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= 001780
(1014 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IAY|A Chain A, Ternary Complex Of Dna Polymerase Delta
Length = 919
Score = 546 bits (1407), Expect = e-155, Method: Compositional matrix adjust.
Identities = 275/492 (55%), Positives = 354/492 (71%), Gaps = 8/492 (1%)
Query: 400 EKEDVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPIS 459
+KEDVH+SIISDLQNG++ETRRRLAVYCLKDAYLP RL++KLM + NY EMARVTGVP S
Sbjct: 424 QKEDVHYSIISDLQNGDSETRRRLAVYCLKDAYLPLRLMEKLMALVNYTEMARVTGVPFS 483
Query: 460 FLLSRGQSIKVLSQLLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLD 519
+LL+RGQ IKV+SQL RK + + VIPN++ S+ YEGATV+E G+Y+ PIATLD
Sbjct: 484 YLLARGQQIKVVSQLFRKCLEIDTVIPNMQSQASDD-QYEGATVIEPIRGYYDVPIATLD 542
Query: 520 FASLYPSIMMAYNLCYSTLVTPEDARKLNLP-PECVNKTPSGETFVKSNLQKGXXXXXXX 578
F SLYPSIMMA+NLCY+TL +LNL E TP+G+ FV + ++G
Sbjct: 543 FNSLYPSIMMAHNLCYTTLCNKATVERLNLKIDEDYVITPNGDYFVTTKRRRGILPIILD 602
Query: 579 XXXXXXXXXXXXXXXXXXPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSSVT 638
P ++ VL+GRQLALKISANSVYGFTGATVG+LPC+ ISSSVT
Sbjct: 603 ELISARKRAKKDLRDEKDPFKRDVLNGRQLALKISANSVYGFTGATVGKLPCLAISSSVT 662
Query: 639 SYGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGREAADY 698
+YGR MI TK V++K+ GY+H+A V+YGDTDSVMV+FG ++ AM LG EAA Y
Sbjct: 663 AYGRTMILKTKTAVQEKYCIKNGYKHDAVVVYGDTDSVMVKFGTTDLKEAMDLGTEAAKY 722
Query: 699 ISGTFIKPIKLEFEKVYYPYLLISKKRYAGLYWTNPEKFDKMDTKGIETVRRDNCLLVKN 758
+S F PI LEFEK Y+PYLLI+KKRYAGL+WTNP+KFDK+D KG+ +VRRD+C LV
Sbjct: 723 VSTLFKHPINLEFEKAYFPYLLINKKRYAGLFWTNPDKFDKLDQKGLASVRRDSCSLVSI 782
Query: 759 LVTECLHKILVDRDIPGAVQYVKSTISDLLMNRMDLSLLVITKGLTKTGDDYEVKAAHVE 818
++ + L KIL++R++ GA+ +V+ TI+D+L NR+D+S L+I+K L +Y H
Sbjct: 783 VMNKVLKKILIERNVDGALAFVRETINDILHNRVDISKLIISKTLAP---NYTNPQPHAV 839
Query: 819 LAERMRKRDAATAPNVGDRVPYVIIKAAKGAKAYERSEDPIYVLENNIPIDTHYYLENQI 878
LAERM++R+ PNVGDRV YVII K Y R+EDP++VLENNI +D+ YYL NQ+
Sbjct: 840 LAERMKRREGV-GPNVGDRVDYVII--GGNDKLYNRAEDPLFVLENNIQVDSRYYLTNQL 896
Query: 879 SKPLLRIFEPIL 890
P++ I PI+
Sbjct: 897 QNPIISIVAPII 908
Score = 265 bits (676), Expect = 1e-70, Method: Compositional matrix adjust.
Identities = 140/355 (39%), Positives = 200/355 (56%), Gaps = 20/355 (5%)
Query: 55 ESLILRDIEQ-RQDFASR----LAKWARPPLSSGYVSQCQSIMFQQLDIDYVIGDSNREL 109
ES +D+ Q D A + L+ + R L + + I FQQ+D + + + ++
Sbjct: 6 ESTFEQDVSQMEHDMADQEEHDLSSFERKKLPTDFDPSLYDISFQQIDAEQSVLNGIKD- 64
Query: 110 LPLSSGSAAIIRIFGVTREGHSVCCKVHGFEPYFYISCPQGMGPDDISHFHQILEGRMRE 169
++ ++R FGVT EGHSV C V GF+ Y Y+ P +D ++ +
Sbjct: 65 ----ENTSTVVRFFGVTSEGHSVLCNVTGFKNYLYVPAPNSSDANDQEQINKFVH----- 115
Query: 170 ANRNSKVPQFVRHIEMVQKRSIMYYQQQKSQPFLKIVVALPTMVASCRGILDRG-IQLDG 228
N + IE+V K+SI Y PF KI V P MV R +RG + +
Sbjct: 116 -YLNETFDHAIDSIEVVSKQSIWGYSGDTKLPFWKIYVTYPHMVNKLRTAFERGHLSFNS 174
Query: 229 LGMKSFMTYESNVLFALRFMIDCNIVGGNWIEVPVGKYR--KTAKTLSYCQLEFDCLYSD 286
TY+ N+ + LR M+DC IVG +WI +P GKY + +S CQLE Y +
Sbjct: 175 WFSNGTTTYD-NIAYTLRLMVDCGIVGMSWITLPKGKYSMIEPNNRVSSCQLEVSINYRN 233
Query: 287 IISRHPEGEFSKMAPFRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNV 346
+I+ EG++S AP RI+SFDIECAGR G FPEP +DPVIQ+AN+V++ G K+PFIRNV
Sbjct: 234 LIAHPAEGDWSHTAPLRIMSFDIECAGRIGVFPEPEYDPVIQIANVVSIAGAKKPFIRNV 293
Query: 347 MTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
TL +C+PI G + S TE ++L WR+FI +VDPDV+IGYN FD+PYL+ +
Sbjct: 294 FTLNTCSPITGSMIFSHATEEEMLSNWRNFIIKVDPDVIIGYNTTNFDIPYLLNR 348
>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 = 177 bits (448), Expect = 4e-44, Method: Compositional matrix adjust.
Identities = 144/538 (26%), Positives = 235/538 (43%), Gaps = 97/538 (18%)
Query: 400 EKEDVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPIS 459
+K+D+ + I R + YC++D+ L +L K + +AR+ G+ I+
Sbjct: 509 KKKDLSYRDIPAYYATGPAQRGVIGEYCIQDSLLVGQLFFKFLPHLELSAVARLAGINIT 568
Query: 460 FLLSRGQSIKVLSQLLRKAKQKNLVIPNV----KQAGSE--------------------- 494
+ GQ I+V + LLR A QK ++P+ + AG E
Sbjct: 569 RTIYDGQQIRVFTCLLRLADQKGFILPDTQGRFRGAGGEAPKRPAAAREDEERPEEEGED 628
Query: 495 ----------------------QGTYEGATVLEARAGFYEKPIATLDFASLYPSIMMAYN 532
Y+GA VL+ +GF+ P+ DFASLYPSI+ A+N
Sbjct: 629 EDEREEGGGEREPEGARETAGRHVGYQGAKVLDPTSGFHVNPVVVFDFASLYPSIIQAHN 688
Query: 533 LCYSTLVTPEDA-RKLNLPPECVNKTPSGET--FVKSNLQKGXXXXXXXXXXXXXXXXXX 589
LC+STL DA L + + G FVK+++++
Sbjct: 689 LCFSTLSLRADAVAHLEAGKDYLEIEVGGRRLFFVKAHVRESLLSILLRDWLAMRKQIRS 748
Query: 590 XXXXXXXPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTK 649
P E +LD +Q A+K+ NSVYGFTG G LPC+ ++++VT+ GR+M+ T+
Sbjct: 749 RIPQSS-PEEAVLLDKQQAAIKVVCNSVYGFTGVQHGLLPCLHVAATVTTIGREMLLATR 807
Query: 650 KLVEDKFTT----VGGYEHNAE----------VIYGDTDSVMVQFGVPTVEAAMKLGREA 695
+ V ++ + + A+ +IYGDTDS+ V T +G +
Sbjct: 808 EYVHARWAAFEQLLADFPEAADMRAPGPYSMRIIYGDTDSIFVLCRGLTAAGLTAMGDKM 867
Query: 696 ADYIS-GTFIKPIKLEFEKVYYPYLLISKKRYAGLYWTNPEKFDKMDTKGIETVRRDNCL 754
A +IS F+ PIKLE EK + LLI+KK+Y G+ + KM KG++ VR++NC
Sbjct: 868 ASHISRALFLPPIKLECEKTFTKLLLIAKKKYIGVIYGG-----KMLIKGVDLVRKNNCA 922
Query: 755 LVKNLVTECLHKILVD--------------------RDIPGAVQYVKSTISD----LLMN 790
+ + + D R +P +Q + + D +
Sbjct: 923 FINRTSRALVDLLFYDDTVSGAAAALAERPAEEWLARPLPEGLQAFGAVLVDAHRRITDP 982
Query: 791 RMDLSLLVITKGLTKTGDDYEVK-AAHVELAERMRKRDAATAPNVGDRVPYVIIKAAK 847
D+ V+T L++ Y K AH+ + ++ R A P++ DR+PYVI+ +
Sbjct: 983 ERDIQDFVLTAELSRHPRAYTNKRLAHLTVYYKLMARRAQV-PSIKDRIPYVIVAQTR 1039
Score = 75.1 bits (183), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 83/328 (25%), Positives = 138/328 (42%), Gaps = 69/328 (21%)
Query: 116 SAAIIRIFGVTREGHSVCCKVHGFEPYFYISCP------QGMGPDDISHFHQILEGRMRE 169
+ +I + G+T EGH V V+G YFY++ Q P D+ RM
Sbjct: 136 TGTVITLLGLTPEGHRVAVHVYGTRQYFYMNKEEVDRHLQCRAPRDLCE-------RMAA 188
Query: 170 ANRNSKVPQF----VRHIEM-VQKRSIMYYQQQKSQPFLKIVVALPTMVAS-CRGILDRG 223
A R S F H E V +R+ +YY + + F ++ V +++ C
Sbjct: 189 ALRESPGASFRGISADHFEAEVVERTDVYYYETRPALFYRVYVRSGRVLSYLCDNFC--- 245
Query: 224 IQLDGLGMKSFMTYESNVLFALRFMIDC-NIVGGNWIEVPVGKYRKTAKTL------SYC 276
+ YE V RF++D V W + G+ A+ +
Sbjct: 246 --------PAIKKYEGGVDATTRFILDNPGFVTFGWYRLKPGRNNTLAQPRAPMAFGTSS 297
Query: 277 QLEFDCLYSDIISRHPEGEFSKMAPFRILSFDIEC-AGRKGH--FPEPTH--DPVIQVAN 331
+EF+C ++ EG S + ++++ FDIEC AG + FP H D VIQ++
Sbjct: 298 DVEFNCTADNLAI---EGGMSDLPAYKLMCFDIECKAGGEDELAFPVAGHPEDLVIQISC 354
Query: 332 LVTLQGEKQPFIRNVM--TLKSC----------------APIVGVDVMSFETERDVLLAW 373
L L + +V+ +L SC P+V + F++E ++LLA+
Sbjct: 355 L--LYDLSTTALEHVLLFSLGSCDLPESHLNELAARGLPTPVV----LEFDSEFEMLLAF 408
Query: 374 RDFIREVDPDVMIGYNICKFDLPYLIEK 401
+++ P+ + GYNI FD P+L+ K
Sbjct: 409 MTLVKQYGPEFVTGYNIINFDWPFLLAK 436
>pdb|2VWK|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography. V93q Polymerase Variant
Length = 773
Score = 166 bits (420), Expect = 7e-41, Method: Compositional matrix adjust.
Identities = 150/517 (29%), Positives = 232/517 (44%), Gaps = 43/517 (8%)
Query: 401 KEDVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISF 460
KE V+ I+ E R+A Y ++DA + L + F +++R+ G + +
Sbjct: 287 KEKVYAEEIAQAWE-TGEGLERVARYSMEDAKVTYELGKE--FFPMEAQLSRLVGQSL-W 342
Query: 461 LLSRGQSIKVLSQ-LLRKAKQKNLVIPNV---KQAGSEQGTYEGATVLEARAGFYEKPIA 516
+SR + ++ LLRKA ++N + PN ++ + +Y G V E G +E I
Sbjct: 343 DVSRSSTGNLVEWFLLRKAYERNELAPNKPDERELARRRESYAGGYVKEPERGLWEN-IV 401
Query: 517 TLDFASLYPSIMMAYNLCYSTLVTPEDARKLNLPPECVNKTPSGETFVKSNLQKGXXXXX 576
LDF SLYPSI++ +N+ TL E + ++ P+ G F K G
Sbjct: 402 YLDFRSLYPSIIITHNVSPDTL-NREGCEEYDVAPQV------GHKFCKDF--PGFIPSL 452
Query: 577 XXXXXXXXXXXXXXXXXXXXPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSS 636
P+EK +LD RQ A+KI ANS YG+ G + C E + S
Sbjct: 453 LGDLLEERQKVKKKMKATIDPIEKKLLDYRQRAIKILANSFYGYYGYAKARWYCKECAES 512
Query: 637 VTSYGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGREAA 696
VT++GRQ IE T + +E+KF +V+Y DTD E K +E
Sbjct: 513 VTAWGRQYIETTIREIEEKF--------GFKVLYADTDGFFATIPGADAETVKKKAKEFL 564
Query: 697 DYISGTFIKPIKLEFEKVYYPYLLISKKRYAGLYWTNPEKFDKMDTKGIETVRRDNCLLV 756
DYI+ ++LE+E Y ++KK+YA + ++ DK+ T+G+E VRRD +
Sbjct: 565 DYINAKLPGLLELEYEGFYKRGFFVTKKKYAVI-----DEEDKITTRGLEIVRRDWSEIA 619
Query: 757 KNLVTECLHKILVDRDIPGAVQYVKSTISDLLMNRMDLSLLVITKGLTKTGDDYEVKAAH 816
K L IL D+ AV+ VK L + LVI + +T+ DY+ H
Sbjct: 620 KETQARVLEAILKHGDVEEAVRIVKEVTEKLSKYEVPPEKLVIYEQITRDLKDYKATGPH 679
Query: 817 VELAERMRKRDAATAPNVGDRVPYVIIKAAK--GAKAYERSE-DPIYVLENNIPIDTHYY 873
V +A+R+ R P G + Y+++K + G +A E DP D YY
Sbjct: 680 VAVAKRLAARGIKIRP--GTVISYIVLKGSGRIGDRAIPFDEFDP-----AKHKYDAEYY 732
Query: 874 LENQISKPLLRIFEPILKNASKELLSGDHTRSISIST 910
+ENQ+ + RI KE L TR + +
Sbjct: 733 IENQVLPAVERILRAF--GYRKEDLRYQKTRQVGLGA 767
Score = 39.7 bits (91), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 66/305 (21%), Positives = 104/305 (34%), Gaps = 90/305 (29%)
Query: 96 LDIDYVIGDSNRELLPLSSGSAAIIRIFGVTREGHSVCCKVHGFEPYFYISCPQGMGPDD 155
LD DY+ D +IRIF G FEPY Y +D
Sbjct: 3 LDTDYITEDGK-----------PVIRIFK-KENGEFKIDYDRNFEPYIYALLKDDSAIED 50
Query: 156 ISHFHQILEGRMREANRNSKVPQ--FVRHIEMVQKRSIMYYQQQKSQPFLKIVVALPTMV 213
+ G R KV + R IE+ + +Y+ + QP A+ +
Sbjct: 51 VKKITAERHGTTVRVVRAEKVKKKFLGRPIEVWK----LYFTHPQDQP------AIRDKI 100
Query: 214 ASCRGILDRGIQLDGLGMKSFMTYESNVLFALRFMIDCNIVGGNWIEVPVGKYRKTAKTL 273
++D YE ++ FA R++ID ++ E
Sbjct: 101 KEHPAVVD--------------IYEYDIPFAKRYLIDKGLIPMEGDE------------- 133
Query: 274 SYCQLEFDCLYSDIISRHPEGEFSKMAPFRILSFDIECAGRKGHFPEPTHDPVIQVANLV 333
E L DI + + EGE P ++S+ E R ++
Sbjct: 134 -----ELKMLAFDIETLYHEGEKFAEGPILMISYADEEGAR-----------------VI 171
Query: 334 TLQGEKQPFIRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKF 393
T + P+ VDV+S TE++++ + ++E DPDV+I YN F
Sbjct: 172 TWRNIDLPY---------------VDVVS--TEKEMIKRFLKVVKEKDPDVLITYNGDNF 214
Query: 394 DLPYL 398
YL
Sbjct: 215 AFAYL 219
>pdb|2XHB|A Chain A, Crystal Structure Of Dna Polymerase From Thermococcus
Gorgonarius In Complex With Hypoxanthine-Containing Dna
Length = 773
Score = 166 bits (419), Expect = 8e-41, Method: Compositional matrix adjust.
Identities = 150/517 (29%), Positives = 232/517 (44%), Gaps = 43/517 (8%)
Query: 401 KEDVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISF 460
KE V+ I+ E R+A Y ++DA + L + F +++R+ G + +
Sbjct: 287 KEKVYAEEIAQAWE-TGEGLERVARYSMEDAKVTYELGKE--FFPMEAQLSRLVGQSL-W 342
Query: 461 LLSRGQSIKVLSQ-LLRKAKQKNLVIPNV---KQAGSEQGTYEGATVLEARAGFYEKPIA 516
+SR + ++ LLRKA ++N + PN ++ + +Y G V E G +E I
Sbjct: 343 DVSRSSTGNLVEWFLLRKAYERNELAPNKPDERELARRRESYAGGYVKEPERGLWEN-IV 401
Query: 517 TLDFASLYPSIMMAYNLCYSTLVTPEDARKLNLPPECVNKTPSGETFVKSNLQKGXXXXX 576
LDF SLYPSI++ +N+ TL E + ++ P+ G F K G
Sbjct: 402 YLDFRSLYPSIIITHNVSPDTL-NREGCEEYDVAPQV------GHKFCKDF--PGFIPSL 452
Query: 577 XXXXXXXXXXXXXXXXXXXXPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSS 636
P+EK +LD RQ A+KI ANS YG+ G + C E + S
Sbjct: 453 LGDLLEERQKVKKKMKATIDPIEKKLLDYRQRAIKILANSFYGYYGYAKARWYCKECAES 512
Query: 637 VTSYGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGREAA 696
VT++GRQ IE T + +E+KF +V+Y DTD E K +E
Sbjct: 513 VTAWGRQYIETTIREIEEKF--------GFKVLYADTDGFFATIPGADAETVKKKAKEFL 564
Query: 697 DYISGTFIKPIKLEFEKVYYPYLLISKKRYAGLYWTNPEKFDKMDTKGIETVRRDNCLLV 756
DYI+ ++LE+E Y ++KK+YA + ++ DK+ T+G+E VRRD +
Sbjct: 565 DYINAKLPGLLELEYEGFYKRGFFVTKKKYAVI-----DEEDKITTRGLEIVRRDWSEIA 619
Query: 757 KNLVTECLHKILVDRDIPGAVQYVKSTISDLLMNRMDLSLLVITKGLTKTGDDYEVKAAH 816
K L IL D+ AV+ VK L + LVI + +T+ DY+ H
Sbjct: 620 KETQARVLEAILKHGDVEEAVRIVKEVTEKLSKYEVPPEKLVIYEQITRDLKDYKATGPH 679
Query: 817 VELAERMRKRDAATAPNVGDRVPYVIIKAAK--GAKAYERSE-DPIYVLENNIPIDTHYY 873
V +A+R+ R P G + Y+++K + G +A E DP D YY
Sbjct: 680 VAVAKRLAARGIKIRP--GTVISYIVLKGSGRIGDRAIPFDEFDP-----AKHKYDAEYY 732
Query: 874 LENQISKPLLRIFEPILKNASKELLSGDHTRSISIST 910
+ENQ+ + RI KE L TR + +
Sbjct: 733 IENQVLPAVERILRAF--GYRKEDLRYQKTRQVGLGA 767
Score = 36.6 bits (83), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 65/305 (21%), Positives = 103/305 (33%), Gaps = 90/305 (29%)
Query: 96 LDIDYVIGDSNRELLPLSSGSAAIIRIFGVTREGHSVCCKVHGFEPYFYISCPQGMGPDD 155
LD DY+ D +IRIF G FEPY Y +D
Sbjct: 3 LDTDYITEDGK-----------PVIRIFK-KENGEFKIDYDRNFEPYIYALLKDDSAIED 50
Query: 156 ISHFHQILEGRMREANRNSKVPQ--FVRHIEMVQKRSIMYYQQQKSQPFLKIVVALPTMV 213
+ G R KV + R IE+ + +Y+ + P A+ +
Sbjct: 51 VKKITAERHGTTVRVVRAEKVKKKFLGRPIEVWK----LYFTHPQDVP------AIRDKI 100
Query: 214 ASCRGILDRGIQLDGLGMKSFMTYESNVLFALRFMIDCNIVGGNWIEVPVGKYRKTAKTL 273
++D YE ++ FA R++ID ++ E
Sbjct: 101 KEHPAVVD--------------IYEYDIPFAKRYLIDKGLIPMEGDE------------- 133
Query: 274 SYCQLEFDCLYSDIISRHPEGEFSKMAPFRILSFDIECAGRKGHFPEPTHDPVIQVANLV 333
E L DI + + EGE P ++S+ E R ++
Sbjct: 134 -----ELKMLAFDIETLYHEGEEFAEGPILMISYADEEGAR-----------------VI 171
Query: 334 TLQGEKQPFIRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKF 393
T + P+ VDV+S TE++++ + ++E DPDV+I YN F
Sbjct: 172 TWKNIDLPY---------------VDVVS--TEKEMIKRFLKVVKEKDPDVLITYNGDNF 214
Query: 394 DLPYL 398
YL
Sbjct: 215 AFAYL 219
>pdb|2VWJ|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography
Length = 773
Score = 166 bits (419), Expect = 8e-41, Method: Compositional matrix adjust.
Identities = 150/517 (29%), Positives = 232/517 (44%), Gaps = 43/517 (8%)
Query: 401 KEDVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISF 460
KE V+ I+ E R+A Y ++DA + L + F +++R+ G + +
Sbjct: 287 KEKVYAEEIAQAWE-TGEGLERVARYSMEDAKVTYELGKE--FFPMEAQLSRLVGQSL-W 342
Query: 461 LLSRGQSIKVLSQ-LLRKAKQKNLVIPNV---KQAGSEQGTYEGATVLEARAGFYEKPIA 516
+SR + ++ LLRKA ++N + PN ++ + +Y G V E G +E I
Sbjct: 343 DVSRSSTGNLVEWFLLRKAYERNELAPNKPDERELARRRESYAGGYVKEPERGLWEN-IV 401
Query: 517 TLDFASLYPSIMMAYNLCYSTLVTPEDARKLNLPPECVNKTPSGETFVKSNLQKGXXXXX 576
LDF SLYPSI++ +N+ TL E + ++ P+ G F K G
Sbjct: 402 YLDFRSLYPSIIITHNVSPDTL-NREGCEEYDVAPQV------GHKFCKDF--PGFIPSL 452
Query: 577 XXXXXXXXXXXXXXXXXXXXPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSS 636
P+EK +LD RQ A+KI ANS YG+ G + C E + S
Sbjct: 453 LGDLLEERQKVKKKMKATIDPIEKKLLDYRQRAIKILANSFYGYYGYAKARWYCKECAES 512
Query: 637 VTSYGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGREAA 696
VT++GRQ IE T + +E+KF +V+Y DTD E K +E
Sbjct: 513 VTAWGRQYIETTIREIEEKF--------GFKVLYADTDGFFATIPGADAETVKKKAKEFL 564
Query: 697 DYISGTFIKPIKLEFEKVYYPYLLISKKRYAGLYWTNPEKFDKMDTKGIETVRRDNCLLV 756
DYI+ ++LE+E Y ++KK+YA + ++ DK+ T+G+E VRRD +
Sbjct: 565 DYINAKLPGLLELEYEGFYKRGFFVTKKKYAVI-----DEEDKITTRGLEIVRRDWSEIA 619
Query: 757 KNLVTECLHKILVDRDIPGAVQYVKSTISDLLMNRMDLSLLVITKGLTKTGDDYEVKAAH 816
K L IL D+ AV+ VK L + LVI + +T+ DY+ H
Sbjct: 620 KETQARVLEAILKHGDVEEAVRIVKEVTEKLSKYEVPPEKLVIYEQITRDLKDYKATGPH 679
Query: 817 VELAERMRKRDAATAPNVGDRVPYVIIKAAK--GAKAYERSE-DPIYVLENNIPIDTHYY 873
V +A+R+ R P G + Y+++K + G +A E DP D YY
Sbjct: 680 VAVAKRLAARGIKIRP--GTVISYIVLKGSGRIGDRAIPFDEFDP-----AKHKYDAEYY 732
Query: 874 LENQISKPLLRIFEPILKNASKELLSGDHTRSISIST 910
+ENQ+ + RI KE L TR + +
Sbjct: 733 IENQVLPAVERILRAF--GYRKEDLRYQKTRQVGLGA 767
Score = 36.2 bits (82), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 65/305 (21%), Positives = 103/305 (33%), Gaps = 90/305 (29%)
Query: 96 LDIDYVIGDSNRELLPLSSGSAAIIRIFGVTREGHSVCCKVHGFEPYFYISCPQGMGPDD 155
LD DY+ D +IRIF G FEPY Y +D
Sbjct: 3 LDTDYITEDGK-----------PVIRIFK-KENGEFKIDYDRNFEPYIYALLKDDSAIED 50
Query: 156 ISHFHQILEGRMREANRNSKVPQ--FVRHIEMVQKRSIMYYQQQKSQPFLKIVVALPTMV 213
+ G R KV + R IE+ + +Y+ + P A+ +
Sbjct: 51 VKKITAERHGTTVRVVRAEKVKKKFLGRPIEVWK----LYFTHPQDVP------AIRDKI 100
Query: 214 ASCRGILDRGIQLDGLGMKSFMTYESNVLFALRFMIDCNIVGGNWIEVPVGKYRKTAKTL 273
++D YE ++ FA R++ID ++ E
Sbjct: 101 KEHPAVVD--------------IYEYDIPFAKRYLIDKGLIPMEGDE------------- 133
Query: 274 SYCQLEFDCLYSDIISRHPEGEFSKMAPFRILSFDIECAGRKGHFPEPTHDPVIQVANLV 333
E L DI + + EGE P ++S+ E R ++
Sbjct: 134 -----ELKMLAFDIETLYHEGEKFAEGPILMISYADEEGAR-----------------VI 171
Query: 334 TLQGEKQPFIRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKF 393
T + P+ VDV+S TE++++ + ++E DPDV+I YN F
Sbjct: 172 TWRNIDLPY---------------VDVVS--TEKEMIKRFLKVVKEKDPDVLITYNGDNF 214
Query: 394 DLPYL 398
YL
Sbjct: 215 AFAYL 219
>pdb|1TGO|A Chain A, Thermostable B Type Dna Polymerase From Thermococcus
Gorgonarius
Length = 773
Score = 166 bits (419), Expect = 9e-41, Method: Compositional matrix adjust.
Identities = 150/517 (29%), Positives = 232/517 (44%), Gaps = 43/517 (8%)
Query: 401 KEDVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISF 460
KE V+ I+ E R+A Y ++DA + L + F +++R+ G + +
Sbjct: 287 KEKVYAEEIAQAWE-TGEGLERVARYSMEDAKVTYELGKE--FFPMEAQLSRLVGQSL-W 342
Query: 461 LLSRGQSIKVLSQ-LLRKAKQKNLVIPNV---KQAGSEQGTYEGATVLEARAGFYEKPIA 516
+SR + ++ LLRKA ++N + PN ++ + +Y G V E G +E I
Sbjct: 343 DVSRSSTGNLVEWFLLRKAYERNELAPNKPDERELARRRESYAGGYVKEPERGLWEN-IV 401
Query: 517 TLDFASLYPSIMMAYNLCYSTLVTPEDARKLNLPPECVNKTPSGETFVKSNLQKGXXXXX 576
LDF SLYPSI++ +N+ TL E + ++ P+ G F K G
Sbjct: 402 YLDFRSLYPSIIITHNVSPDTL-NREGCEEYDVAPQV------GHKFCKDF--PGFIPSL 452
Query: 577 XXXXXXXXXXXXXXXXXXXXPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSS 636
P+EK +LD RQ A+KI ANS YG+ G + C E + S
Sbjct: 453 LGDLLEERQKVKKKMKATIDPIEKKLLDYRQRAIKILANSFYGYYGYAKARWYCKECAES 512
Query: 637 VTSYGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGREAA 696
VT++GRQ IE T + +E+KF +V+Y DTD E K +E
Sbjct: 513 VTAWGRQYIETTIREIEEKF--------GFKVLYADTDGFFATIPGADAETVKKKAKEFL 564
Query: 697 DYISGTFIKPIKLEFEKVYYPYLLISKKRYAGLYWTNPEKFDKMDTKGIETVRRDNCLLV 756
DYI+ ++LE+E Y ++KK+YA + ++ DK+ T+G+E VRRD +
Sbjct: 565 DYINAKLPGLLELEYEGFYKRGFFVTKKKYAVI-----DEEDKITTRGLEIVRRDWSEIA 619
Query: 757 KNLVTECLHKILVDRDIPGAVQYVKSTISDLLMNRMDLSLLVITKGLTKTGDDYEVKAAH 816
K L IL D+ AV+ VK L + LVI + +T+ DY+ H
Sbjct: 620 KETQARVLEAILKHGDVEEAVRIVKEVTEKLSKYEVPPEKLVIYEQITRDLKDYKATGPH 679
Query: 817 VELAERMRKRDAATAPNVGDRVPYVIIKAAK--GAKAYERSE-DPIYVLENNIPIDTHYY 873
V +A+R+ R P G + Y+++K + G +A E DP D YY
Sbjct: 680 VAVAKRLAARGIKIRP--GTVISYIVLKGSGRIGDRAIPFDEFDP-----AKHKYDAEYY 732
Query: 874 LENQISKPLLRIFEPILKNASKELLSGDHTRSISIST 910
+ENQ+ + RI KE L TR + +
Sbjct: 733 IENQVLPAVERILRAF--GYRKEDLRYQKTRQVGLGA 767
Score = 39.7 bits (91), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 66/305 (21%), Positives = 104/305 (34%), Gaps = 90/305 (29%)
Query: 96 LDIDYVIGDSNRELLPLSSGSAAIIRIFGVTREGHSVCCKVHGFEPYFYISCPQGMGPDD 155
LD DY+ D +IRIF G FEPY Y +D
Sbjct: 3 LDTDYITEDGK-----------PVIRIFK-KENGEFKIDYDRNFEPYIYALLKDDSAIED 50
Query: 156 ISHFHQILEGRMREANRNSKVPQ--FVRHIEMVQKRSIMYYQQQKSQPFLKIVVALPTMV 213
+ G R KV + R IE+ + +Y+ + P A+ +
Sbjct: 51 VKKITAERHGTTVRVVRAEKVKKKFLGRPIEVWK----LYFTHPQDVP------AIRDKI 100
Query: 214 ASCRGILDRGIQLDGLGMKSFMTYESNVLFALRFMIDCNIVGGNWIEVPVGKYRKTAKTL 273
++D YE ++ FA R++ID ++ E
Sbjct: 101 KEHPAVVD--------------IYEYDIPFAKRYLIDKGLIPMEGDE------------- 133
Query: 274 SYCQLEFDCLYSDIISRHPEGEFSKMAPFRILSFDIECAGRKGHFPEPTHDPVIQVANLV 333
E L DI + + EGE P ++S+ E R ++
Sbjct: 134 -----ELKMLAFDIETLYHEGEEFAEGPILMISYADEEGAR-----------------VI 171
Query: 334 TLQGEKQPFIRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKF 393
T + P+ VDV+S TE++++ + ++E DPDV+I YN F
Sbjct: 172 TWKNIDLPY---------------VDVVS--TEKEMIKRFLKVVKEKDPDVLITYNGDNF 214
Query: 394 DLPYL 398
D YL
Sbjct: 215 DFAYL 219
>pdb|1QHT|A Chain A, Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon
Length = 775
Score = 159 bits (401), Expect = 1e-38, Method: Compositional matrix adjust.
Identities = 147/517 (28%), Positives = 233/517 (45%), Gaps = 43/517 (8%)
Query: 401 KEDVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISF 460
KE V+ I+ + E R+A Y ++DA + L + F +++R+ G + +
Sbjct: 287 KEKVYAEEIAQAWE-SGEGLERVARYSMEDAKVTYELGRE--FFPMEAQLSRLIGQSL-W 342
Query: 461 LLSRGQSIKVLSQ-LLRKAKQKNLVIPNV---KQAGSEQGTYEGATVLEARAGFYEKPIA 516
+SR + ++ LLRKA ++N + PN ++ +G Y G V E G ++ I
Sbjct: 343 DVSRSSTGNLVEWFLLRKAYKRNELAPNKPDERELARRRGGYAGGYVKEPERGLWDN-IV 401
Query: 517 TLDFASLYPSIMMAYNLCYSTLVTPEDARKLNLPPECVNKTPSGETFVKSNLQKGXXXXX 576
LDF SLYPSI++ +N+ TL E ++ ++ PE G F K G
Sbjct: 402 YLDFRSLYPSIIITHNVSPDTL-NREGCKEYDVAPEV------GHKFCKDF--PGFIPSL 452
Query: 577 XXXXXXXXXXXXXXXXXXXXPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSS 636
PLEK +LD RQ A+KI ANS YG+ G + C E + S
Sbjct: 453 LGDLLEERQKIKRKMKATVDPLEKKLLDYRQRAIKILANSFYGYYGYAKARWYCKECAES 512
Query: 637 VTSYGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGREAA 696
VT++GR+ IE + +E+KF +V+Y DTD + E K +E
Sbjct: 513 VTAWGREYIEMVIRELEEKF--------GFKVLYADTDGLHATIPGADAETVKKKAKEFL 564
Query: 697 DYISGTFIKPIKLEFEKVYYPYLLISKKRYAGLYWTNPEKFDKMDTKGIETVRRDNCLLV 756
YI+ ++LE+E Y ++KK+YA + ++ K+ T+G+E VRRD +
Sbjct: 565 KYINPKLPGLLELEYEGFYVRGFFVTKKKYAVI-----DEEGKITTRGLEIVRRDWSEIA 619
Query: 757 KNLVTECLHKILVDRDIPGAVQYVKSTISDLLMNRMDLSLLVITKGLTKTGDDYEVKAAH 816
K L IL D+ AV+ VK L + LVI + +T+ DY+ H
Sbjct: 620 KETQARVLEAILKHGDVEEAVRIVKEVTEKLSKYEVPPEKLVIHEQITRDLRDYKATGPH 679
Query: 817 VELAERMRKRDAATAPNVGDRVPYVIIKAAK--GAKAYERSE-DPIYVLENNIPIDTHYY 873
V +A+R+ R P G + Y+++K + G +A E DP D YY
Sbjct: 680 VAVAKRLAARGVKIRP--GTVISYIVLKGSGRIGDRAIPADEFDP-----TKHRYDAEYY 732
Query: 874 LENQISKPLLRIFEPILKNASKELLSGDHTRSISIST 910
+ENQ+ + RI + KE L T+ + +
Sbjct: 733 IENQVLPAVERILKAF--GYRKEDLRYQKTKQVGLGA 767
Score = 38.5 bits (88), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 65/305 (21%), Positives = 108/305 (35%), Gaps = 90/305 (29%)
Query: 96 LDIDYVIGDSNRELLPLSSGSAAIIRIFGVTREGHSVCCKVHGFEPYFYISCPQGMGPDD 155
LD DY+ + +IR+F G FEPYFY +D
Sbjct: 3 LDTDYI-----------TENGKPVIRVFK-KENGEFKIEYDRTFEPYFYALLKDDSAIED 50
Query: 156 ISHFHQILEGRMREANRNSKVPQ--FVRHIEMVQKRSIMYYQQQKSQPFLKIVVALPTMV 213
+ G + + R KV + R IE+ + +Y+ + P A+ +
Sbjct: 51 VKKVTAKRHGTVVKVKRAEKVQKKFLGRPIEVWK----LYFNHPQDVP------AIRDRI 100
Query: 214 ASCRGILDRGIQLDGLGMKSFMTYESNVLFALRFMIDCNIVGGNWIEVPVGKYRKTAKTL 273
+ ++D YE ++ FA R++ID ++ E
Sbjct: 101 RAHPAVVD--------------IYEYDIPFAKRYLIDKGLIPMEGDE------------- 133
Query: 274 SYCQLEFDCLYSDIISRHPEGEFSKMAPFRILSFDIECAGRKGHFPEPTHDPVIQVANLV 333
E L I + + EGE P ++S+ G + A ++
Sbjct: 134 -----ELTMLAFAIATLYHEGEEFGTGPILMISY---ADGSE--------------ARVI 171
Query: 334 TLQGEKQPFIRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKF 393
T + P+ VDV+S TE++++ + +RE DPDV+I YN F
Sbjct: 172 TWKKIDLPY---------------VDVVS--TEKEMIKRFLRVVREKDPDVLITYNGDNF 214
Query: 394 DLPYL 398
D YL
Sbjct: 215 DFAYL 219
>pdb|1WNS|A Chain A, Crystal Structure Of Family B Dna Polymerase From
Hyperthermophilic Archaeon Pyrococcus Kodakaraensis Kod1
Length = 774
Score = 153 bits (387), Expect = 4e-37, Method: Compositional matrix adjust.
Identities = 151/518 (29%), Positives = 237/518 (45%), Gaps = 45/518 (8%)
Query: 401 KEDVH-HSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPIS 459
KE V+ I + + G E R+A Y ++DA + L + F+ +++R+ G +
Sbjct: 287 KEKVYAEEITTAWETG--ENLERVARYSMEDAKVTYELGKE--FLPMEAQLSRLIGQSL- 341
Query: 460 FLLSRGQSIKVLSQ-LLRKAKQKNLVIPNV---KQAGSEQGTYEGATVLEARAGFYEKPI 515
+ +SR + ++ LLRKA ++N + PN K+ + +YEG V E G +E I
Sbjct: 342 WDVSRSSTGNLVEWFLLRKAYERNELAPNKPDEKELARRRQSYEGGYVKEPERGLWEN-I 400
Query: 516 ATLDFASLYPSIMMAYNLCYSTLVTPEDARKLNLPPECVNKTPSGETFVKSNLQKGXXXX 575
LDF SLYPSI++ +N+ TL E ++ ++ P+ G F K G
Sbjct: 401 VYLDFRSLYPSIIITHNVSPDTL-NREGCKEYDVAPQV------GHRFCKDF--PGFIPS 451
Query: 576 XXXXXXXXXXXXXXXXXXXXXPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISS 635
P+E+ +LD RQ A+KI ANS YG+ G + C E +
Sbjct: 452 LLGDLLEERQKIKKKMKATIDPIERKLLDYRQRAIKILANSYYGYYGYARARWYCKECAE 511
Query: 636 SVTSYGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGREA 695
SVT++GR+ I T K +E+K+ G+ +VIY DTD E K E
Sbjct: 512 SVTAWGREYITMTIKEIEEKY----GF----KVIYSDTDGFFATIPGADAETVKKKAMEF 563
Query: 696 ADYISGTFIKPIKLEFEKVYYPYLLISKKRYAGLYWTNPEKFDKMDTKGIETVRRDNCLL 755
YI+ ++LE+E Y ++KK+YA + ++ K+ T+G+E VRRD +
Sbjct: 564 LKYINAKLPGALELEYEGFYKRGFFVTKKKYAVI-----DEEGKITTRGLEIVRRDWSEI 618
Query: 756 VKNLVTECLHKILVDRDIPGAVQYVKSTISDLLMNRMDLSLLVITKGLTKTGDDYEVKAA 815
K L +L D D+ AV+ VK L + LVI + +T+ DY+
Sbjct: 619 AKETQARVLEALLKDGDVEKAVRIVKEVTEKLSKYEVPPEKLVIHEQITRDLKDYKATGP 678
Query: 816 HVELAERMRKRDAATAPNVGDRVPYVIIKAAK--GAKAYERSE-DPIYVLENNIPIDTHY 872
HV +A+R+ R P G + Y+++K + G +A E DP D Y
Sbjct: 679 HVAVAKRLAARGVKIRP--GTVISYIVLKGSGRIGDRAIPFDEFDP-----TKHKYDAEY 731
Query: 873 YLENQISKPLLRIFEPILKNASKELLSGDHTRSISIST 910
Y+ENQ+ + RI KE L TR + +S
Sbjct: 732 YIENQVLPAVERILRAF--GYRKEDLRYQKTRQVGLSA 767
Score = 44.7 bits (104), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 75/304 (24%), Positives = 112/304 (36%), Gaps = 88/304 (28%)
Query: 96 LDIDYVIGDSNRELLPLSSGSAAIIRIFGVTREGHSVCCKVHGFEPYFYISCPQGMGPDD 155
LD DY+ D +IRIF G FEPYFY + DD
Sbjct: 3 LDTDYITEDGK-----------PVIRIFK-KENGEFKIEYDRTFEPYFY-----ALLKDD 45
Query: 156 ISHFHQILEGRMREANRNSKVPQFVRHIEMVQKRSIMYYQQQKSQPFLKIVVALPTMVAS 215
+ I E + A R+ V V+ +E VQK+ + + K+ P V +
Sbjct: 46 SA----IEEVKKITAERHGTVVT-VKRVEKVQKKFL-----GRPVEVWKLYFTHPQDVPA 95
Query: 216 CRG-ILDRGIQLDGLGMKSFMTYESNVLFALRFMIDCNIVGGNWIEVPVGKYRKTAKTLS 274
R I + +D YE ++ FA R++ID +V E
Sbjct: 96 IRDKIREHPAVID--------IYEYDIPFAKRYLIDKGLVPMEGDE-------------- 133
Query: 275 YCQLEFDCLYSDIISRHPEGEFSKMAPFRILSFDIECAGRKGHFPEPTHDPVIQVANLVT 334
E L DI + + EGE P ++S+ E R ++T
Sbjct: 134 ----ELKMLAFDIETLYHEGEEFAEGPILMISYADEEGAR-----------------VIT 172
Query: 335 LQGEKQPFIRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFD 394
+ P+ VDV+S TER+++ + ++E DPDV+I YN FD
Sbjct: 173 WKNVDLPY---------------VDVVS--TEREMIKRFLRVVKEKDPDVLITYNGDNFD 215
Query: 395 LPYL 398
YL
Sbjct: 216 FAYL 219
>pdb|1WN7|A Chain A, Crystal Structure Of Archaeal Family B Dna Polymerase
Mutant
Length = 774
Score = 153 bits (387), Expect = 4e-37, Method: Compositional matrix adjust.
Identities = 151/518 (29%), Positives = 237/518 (45%), Gaps = 45/518 (8%)
Query: 401 KEDVH-HSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPIS 459
KE V+ I + + G E R+A Y ++DA + L + F+ +++R+ G +
Sbjct: 287 KEKVYAEEITTAWETG--ENLERVARYSMEDAKVTYELGKE--FLPMEAQLSRLIGQSL- 341
Query: 460 FLLSRGQSIKVLSQ-LLRKAKQKNLVIPNV---KQAGSEQGTYEGATVLEARAGFYEKPI 515
+ +SR + ++ LLRKA ++N + PN K+ + +YEG V E G +E I
Sbjct: 342 WDVSRSSTGNLVEWFLLRKAYERNELAPNKPDEKELARRRQSYEGGYVKEPERGLWEN-I 400
Query: 516 ATLDFASLYPSIMMAYNLCYSTLVTPEDARKLNLPPECVNKTPSGETFVKSNLQKGXXXX 575
LDF SLYPSI++ +N+ TL E ++ ++ P+ G F K G
Sbjct: 401 VYLDFRSLYPSIIITHNVSPDTL-NREGCKEYDVAPQV------GHRFCKDF--PGFIPS 451
Query: 576 XXXXXXXXXXXXXXXXXXXXXPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISS 635
P+E+ +LD RQ A+KI ANS YG+ G + C E +
Sbjct: 452 LLGDLLEERQKIKKKMKATIDPIERKLLDYRQRAIKILANSYYGYYGYARARWYCKECAE 511
Query: 636 SVTSYGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGREA 695
SVT++GR+ I T K +E+K+ G+ +VIY DTD E K E
Sbjct: 512 SVTAWGREYITMTIKEIEEKY----GF----KVIYSDTDGFFATIPGADAETVKKKAMEF 563
Query: 696 ADYISGTFIKPIKLEFEKVYYPYLLISKKRYAGLYWTNPEKFDKMDTKGIETVRRDNCLL 755
YI+ ++LE+E Y ++KK+YA + ++ K+ T+G+E VRRD +
Sbjct: 564 LKYINAKLPGALELEYEGFYERGFFVTKKKYAVI-----DEEGKITTRGLEIVRRDWSEI 618
Query: 756 VKNLVTECLHKILVDRDIPGAVQYVKSTISDLLMNRMDLSLLVITKGLTKTGDDYEVKAA 815
K L +L D D+ AV+ VK L + LVI + +T+ DY+
Sbjct: 619 AKETQARVLEALLKDGDVEKAVRIVKEVTEKLSKYEVPPEKLVIHEQITRDLKDYKATGP 678
Query: 816 HVELAERMRKRDAATAPNVGDRVPYVIIKAAK--GAKAYERSE-DPIYVLENNIPIDTHY 872
HV +A+R+ R P G + Y+++K + G +A E DP D Y
Sbjct: 679 HVAVAKRLAARGVKIRP--GTVISYIVLKGSGRIGDRAIPFDEFDP-----TKHKYDAEY 731
Query: 873 YLENQISKPLLRIFEPILKNASKELLSGDHTRSISIST 910
Y+ENQ+ + RI KE L TR + +S
Sbjct: 732 YIENQVLPAVERILRAF--GYRKEDLRYQKTRQVGLSA 767
Score = 45.1 bits (105), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 75/304 (24%), Positives = 112/304 (36%), Gaps = 88/304 (28%)
Query: 96 LDIDYVIGDSNRELLPLSSGSAAIIRIFGVTREGHSVCCKVHGFEPYFYISCPQGMGPDD 155
LD DY+ D +IRIF G FEPYFY + DD
Sbjct: 3 LDTDYITEDGK-----------PVIRIFK-KENGEFKIEYDRTFEPYFY-----ALLKDD 45
Query: 156 ISHFHQILEGRMREANRNSKVPQFVRHIEMVQKRSIMYYQQQKSQPFLKIVVALPTMVAS 215
+ I E + A R+ V V+ +E VQK+ + + K+ P V +
Sbjct: 46 SA----IEEVKKITAERHGTVVT-VKRVEKVQKKFL-----GRPVEVWKLYFTHPQDVPA 95
Query: 216 CRG-ILDRGIQLDGLGMKSFMTYESNVLFALRFMIDCNIVGGNWIEVPVGKYRKTAKTLS 274
R I + +D YE ++ FA R++ID +V E
Sbjct: 96 IRDKIREHPAVID--------IYEYDIPFAKRYLIDKGLVPMEGDE-------------- 133
Query: 275 YCQLEFDCLYSDIISRHPEGEFSKMAPFRILSFDIECAGRKGHFPEPTHDPVIQVANLVT 334
E L DI + + EGE P ++S+ E R ++T
Sbjct: 134 ----ELKMLAFDIETLYEEGEEFAEGPILMISYADEEGAR-----------------VIT 172
Query: 335 LQGEKQPFIRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFD 394
+ P+ VDV+S TER+++ + ++E DPDV+I YN FD
Sbjct: 173 WKNVDLPY---------------VDVVS--TEREMIKRFLRVVKEKDPDVLITYNGDNFD 215
Query: 395 LPYL 398
YL
Sbjct: 216 FAYL 219
>pdb|2JGU|A Chain A, Crystal Structure Of Dna-directed Dna Polymerase
Length = 775
Score = 152 bits (383), Expect = 1e-36, Method: Compositional matrix adjust.
Identities = 144/510 (28%), Positives = 228/510 (44%), Gaps = 51/510 (10%)
Query: 416 NAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLLSRGQSIKVLSQ-L 474
+ E R+A Y ++DA L + F+ ++++R+ G P+ + +SR + ++ L
Sbjct: 301 SGENLERVAKYSMEDAKATYELGKE--FLPMEIQLSRLVGQPL-WDVSRSSTGNLVEWFL 357
Query: 475 LRKAKQKNLVIPNVKQAGSEQ----GTYEGATVLEARAGFYEKPIATLDFASLYPSIMMA 530
LRKA ++N V PN Q +Y G V E G +E I LD+ SLYPSI++
Sbjct: 358 LRKAYERNEVAPNKPSEEEYQRRLRESYTGGFVKEPEKGLWEN-IVYLDYKSLYPSIIIT 416
Query: 531 YNLCYSTLVTPEDARKLNLPPECVNKTPSGETFVKSNLQKGXXXXXXXXXXXXXXXXXXX 590
+N+ TL E + ++ P+ G F K G
Sbjct: 417 HNVSPDTL-NLEGCKNYDIAPQV------GHKFCKD--IPGFIPSLLGHLLEERQKIKTK 467
Query: 591 XXXXXXPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKK 650
P+EK +LD RQ A+K+ ANS YG+ G + C E + SVT++GR+ IE K
Sbjct: 468 MKETQDPIEKILLDYRQKAIKLLANSFYGYYGYAKARWYCKECAESVTAWGRKYIELVWK 527
Query: 651 LVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGREAADYISGTFIKPIKLE 710
+E+KF +V+Y DTD + E K E YI+ ++LE
Sbjct: 528 ELEEKF--------GFKVLYIDTDGLYATIPGGESEEIKKKALEFVKYINSKLPGLLELE 579
Query: 711 FEKVYYPYLLISKKRYAGLYWTNPEKFDKMDTKGIETVRRDNCLLVKNLVTECLHKILVD 770
+E Y ++KKRYA + ++ K+ T+G+E VRRD + K L IL
Sbjct: 580 YEGFYKRGFFVTKKRYAVI-----DEEGKVITRGLEIVRRDWSEIAKETQARVLETILKH 634
Query: 771 RDIPGAVQYVKSTISDLLMNRMDLSLLVITKGLTKTGDDYEVKAAHVELAERMRKRDAAT 830
D+ AV+ VK I L + L I + +T+ +Y+ HV +A+++ +
Sbjct: 635 GDVEEAVRIVKEVIQKLANYEIPPEKLAIYEQITRPLHEYKAIGPHVAVAKKLAAKGVKI 694
Query: 831 APNVGDRVPYVIIKA-------AKGAKAYERSEDPIYVLENNIPIDTHYYLENQISKPLL 883
P G + Y++++ A A+ Y DP D YY+ENQ+ +L
Sbjct: 695 KP--GMVIGYIVLRGDGPISNRAILAEEY----DP-----KKHKYDAEYYIENQVLPAVL 743
Query: 884 RIFEPILKNASKELLSGDHTRSISISTPSN 913
RI E KE L TR + +++ N
Sbjct: 744 RILEGF--GYRKEDLRYQKTRQVGLTSWLN 771
Score = 43.1 bits (100), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 29/107 (27%), Positives = 50/107 (46%), Gaps = 26/107 (24%)
Query: 302 FRILSFDIECAGRKGHFPEPTHDPVIQV-------ANLVTLQGEKQPFIRNVMTLKSCAP 354
+IL+FDIE +G E P+I + A ++T + P++ +V
Sbjct: 135 LKILAFDIETLYHEGE--EFGKGPIIMISYADENEARVITWKNIDLPYVESV-------- 184
Query: 355 IVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
TE++++ + IRE DPD+++ YN FD PYL ++
Sbjct: 185 ---------STEKEMIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKR 222
>pdb|3A2F|A Chain A, Crystal Structure Of Pyrococcus Furiosus Dna
PolymerasePCNA Monomer Mutant Complex
Length = 775
Score = 151 bits (382), Expect = 1e-36, Method: Compositional matrix adjust.
Identities = 145/510 (28%), Positives = 228/510 (44%), Gaps = 51/510 (10%)
Query: 416 NAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLLSRGQSIKVLSQ-L 474
+ E R+A Y +DA L + F+ ++++R+ G P+ + +SR + ++ L
Sbjct: 301 SGENLERVAKYSXEDAKATYELGKE--FLPXEIQLSRLVGQPL-WDVSRSSTGNLVEWFL 357
Query: 475 LRKAKQKNLVIPNVKQAGSEQ----GTYEGATVLEARAGFYEKPIATLDFASLYPSIMMA 530
LRKA ++N V PN Q +Y G V E G +E I LDF +LYPSI++
Sbjct: 358 LRKAYERNEVAPNKPSEEEYQRRLRESYTGGFVKEPEKGLWEN-IVYLDFRALYPSIIIT 416
Query: 531 YNLCYSTLVTPEDARKLNLPPECVNKTPSGETFVKSNLQKGXXXXXXXXXXXXXXXXXXX 590
+N+ TL E + ++ P+ G F K G
Sbjct: 417 HNVSPDTL-NLEGCKNYDIAPQV------GHKFCKD--IPGFIPSLLGHLLEERQKIKTK 467
Query: 591 XXXXXXPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKK 650
P+EK +LD RQ A+K+ ANS YG+ G + C E + SVT++GR+ IE K
Sbjct: 468 XKETQDPIEKILLDYRQKAIKLLANSFYGYYGYAKARWYCKECAESVTAWGRKYIELVWK 527
Query: 651 LVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGREAADYISGTFIKPIKLE 710
+E+KF +V+Y DTD + E K E YI+ ++LE
Sbjct: 528 ELEEKF--------GFKVLYIDTDGLYATIPGGESEEIKKKALEFVKYINSKLPGLLELE 579
Query: 711 FEKVYYPYLLISKKRYAGLYWTNPEKFDKMDTKGIETVRRDNCLLVKNLVTECLHKILVD 770
+E Y ++KKRYA + ++ K+ T+G+E VRRD + K L IL
Sbjct: 580 YEGFYKRGFFVTKKRYAVI-----DEEGKVITRGLEIVRRDWSEIAKETQARVLETILKH 634
Query: 771 RDIPGAVQYVKSTISDLLMNRMDLSLLVITKGLTKTGDDYEVKAAHVELAERMRKRDAAT 830
D+ AV+ VK I L + L I + +T+ +Y+ HV +A+++ +
Sbjct: 635 GDVEEAVRIVKEVIQKLANYEIPPEKLAIYEQITRPLHEYKAIGPHVAVAKKLAAKGVKI 694
Query: 831 APNVGDRVPYVIIKA-------AKGAKAYERSEDPIYVLENNIPIDTHYYLENQISKPLL 883
P G + Y++++ A A+ Y DP D YY+ENQ+ +L
Sbjct: 695 KP--GXVIGYIVLRGDGPISNRAILAEEY----DP-----KKHKYDAEYYIENQVLPAVL 743
Query: 884 RIFEPILKNASKELLSGDHTRSISISTPSN 913
RI E KE L TR + +++ N
Sbjct: 744 RILEGF--GYRKEDLRYQKTRQVGLTSWLN 771
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 31/100 (31%), Positives = 52/100 (52%), Gaps = 12/100 (12%)
Query: 302 FRILSFDIECAGRKGHFPEPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAPIVGVDVM 361
+IL+FDIE +G E P+I ++ + V+T K+ + V+V+
Sbjct: 135 LKILAFDIETLYHEGE--EFGKGPIIXISYADENEA-------KVITWKNID-LPYVEVV 184
Query: 362 SFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
S +ER+ + + IRE DPD+++ YN FD PYL ++
Sbjct: 185 S--SEREXIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKR 222
>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 = 150 bits (378), Expect = 5e-36, Method: Compositional matrix adjust.
Identities = 143/510 (28%), Positives = 228/510 (44%), Gaps = 51/510 (10%)
Query: 416 NAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLLSRGQSIKVLSQ-L 474
+ E R+A Y ++DA L + F+ ++++R+ G P+ + +SR + ++ L
Sbjct: 301 SGENLERVAKYSMEDAKATYELGKE--FLPMEIQLSRLIGQPL-WDVSRSSTGNLVEWFL 357
Query: 475 LRKAKQKNLVIPNVKQAGSEQ----GTYEGATVLEARAGFYEKPIATLDFASLYPSIMMA 530
LRKA ++N V PN Q +Y G V E G ++ I LDF +LYPSI++
Sbjct: 358 LRKAYERNEVAPNKPSEEEYQRRLRESYTGGFVKEPEKGLWDD-IVYLDFIALYPSIIIT 416
Query: 531 YNLCYSTLVTPEDARKLNLPPECVNKTPSGETFVKSNLQKGXXXXXXXXXXXXXXXXXXX 590
+N+ TL E + ++ P+ G F K G
Sbjct: 417 HNVSPDTL-NLEGCKNYDIAPQV------GHKFCKDI--PGFIPSLLGHLLEERQKIKTK 467
Query: 591 XXXXXXPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKK 650
P+EK +LD RQ A+K+ ANS YG+ G + C E + SVT++GR+ IE K
Sbjct: 468 MKETQDPIEKILLDYRQKAIKLLANSFYGYYGYAKARWYCKECAESVTAWGRKYIELVWK 527
Query: 651 LVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGREAADYISGTFIKPIKLE 710
+E+KF +V+Y DTD + E K E YI+ ++LE
Sbjct: 528 ELEEKF--------GFKVLYIDTDGLHATIPGGESEEIKKKALEFVKYINSKLPGLLELE 579
Query: 711 FEKVYYPYLLISKKRYAGLYWTNPEKFDKMDTKGIETVRRDNCLLVKNLVTECLHKILVD 770
+E Y ++KKRYA + ++ K+ T+G+E VRRD + K L IL
Sbjct: 580 YEGFYKRGFFVTKKRYAVI-----DEEGKVITRGLEIVRRDWSEIAKETQARVLETILKH 634
Query: 771 RDIPGAVQYVKSTISDLLMNRMDLSLLVITKGLTKTGDDYEVKAAHVELAERMRKRDAAT 830
D+ AV+ VK I L + L I + +T+ +Y+ HV +A+++ +
Sbjct: 635 GDVEEAVRIVKEVIQKLANYEIPPEKLAIYEQITRPLHEYKAIGPHVAVAKKLAAKGVKI 694
Query: 831 APNVGDRVPYVIIKA-------AKGAKAYERSEDPIYVLENNIPIDTHYYLENQISKPLL 883
P G + Y++++ A A+ Y DP D YY+ENQ+ +L
Sbjct: 695 KP--GMVIGYIVLRGDGPISNRAILAEEY----DP-----KKHKYDAEYYIENQVLPAVL 743
Query: 884 RIFEPILKNASKELLSGDHTRSISISTPSN 913
RI E KE L TR + +++ N
Sbjct: 744 RILEGF--GYRKEDLRYQKTRQVGLTSWLN 771
Score = 39.7 bits (91), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 32/114 (28%), Positives = 53/114 (46%), Gaps = 16/114 (14%)
Query: 304 ILSFDIECAGR----KGHFP-EPTHDPVIQVANLVTLQGEKQPFIRNVMTLKSCAPIVGV 358
I +DI A R KG P E + I + TL E + F + + + S A
Sbjct: 109 IFEYDIPFAKRYLIDKGLIPMEGEEELKILAFAIATLYHEGEEFGKGPIIMISYADENEA 168
Query: 359 DVMSFE-----------TERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
V++++ +ER+++ + IRE DPD+++ YN FD PYL ++
Sbjct: 169 KVITWKNIDLPYVEVVSSEREMIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKR 222
>pdb|1QQC|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
D.Tok
Length = 773
Score = 139 bits (351), Expect = 7e-33, Method: Compositional matrix adjust.
Identities = 137/478 (28%), Positives = 215/478 (44%), Gaps = 40/478 (8%)
Query: 416 NAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLLSRGQSIKVLSQ-L 474
+ E R+A Y ++DA L + F +++R+ G + + +SR + ++ L
Sbjct: 301 SGEGLERVARYSMEDAKATYELGKE--FFPMEAQLSRLVGQSL-WDVSRSSTGNLVEWFL 357
Query: 475 LRKAKQKNLVIPNV---KQAGSEQGTYEGATVLEARAGFYEKPIATLDFASLYPSIMMAY 531
LRKA ++N V PN ++ +Y G V E G +E I LD+ SLYPSI++ +
Sbjct: 358 LRKAYERNDVAPNKPDERELARRTESYAGGYVKEPEKGLWEN-IVYLDYKSLYPSIIITH 416
Query: 532 NLCYSTLVTPEDARKLNLPPECVNKTPSGETFVKSNLQKGXXXXXXXXXXXXXXXXXXXX 591
N+ TL E R+ ++ P+ G F K G
Sbjct: 417 NVSPDTL-NREGCREYDVAPQV------GHRFCKDF--PGFIPSLLGDLLEERQKVKKKM 467
Query: 592 XXXXXPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKL 651
P+E+ +LD RQ A+KI ANS YG+ + C E + SVT++GRQ IE T +
Sbjct: 468 KATVDPIERKLLDYRQRAIKILANSYYGYYAYANARWYCRECAESVTAWGRQYIETTMRE 527
Query: 652 VEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGREAADYISGTFIKPIKLEF 711
+E+KF +V+Y DTD E +E +YI+ ++LE+
Sbjct: 528 IEEKF--------GFKVLYADTDGFFATIPGADAETVKNKAKEFLNYINPRLPGLLELEY 579
Query: 712 EKVYYPYLLISKKRYAGLYWTNPEKFDKMDTKGIETVRRDNCLLVKNLVTECLHKILVDR 771
E Y ++KK+YA + ++ DK+ T+G+E VRRD + K L IL
Sbjct: 580 EGFYRRGFFVTKKKYAVI-----DEEDKITTRGLEIVRRDWSEIAKETQARVLEAILKHG 634
Query: 772 DIPGAVQYVKSTISDLLMNRMDLSLLVITKGLTKTGDDYEVKAAHVELAERMRKRDAATA 831
D+ AV+ VK L + + LVI + +T+ Y HV +A+R+ R
Sbjct: 635 DVEEAVRIVKEVTEKLSRHEVPPEKLVIYEQITRDLRSYRATGPHVAVAKRLAARGIKIR 694
Query: 832 PNVGDRVPYVIIKAAK--GAKAYERSE-DPIYVLENNIPIDTHYYLENQISKPLLRIF 886
P G + Y+++K G +A E DP D YY+ENQ+ + RI
Sbjct: 695 P--GTVISYIVLKGPGRVGDRAIPFDEFDP-----AKHRYDAEYYIENQVLPAVERIL 745
Score = 38.1 bits (87), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 28/110 (25%), Positives = 51/110 (46%), Gaps = 26/110 (23%)
Query: 302 FRILSFDIECAGRKGHFPEPTHDPVIQV-------ANLVTLQGEKQPFIRNVMTLKSCAP 354
R+L+FDIE +G E P++ + A ++T + P++ +V
Sbjct: 135 LRMLAFDIETLYHEGE--EFGEGPILMISYADEEGARVITWKNIDLPYVESV-------- 184
Query: 355 IVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEKEDV 404
TE++++ + I+E DPDV+I YN FD YL ++ ++
Sbjct: 185 ---------STEKEMIKRFLKVIQEKDPDVLITYNGDNFDFAYLKKRSEM 225
>pdb|4FM2|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase (Triple Mutant)
Bound To A Dsdna, In Edition Mode
Length = 793
Score = 135 bits (340), Expect = 1e-31, Method: Compositional matrix adjust.
Identities = 143/520 (27%), Positives = 237/520 (45%), Gaps = 49/520 (9%)
Query: 401 KEDVH-HSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPIS 459
KE V+ H I + G R+A Y ++DA + L + F ++AR+ G P+
Sbjct: 309 KEKVYAHEIAEAWETGKG--LERVAKYSMEDAKVTFELGKE--FFPMEAQLARLVGQPV- 363
Query: 460 FLLSRGQSIKVLSQ-LLRKAKQKNLVIPN----VKQAGSEQGTYEGATVLEARAGFYEKP 514
+ +SR + ++ LLRKA ++N + PN + + +YEG V E G +E
Sbjct: 364 WAVSRSSTGNLVEWFLLRKAYERNELAPNKPDEREYERRLRESYEGGYVKEPEKGLWEG- 422
Query: 515 IATLDFASLYPSIMMAYNLCYSTLVTPEDARKLNLPPECVNKTPSGETFVKSNLQKGXXX 574
I +LDF SLYPSI++ +N+ TL E+ ++ ++ P+ G F K G
Sbjct: 423 IVSLDFRSLYPSIIITHNVSPDTL-NRENCKEYDVAPQV------GHRFCKDF--PGFIP 473
Query: 575 XXXXXXXXXXXXXXXXXXXXXXPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEIS 634
P+EK +LD RQ A+KI ANS YG+ G + C E +
Sbjct: 474 SLLGNLLEERQKIKKRMKESKDPVEKKLLDYRQRAIKILANSYYGYYGYAKARWYCKECA 533
Query: 635 SSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGRE 694
SVT++GRQ I+ ++ +E + G+ +V+Y DTD + E + +
Sbjct: 534 ESVTAWGRQYIDLVRRELESR-----GF----KVLYIDTDGLYATIPGAKHEEIKEKALK 584
Query: 695 AADYISGTFIKPIKLEFEKVYYPYLLISKKRYAGLYWTNPEKFDKMDTKGIETVRRDNCL 754
+YI+ ++LE+E Y ++KK+YA + ++ K+ T+G+E VRRD
Sbjct: 585 FVEYINSKLPGLLELEYEGFYARGFFVTKKKYALI-----DEEGKIVTRGLEIVRRDWSE 639
Query: 755 LVKNLVTECLHKILVDRDIPGAVQYVKSTISDLLMNRMDLSLLVITKGLTKTGDDYEVKA 814
+ K + L IL ++ AV+ VK L + LVI + +T+ +Y+
Sbjct: 640 IAKETQAKVLEAILKHGNVDEAVKIVKEVTEKLSKYEIPPEKLVIYEQITRPLSEYKAIG 699
Query: 815 AHVELAERMRKRDAATAPNVGDRVPYVIIKA----AKGAKAYERSEDPIYVLENNIPIDT 870
HV +A+R+ + P G + Y++++ +K A A E DP D
Sbjct: 700 PHVAVAKRLAAKGVKVKP--GMVIGYIVLRGDGPISKRAIAIEEF-DP-----KKHKYDA 751
Query: 871 HYYLENQISKPLLRIFEPILKNASKELLSGDHTRSISIST 910
YY+ENQ+ + RI KE L T+ + +
Sbjct: 752 EYYIENQVLPAVERILRAF--GYRKEDLKYQKTKQVGLGA 789
Score = 40.8 bits (94), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 37/132 (28%), Positives = 58/132 (43%), Gaps = 23/132 (17%)
Query: 288 ISRHPEGEFSKMAPFRILSFDIECAGR----KGHFP-EPTHDPVIQVANLVTLQGEKQPF 342
I HP A I +DI A R KG P E + ++ TL E + F
Sbjct: 122 IREHP-------AVVDIFEYDIPFAKRYLIDKGLTPMEGNEELTFLAVDIETLYHEGEEF 174
Query: 343 IRNVMTLKSCAPIVGVDVMSFET-----------ERDVLLAWRDFIREVDPDVMIGYNIC 391
+ + + S A G V+++++ ER+++ IRE DPDV+I YN
Sbjct: 175 GKGPIIMISYADEEGAKVITWKSIDLPYVEVVSSEREMIKRLVKVIREKDPDVIITYNGD 234
Query: 392 KFDLPYLIEKED 403
F PYL+++ +
Sbjct: 235 NFAFPYLLKRAE 246
>pdb|4FLT|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FLU|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FLV|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FLW|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FLX|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FLY|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FLZ|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FM0|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
pdb|4FM1|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
Dsdna, In Edition Mode
Length = 793
Score = 134 bits (338), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 143/520 (27%), Positives = 237/520 (45%), Gaps = 49/520 (9%)
Query: 401 KEDVH-HSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPIS 459
KE V+ H I + G R+A Y ++DA + L + F ++AR+ G P+
Sbjct: 309 KEKVYAHEIAEAWETGKG--LERVAKYSMEDAKVTFELGKE--FFPMEAQLARLVGQPV- 363
Query: 460 FLLSRGQSIKVLSQ-LLRKAKQKNLVIPN----VKQAGSEQGTYEGATVLEARAGFYEKP 514
+ +SR + ++ LLRKA ++N + PN + + +YEG V E G +E
Sbjct: 364 WDVSRSSTGNLVEWFLLRKAYERNELAPNKPDEREYERRLRESYEGGYVKEPEKGLWEG- 422
Query: 515 IATLDFASLYPSIMMAYNLCYSTLVTPEDARKLNLPPECVNKTPSGETFVKSNLQKGXXX 574
I +LDF SLYPSI++ +N+ TL E+ ++ ++ P+ G F K G
Sbjct: 423 IVSLDFRSLYPSIIITHNVSPDTL-NRENCKEYDVAPQV------GHRFCKDF--PGFIP 473
Query: 575 XXXXXXXXXXXXXXXXXXXXXXPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEIS 634
P+EK +LD RQ A+KI ANS YG+ G + C E +
Sbjct: 474 SLLGNLLEERQKIKKRMKESKDPVEKKLLDYRQRAIKILANSYYGYYGYAKARWYCKECA 533
Query: 635 SSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGRE 694
SVT++GRQ I+ ++ +E + G+ +V+Y DTD + E + +
Sbjct: 534 ESVTAWGRQYIDLVRRELESR-----GF----KVLYIDTDGLYATIPGAKHEEIKEKALK 584
Query: 695 AADYISGTFIKPIKLEFEKVYYPYLLISKKRYAGLYWTNPEKFDKMDTKGIETVRRDNCL 754
+YI+ ++LE+E Y ++KK+YA + ++ K+ T+G+E VRRD
Sbjct: 585 FVEYINSKLPGLLELEYEGFYARGFFVTKKKYALI-----DEEGKIVTRGLEIVRRDWSE 639
Query: 755 LVKNLVTECLHKILVDRDIPGAVQYVKSTISDLLMNRMDLSLLVITKGLTKTGDDYEVKA 814
+ K + L IL ++ AV+ VK L + LVI + +T+ +Y+
Sbjct: 640 IAKETQAKVLEAILKHGNVDEAVKIVKEVTEKLSKYEIPPEKLVIYEQITRPLSEYKAIG 699
Query: 815 AHVELAERMRKRDAATAPNVGDRVPYVIIKA----AKGAKAYERSEDPIYVLENNIPIDT 870
HV +A+R+ + P G + Y++++ +K A A E DP D
Sbjct: 700 PHVAVAKRLAAKGVKVKP--GMVIGYIVLRGDGPISKRAIAIEEF-DP-----KKHKYDA 751
Query: 871 HYYLENQISKPLLRIFEPILKNASKELLSGDHTRSISIST 910
YY+ENQ+ + RI KE L T+ + +
Sbjct: 752 EYYIENQVLPAVERILRAF--GYRKEDLKYQKTKQVGLGA 789
Score = 40.8 bits (94), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 37/130 (28%), Positives = 57/130 (43%), Gaps = 23/130 (17%)
Query: 288 ISRHPEGEFSKMAPFRILSFDIECAGR----KGHFP-EPTHDPVIQVANLVTLQGEKQPF 342
I HP A I +DI A R KG P E + ++ TL E + F
Sbjct: 122 IREHP-------AVVDIFEYDIPFAKRYLIDKGLTPMEGNEELTFLAVDIETLYHEGEEF 174
Query: 343 IRNVMTLKSCAPIVGVDVMSFET-----------ERDVLLAWRDFIREVDPDVMIGYNIC 391
+ + + S A G V+++++ ER+++ IRE DPDV+I YN
Sbjct: 175 GKGPIIMISYADEEGAKVITWKSIDLPYVEVVSSEREMIKRLVKVIREKDPDVIITYNGD 234
Query: 392 KFDLPYLIEK 401
F PYL+++
Sbjct: 235 NFAFPYLLKR 244
>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 = 125 bits (315), Expect = 9e-29, Method: Compositional matrix adjust.
Identities = 114/420 (27%), Positives = 192/420 (45%), Gaps = 47/420 (11%)
Query: 491 AGSEQGTYEGATVLEARAGFYEKPIATLDFASLYPSIMMAYNLCYSTL-VTPEDARKL-N 548
S++ Y+G V E G ++ + +DF SLYPSI+ +N+C++T+ ED +L +
Sbjct: 488 VNSKKAKYQGGLVFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVDRNKEDIDELPS 547
Query: 549 LPPECVNKTPSGETFVKSNLQKGXXXXXXXXXXXXXXXXXXXXXXXXXPLEKAVLDGRQL 608
+PP S + +G P ++ D RQ
Sbjct: 548 VPP--------------SEVDQGVLPRLLANLVDRRREVKKVMKTETDPHKRVQCDIRQQ 593
Query: 609 ALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNAEV 668
ALK++ANS+YG G + ++ VT+ GR+++ +T++L E N V
Sbjct: 594 ALKLTANSMYGCLGYVNSRFYAKPLAMLVTNKGREILMNTRQLAE---------SMNLLV 644
Query: 669 IYGDTDSVMVQFGVPTVEAAMKLGREAADYISGTFIKPIKLEFEKVYYPYLLISKKRYAG 728
+YGDTDSVM+ G A+K+G ++ + + ++++ + V+ LL +KK+YA
Sbjct: 645 VYGDTDSVMIDTGCDNYADAIKIGLGFKRLVNERY-RLLEIDIDNVFKKLLLHAKKKYAA 703
Query: 729 LYWT---NPEKFDKMDTKGIETVRRDNCLLVKNLVTECLHKILVDRDIPGAVQYVKSTIS 785
L N ++ KG++ RR+ C L +++ L+ IL D+D A+Q V +
Sbjct: 704 LTVNLDKNGNGTTVLEVKGLDMKRREFCPLSRDVSIHVLNTILSDKDPEEALQEVYDYLE 763
Query: 786 DLLM----NRMDLSLLVITKGLTKTGDDYE--VKAAHVELAERMRKRDAATAPNVGDRVP 839
D+ + N + + I L+K Y V++A RMRK A G +
Sbjct: 764 DIRIKVETNNIRIDKYKINMKLSKDPKAYPGGKNMPAVQVALRMRK--AGRVVKAGSVIT 821
Query: 840 YVIIKAAKGAKA--------YERSE--DPIYVLENNIPIDTHYYLENQISKPLLRIFEPI 889
+VI K + A ER+ + + + NN+ D YYLE QI P+ R+ E I
Sbjct: 822 FVITKQDEIDNAADTPALSVAERAHALNEVMIKSNNLIPDPQYYLEKQIFAPVERLLERI 881
>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 = 124 bits (310), Expect = 3e-28, Method: Compositional matrix adjust.
Identities = 113/420 (26%), Positives = 192/420 (45%), Gaps = 47/420 (11%)
Query: 491 AGSEQGTYEGATVLEARAGFYEKPIATLDFASLYPSIMMAYNLCYSTL-VTPEDARKL-N 548
S++ Y+G V E G ++ + +DF SLYPSI+ +N+C++T+ ED +L +
Sbjct: 488 VNSKKAKYQGGLVFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVDRNKEDIDELPS 547
Query: 549 LPPECVNKTPSGETFVKSNLQKGXXXXXXXXXXXXXXXXXXXXXXXXXPLEKAVLDGRQL 608
+PP S + +G P ++ D RQ
Sbjct: 548 VPP--------------SEVDQGVLPRLLANLVDRRREVKKVMKTETDPHKRVQCDIRQQ 593
Query: 609 ALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNAEV 668
ALK++ANS+YG G + ++ VT+ GR+++ +T++L E N V
Sbjct: 594 ALKLTANSMYGCLGYVNSRFYAKPLAMLVTNKGREILMNTRQLAE---------SMNLLV 644
Query: 669 IYGDTDSVMVQFGVPTVEAAMKLGREAADYISGTFIKPIKLEFEKVYYPYLLISKKRYAG 728
+YGDT+SVM+ G A+K+G ++ + + ++++ + V+ LL +KK+YA
Sbjct: 645 VYGDTNSVMIDTGCDNYADAIKIGLGFKRLVNERY-RLLEIDIDNVFKKLLLHAKKKYAA 703
Query: 729 LYWT---NPEKFDKMDTKGIETVRRDNCLLVKNLVTECLHKILVDRDIPGAVQYVKSTIS 785
L N ++ KG++ RR+ C L +++ L+ IL D+D A+Q V +
Sbjct: 704 LTVNLDKNGNGTTVLEVKGLDMKRREFCPLSRDVSIHVLNTILSDKDPEEALQEVYDYLE 763
Query: 786 DLLM----NRMDLSLLVITKGLTKTGDDYE--VKAAHVELAERMRKRDAATAPNVGDRVP 839
D+ + N + + I L+K Y V++A RMRK A G +
Sbjct: 764 DIRIKVETNNIRIDKYKINMKLSKDPKAYPGGKNMPAVQVALRMRK--AGRVVKAGSVIT 821
Query: 840 YVIIKAAKGAKA--------YERSE--DPIYVLENNIPIDTHYYLENQISKPLLRIFEPI 889
+VI K + A ER+ + + + NN+ D YYLE QI P+ R+ E I
Sbjct: 822 FVITKQDEIDNAADTPALSVAERAHALNEVMIKSNNLIPDPQYYLEKQIFAPVERLLERI 881
>pdb|4B08|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha,
Selenomethionine Protein
Length = 910
Score = 122 bits (305), Expect = 1e-27, Method: Compositional matrix adjust.
Identities = 110/417 (26%), Positives = 186/417 (44%), Gaps = 43/417 (10%)
Query: 492 GSEQGTYEGATVLEARAGFYEKPIATLDFASLYPSIMMAYNLCYSTL-VTPEDARKL-NL 549
S++ Y+G V E G ++ + DF SLYPSI+ +N+C++T+ ED +L ++
Sbjct: 489 NSKKAKYQGGLVFEPEKGLHKNYVLVXDFNSLYPSIIQEFNICFTTVDRNKEDIDELPSV 548
Query: 550 PPECVNKTPSGETFVKSNLQKGXXXXXXXXXXXXXXXXXXXXXXXXXPLEKAVLDGRQLA 609
PP S + +G P ++ D RQ A
Sbjct: 549 PP--------------SEVDQGVLPRLLANLVDRRREVKKVXKTETDPHKRVQCDIRQQA 594
Query: 610 LKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNAEVI 669
LK++ANS YG G + ++ VT+ GR+++ +T++L E N V+
Sbjct: 595 LKLTANSXYGCLGYVNSRFYAKPLAXLVTNKGREILXNTRQLAE---------SXNLLVV 645
Query: 670 YGDTDSVMVQFGVPTVEAAMKLGREAADYISGTFIKPIKLEFEKVYYPYLLISKKRYAGL 729
YGDTDSV + G A+K+G ++ + + ++++ + V+ LL +KK+YA L
Sbjct: 646 YGDTDSVXIDTGCDNYADAIKIGLGFKRLVNERY-RLLEIDIDNVFKKLLLHAKKKYAAL 704
Query: 730 YWT---NPEKFDKMDTKGIETVRRDNCLLVKNLVTECLHKILVDRDIPGAVQYVKSTISD 786
N ++ KG++ RR+ C L +++ L+ IL D+D A+Q V + D
Sbjct: 705 TVNLDKNGNGTTVLEVKGLDXKRREFCPLSRDVSIHVLNTILSDKDPEEALQEVYDYLED 764
Query: 787 LLM----NRMDLSLLVITKGLTKTGDDYEVKAAHVELAERMRKRDAATAPNVGDRVPYVI 842
+ + N + + I L+K Y + +R R A G + +VI
Sbjct: 765 IRIKVETNNIRIDKYKINXKLSKDPKAYPGGKNXPAVQVALRXRKAGRVVKAGSVITFVI 824
Query: 843 IKAAKGAKA--------YERSE--DPIYVLENNIPIDTHYYLENQISKPLLRIFEPI 889
K + A ER+ + + + NN+ D YYLE QI P+ R+ E I
Sbjct: 825 TKQDEIDNAADTPALSVAERAHALNEVXIKSNNLIPDPQYYLEKQIFAPVERLLERI 881
>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 = 121 bits (303), Expect = 2e-27, Method: Compositional matrix adjust.
Identities = 135/478 (28%), Positives = 206/478 (43%), Gaps = 61/478 (12%)
Query: 415 GNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLLSRGQSIKVLSQ- 473
+ E R+A Y ++DA L + F +++R+ G + + +SR + ++
Sbjct: 300 ASGEGLERVARYSMEDAKATYELGKE--FFPMEAQLSRLVGQSL-WDVSRSSTGNLVEWF 356
Query: 474 LLRKAKQKNLVIPNV---KQAGSEQGTYEGATVLEARAGFYEKPIATLDFASLYPSIMMA 530
LLRKA ++N V PN ++ +Y G V E G +E I LD+ SLYPSI++
Sbjct: 357 LLRKAYERNDVAPNKPDERELARRTESYAGGYVKEPEKGLWEN-IVYLDYKSLYPSIIIT 415
Query: 531 YNLCYSTLVTPEDARKLNLPPECVNKTPSGETFVKSNLQKGXXXXXXXXXXXXXXXXXXX 590
+N+ TL E R+ ++ P+ G F K G
Sbjct: 416 HNVSPDTL-NREGCREYDVAPQV------GHRFCKDF--PGFIPSLLGDLLEERQKVKKK 466
Query: 591 XXXXXXPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKK 650
P+E+ +LD RQ A+KI ANS YG+ + C E + SVT++GRQ IE T +
Sbjct: 467 MKATVDPIERKLLDYRQRAIKILANSYYGYYAYANARWYCRECAESVTAWGRQYIETTMR 526
Query: 651 LVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVPTVEAAMKLGREAADYISGTFIKPIKLE 710
+E+KF G+ +V+Y DTD E +E +YI+ ++LE
Sbjct: 527 EIEEKF----GF----KVLYADTDGFFATIPGADAETVKNKAKEFLNYINPRLPGLLELE 578
Query: 711 FEKVYYPYLLISKKRYAGLYWTNPEKFDKMDTKGIETVRRDNCLLVKNLVTECLHKILVD 770
+E Y ++KK+YA + ++ DK+ T+G+E VRRD + K L IL
Sbjct: 579 YEGFYRRGFFVTKKKYAVI-----DEEDKITTRGLEIVRRDWSEIAKETQARVLEAILKH 633
Query: 771 RDIPGAVQYVKSTISDLLMNRMDLSLLVITKGLTKTGDDYEVKAAHVELAERMRKRDAAT 830
D+ AV+ VK L + + LVI YE HV A +
Sbjct: 634 GDVEEAVRIVKEVTEKLSRHEVPPEKLVI----------YEA-GPHVAAAATVISYIVLK 682
Query: 831 APN-VGDR-VPYVIIKAAKGAKAYERSEDPIYVLENNIPIDTHYYLENQISKPLLRIF 886
P VGDR +P+ AK D YY+ENQ+ + RI
Sbjct: 683 GPGRVGDRAIPFDEFDPAKHR------------------YDAEYYIENQVLPAVERIL 722
Score = 34.7 bits (78), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 28/45 (62%)
Query: 360 VMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEKEDV 404
V S TE++++ + I+E DPDV+I YN FD YL ++ ++
Sbjct: 181 VESVSTEKEMIKRFLKVIQEKDPDVLITYNGDNFDFAYLKKRSEM 225
>pdb|1Q8I|A Chain A, Crystal Structure Of Escherichia Coli Dna Polymerase Ii
Length = 783
Score = 114 bits (284), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 138/525 (26%), Positives = 217/525 (41%), Gaps = 109/525 (20%)
Query: 417 AETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLLSRGQSIKVLSQL-L 475
AE + LA Y LKD L ++ K + +E A V G+P+ G S+ L
Sbjct: 322 AEDKPALATYNLKDCELVTQIFHKTEIMPFLLERATVNGLPVD---RHGGSVAAFGHLYF 378
Query: 476 RKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFASLYPSIMMAYNLCY 535
+ + V PN+ + G V+++R G Y+ + LD+ SLYPSI+ + +
Sbjct: 379 PRMHRAGYVAPNLGEVPPHASP--GGYVMDSRPGLYDS-VLVLDYKSLYPSIVRTFLIDP 435
Query: 536 STLVT------PEDA----------RKLNLPPECVNKTPSGETFVKSNLQKGXXXXXXXX 579
LV PE + R+ + PE V G K K
Sbjct: 436 VGLVEGMAQPDPEHSTEGFLDAWFSREKHCLPEIVTNIWHGRDEAKRQGNK--------- 486
Query: 580 XXXXXXXXXXXXXXXXXPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSSVTS 639
PL +A LKI N+ YG G T + ++SS+T
Sbjct: 487 -----------------PLSQA--------LKIIMNAFYGVLGTTACRFFDPRLASSITM 521
Query: 640 YGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQF-GVPTVEAAMKLGREAADY 698
G Q++ TK L+E + GY +VIYGDTDS V G + E A K+GR +
Sbjct: 522 RGHQIMRQTKALIEAQ-----GY----DVIYGDTDSTFVWLKGAHSEEEAAKIGRALVQH 572
Query: 699 ISGTFIKPIK---------LEFEKVYYPYLLI--------SKKRYAGLYWTNPEKFDKMD 741
++ + + ++ LE+E + +L+ SKKRYAGL ++ +M
Sbjct: 573 VNAWWAETLQKQRLTSALELEYETHFCRFLMPTIRGADTGSKKRYAGLIQEGDKQ--RMV 630
Query: 742 TKGIETVRRDNCLLVKNLVTECLHKILVDRDIPGAVQYVKSTISDLLMNRMDLSLLVITK 801
KG+ETVR D L + E +I R+ P +YV+ TI L+ +D + LV K
Sbjct: 631 FKGLETVRTDWTPLAQQFQQELYLRIF--RNEP-YQEYVRETIDKLMAGELD-ARLVYRK 686
Query: 802 GLTKTGDDYE------VKAAHVELAERMRKRDAATAPNVGDRVPYVIIKAAKGAKAYERS 855
L + +Y+ V+AA + E ++ N G + YV Y+RS
Sbjct: 687 RLRRPLSEYQRNVPPHVRAARLADEENQKRGRPLQYQNRGT-IKYVWTTNGPEPLDYQRS 745
Query: 856 EDPIYVLENNIPIDTHYYLENQISKPLLRIFEPILKNASKELLSG 900
P+D +YL Q+ +P+ P +++ L++G
Sbjct: 746 -----------PLDYEHYLTRQL-QPVAEGILPFIEDNFATLMTG 778
>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 = 112 bits (280), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 137/525 (26%), Positives = 217/525 (41%), Gaps = 109/525 (20%)
Query: 417 AETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLLSRGQSIKVLSQL-L 475
AE + LA Y LK+ L ++ K + +E A V G+P+ G S+ L
Sbjct: 325 AEDKPALATYNLKNCELVTQIFHKTEIMPFLLERATVNGLPVD---RHGGSVAAFGHLYF 381
Query: 476 RKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFASLYPSIMMAYNLCY 535
+ + V PN+ + G V+++R G Y+ + LD+ SLYPSI+ + +
Sbjct: 382 PRMHRAGYVAPNLGEVPPHASP--GGYVMDSRPGLYDS-VLVLDYKSLYPSIIRTFLIDP 438
Query: 536 STLVT------PEDA----------RKLNLPPECVNKTPSGETFVKSNLQKGXXXXXXXX 579
LV PE + R+ + PE V G K K
Sbjct: 439 VGLVEGMAQPDPEHSTEGFLDAWFSREKHCLPEIVTNIWHGRDEAKRQGNK--------- 489
Query: 580 XXXXXXXXXXXXXXXXXPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEISSSVTS 639
PL +A LKI N+ YG G T + ++SS+T
Sbjct: 490 -----------------PLSQA--------LKIIMNAFYGVLGTTACRFFDPRLASSITM 524
Query: 640 YGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQF-GVPTVEAAMKLGREAADY 698
G Q++ TK L+E + GY +VIYGDTDS V G + E A K+GR +
Sbjct: 525 RGHQIMRQTKALIEAQ-----GY----DVIYGDTDSTFVWLKGAHSEEEAAKIGRALVQH 575
Query: 699 ISGTFIKPIK---------LEFEKVYYPYLLI--------SKKRYAGLYWTNPEKFDKMD 741
++ + + ++ LE+E + +L+ SKKRYAGL ++ +M
Sbjct: 576 VNAWWAETLQKQRLTSALELEYETHFCRFLMPTIRGADTGSKKRYAGLIQEGDKQ--RMV 633
Query: 742 TKGIETVRRDNCLLVKNLVTECLHKILVDRDIPGAVQYVKSTISDLLMNRMDLSLLVITK 801
KG+ETVR D L + E +I R+ P +YV+ TI L+ +D + LV K
Sbjct: 634 FKGLETVRTDWTPLAQQFQQELYLRIF--RNEP-YQEYVRETIDKLMAGELD-ARLVYRK 689
Query: 802 GLTKTGDDYE------VKAAHVELAERMRKRDAATAPNVGDRVPYVIIKAAKGAKAYERS 855
L + +Y+ V+AA + E ++ N G + YV Y+RS
Sbjct: 690 RLRRPLSEYQRNVPPHVRAARLADEENQKRGRPLQYQNRGT-IKYVWTTNGPEPLDYQRS 748
Query: 856 EDPIYVLENNIPIDTHYYLENQISKPLLRIFEPILKNASKELLSG 900
P+D +YL Q+ +P+ P +++ L++G
Sbjct: 749 -----------PLDYEHYLTRQL-QPVAEGILPFIEDNFATLMTG 781
>pdb|1S5J|A Chain A, Insight In Dna Replication: The Crystal Structure Of Dna
Polymerase B1 From The Archaeon Sulfolobus Solfataricus
Length = 847
Score = 82.0 bits (201), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 131/511 (25%), Positives = 212/511 (41%), Gaps = 101/511 (19%)
Query: 422 RLAVYCLKDAYLPQRLLD-------KLMFIFNYVEMARVTGVPISFLLSRGQSIKVLSQL 474
+L Y +DA + +L KL+ +F +R++ + I L S V +
Sbjct: 370 KLIEYNFRDAEITLQLTTFNNDLTMKLIVLF-----SRISRLGIEELTRTEISTWVKNLY 424
Query: 475 LRKAKQKNLVIP----------NVKQAGSEQGT-YEGATVLEARAGFYEKPIATLDFASL 523
+ +++N +IP N++ + +G Y+GA V++ AG + I LDFASL
Sbjct: 425 YWEHRKRNWLIPLKEEILAKSSNIRTSALIKGKGYKGAVVIDPPAGIFFN-ITVLDFASL 483
Query: 524 YPSIMMAYNLCYSTLVTPEDARKLNLPPECVNKTPS----------GETFVKSNLQKGXX 573
YPSI+ +NL Y T+ D ++ P E ++T G T V + L +
Sbjct: 484 YPSIIRTWNLSYETV----DIQQCKKPYEVKDETGEVLHIVCMDRPGITAVITGLLRDFR 539
Query: 574 XXXXXXXXXXXXXXXXXXXXXXXPLEKAVLDGRQLALKISANSVYGFTGATVGQLPCIEI 633
+K + D Q A+K+ N+ YG GA L +
Sbjct: 540 VKIYKKKAKNPNNSEE---------QKLLYDVVQRAMKVFINATYGVFGAETFPLYAPRV 590
Query: 634 SSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNAEVIYGDTDSVMVQFGVP--TVEAAMKL 691
+ SVT+ GR +I T K E V+YGDTDS+ + P ++E +K
Sbjct: 591 AESVTALGRYVITSTVK---------KAREEGLTVLYGDTDSLFL-LNPPKNSLENIIK- 639
Query: 692 GREAADYISGTFIKPIKLEFEKVYYPYLLIS--KKRYAGLYWTNPEKFDKMDTKGIETVR 749
++ TF + LE +K Y ++ S KK Y G+Y K+D KG+ +
Sbjct: 640 ------WVKTTF--NLDLEVDKT-YKFVAFSGLKKNYFGVYQDG-----KVDIKGMLVKK 685
Query: 750 RDNCLLVKNLVTECLHKILVDRDIPGAVQYVKSTISDL-------LMNR-MDLSLLVITK 801
R+ VK + E ++++ + P V+ +K I D+ L N+ +L L
Sbjct: 686 RNTPEFVKKVFNEV-KELMISINSPNDVKEIKRKIVDVVKGSYEKLKNKGYNLDELAFKV 744
Query: 802 GLTKTGDDYEVKA-AHVELAERMRKRDAATAPNVGDRVPYVIIKAAKGAKAYERSEDPIY 860
L+K D Y+ HV+ A ++R P D + YV +++ G K +
Sbjct: 745 MLSKPLDAYKKNTPQHVKAALQLRPFGVNVLPR--DIIYYVKVRSKDGVKPVQ------- 795
Query: 861 VLENNIPIDTHYYLENQISKPLLRIFEPILK 891
L ID YLE L FE IL+
Sbjct: 796 -LAKVTEIDAEKYLE-----ALRSTFEQILR 820
>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 = 50.4 bits (119), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 44/72 (61%)
Query: 607 QLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNA 666
Q+ALK++ NS+YG G + + ++++T++G+ ++ ++ V + V G E A
Sbjct: 556 QMALKVTCNSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEA 615
Query: 667 EVIYGDTDSVMV 678
V+YGDTDS+ V
Sbjct: 616 FVLYGDTDSIYV 627
Score = 34.7 bits (78), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 48/197 (24%), Positives = 81/197 (41%), Gaps = 18/197 (9%)
Query: 343 IRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEKE 402
I N+ + + G+ V+ D + ++ F P + Y I +F+L K
Sbjct: 253 IENMYGSREIITLFGISVL------DYIDLYKKFSFTNQPSYSLDY-ISEFELNVGKLKY 305
Query: 403 DVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLL 462
D IS L+ N +R Y + D Y ++ K FI ++M + I +
Sbjct: 306 D---GPISKLRESN---HQRYISYNIIDVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVF 359
Query: 463 SRGQSIKVLSQLLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFAS 522
S ++ + + K++N VIP + + Y GA V E Y K + + D S
Sbjct: 360 SPIKTWDAI--IFNSLKEQNKVIPQGRSHPVQ--PYPGAFVKEPIPNRY-KYVMSFDLTS 414
Query: 523 LYPSIMMAYNLCYSTLV 539
LYPSI+ N+ T+
Sbjct: 415 LYPSIIRQVNISPETIA 431
Score = 34.3 bits (77), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 27/41 (65%)
Query: 361 MSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
M F+ E+++L+ + +F ++ P ++ G+N+ F +PY+ +
Sbjct: 189 MPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
>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 = 43.5 bits (101), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 41/72 (56%)
Query: 607 QLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNA 666
Q+ K+ NS+YG G + + ++++T++G+ ++ ++ V + V G E A
Sbjct: 549 QINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEA 608
Query: 667 EVIYGDTDSVMV 678
V+YGDTDS+ V
Sbjct: 609 FVLYGDTDSIYV 620
Score = 34.3 bits (77), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 27/41 (65%)
Query: 361 MSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
M F+ E+++L+ + +F ++ P ++ G+N+ F +PY+ +
Sbjct: 189 MPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
Score = 31.2 bits (69), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 34/131 (25%), Positives = 56/131 (42%), Gaps = 8/131 (6%)
Query: 409 ISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLLSRGQSI 468
IS L+ N +R Y + Y ++ K FI ++M + I + S ++
Sbjct: 302 ISKLRESN---HQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVFSPIKTW 358
Query: 469 KVLSQLLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFASLYPSIM 528
+ + K++N VIP + + Y GA V E Y K + + D SLYPSI+
Sbjct: 359 DAI--IFNSLKEQNKVIPQGRSHPVQ--PYPGAFVKEPIPNRY-KYVMSFDLTSLYPSII 413
Query: 529 MAYNLCYSTLV 539
N+ T+
Sbjct: 414 RQVNISPETIA 424
>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 = 43.5 bits (101), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 41/72 (56%)
Query: 607 QLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNA 666
Q+ K+ NS+YG G + + ++++T++G+ ++ ++ V + V G E A
Sbjct: 556 QINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEA 615
Query: 667 EVIYGDTDSVMV 678
V+YGDTDS+ V
Sbjct: 616 FVLYGDTDSIYV 627
Score = 33.9 bits (76), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 27/41 (65%)
Query: 361 MSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
M F+ E+++L+ + +F ++ P ++ G+N+ F +PY+ +
Sbjct: 189 MPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
Score = 31.6 bits (70), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 47/197 (23%), Positives = 80/197 (40%), Gaps = 18/197 (9%)
Query: 343 IRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEKE 402
I N+ + + G+ V+ D + ++ F P + Y I +F+L K
Sbjct: 253 IENMYGSREIITLFGISVL------DYIDLYKKFSFTNQPSYSLDY-ISEFELNVGKLKY 305
Query: 403 DVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLL 462
D IS L+ N +R Y + Y ++ K FI ++M + I +
Sbjct: 306 D---GPISKLRESN---HQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVF 359
Query: 463 SRGQSIKVLSQLLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFAS 522
S ++ + + K++N VIP + + Y GA V E Y K + + D S
Sbjct: 360 SPIKTWDAI--IFNSLKEQNKVIPQGRSHPVQ--PYPGAFVKEPIPNRY-KYVMSFDLTS 414
Query: 523 LYPSIMMAYNLCYSTLV 539
LYPSI+ N+ T+
Sbjct: 415 LYPSIIRQVNISPETIA 431
>pdb|3CQ8|A Chain A, Ternary Complex Of The L415f Mutant Rb69 Exo(-)polymerase
Length = 903
Score = 43.5 bits (101), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 41/72 (56%)
Query: 607 QLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNA 666
Q+ K+ NS+YG G + + ++++T++G+ ++ ++ V + V G E A
Sbjct: 556 QINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEA 615
Query: 667 EVIYGDTDSVMV 678
V+YGDTDS+ V
Sbjct: 616 FVLYGDTDSIYV 627
Score = 33.9 bits (76), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 27/41 (65%)
Query: 361 MSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
M F+ E+++L+ + +F ++ P ++ G+N+ F +PY+ +
Sbjct: 189 MPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
Score = 30.0 bits (66), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 46/197 (23%), Positives = 79/197 (40%), Gaps = 18/197 (9%)
Query: 343 IRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEKE 402
I N+ + + G+ V+ D + ++ F P + Y I +F+L K
Sbjct: 253 IENMYGSREIITLFGISVL------DYIDLYKKFSFTNQPSYSLDY-ISEFELNVGKLKY 305
Query: 403 DVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLL 462
D IS L+ N +R Y + Y ++ K FI ++M + I +
Sbjct: 306 D---GPISKLRESN---HQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVF 359
Query: 463 SRGQSIKVLSQLLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFAS 522
S ++ + + K++N VIP + + Y GA V E Y K + + D S
Sbjct: 360 SPIKTWDAI--IFNSLKEQNKVIPQGRSHPVQ--PYPGAFVKEPIPNRY-KYVMSFDLTS 414
Query: 523 LYPSIMMAYNLCYSTLV 539
YPSI+ N+ T+
Sbjct: 415 FYPSIIRQVNISPETIA 431
>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 = 43.5 bits (101), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 41/72 (56%)
Query: 607 QLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNA 666
Q+ K+ NS+YG G + + ++++T++G+ ++ ++ V + V G E A
Sbjct: 556 QINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEA 615
Query: 667 EVIYGDTDSVMV 678
V+YGDTDS+ V
Sbjct: 616 FVLYGDTDSIYV 627
Score = 34.3 bits (77), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 27/41 (65%)
Query: 361 MSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
M F+ E+++L+ + +F ++ P ++ G+N+ F +PY+ +
Sbjct: 189 MPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
Score = 31.6 bits (70), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 47/197 (23%), Positives = 80/197 (40%), Gaps = 18/197 (9%)
Query: 343 IRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEKE 402
I N+ + + G+ V+ D + ++ F P + Y I +F+L K
Sbjct: 253 IENMYGSREIITLFGISVL------DYIDLYKKFSFTNQPSYSLDY-ISEFELNVGKLKY 305
Query: 403 DVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLL 462
D IS L+ N +R Y + Y ++ K FI ++M + I +
Sbjct: 306 D---GPISKLRESN---HQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVF 359
Query: 463 SRGQSIKVLSQLLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFAS 522
S ++ + + K++N VIP + + Y GA V E Y K + + D S
Sbjct: 360 SPIKTWDAI--IFNSLKEQNKVIPQGRSHPVQ--PYPGAFVKEPIPNRY-KYVMSFDLTS 414
Query: 523 LYPSIMMAYNLCYSTLV 539
LYPSI+ N+ T+
Sbjct: 415 LYPSIIRQVNISPETIA 431
>pdb|3SQ1|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dupcpp Opposite
Da
Length = 901
Score = 43.5 bits (101), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 41/72 (56%)
Query: 607 QLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNA 666
Q+ K+ NS+YG G + + ++++T++G+ ++ ++ V + V G E A
Sbjct: 556 QINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEA 615
Query: 667 EVIYGDTDSVMV 678
V+YGDTDS+ V
Sbjct: 616 FVLYGDTDSIYV 627
Score = 33.9 bits (76), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 27/41 (65%)
Query: 361 MSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
M F+ E+++L+ + +F ++ P ++ G+N+ F +PY+ +
Sbjct: 189 MPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
Score = 31.2 bits (69), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 47/197 (23%), Positives = 80/197 (40%), Gaps = 18/197 (9%)
Query: 343 IRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEKE 402
I N+ + + G+ V+ D + ++ F P + Y I +F+L K
Sbjct: 253 IENMYGSREIITLFGISVL------DYIDLYKKFSFTNQPSYSLDY-ISEFELNVGKLKY 305
Query: 403 DVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLL 462
D IS L+ N +R Y + Y ++ K FI ++M + I +
Sbjct: 306 D---GPISKLRESN---HQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVF 359
Query: 463 SRGQSIKVLSQLLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFAS 522
S ++ + + K++N VIP + + Y GA V E Y K + + D S
Sbjct: 360 SPIKTWDAI--IFNSLKEQNKVIPQGRSHPVQ--PYPGAFVKEPIPNRY-KYVMSFDLTS 414
Query: 523 LYPSIMMAYNLCYSTLV 539
LYPSI+ N+ T+
Sbjct: 415 LYPSIIRQVNISPETIA 431
>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 = 43.5 bits (101), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 41/72 (56%)
Query: 607 QLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNA 666
Q+ K+ NS+YG G + + ++++T++G+ ++ ++ V + V G E A
Sbjct: 556 QINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEA 615
Query: 667 EVIYGDTDSVMV 678
V+YGDTDS+ V
Sbjct: 616 FVLYGDTDSIYV 627
Score = 37.0 bits (84), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 28/41 (68%)
Query: 361 MSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
M F+ E+++L+ + +F ++ P ++ G+N+ FD+PY+ +
Sbjct: 189 MPFDNEKELLMEYLNFWQQKTPVILTGWNVESFDIPYVYNR 229
Score = 34.7 bits (78), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 48/197 (24%), Positives = 81/197 (41%), Gaps = 18/197 (9%)
Query: 343 IRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEKE 402
I N+ + + G+ V+ D + ++ F P + Y I +F+L K
Sbjct: 253 IENMYGSREIITLFGISVL------DYIDLYKKFSFTNQPSYSLDY-ISEFELNVGKLKY 305
Query: 403 DVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLL 462
D IS L+ N +R Y + D Y ++ K FI ++M + I +
Sbjct: 306 D---GPISKLRESN---HQRYISYNIIDVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVF 359
Query: 463 SRGQSIKVLSQLLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFAS 522
S ++ + + K++N VIP + + Y GA V E Y K + + D S
Sbjct: 360 SPIKTWDAI--IFNSLKEQNKVIPQGRSHPVQ--PYPGAFVKEPIPNRY-KYVMSFDLTS 414
Query: 523 LYPSIMMAYNLCYSTLV 539
LYPSI+ N+ T+
Sbjct: 415 LYPSIIRQVNISPETIA 431
>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 = 43.5 bits (101), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 41/72 (56%)
Query: 607 QLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNA 666
Q+ K+ NS+YG G + + ++++T++G+ ++ ++ V + V G E A
Sbjct: 556 QINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEA 615
Query: 667 EVIYGDTDSVMV 678
V+YGDTDS+ V
Sbjct: 616 FVLYGDTDSIYV 627
Score = 34.3 bits (77), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 27/41 (65%)
Query: 361 MSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
M F+ E+++L+ + +F ++ P ++ G+N+ F +PY+ +
Sbjct: 189 MPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
Score = 31.6 bits (70), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 47/197 (23%), Positives = 80/197 (40%), Gaps = 18/197 (9%)
Query: 343 IRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEKE 402
I N+ + + G+ V+ D + ++ F P + Y I +F+L K
Sbjct: 253 IENMYGSREIITLFGISVL------DYIDLYKKFSFTNQPSYSLDY-ISEFELNVGKLKY 305
Query: 403 DVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLL 462
D IS L+ N +R Y + Y ++ K FI ++M + I +
Sbjct: 306 D---GPISKLRESN---HQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVF 359
Query: 463 SRGQSIKVLSQLLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFAS 522
S ++ + + K++N VIP + + Y GA V E Y K + + D S
Sbjct: 360 SPIKTWDAI--IFNSLKEQNKVIPQGRSHPVQ--PYPGAFVKEPIPNRY-KYVMSFDLTS 414
Query: 523 LYPSIMMAYNLCYSTLV 539
LYPSI+ N+ T+
Sbjct: 415 LYPSIIRQVNISPETIA 431
>pdb|1Q9Y|A Chain A, Crystal Structure Of Enterobacteria Phage Rb69 Gp43 Dna
Polymerase Complexed With 8-Oxoguanosine Containing Dna
Length = 906
Score = 43.5 bits (101), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 41/72 (56%)
Query: 607 QLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNA 666
Q+ K+ NS+YG G + + ++++T++G+ ++ ++ V + V G E A
Sbjct: 559 QINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEA 618
Query: 667 EVIYGDTDSVMV 678
V+YGDTDS+ V
Sbjct: 619 FVLYGDTDSIYV 630
Score = 34.3 bits (77), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 27/41 (65%)
Query: 361 MSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
M F+ E+++L+ + +F ++ P ++ G+N+ F +PY+ +
Sbjct: 192 MPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 232
Score = 31.6 bits (70), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 47/197 (23%), Positives = 80/197 (40%), Gaps = 18/197 (9%)
Query: 343 IRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEKE 402
I N+ + + G+ V+ D + ++ F P + Y I +F+L K
Sbjct: 256 IENMYGSREIITLFGISVL------DYIDLYKKFSFTNQPSYSLDY-ISEFELNVGKLKY 308
Query: 403 DVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLL 462
D IS L+ N +R Y + Y ++ K FI ++M + I +
Sbjct: 309 D---GPISKLRESN---HQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVF 362
Query: 463 SRGQSIKVLSQLLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFAS 522
S ++ + + K++N VIP + + Y GA V E Y K + + D S
Sbjct: 363 SPIKTWDAI--IFNSLKEQNKVIPQGRSHPVQ--PYPGAFVKEPIPNRY-KYVMSFDLTS 417
Query: 523 LYPSIMMAYNLCYSTLV 539
LYPSI+ N+ T+
Sbjct: 418 LYPSIIRQVNISPETIA 434
>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 = 43.1 bits (100), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 41/72 (56%)
Query: 607 QLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNA 666
Q+ K+ NS+YG G + + ++++T++G+ ++ ++ V + V G E A
Sbjct: 556 QINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQXALQWIERKVNEYLNEVCGTEGEA 615
Query: 667 EVIYGDTDSVMV 678
V+YGDTDS+ V
Sbjct: 616 FVLYGDTDSIYV 627
Score = 30.8 bits (68), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 10/39 (25%), Positives = 25/39 (64%)
Query: 363 FETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
F+ E+++L + +F ++ P ++ G+N+ F +PY+ +
Sbjct: 191 FDNEKELLXEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
Score = 29.6 bits (65), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 3/66 (4%)
Query: 474 LLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFASLYPSIMMAYNL 533
+ K++N VIP + + Y GA V E Y K + + D SLYPSI+ N+
Sbjct: 369 IFNSLKEQNKVIPQGRSHPVQ--PYPGAFVKEPIPNRY-KYVXSFDLTSLYPSIIRQVNI 425
Query: 534 CYSTLV 539
T+
Sbjct: 426 SPETIA 431
>pdb|3LDS|A Chain A, Crystal Structure Of Rb69 Gp43 With Dna And Datp Opposite
8-
Length = 903
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 40/72 (55%)
Query: 607 QLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNA 666
Q+ K NS+YG G + + ++++T++G+ ++ ++ V + V G E A
Sbjct: 556 QINRKALINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEA 615
Query: 667 EVIYGDTDSVMV 678
V+YGDTDS+ V
Sbjct: 616 FVLYGDTDSIYV 627
Score = 34.3 bits (77), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 27/41 (65%)
Query: 361 MSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
M F+ E+++L+ + +F ++ P ++ G+N+ F +PY+ +
Sbjct: 189 MPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
Score = 31.6 bits (70), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 47/197 (23%), Positives = 80/197 (40%), Gaps = 18/197 (9%)
Query: 343 IRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEKE 402
I N+ + + G+ V+ D + ++ F P + Y I +F+L K
Sbjct: 253 IENMYGSREIITLFGISVL------DYIDLYKKFSFTNQPSYSLDY-ISEFELNVGKLKY 305
Query: 403 DVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLL 462
D IS L+ N +R Y + Y ++ K FI ++M + I +
Sbjct: 306 D---GPISKLRESN---HQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVF 359
Query: 463 SRGQSIKVLSQLLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFAS 522
S ++ + + K++N VIP + + Y GA V E Y K + + D S
Sbjct: 360 SPIKTWDAI--IFNSLKEQNKVIPQGRSHPVQ--PYPGAFVKEPIPNRY-KYVMSFDLTS 414
Query: 523 LYPSIMMAYNLCYSTLV 539
LYPSI+ N+ T+
Sbjct: 415 LYPSIIRQVNISPETIA 431
>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 = 40.0 bits (92), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 40/72 (55%)
Query: 607 QLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNA 666
Q+ K+ NS+ G G + + ++++T++G+ ++ ++ V + V G E A
Sbjct: 556 QINRKLLINSLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEA 615
Query: 667 EVIYGDTDSVMV 678
V+YGDTDS+ V
Sbjct: 616 FVLYGDTDSIYV 627
Score = 33.9 bits (76), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 27/41 (65%)
Query: 361 MSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
M F+ E+++L+ + +F ++ P ++ G+N+ F +PY+ +
Sbjct: 189 MPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
Score = 31.2 bits (69), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 47/197 (23%), Positives = 80/197 (40%), Gaps = 18/197 (9%)
Query: 343 IRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEKE 402
I N+ + + G+ V+ D + ++ F P + Y I +F+L K
Sbjct: 253 IENMYGSREIITLFGISVL------DYIDLYKKFSFTNQPSYSLDY-ISEFELNVGKLKY 305
Query: 403 DVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLL 462
D IS L+ N +R Y + Y ++ K FI ++M + I +
Sbjct: 306 D---GPISKLRESN---HQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVF 359
Query: 463 SRGQSIKVLSQLLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFAS 522
S ++ + + K++N VIP + + Y GA V E Y K + + D S
Sbjct: 360 SPIKTWDAI--IFNSLKEQNKVIPQGRSHPVQ--PYPGAFVKEPIPNRY-KYVMSFDLTS 414
Query: 523 LYPSIMMAYNLCYSTLV 539
LYPSI+ N+ T+
Sbjct: 415 LYPSIIRQVNISPETIA 431
>pdb|3SUO|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dttp
Opposite 2ap (Gc Rich Sequence)
Length = 900
Score = 40.0 bits (92), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 40/72 (55%)
Query: 607 QLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNA 666
Q+ K+ NS+ G G + + ++++T++G+ ++ ++ V + V G E A
Sbjct: 556 QINRKLLINSLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEA 615
Query: 667 EVIYGDTDSVMV 678
V+YGDTDS+ V
Sbjct: 616 FVLYGDTDSIYV 627
Score = 34.3 bits (77), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 27/41 (65%)
Query: 361 MSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
M F+ E+++L+ + +F ++ P ++ G+N+ F +PY+ +
Sbjct: 189 MPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
Score = 31.6 bits (70), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 47/197 (23%), Positives = 80/197 (40%), Gaps = 18/197 (9%)
Query: 343 IRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEKE 402
I N+ + + G+ V+ D + ++ F P + Y I +F+L K
Sbjct: 253 IENMYGSREIITLFGISVL------DYIDLYKKFSFTNQPSYSLDY-ISEFELNVGKLKY 305
Query: 403 DVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLL 462
D IS L+ N +R Y + Y ++ K FI ++M + I +
Sbjct: 306 D---GPISKLRESN---HQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVF 359
Query: 463 SRGQSIKVLSQLLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFAS 522
S ++ + + K++N VIP + + Y GA V E Y K + + D S
Sbjct: 360 SPIKTWDAI--IFNSLKEQNKVIPQGRSHPVQ--PYPGAFVKEPIPNRY-KYVMSFDLTS 414
Query: 523 LYPSIMMAYNLCYSTLV 539
LYPSI+ N+ T+
Sbjct: 415 LYPSIIRQVNISPETIA 431
>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 = 40.0 bits (92), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 40/72 (55%)
Query: 607 QLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNA 666
Q+ K+ NS+ G G + + ++++T++G+ ++ ++ V + V G E A
Sbjct: 556 QINRKLLINSLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEA 615
Query: 667 EVIYGDTDSVMV 678
V+YGDTDS+ V
Sbjct: 616 FVLYGDTDSIYV 627
Score = 34.3 bits (77), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 27/41 (65%)
Query: 361 MSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
M F+ E+++L+ + +F ++ P ++ G+N+ F +PY+ +
Sbjct: 189 MPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
Score = 31.2 bits (69), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 47/197 (23%), Positives = 80/197 (40%), Gaps = 18/197 (9%)
Query: 343 IRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEKE 402
I N+ + + G+ V+ D + ++ F P + Y I +F+L K
Sbjct: 253 IENMYGSREIITLFGISVL------DYIDLYKKFSFTNQPSYSLDY-ISEFELNVGKLKY 305
Query: 403 DVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLL 462
D IS L+ N +R Y + Y ++ K FI ++M + I +
Sbjct: 306 D---GPISKLRESN---HQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVF 359
Query: 463 SRGQSIKVLSQLLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFAS 522
S ++ + + K++N VIP + + Y GA V E Y K + + D S
Sbjct: 360 SPIKTWDAI--IFNSLKEQNKVIPQGRSHPVQ--PYPGAFVKEPIPNRY-KYVMSFDLTS 414
Query: 523 LYPSIMMAYNLCYSTLV 539
LYPSI+ N+ T+
Sbjct: 415 LYPSIIRQVNISPETIA 431
>pdb|3SUN|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dttp
Opposite 2ap (At Rich Sequence)
Length = 895
Score = 40.0 bits (92), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 40/72 (55%)
Query: 607 QLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNA 666
Q+ K+ NS+ G G + + ++++T++G+ ++ ++ V + V G E A
Sbjct: 556 QINRKLLINSLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEA 615
Query: 667 EVIYGDTDSVMV 678
V+YGDTDS+ V
Sbjct: 616 FVLYGDTDSIYV 627
Score = 34.3 bits (77), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 27/41 (65%)
Query: 361 MSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
M F+ E+++L+ + +F ++ P ++ G+N+ F +PY+ +
Sbjct: 189 MPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
Score = 31.6 bits (70), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 47/197 (23%), Positives = 80/197 (40%), Gaps = 18/197 (9%)
Query: 343 IRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEKE 402
I N+ + + G+ V+ D + ++ F P + Y I +F+L K
Sbjct: 253 IENMYGSREIITLFGISVL------DYIDLYKKFSFTNQPSYSLDY-ISEFELNVGKLKY 305
Query: 403 DVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLL 462
D IS L+ N +R Y + Y ++ K FI ++M + I +
Sbjct: 306 D---GPISKLRESN---HQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVF 359
Query: 463 SRGQSIKVLSQLLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFAS 522
S ++ + + K++N VIP + + Y GA V E Y K + + D S
Sbjct: 360 SPIKTWDAI--IFNSLKEQNKVIPQGRSHPVQ--PYPGAFVKEPIPNRY-KYVMSFDLTS 414
Query: 523 LYPSIMMAYNLCYSTLV 539
LYPSI+ N+ T+
Sbjct: 415 LYPSIIRQVNISPETIA 431
>pdb|3SUQ|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dctp
Opposite 2ap (At Rich Sequence)
Length = 897
Score = 40.0 bits (92), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 40/72 (55%)
Query: 607 QLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNA 666
Q+ K+ NS+ G G + + ++++T++G+ ++ ++ V + V G E A
Sbjct: 556 QINRKLLINSLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEA 615
Query: 667 EVIYGDTDSVMV 678
V+YGDTDS+ V
Sbjct: 616 FVLYGDTDSIYV 627
Score = 34.3 bits (77), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 27/41 (65%)
Query: 361 MSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
M F+ E+++L+ + +F ++ P ++ G+N+ F +PY+ +
Sbjct: 189 MPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
Score = 31.6 bits (70), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 47/197 (23%), Positives = 80/197 (40%), Gaps = 18/197 (9%)
Query: 343 IRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEKE 402
I N+ + + G+ V+ D + ++ F P + Y I +F+L K
Sbjct: 253 IENMYGSREIITLFGISVL------DYIDLYKKFSFTNQPSYSLDY-ISEFELNVGKLKY 305
Query: 403 DVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLL 462
D IS L+ N +R Y + Y ++ K FI ++M + I +
Sbjct: 306 D---GPISKLRESN---HQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVF 359
Query: 463 SRGQSIKVLSQLLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFAS 522
S ++ + + K++N VIP + + Y GA V E Y K + + D S
Sbjct: 360 SPIKTWDAI--IFNSLKEQNKVIPQGRSHPVQ--PYPGAFVKEPIPNRY-KYVMSFDLTS 414
Query: 523 LYPSIMMAYNLCYSTLV 539
LYPSI+ N+ T+
Sbjct: 415 LYPSIIRQVNISPETIA 431
>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 = 38.5 bits (88), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 39/72 (54%)
Query: 607 QLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNA 666
Q+ K+ N + G G + + ++++T++G+ ++ ++ V + V G E A
Sbjct: 556 QINRKLLINGLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEA 615
Query: 667 EVIYGDTDSVMV 678
V+YGDTDS+ V
Sbjct: 616 FVLYGDTDSIYV 627
Score = 34.3 bits (77), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 27/41 (65%)
Query: 361 MSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
M F+ E+++L+ + +F ++ P ++ G+N+ F +PY+ +
Sbjct: 189 MPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
Score = 31.2 bits (69), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 47/197 (23%), Positives = 80/197 (40%), Gaps = 18/197 (9%)
Query: 343 IRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEKE 402
I N+ + + G+ V+ D + ++ F P + Y I +F+L K
Sbjct: 253 IENMYGSREIITLFGISVL------DYIDLYKKFSFTNQPSYSLDY-ISEFELNVGKLKY 305
Query: 403 DVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLL 462
D IS L+ N +R Y + Y ++ K FI ++M + I +
Sbjct: 306 D---GPISKLRESN---HQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVF 359
Query: 463 SRGQSIKVLSQLLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFAS 522
S ++ + + K++N VIP + + Y GA V E Y K + + D S
Sbjct: 360 SPIKTWDAI--IFNSLKEQNKVIPQGRSHPVQ--PYPGAFVKEPIPNRY-KYVMSFDLTS 414
Query: 523 LYPSIMMAYNLCYSTLV 539
LYPSI+ N+ T+
Sbjct: 415 LYPSIIRQVNISPETIA 431
>pdb|3SCX|A Chain A, Rb69 Dna Polymerase Triple Mutant(L561aS565GY567A) TERNARY
COMPLEX With Dupnpp And A Deoxy-Terminated Primer In The
Presence Of Ca2+
pdb|3SI6|A Chain A, Rb69 Dna Polymerase Triple Mutant (L561aS565GY567A)
TERNARY COMPLEX With Dupnpp And A Deoxy-Terminated
Primer In The Presence Of Mg2+
pdb|3SJJ|A Chain A, Rb69 Dna Polymerase Triple Mutant (L561aS565GY567A)
TERNARY COMPLEX With Dupnpp And A Deoxy-Terminated
Primer In The Presence Of Mn2+
pdb|3SNN|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DCTP Opposite Dg In The Presence Of Mg2+
Length = 903
Score = 37.4 bits (85), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 38/72 (52%)
Query: 607 QLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNA 666
Q+ K N + G G + + ++++T++G+ ++ ++ V + V G E A
Sbjct: 556 QINRKALINGLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEA 615
Query: 667 EVIYGDTDSVMV 678
V+YGDTDS+ V
Sbjct: 616 FVLYGDTDSIYV 627
Score = 34.3 bits (77), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 27/41 (65%)
Query: 361 MSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
M F+ E+++L+ + +F ++ P ++ G+N+ F +PY+ +
Sbjct: 189 MPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
Score = 31.2 bits (69), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 47/197 (23%), Positives = 80/197 (40%), Gaps = 18/197 (9%)
Query: 343 IRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEKE 402
I N+ + + G+ V+ D + ++ F P + Y I +F+L K
Sbjct: 253 IENMYGSREIITLFGISVL------DYIDLYKKFSFTNQPSYSLDY-ISEFELNVGKLKY 305
Query: 403 DVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLL 462
D IS L+ N +R Y + Y ++ K FI ++M + I +
Sbjct: 306 D---GPISKLRESN---HQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVF 359
Query: 463 SRGQSIKVLSQLLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFAS 522
S ++ + + K++N VIP + + Y GA V E Y K + + D S
Sbjct: 360 SPIKTWDAI--IFNSLKEQNKVIPQGRSHPVQ--PYPGAFVKEPIPNRY-KYVMSFDLTS 414
Query: 523 LYPSIMMAYNLCYSTLV 539
LYPSI+ N+ T+
Sbjct: 415 LYPSIIRQVNISPETIA 431
>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 = 37.4 bits (85), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 38/72 (52%)
Query: 607 QLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNA 666
Q+ K N + G G + + ++++T++G+ ++ ++ V + V G E A
Sbjct: 556 QINRKALINGLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEA 615
Query: 667 EVIYGDTDSVMV 678
V+YGDTDS+ V
Sbjct: 616 FVLYGDTDSIYV 627
Score = 33.9 bits (76), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 27/41 (65%)
Query: 361 MSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
M F+ E+++L+ + +F ++ P ++ G+N+ F +PY+ +
Sbjct: 189 MPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
>pdb|3QEP|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DTTP Opposite Difluorotoluene Nucleoside
pdb|3S9H|A Chain A, Rb69 Dna Polymerase Triple Mutant(L561aS565GY567A) TERNARY
COMPLEX With Dupnpp And A Dideoxy-Terminated Primer In
The Presence Of Ca2+
pdb|3SQ0|A Chain A, Dna Polymerase(L561aS565GY567A) TERNARY COMPLEX WITH
DUPNPP OPPOSITE Da (Mn2+)
pdb|3QEI|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DCTP Opposite Difluorotoluene Nucleoside
pdb|3QER|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DATP Opposite Difluorotoluene Nucleoside
pdb|3QES|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DGTP Opposite Difluorotoluene Nucleoside
pdb|3QET|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DTTP Opposite Dt
pdb|3QEV|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DCTP Opposite Dt
pdb|3QEW|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DDTP Opposite Dt
pdb|3QEX|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DGTP Opposite Dt
pdb|4E3S|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dqtp Opposite Dt
pdb|4DTN|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp Opposite An
Abasic Site And DdaDT AS THE PENULTIMATE BASE-Pair
pdb|4DTO|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp Opposite An
Abasic Site And DdaDT AS THE PENULTIMATE BASE-Pair
pdb|4DTP|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dgtp Opposite An
Abasic Site And DdaDT AS THE PENULTIMATE BASE-Pair
pdb|4DTR|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp Opposite An
Abasic Site And DdcDG AS THE PENULTIMATE BASE-Pair
pdb|4DTS|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp Opposite An
Abasic Site And DdcDG AS THE PENULTIMATE BASE-Pair
pdb|4DTU|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dgtp Opposite An
Abasic Site And DdcDG AS THE PENULTIMATE BASE-Pair
pdb|4DTX|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp Opposite An
Abasic Site And DdcDG AS THE PENULTIMATE BASE-Pair
pdb|4FJM|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp/da
Length = 903
Score = 37.4 bits (85), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 38/72 (52%)
Query: 607 QLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNA 666
Q+ K N + G G + + ++++T++G+ ++ ++ V + V G E A
Sbjct: 556 QINRKALINGLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEA 615
Query: 667 EVIYGDTDSVMV 678
V+YGDTDS+ V
Sbjct: 616 FVLYGDTDSIYV 627
Score = 33.9 bits (76), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 27/41 (65%)
Query: 361 MSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
M F+ E+++L+ + +F ++ P ++ G+N+ F +PY+ +
Sbjct: 189 MPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
Score = 31.2 bits (69), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 47/197 (23%), Positives = 80/197 (40%), Gaps = 18/197 (9%)
Query: 343 IRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEKE 402
I N+ + + G+ V+ D + ++ F P + Y I +F+L K
Sbjct: 253 IENMYGSREIITLFGISVL------DYIDLYKKFSFTNQPSYSLDY-ISEFELNVGKLKY 305
Query: 403 DVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLL 462
D IS L+ N +R Y + Y ++ K FI ++M + I +
Sbjct: 306 D---GPISKLRESN---HQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVF 359
Query: 463 SRGQSIKVLSQLLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFAS 522
S ++ + + K++N VIP + + Y GA V E Y K + + D S
Sbjct: 360 SPIKTWDAI--IFNSLKEQNKVIPQGRSHPVQ--PYPGAFVKEPIPNRY-KYVMSFDLTS 414
Query: 523 LYPSIMMAYNLCYSTLV 539
LYPSI+ N+ T+
Sbjct: 415 LYPSIIRQVNISPETIA 431
>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 = 37.4 bits (85), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 38/72 (52%)
Query: 607 QLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNA 666
Q+ K N + G G + + ++++T++G+ ++ ++ V + V G E A
Sbjct: 556 QINRKALINGLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEA 615
Query: 667 EVIYGDTDSVMV 678
V+YGDTDS+ V
Sbjct: 616 FVLYGDTDSIYV 627
Score = 37.0 bits (84), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 28/41 (68%)
Query: 361 MSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
M F+ E+++L+ + +F ++ P ++ G+N+ FD+PY+ +
Sbjct: 189 MPFDNEKELLMEYLNFWQQKTPVILTGWNVESFDIPYVYNR 229
Score = 34.7 bits (78), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 48/197 (24%), Positives = 81/197 (41%), Gaps = 18/197 (9%)
Query: 343 IRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEKE 402
I N+ + + G+ V+ D + ++ F P + Y I +F+L K
Sbjct: 253 IENMYGSREIITLFGISVL------DYIDLYKKFSFTNQPSYSLDY-ISEFELNVGKLKY 305
Query: 403 DVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLL 462
D IS L+ N +R Y + D Y ++ K FI ++M + I +
Sbjct: 306 D---GPISKLRESN---HQRYISYNIIDVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVF 359
Query: 463 SRGQSIKVLSQLLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFAS 522
S ++ + + K++N VIP + + Y GA V E Y K + + D S
Sbjct: 360 SPIKTWDAI--IFNSLKEQNKVIPQGRSHPVQ--PYPGAFVKEPIPNRY-KYVMSFDLTS 414
Query: 523 LYPSIMMAYNLCYSTLV 539
LYPSI+ N+ T+
Sbjct: 415 LYPSIIRQVNISPETIA 431
>pdb|4DTJ|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp Opposite An
Abasic Site And DdtDA AS THE PENULTIMATE BASE-Pair
pdb|4DTM|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp Opposite An
Abasic Site And DdgDC AS THE PENULTIMATE BASE-Pair
Length = 901
Score = 37.4 bits (85), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 38/72 (52%)
Query: 607 QLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNA 666
Q+ K N + G G + + ++++T++G+ ++ ++ V + V G E A
Sbjct: 556 QINRKALINGLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEA 615
Query: 667 EVIYGDTDSVMV 678
V+YGDTDS+ V
Sbjct: 616 FVLYGDTDSIYV 627
Score = 33.9 bits (76), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 27/41 (65%)
Query: 361 MSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
M F+ E+++L+ + +F ++ P ++ G+N+ F +PY+ +
Sbjct: 189 MPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
Score = 31.2 bits (69), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 47/197 (23%), Positives = 80/197 (40%), Gaps = 18/197 (9%)
Query: 343 IRNVMTLKSCAPIVGVDVMSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEKE 402
I N+ + + G+ V+ D + ++ F P + Y I +F+L K
Sbjct: 253 IENMYGSREIITLFGISVL------DYIDLYKKFSFTNQPSYSLDY-ISEFELNVGKLKY 305
Query: 403 DVHHSIISDLQNGNAETRRRLAVYCLKDAYLPQRLLDKLMFIFNYVEMARVTGVPISFLL 462
D IS L+ N +R Y + Y ++ K FI ++M + I +
Sbjct: 306 D---GPISKLRESN---HQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVF 359
Query: 463 SRGQSIKVLSQLLRKAKQKNLVIPNVKQAGSEQGTYEGATVLEARAGFYEKPIATLDFAS 522
S ++ + + K++N VIP + + Y GA V E Y K + + D S
Sbjct: 360 SPIKTWDAI--IFNSLKEQNKVIPQGRSHPVQ--PYPGAFVKEPIPNRY-KYVMSFDLTS 414
Query: 523 LYPSIMMAYNLCYSTLV 539
LYPSI+ N+ T+
Sbjct: 415 LYPSIIRQVNISPETIA 431
>pdb|3SPY|A Chain A, Rb69 Dna Polymerase(L415aL561AS565GY567A) TERNARY COMPLEX
WITH Dupcpp Opposite Da
Length = 901
Score = 37.4 bits (85), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 38/72 (52%)
Query: 607 QLALKISANSVYGFTGATVGQLPCIEISSSVTSYGRQMIEHTKKLVEDKFTTVGGYEHNA 666
Q+ K N + G G + + ++++T++G+ ++ ++ V + V G E A
Sbjct: 556 QINRKALINGLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEA 615
Query: 667 EVIYGDTDSVMV 678
V+YGDTDS+ V
Sbjct: 616 FVLYGDTDSIYV 627
Score = 34.3 bits (77), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 27/41 (65%)
Query: 361 MSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
M F+ E+++L+ + +F ++ P ++ G+N+ F +PY+ +
Sbjct: 189 MPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
>pdb|1NOZ|A Chain A, T4 Dna Polymerase Fragment (Residues 1-388) At 110k
pdb|1NOZ|B Chain B, T4 Dna Polymerase Fragment (Residues 1-388) At 110k
pdb|1NOY|A Chain A, Dna Polymerase (e.c.2.7.7.7)/dna Complex
pdb|1NOY|B Chain B, Dna Polymerase (e.c.2.7.7.7)/dna Complex
Length = 388
Score = 37.4 bits (85), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 26/41 (63%)
Query: 361 MSFETERDVLLAWRDFIREVDPDVMIGYNICKFDLPYLIEK 401
M F+ ERD+L+ + + + P + G+NI FD+PY++ +
Sbjct: 186 MPFDNERDMLMEYINLWEQKRPAIFTGWNIEGFDVPYIMNR 226
>pdb|2VQD|A Chain A, Crystal Structure Of Biotin Carboxylase From Pseudomonas
Aeruginosa Complexed With Ampcp
pdb|2C00|A Chain A, Crystal Structure Of Biotin Carboxylase From Pseudomonas
Aeruginosa In Apo Form
pdb|2C00|B Chain B, Crystal Structure Of Biotin Carboxylase From Pseudomonas
Aeruginosa In Apo Form
Length = 464
Score = 31.6 bits (70), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 5/57 (8%)
Query: 104 DSNRELLPLSSGSAAIIRIFGVTREGHSVCCKVHGFEPYFYISCPQGMGPDDISHFH 160
D +E+L ++SG IR V GH++ C+++ +P ++ P + HFH
Sbjct: 307 DIVKEMLRIASGEKLSIRQEDVVIRGHALECRINAEDPKTFMPS-----PGKVKHFH 358
>pdb|1XNG|A Chain A, Crystal Structure Of Nh3-Dependent Nad+ Synthetase From
Helicobacter Pylori
pdb|1XNG|B Chain B, Crystal Structure Of Nh3-Dependent Nad+ Synthetase From
Helicobacter Pylori
pdb|1XNH|A Chain A, Crystal Structure Of Nh3-dependent Nad+ Synthetase From
Helicobacter Pylori
Length = 268
Score = 29.6 bits (65), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 20/29 (68%)
Query: 542 EDARKLNLPPECVNKTPSGETFVKSNLQK 570
E AR+LN+P + +NK PS + FV + +K
Sbjct: 166 ELARRLNIPKKILNKPPSADLFVGQSDEK 194
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.321 0.136 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 28,339,440
Number of Sequences: 62578
Number of extensions: 1143233
Number of successful extensions: 2517
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 47
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 2272
Number of HSP's gapped (non-prelim): 168
length of query: 1014
length of database: 14,973,337
effective HSP length: 108
effective length of query: 906
effective length of database: 8,214,913
effective search space: 7442711178
effective search space used: 7442711178
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)