994 --------MYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLN--------LEV 1037
+YG LG R+Y A IT G+ L+ V LN V
Sbjct: 558 NRKLLINSLYGALGNVWFRYYDLRNATAITTFGQXALQWIERKVNEYLNEVCGTEGEAFV 617
Query: 1038 IYGDTDSIMIHS 1049
+YGDTDSI + +
Sbjct: 618 LYGDTDSIYVSA 629
>pdb|3SPY|A Chain A, Rb69 Dna Polymerase(L415aL561AS565GY567A) TERNARY COMPLEX
WITH Dupcpp Opposite Da
Length = 901
Score = 37.4 bits (85), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 60/252 (23%), Positives = 92/252 (36%), Gaps = 90/252 (35%)
Query: 884 KGKRGPA--YAGGLVLEPKKGLYDKYILLLDFNSLYPSIIQEYNICFTTV---------- 931
+G+ P Y G V EP Y KY++ D S YPSII++ NI T+
Sbjct: 382 QGRSHPVQPYPGAFVKEPIPNRY-KYVMSFDLTSAYPSIIRQVNISPETIAGTFKVAPLH 440
Query: 932 -------ER-------SPDGLVPHLPSSKTTGVLPELLKNLVQRRRMVKTWMKTA--SGL 975
ER SP+G++ + GV+P + + +R+ K +M A +G
Sbjct: 441 DYINAVAERPSDVYSCSPNGMMYY---KDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGE 497
Query: 976 KIQQL----------------------DIQQQALKLTA---------------------- 991
I++ +I+++ KL+A
Sbjct: 498 IIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQI 557
Query: 992 ------NSMYGCLGFSNSRFYAKPLAELITQQGREILRSTVDLVQNNLN--------LEV 1037
N + G LG R+Y A IT G+ L+ V LN V
Sbjct: 558 NRKALINGLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFV 617
Query: 1038 IYGDTDSIMIHS 1049
+YGDTDSI + +
Sbjct: 618 LYGDTDSIYVSA 629
>pdb|3SC3|A Chain A, Crystal Structure Of A Putative Dna Replication Regulator
Hda (Sama_1916) From Shewanella Amazonensis Sb2b At 3.00
A Resolution
pdb|3SC3|B Chain B, Crystal Structure Of A Putative Dna Replication Regulator
Hda (Sama_1916) From Shewanella Amazonensis Sb2b At 3.00
A Resolution
Length = 225
Score = 34.7 bits (78), Expect = 0.43, Method: Composition-based stats.
Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 10/67 (14%)
Query: 330 DDDGSLPFYILDAHEQL--------SGANMGTLYLFGKVKAGSTH--HSCCVVVKNMQRC 379
DD+ +Y +++L SG + +YL+G VK+G TH H+ C ++R
Sbjct: 6 DDETFTSYYPAAGNDELIGALKSAASGDGVQAIYLWGPVKSGRTHLIHAACARANELERR 65
Query: 380 VYAIPNG 386
+ IP G
Sbjct: 66 SFYIPLG 72
>pdb|3BOS|A Chain A, Crystal Structure Of A Putative Dna Replication Regulator
Hda (Sama_1916) From Shewanella Amazonensis Sb2b At 1.75
A Resolution
pdb|3BOS|B Chain B, Crystal Structure Of A Putative Dna Replication Regulator
Hda (Sama_1916) From Shewanella Amazonensis Sb2b At 1.75
A Resolution
Length = 242
Score = 34.3 bits (77), Expect = 0.50, Method: Composition-based stats.
Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 10/67 (14%)
Query: 330 DDDGSLPFYILDAHEQL--------SGANMGTLYLFGKVKAGSTH--HSCCVVVKNMQRC 379
DD+ +Y +++L SG + +YL+G VK+G TH H+ C ++R
Sbjct: 23 DDETFTSYYPAAGNDELIGALKSAASGDGVQAIYLWGPVKSGRTHLIHAACARANELERR 82
Query: 380 VYAIPNG 386
+ IP G
Sbjct: 83 SFYIPLG 89
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
0.317 0.133 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 40,862,832
Number of Sequences: 62578
Number of extensions: 1644944
Number of successful extensions: 3829
Number of sequences better than 100.0: 49
Number of HSP's better than 100.0 without gapping: 42
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 3582
Number of HSP's gapped (non-prelim): 95
length of query: 1517
length of database: 14,973,337
effective HSP length: 111
effective length of query: 1406
effective length of database: 8,027,179
effective search space: 11286213674
effective search space used: 11286213674
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.9 bits)