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= 000501
(1459 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 = 187 bits (475), Expect = 3e-47, Method: Compositional matrix adjust.
Identities = 144/512 (28%), Positives = 238/512 (46%), Gaps = 69/512 (13%)
Query: 957 LTLLSIEVQAESRGDLRPDPRYDSI----NVVALAFENDSDHAVEIYVLLYCKSESHQRS 1012
L ++S +++ R + P+P YD + NVV++A ++ L C
Sbjct: 249 LRIMSFDIECAGRIGVFPEPEYDPVIQIANVVSIAGAKKP-FIRNVFTLNTCSP------ 301
Query: 1013 LVGIPDCKVFVCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLN 1072
I +F + E + S++ + DPD+++G++ + +L RA L + N
Sbjct: 302 ---ITGSMIFSHATEEEMLSNWRNFIIKVDPDVIIGYNTTNFDIPYLLNRAKALKV---N 355
Query: 1073 DISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGG 1132
D P ++ EI E S+ + A +G +++ G
Sbjct: 356 DF---PYFGRLKTVKQEIKE---------------SVFSSKA-----YGTRETKNVNIDG 392
Query: 1133 RIVLNVWRLMRGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYV 1192
R+ L++ + ++ E KL YT+ AV+ L + + + +++ +G R R Y
Sbjct: 393 RLQLDLLQFIQREYKLRSYTLNAVSAHFLGEQKEDVHYSIISD-LQNGDSETRRRLAVYC 451
Query: 1193 VGRAKLNLEIMNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAIS 1252
+ A L L +M +L + +E+ARV G+ F +L+RG Q +V S L R + +
Sbjct: 452 LKDAYLPLRLMEKLMALVNYTEMARVTGVPFSYLLARGQQIKVVSQLFRKCLEID--TVI 509
Query: 1253 PGNHQVASQPAMECLPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPS 1312
P AS E V+EP G+Y P+ LDF SLYPS+M+A+NLC+ T K
Sbjct: 510 PNMQSQASDDQYEG-ATVIEPIRGYYDVPIATLDFNSLYPSIMMAHNLCYTTLCNKATVE 568
Query: 1313 KENTLGVSSFRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQA 1372
+ N + ++ +I PNG +V K R+G+LP +L+E++S R K+A
Sbjct: 569 RLNL--------------KIDEDYVITPNGDYFVTTKRRRGILPIILDELISAR---KRA 611
Query: 1373 IKKLAPSQQILHR-IFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLE 1431
K L + R + N RQLALK+ AN YG+T A G++PC ++ S+ GR+ +
Sbjct: 612 KKDLRDEKDPFKRDVLNGRQLALKISANSVYGFTGATV-GKLPCLAISSSVTAYGRTMIL 670
Query: 1432 KAISFVNEN------EKWKAKVIYGDTDRYTV 1457
K + V E K A V+YGDTD V
Sbjct: 671 KTKTAVQEKYCIKNGYKHDAVVVYGDTDSVMV 702
>pdb|2VWK|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography. V93q Polymerase Variant
Length = 773
Score = 119 bits (298), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 113/438 (25%), Positives = 189/438 (43%), Gaps = 73/438 (16%)
Query: 1023 VCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESK 1082
V S E + F+K++ DPD+L+ ++ + +L +R+ LG+ + + R E K
Sbjct: 183 VVSTEKEMIKRFLKVVKEKDPDVLITYNGDNFAFAYLKKRSEKLGVKFI--LGREGSEPK 240
Query: 1083 IAAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWRLM 1142
I + + D E V GRI +++ ++
Sbjct: 241 I---------QRMGDRFAVE---------------------------VKGRIHFDLYPVI 264
Query: 1143 RGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLEI 1202
R + L YT+EAV E + + + + + + +G G R Y + AK+ E+
Sbjct: 265 RRTINLPTYTLEAVYEAIFGQPKEKVYAEEIAQAWETGEGLER--VARYSMEDAKVTYEL 322
Query: 1203 MNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAIS-PGNHQVASQ 1261
+ ++L+R+ G + V + VE LLR A+ +N LA + P ++A +
Sbjct: 323 GKEF--FPMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKPDERELARR 380
Query: 1262 PAMECLPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSS 1321
V EPE G + + +V LDF+SLYPS++I +N+ P N G
Sbjct: 381 RESYAGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVS---------PDTLNREGCEE 430
Query: 1322 FRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQ 1381
+ + P G + K G +P LL ++L R VK+ +K A
Sbjct: 431 YD-------------VAPQVGHKFC--KDFPGFIPSLLGDLLEERQKVKKKMK--ATIDP 473
Query: 1382 ILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNENE 1441
I ++ + RQ A+K++AN YGY R C E A+S+ GR +E I + E
Sbjct: 474 IEKKLLDYRQRAIKILANSFYGYYGYA-KARWYCKECAESVTAWGRQYIETTIREI--EE 530
Query: 1442 KWKAKVIYGDTDRYTVCI 1459
K+ KV+Y DTD + I
Sbjct: 531 KFGFKVLYADTDGFFATI 548
>pdb|2XHB|A Chain A, Crystal Structure Of Dna Polymerase From Thermococcus
Gorgonarius In Complex With Hypoxanthine-Containing Dna
Length = 773
Score = 119 bits (298), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 113/438 (25%), Positives = 189/438 (43%), Gaps = 73/438 (16%)
Query: 1023 VCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESK 1082
V S E + F+K++ DPD+L+ ++ + +L +R+ LG+ + + R E K
Sbjct: 183 VVSTEKEMIKRFLKVVKEKDPDVLITYNGDNFAFAYLKKRSEKLGVKFI--LGREGSEPK 240
Query: 1083 IAAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWRLM 1142
I + + D E V GRI +++ ++
Sbjct: 241 I---------QRMGDRFAVE---------------------------VKGRIHFDLYPVI 264
Query: 1143 RGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLEI 1202
R + L YT+EAV E + + + + + + +G G R Y + AK+ E+
Sbjct: 265 RRTINLPTYTLEAVYEAIFGQPKEKVYAEEIAQAWETGEGLER--VARYSMEDAKVTYEL 322
Query: 1203 MNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAIS-PGNHQVASQ 1261
+ ++L+R+ G + V + VE LLR A+ +N LA + P ++A +
Sbjct: 323 GKEF--FPMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKPDERELARR 380
Query: 1262 PAMECLPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSS 1321
V EPE G + + +V LDF+SLYPS++I +N+ P N G
Sbjct: 381 RESYAGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVS---------PDTLNREGCEE 430
Query: 1322 FRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQ 1381
+ + P G + K G +P LL ++L R VK+ +K A
Sbjct: 431 YD-------------VAPQVGHKFC--KDFPGFIPSLLGDLLEERQKVKKKMK--ATIDP 473
Query: 1382 ILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNENE 1441
I ++ + RQ A+K++AN YGY R C E A+S+ GR +E I + E
Sbjct: 474 IEKKLLDYRQRAIKILANSFYGYYGYA-KARWYCKECAESVTAWGRQYIETTIREI--EE 530
Query: 1442 KWKAKVIYGDTDRYTVCI 1459
K+ KV+Y DTD + I
Sbjct: 531 KFGFKVLYADTDGFFATI 548
>pdb|2VWJ|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography
Length = 773
Score = 119 bits (298), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 113/438 (25%), Positives = 189/438 (43%), Gaps = 73/438 (16%)
Query: 1023 VCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESK 1082
V S E + F+K++ DPD+L+ ++ + +L +R+ LG+ + + R E K
Sbjct: 183 VVSTEKEMIKRFLKVVKEKDPDVLITYNGDNFAFAYLKKRSEKLGVKFI--LGREGSEPK 240
Query: 1083 IAAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWRLM 1142
I + + D E V GRI +++ ++
Sbjct: 241 I---------QRMGDRFAVE---------------------------VKGRIHFDLYPVI 264
Query: 1143 RGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLEI 1202
R + L YT+EAV E + + + + + + +G G R Y + AK+ E+
Sbjct: 265 RRTINLPTYTLEAVYEAIFGQPKEKVYAEEIAQAWETGEGLER--VARYSMEDAKVTYEL 322
Query: 1203 MNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAIS-PGNHQVASQ 1261
+ ++L+R+ G + V + VE LLR A+ +N LA + P ++A +
Sbjct: 323 GKEF--FPMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKPDERELARR 380
Query: 1262 PAMECLPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSS 1321
V EPE G + + +V LDF+SLYPS++I +N+ P N G
Sbjct: 381 RESYAGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVS---------PDTLNREGCEE 430
Query: 1322 FRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQ 1381
+ + P G + K G +P LL ++L R VK+ +K A
Sbjct: 431 YD-------------VAPQVGHKFC--KDFPGFIPSLLGDLLEERQKVKKKMK--ATIDP 473
Query: 1382 ILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNENE 1441
I ++ + RQ A+K++AN YGY R C E A+S+ GR +E I + E
Sbjct: 474 IEKKLLDYRQRAIKILANSFYGYYGYA-KARWYCKECAESVTAWGRQYIETTIREI--EE 530
Query: 1442 KWKAKVIYGDTDRYTVCI 1459
K+ KV+Y DTD + I
Sbjct: 531 KFGFKVLYADTDGFFATI 548
>pdb|1TGO|A Chain A, Thermostable B Type Dna Polymerase From Thermococcus
Gorgonarius
Length = 773
Score = 119 bits (297), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 113/438 (25%), Positives = 188/438 (42%), Gaps = 73/438 (16%)
Query: 1023 VCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESK 1082
V S E + F+K++ DPD+L+ ++ +L +R+ LG+ + + R E K
Sbjct: 183 VVSTEKEMIKRFLKVVKEKDPDVLITYNGDNFDFAYLKKRSEKLGVKFI--LGREGSEPK 240
Query: 1083 IAAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWRLM 1142
I + + D E V GRI +++ ++
Sbjct: 241 I---------QRMGDRFAVE---------------------------VKGRIHFDLYPVI 264
Query: 1143 RGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLEI 1202
R + L YT+EAV E + + + + + + +G G R Y + AK+ E+
Sbjct: 265 RRTINLPTYTLEAVYEAIFGQPKEKVYAEEIAQAWETGEGLER--VARYSMEDAKVTYEL 322
Query: 1203 MNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAIS-PGNHQVASQ 1261
+ ++L+R+ G + V + VE LLR A+ +N LA + P ++A +
Sbjct: 323 GKEF--FPMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKPDERELARR 380
Query: 1262 PAMECLPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSS 1321
V EPE G + + +V LDF+SLYPS++I +N+ P N G
Sbjct: 381 RESYAGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVS---------PDTLNREGCEE 430
Query: 1322 FRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQ 1381
+ + P G + K G +P LL ++L R VK+ +K A
Sbjct: 431 YD-------------VAPQVGHKFC--KDFPGFIPSLLGDLLEERQKVKKKMK--ATIDP 473
Query: 1382 ILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNENE 1441
I ++ + RQ A+K++AN YGY R C E A+S+ GR +E I + E
Sbjct: 474 IEKKLLDYRQRAIKILANSFYGYYGYA-KARWYCKECAESVTAWGRQYIETTIREI--EE 530
Query: 1442 KWKAKVIYGDTDRYTVCI 1459
K+ KV+Y DTD + I
Sbjct: 531 KFGFKVLYADTDGFFATI 548
>pdb|1QHT|A Chain A, Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon
Length = 775
Score = 116 bits (290), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 113/432 (26%), Positives = 184/432 (42%), Gaps = 73/432 (16%)
Query: 1023 VCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESK 1082
V S E + F++++ DPD+L+ ++ +L +R LGI + R E K
Sbjct: 183 VVSTEKEMIKRFLRVVREKDPDVLITYNGDNFDFAYLKKRCEELGIKFT--LGRDGSEPK 240
Query: 1083 IAAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWRLM 1142
I + + D E V GRI +++ ++
Sbjct: 241 I---------QRMGDRFAVE---------------------------VKGRIHFDLYPVI 264
Query: 1143 RGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLEI 1202
R + L YT+EAV E V + + + + + SG G R Y + AK+ E+
Sbjct: 265 RRTINLPTYTLEAVYEAVFGKPKEKVYAEEIAQAWESGEGLER--VARYSMEDAKVTYEL 322
Query: 1203 MNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAIS-PGNHQVASQ 1261
+ ++L+R+ G + V + VE LLR A+ +N LA + P ++A +
Sbjct: 323 GREF--FPMEAQLSRLIGQSLWDVSRSSTGNLVEWFLLRKAYKRNELAPNKPDERELARR 380
Query: 1262 PAMECLPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSS 1321
V EPE G + D +V LDF+SLYPS++I +N+
Sbjct: 381 RGGYAGGYVKEPERGLW-DNIVYLDFRSLYPSIIITHNVS-------------------- 419
Query: 1322 FRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQ 1381
PD K+ + P G + K G +P LL ++L R +K+ +K A
Sbjct: 420 --PDTLNREGCKEYDVAPEVGHKFC--KDFPGFIPSLLGDLLEERQKIKRKMK--ATVDP 473
Query: 1382 ILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNENE 1441
+ ++ + RQ A+K++AN YGY R C E A+S+ GR +E I + E
Sbjct: 474 LEKKLLDYRQRAIKILANSFYGYYGYA-KARWYCKECAESVTAWGREYIEMVIREL--EE 530
Query: 1442 KWKAKVIYGDTD 1453
K+ KV+Y DTD
Sbjct: 531 KFGFKVLYADTD 542
>pdb|2JGU|A Chain A, Crystal Structure Of Dna-directed Dna Polymerase
Length = 775
Score = 109 bits (272), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 113/436 (25%), Positives = 185/436 (42%), Gaps = 82/436 (18%)
Query: 1024 CSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESKI 1083
S E + F++I+ DPDI++ ++ +LA+RA LGI L I
Sbjct: 184 VSTEKEMIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKRAEKLGIKLT-----------I 232
Query: 1084 AAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWRLMR 1143
SE + I D + + V GRI +++ ++R
Sbjct: 233 GRDGSEPKMQRIGD---------------------------MTAVEVKGRIHFDLYHVIR 265
Query: 1144 GEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLEIM 1203
+ L YT+EAV E + + + + K + SG R +Y + AK E+
Sbjct: 266 TTINLPTYTLEAVYEAIFGKPKEKVYADEIAKAWESGENLE--RVAKYSMEDAKATYELG 323
Query: 1204 NQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNHQVASQPA 1263
+ + +L+R+ G + V + VE LLR A+ +N +A + + + +
Sbjct: 324 KEF--LPMEIQLSRLVGQPLWDVSRSSTGNLVEWFLLRKAYERNEVAPNKPSEEEYQRRL 381
Query: 1264 MECLP--LVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSS 1321
E V EPE G + + +V LD++SLYPS++I +N+
Sbjct: 382 RESYTGGFVKEPEKGLWEN-IVYLDYKSLYPSIIITHNVS-------------------- 420
Query: 1322 FRPDLHVLRDLKDELLIPPNGVMY---VPPKVRKGVLPRLLEEILSTRIMVKQAIKKLA- 1377
PD L K+ + P G + +P G +P LL +L R +K +K+
Sbjct: 421 --PDTLNLEGCKNYDIAPQVGHKFCKDIP-----GFIPSLLGHLLEERQKIKTKMKETQD 473
Query: 1378 PSQQILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFV 1437
P ++IL + RQ A+KL+AN YGY R C E A+S+ GR +E + +
Sbjct: 474 PIEKIL---LDYRQKAIKLLANSFYGYYGYA-KARWYCKECAESVTAWGRKYIE--LVWK 527
Query: 1438 NENEKWKAKVIYGDTD 1453
EK+ KV+Y DTD
Sbjct: 528 ELEEKFGFKVLYIDTD 543
>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 = 107 bits (268), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 115/439 (26%), Positives = 185/439 (42%), Gaps = 82/439 (18%)
Query: 1021 VFVCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLE 1080
V V S E + F++I+ DPDI++ ++ +LA+RA LGI L
Sbjct: 181 VEVVSSEREMIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKRAEKLGIKLT--------- 231
Query: 1081 SKIAAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWR 1140
I SE + I D + + V GRI +++
Sbjct: 232 --IGRDGSEPKMQRIGD---------------------------MTAVEVKGRIHFDLYH 262
Query: 1141 LMRGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNL 1200
++ + L YT+EAV E + + + + K + SG R +Y + AK
Sbjct: 263 VITRTINLPTYTLEAVYEAIFGKPKEKVYADEIAKAWESGENLER--VAKYSMEDAKATY 320
Query: 1201 EIMNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNHQVAS 1260
E+ + + +L+R+ G + V + VE LLR A+ +N +A + + +
Sbjct: 321 ELGKEF--LPMEIQLSRLIGQPLWDVSRSSTGNLVEWFLLRKAYERNEVAPNKPSEEEYQ 378
Query: 1261 QPAMECLP--LVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLG 1318
+ E V EPE G + D +V LDF +LYPS++I +N+
Sbjct: 379 RRLRESYTGGFVKEPEKGLW-DDIVYLDFIALYPSIIITHNVS----------------- 420
Query: 1319 VSSFRPDLHVLRDLKDELLIPPNGVMY---VPPKVRKGVLPRLLEEILSTRIMVKQAIKK 1375
PD L K+ + P G + +P G +P LL +L R +K +K+
Sbjct: 421 -----PDTLNLEGCKNYDIAPQVGHKFCKDIP-----GFIPSLLGHLLEERQKIKTKMKE 470
Query: 1376 LA-PSQQILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAI 1434
P ++IL + RQ A+KL+AN YGY R C E A+S+ GR +E +
Sbjct: 471 TQDPIEKIL---LDYRQKAIKLLANSFYGYYGYA-KARWYCKECAESVTAWGRKYIE--L 524
Query: 1435 SFVNENEKWKAKVIYGDTD 1453
+ EK+ KV+Y DTD
Sbjct: 525 VWKELEEKFGFKVLYIDTD 543
>pdb|3A2F|A Chain A, Crystal Structure Of Pyrococcus Furiosus Dna PolymerasePCNA
Monomer Mutant Complex
Length = 775
Score = 107 bits (266), Expect = 7e-23, Method: Compositional matrix adjust.
Identities = 114/439 (25%), Positives = 183/439 (41%), Gaps = 82/439 (18%)
Query: 1021 VFVCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLE 1080
V V S E F++I+ DPDI++ ++ +LA+RA LGI L
Sbjct: 181 VEVVSSEREXIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKRAEKLGIKLT--------- 231
Query: 1081 SKIAAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWR 1140
I SE + I D + + V GRI +++
Sbjct: 232 --IGRDGSEPKXQRIGD---------------------------XTAVEVKGRIHFDLYH 262
Query: 1141 LMRGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNL 1200
++ + L YT+EAV E + + + + K + SG R +Y AK
Sbjct: 263 VITRTINLPTYTLEAVYEAIFGKPKEKVYADEIAKAWESGENLER--VAKYSXEDAKATY 320
Query: 1201 EIMNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNHQVAS 1260
E+ + + +L+R+ G + V + VE LLR A+ +N +A + + +
Sbjct: 321 ELGKEF--LPXEIQLSRLVGQPLWDVSRSSTGNLVEWFLLRKAYERNEVAPNKPSEEEYQ 378
Query: 1261 QPAMECLP--LVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLG 1318
+ E V EPE G + + +V LDF++LYPS++I +N+
Sbjct: 379 RRLRESYTGGFVKEPEKGLWEN-IVYLDFRALYPSIIITHNVS----------------- 420
Query: 1319 VSSFRPDLHVLRDLKDELLIPPNGVMY---VPPKVRKGVLPRLLEEILSTRIMVKQAIKK 1375
PD L K+ + P G + +P G +P LL +L R +K K+
Sbjct: 421 -----PDTLNLEGCKNYDIAPQVGHKFCKDIP-----GFIPSLLGHLLEERQKIKTKXKE 470
Query: 1376 LA-PSQQILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAI 1434
P ++IL + RQ A+KL+AN YGY R C E A+S+ GR +E +
Sbjct: 471 TQDPIEKIL---LDYRQKAIKLLANSFYGYYGYA-KARWYCKECAESVTAWGRKYIE--L 524
Query: 1435 SFVNENEKWKAKVIYGDTD 1453
+ EK+ KV+Y DTD
Sbjct: 525 VWKELEEKFGFKVLYIDTD 543
>pdb|1WN7|A Chain A, Crystal Structure Of Archaeal Family B Dna Polymerase Mutant
Length = 774
Score = 100 bits (250), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 111/439 (25%), Positives = 183/439 (41%), Gaps = 75/439 (17%)
Query: 1023 VCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESK 1082
V S E + F++++ DPD+L+ ++ +L +R LGI + R E K
Sbjct: 183 VVSTEREMIKRFLRVVKEKDPDVLITYNGDNFDFAYLKKRCEKLGINFA--LGRDGSEPK 240
Query: 1083 IA-AGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWRL 1141
I GD + V GRI +++ +
Sbjct: 241 IQRMGDR-------------------------------------FAVEVKGRIHFDLYPV 263
Query: 1142 MRGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLE 1201
+R + L YT+EAV E V + + +T + +G R Y + AK+ E
Sbjct: 264 IRRTINLPTYTLEAVYEAVFGQPKEKVYAEEITTAWETGENLER--VARYSMEDAKVTYE 321
Query: 1202 IMNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAIS-PGNHQVAS 1260
+ + + ++L+R+ G + V + VE LLR A+ +N LA + P ++A
Sbjct: 322 LGKEF--LPMEAQLSRLIGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKPDEKELAR 379
Query: 1261 QPAMECLPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVS 1320
+ V EPE G + + +V LDF+SLYPS++I +N+ P N G
Sbjct: 380 RRQSYEGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVS---------PDTLNREGCK 429
Query: 1321 SFRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQ 1380
+ + P G + K G +P LL ++L R +K+ +K A
Sbjct: 430 EYD-------------VAPQVGHRFC--KDFPGFIPSLLGDLLEERQKIKKKMK--ATID 472
Query: 1381 QILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNEN 1440
I ++ + RQ A+K++AN +Y R C E A+S+ GR + I +
Sbjct: 473 PIERKLLDYRQRAIKILAN-SYYGYYGYARARWYCKECAESVTAWGREYITMTIKEI--E 529
Query: 1441 EKWKAKVIYGDTDRYTVCI 1459
EK+ KVIY DTD + I
Sbjct: 530 EKYGFKVIYSDTDGFFATI 548
>pdb|1WNS|A Chain A, Crystal Structure Of Family B Dna Polymerase From
Hyperthermophilic Archaeon Pyrococcus Kodakaraensis Kod1
Length = 774
Score = 100 bits (250), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 111/439 (25%), Positives = 183/439 (41%), Gaps = 75/439 (17%)
Query: 1023 VCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESK 1082
V S E + F++++ DPD+L+ ++ +L +R LGI + R E K
Sbjct: 183 VVSTEREMIKRFLRVVKEKDPDVLITYNGDNFDFAYLKKRCEKLGINFA--LGRDGSEPK 240
Query: 1083 IA-AGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWRL 1141
I GD + V GRI +++ +
Sbjct: 241 IQRMGDR-------------------------------------FAVEVKGRIHFDLYPV 263
Query: 1142 MRGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLE 1201
+R + L YT+EAV E V + + +T + +G R Y + AK+ E
Sbjct: 264 IRRTINLPTYTLEAVYEAVFGQPKEKVYAEEITTAWETGENLER--VARYSMEDAKVTYE 321
Query: 1202 IMNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAIS-PGNHQVAS 1260
+ + + ++L+R+ G + V + VE LLR A+ +N LA + P ++A
Sbjct: 322 LGKEF--LPMEAQLSRLIGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKPDEKELAR 379
Query: 1261 QPAMECLPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVS 1320
+ V EPE G + + +V LDF+SLYPS++I +N+
Sbjct: 380 RRQSYEGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVS------------------- 419
Query: 1321 SFRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQ 1380
PD K+ + P G + K G +P LL ++L R +K+ +K A
Sbjct: 420 ---PDTLNREGCKEYDVAPQVGHRFC--KDFPGFIPSLLGDLLEERQKIKKKMK--ATID 472
Query: 1381 QILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNEN 1440
I ++ + RQ A+K++AN +Y R C E A+S+ GR + I +
Sbjct: 473 PIERKLLDYRQRAIKILAN-SYYGYYGYARARWYCKECAESVTAWGREYITMTIKEI--E 529
Query: 1441 EKWKAKVIYGDTDRYTVCI 1459
EK+ KVIY DTD + I
Sbjct: 530 EKYGFKVIYSDTDGFFATI 548
>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 = 99.4 bits (246), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 109/438 (24%), Positives = 184/438 (42%), Gaps = 75/438 (17%)
Query: 1024 CSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESKI 1083
S E + F+K++ DPD+L+ ++ +L +R+ LG+ + + R E KI
Sbjct: 184 VSTEKEMIKRFLKVIQEKDPDVLITYNGDNFDFAYLKKRSEMLGVKFI--LGRDGSEPKI 241
Query: 1084 A-AGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWRLM 1142
GD + V GRI +++ ++
Sbjct: 242 QRMGDR-------------------------------------FAVEVKGRIHFDLYPVI 264
Query: 1143 RGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLEI 1202
R + L YT+E V E V + + + + +ASG G R Y + AK E+
Sbjct: 265 RRTINLPTYTLETVYEPVFGQPAEKVYAEEIAEAWASGEGLE--RVARYSMEDAKATYEL 322
Query: 1203 MNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAIS-PGNHQVASQ 1261
+ ++L+R+ G + V + VE LLR A+ +N +A + P ++A +
Sbjct: 323 GKEF--FPMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKAYERNDVAPNKPDERELARR 380
Query: 1262 PAMECLPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSS 1321
V EPE G + + +V LD++SLYPS++I +N+ P N G
Sbjct: 381 TESYAGGYVKEPEKGLWEN-IVYLDYKSLYPSIIITHNVS---------PDTLNREGCRE 430
Query: 1322 FRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQ 1381
+ + P G + K G +P LL ++L R VK+ +K A
Sbjct: 431 YD-------------VAPQVGHRFC--KDFPGFIPSLLGDLLEERQKVKKKMK--ATVDP 473
Query: 1382 ILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNENE 1441
I ++ + RQ A+K++AN A + R C E A+S+ GR +E + + E
Sbjct: 474 IERKLLDYRQRAIKILANSY-YGYYAYANARWYCRECAESVTAWGRQYIETTMREI--EE 530
Query: 1442 KWKAKVIYGDTDRYTVCI 1459
K+ KV+Y DTD + I
Sbjct: 531 KFGFKVLYADTDGFFATI 548
>pdb|1QQC|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase D.Tok
Length = 773
Score = 97.1 bits (240), Expect = 6e-20, Method: Compositional matrix adjust.
Identities = 108/438 (24%), Positives = 183/438 (41%), Gaps = 75/438 (17%)
Query: 1024 CSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESKI 1083
S E + F+K++ DPD+L+ ++ +L +R+ LG+ + + R E KI
Sbjct: 184 VSTEKEMIKRFLKVIQEKDPDVLITYNGDNFDFAYLKKRSEMLGVKFI--LGRDGSEPKI 241
Query: 1084 A-AGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWRLM 1142
GD + V GRI +++ ++
Sbjct: 242 QRMGDR-------------------------------------FAVEVKGRIHFDLYPVI 264
Query: 1143 RGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLEI 1202
R + L YT+E V E V + + + + + SG G R Y + AK E+
Sbjct: 265 RRTINLPTYTLETVYEPVFGQPKEKVYAEEIARAWESGEGLE--RVARYSMEDAKATYEL 322
Query: 1203 MNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAIS-PGNHQVASQ 1261
+ ++L+R+ G + V + VE LLR A+ +N +A + P ++A +
Sbjct: 323 GKEF--FPMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKAYERNDVAPNKPDERELARR 380
Query: 1262 PAMECLPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSS 1321
V EPE G + + +V LD++SLYPS++I +N+ P N G
Sbjct: 381 TESYAGGYVKEPEKGLWEN-IVYLDYKSLYPSIIITHNVS---------PDTLNREGCRE 430
Query: 1322 FRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQ 1381
+ + P G + K G +P LL ++L R VK+ +K A
Sbjct: 431 YD-------------VAPQVGHRFC--KDFPGFIPSLLGDLLEERQKVKKKMK--ATVDP 473
Query: 1382 ILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNENE 1441
I ++ + RQ A+K++AN A + R C E A+S+ GR +E + + E
Sbjct: 474 IERKLLDYRQRAIKILANSY-YGYYAYANARWYCRECAESVTAWGRQYIETTMREI--EE 530
Query: 1442 KWKAKVIYGDTDRYTVCI 1459
K+ KV+Y DTD + I
Sbjct: 531 KFGFKVLYADTDGFFATI 548
>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 = 91.3 bits (225), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 66/215 (30%), Positives = 103/215 (47%), Gaps = 47/215 (21%)
Query: 1270 VMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSSFRPD-LHV 1328
V++P SGF+ +PVVV DF SLYPS++ A+NLCF T S R D +
Sbjct: 659 VLDPTSGFHVNPVVVFDFASLYPSIIQAHNLCFSTL---------------SLRADAVAH 703
Query: 1329 LRDLKDELLIPPNG--VMYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQILHRI 1386
L KD L I G + +V VR+ +L LL + L+ R ++ I + +P + +L
Sbjct: 704 LEAGKDYLEIEVGGRRLFFVKAHVRESLLSILLRDWLAMRKQIRSRIPQSSPEEAVL--- 760
Query: 1387 FNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNENEKWKA- 1445
+ +Q A+K++ N YG+T G +PC +A ++ GR L +V + +W A
Sbjct: 761 LDKQQAAIKVVCNSVYGFTGVQ-HGLLPCLHVAATVTTIGREMLLATREYV--HARWAAF 817
Query: 1446 ---------------------KVIYGDTDR-YTVC 1458
++IYGDTD + +C
Sbjct: 818 EQLLADFPEAADMRAPGPYSMRIIYGDTDSIFVLC 852
Score = 66.2 bits (160), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 59/251 (23%), Positives = 113/251 (45%), Gaps = 44/251 (17%)
Query: 1007 ESHQRSLV--GIPDCKVFVCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAA 1064
ESH L G+P V E + F+ ++ + P+ + G++I FL +
Sbjct: 379 ESHLNELAARGLPTPVVLEFDSEFEMLLAFMTLVKQYGPEFVTGYNIINFDWPFLLAK-- 436
Query: 1065 HLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTH 1124
L DI + PL+ G ++ RG+ + G++H
Sbjct: 437 ------LTDIYKVPLD-----GYGRMNGRGVFRVW-------------------DIGQSH 466
Query: 1125 ---ASGLHVGGRIVLNVWRLMRGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGP 1181
S + V G + ++++ ++ ++KL+ Y + AVAE VL+ K + +R + ++A+GP
Sbjct: 467 FQKRSKIKVNGMVNIDMYGIITDKIKLSSYKLNAVAEAVLKDKKKDLSYRDIPAYYATGP 526
Query: 1182 ---GRARYRCVEYVVGRAKLNLEIMNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESM 1238
G C++ + +L + + L++ S +AR+ GI+ + G Q RV +
Sbjct: 527 AQRGVIGEYCIQDSLLVGQLFFKFLPHLEL----SAVARLAGINITRTIYDGQQIRVFTC 582
Query: 1239 LLRLAHTQNYL 1249
LLRLA + ++
Sbjct: 583 LLRLADQKGFI 593
>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 = 90.5 bits (223), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 108/435 (24%), Positives = 186/435 (42%), Gaps = 75/435 (17%)
Query: 1021 VFVCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLE 1080
V V S E + +K++ DPD+++ ++ + +L +RA LGI L PL
Sbjct: 203 VEVVSSEREMIKRLVKVIREKDPDVIITYNGDNFAFPYLLKRAEKLGIKL-------PL- 254
Query: 1081 SKIAAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWR 1140
+SE + + D++ E + GRI +++
Sbjct: 255 ---GRDNSEPKMQRMGDSLAVE---------------------------IKGRIHFDLFP 284
Query: 1141 LMRGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNL 1200
++R + L YT+EAV E + + + + + + +G G R +Y + AK+
Sbjct: 285 VIRRTINLPTYTLEAVYEAIFGKSKEKVYAHEIAEAWETGKGLER--VAKYSMEDAKVTF 342
Query: 1201 EIMNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNHQVAS 1260
E+ + ++LAR+ G + V + VE LLR A+ +N LA + + +
Sbjct: 343 ELGKEF--FPMEAQLARLVGQPVWDVSRSSTGNLVEWFLLRKAYERNELAPNKPDEREYE 400
Query: 1261 QPAMECLP--LVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLG 1318
+ E V EPE G + + +V LDF+SLYPS++I +N+
Sbjct: 401 RRLRESYEGGYVKEPEKGLW-EGIVSLDFRSLYPSIIITHNVS----------------- 442
Query: 1319 VSSFRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAP 1378
PD + K+ + P G + K G +P LL +L R +K+ +K+
Sbjct: 443 -----PDTLNRENCKEYDVAPQVGHRFC--KDFPGFIPSLLGNLLEERQKIKKRMKE--S 493
Query: 1379 SQQILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVN 1438
+ ++ + RQ A+K++AN YGY R C E A+S+ GR ++
Sbjct: 494 KDPVEKKLLDYRQRAIKILANSYYGYYGYA-KARWYCKECAESVTAWGRQYID---LVRR 549
Query: 1439 ENEKWKAKVIYGDTD 1453
E E KV+Y DTD
Sbjct: 550 ELESRGFKVLYIDTD 564
>pdb|4FM2|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase (Triple Mutant)
Bound To A Dsdna, In Edition Mode
Length = 793
Score = 89.7 bits (221), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 107/435 (24%), Positives = 187/435 (42%), Gaps = 75/435 (17%)
Query: 1021 VFVCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLE 1080
V V S E + +K++ DPD+++ ++ + +L +RA LGI L PL
Sbjct: 203 VEVVSSEREMIKRLVKVIREKDPDVIITYNGDNFAFPYLLKRAEKLGIKL-------PL- 254
Query: 1081 SKIAAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWR 1140
+SE + + D++ + + GRI +++
Sbjct: 255 ---GRDNSEPKMQRMGDSL---------------------------AVAIKGRIHFDLFP 284
Query: 1141 LMRGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNL 1200
++R + L YT+EAV E + + + + + + +G G R +Y + AK+
Sbjct: 285 VIRRTINLPTYTLEAVYEAIFGKSKEKVYAHEIAEAWETGKGLER--VAKYSMEDAKVTF 342
Query: 1201 EIMNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNHQVAS 1260
E+ + ++LAR+ G ++V + VE LLR A+ +N LA + + +
Sbjct: 343 ELGKEF--FPMEAQLARLVGQPVWAVSRSSTGNLVEWFLLRKAYERNELAPNKPDEREYE 400
Query: 1261 QPAMECLP--LVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLG 1318
+ E V EPE G + + +V LDF+SLYPS++I +N+
Sbjct: 401 RRLRESYEGGYVKEPEKGLW-EGIVSLDFRSLYPSIIITHNVS----------------- 442
Query: 1319 VSSFRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAP 1378
PD + K+ + P G + K G +P LL +L R +K+ +K+
Sbjct: 443 -----PDTLNRENCKEYDVAPQVGHRFC--KDFPGFIPSLLGNLLEERQKIKKRMKE--S 493
Query: 1379 SQQILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVN 1438
+ ++ + RQ A+K++AN YGY R C E A+S+ GR ++
Sbjct: 494 KDPVEKKLLDYRQRAIKILANSYYGYYGYA-KARWYCKECAESVTAWGRQYID---LVRR 549
Query: 1439 ENEKWKAKVIYGDTD 1453
E E KV+Y DTD
Sbjct: 550 ELESRGFKVLYIDTD 564
>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 = 76.3 bits (186), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 64/187 (34%), Positives = 88/187 (47%), Gaps = 37/187 (19%)
Query: 1269 LVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSSFRPDLHV 1328
LV EPE G + + V+V+DF SLYPS++ +N+CF T V + D+
Sbjct: 499 LVFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTT--------------VDRNKEDI-- 542
Query: 1329 LRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIK-KLAPSQQILHRIF 1387
DEL P P +V +GVLPRLL ++ R VK+ +K + P +++ I
Sbjct: 543 -----DELPSVP------PSEVDQGVLPRLLANLVDRRREVKKVMKTETDPHKRVQCDI- 590
Query: 1388 NARQLALKLIANVTYGYTAAGF-SGRMPCAELADSIVQCGRSTLEKAISFVNENEKWKAK 1446
RQ ALKL AN YG G+ + R LA + GR L E
Sbjct: 591 --RQQALKLTANSMYG--CLGYVNSRFYAKPLAMLVTNKGREILMNTRQLA---ESMNLL 643
Query: 1447 VIYGDTD 1453
V+YGDTD
Sbjct: 644 VVYGDTD 650
>pdb|4B08|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha,
Selenomethionine Protein
Length = 910
Score = 75.5 bits (184), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 64/187 (34%), Positives = 86/187 (45%), Gaps = 37/187 (19%)
Query: 1269 LVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSSFRPDLHV 1328
LV EPE G + + V+V DF SLYPS++ +N+CF T V + D+
Sbjct: 499 LVFEPEKGLHKNYVLVXDFNSLYPSIIQEFNICFTT--------------VDRNKEDI-- 542
Query: 1329 LRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIK-KLAPSQQILHRIF 1387
DEL P P +V +GVLPRLL ++ R VK+ K + P +++ I
Sbjct: 543 -----DELPSVP------PSEVDQGVLPRLLANLVDRRREVKKVXKTETDPHKRVQCDI- 590
Query: 1388 NARQLALKLIANVTYGYTAAGF-SGRMPCAELADSIVQCGRSTLEKAISFVNENEKWKAK 1446
RQ ALKL AN YG G+ + R LA + GR L E
Sbjct: 591 --RQQALKLTANSXYG--CLGYVNSRFYAKPLAXLVTNKGREILXNTRQLA---ESXNLL 643
Query: 1447 VIYGDTD 1453
V+YGDTD
Sbjct: 644 VVYGDTD 650
>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 = 74.7 bits (182), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 63/187 (33%), Positives = 88/187 (47%), Gaps = 37/187 (19%)
Query: 1269 LVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSSFRPDLHV 1328
LV EPE G + + V+V+DF SLYPS++ +N+CF T V + D+
Sbjct: 499 LVFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTT--------------VDRNKEDI-- 542
Query: 1329 LRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIK-KLAPSQQILHRIF 1387
DEL P P +V +GVLPRLL ++ R VK+ +K + P +++ I
Sbjct: 543 -----DELPSVP------PSEVDQGVLPRLLANLVDRRREVKKVMKTETDPHKRVQCDI- 590
Query: 1388 NARQLALKLIANVTYGYTAAGF-SGRMPCAELADSIVQCGRSTLEKAISFVNENEKWKAK 1446
RQ ALKL AN YG G+ + R LA + GR L E
Sbjct: 591 --RQQALKLTANSMYG--CLGYVNSRFYAKPLAMLVTNKGREILMNTRQLA---ESMNLL 643
Query: 1447 VIYGDTD 1453
V+YGDT+
Sbjct: 644 VVYGDTN 650
>pdb|1S5J|A Chain A, Insight In Dna Replication: The Crystal Structure Of Dna
Polymerase B1 From The Archaeon Sulfolobus Solfataricus
Length = 847
Score = 44.7 bits (104), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 45/189 (23%), Positives = 83/189 (43%), Gaps = 33/189 (17%)
Query: 1269 LVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSSFRPDLHV 1328
+V++P +G + + + VLDF SLYPS++ +NL + T D+
Sbjct: 463 VVIDPPAGIFFN-ITVLDFASLYPSIIRTWNLSYETV-------------------DIQQ 502
Query: 1329 LR---DLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQILHR 1385
+ ++KDE V+++ R G+ + + R+ + + K + +
Sbjct: 503 CKKPYEVKDE----TGEVLHIVCMDRPGITAVITGLLRDFRVKIYKKKAKNPNNSEEQKL 558
Query: 1386 IFNARQLALKLIANVTYG-YTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNENEKWK 1444
+++ Q A+K+ N TYG + A F P +A+S+ GR + + E
Sbjct: 559 LYDVVQRAMKVFINATYGVFGAETFPLYAP--RVAESVTALGRYVITSTVKKAREE---G 613
Query: 1445 AKVIYGDTD 1453
V+YGDTD
Sbjct: 614 LTVLYGDTD 622
>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 = 35.4 bits (80), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 49/191 (25%), Positives = 71/191 (37%), Gaps = 42/191 (21%)
Query: 1270 VMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCL-GKILPSKENTLGVSSFRPDLHV 1328
VM+ G Y D V+VLD++SLYPS++ + + + G P E++
Sbjct: 407 VMDSRPGLY-DSVLVLDYKSLYPSIIRTFLIDPVGLVEGMAQPDPEHST----------- 454
Query: 1329 LRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQILHRIFN 1388
G + K LP ++ I R K+ K P Q
Sbjct: 455 ------------EGFLDAWFSREKHCLPEIVTNIWHGRDEAKRQGNK--PLSQ------- 493
Query: 1389 ARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNENEKWKAKVI 1448
ALK+I N YG + R LA SI G + + + + E VI
Sbjct: 494 ----ALKIIMNAFYGVLGTT-ACRFFDPRLASSITMRGHQIMRQTKALI---EAQGYDVI 545
Query: 1449 YGDTDRYTVCI 1459
YGDTD V +
Sbjct: 546 YGDTDSTFVWL 556
>pdb|1Q8I|A Chain A, Crystal Structure Of Escherichia Coli Dna Polymerase Ii
Length = 783
Score = 35.0 bits (79), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 49/191 (25%), Positives = 71/191 (37%), Gaps = 42/191 (21%)
Query: 1270 VMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCL-GKILPSKENTLGVSSFRPDLHV 1328
VM+ G Y D V+VLD++SLYPS++ + + + G P E++
Sbjct: 404 VMDSRPGLY-DSVLVLDYKSLYPSIVRTFLIDPVGLVEGMAQPDPEHST----------- 451
Query: 1329 LRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQILHRIFN 1388
G + K LP ++ I R K+ K P Q
Sbjct: 452 ------------EGFLDAWFSREKHCLPEIVTNIWHGRDEAKRQGNK--PLSQ------- 490
Query: 1389 ARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNENEKWKAKVI 1448
ALK+I N YG + R LA SI G + + + + E VI
Sbjct: 491 ----ALKIIMNAFYGVLGTT-ACRFFDPRLASSITMRGHQIMRQTKALI---EAQGYDVI 542
Query: 1449 YGDTDRYTVCI 1459
YGDTD V +
Sbjct: 543 YGDTDSTFVWL 553
>pdb|1VMD|A Chain A, Crystal Structure Of Methylglyoxal Synthase (Tm1185) From
Thermotoga Maritima At 2.06 A Resolution
pdb|1VMD|B Chain B, Crystal Structure Of Methylglyoxal Synthase (Tm1185) From
Thermotoga Maritima At 2.06 A Resolution
Length = 178
Score = 34.7 bits (78), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 38/139 (27%), Positives = 61/139 (43%), Gaps = 28/139 (20%)
Query: 403 LSALAPQGLVHQEKISLMPSKGKDTCPELPFGGEIHSSEMVGAPGQKEPLIFGID--IPQ 460
L A G + QEK+ L + K P GG+ M+ A G+ + LIF D PQ
Sbjct: 58 LYATGTTGALLQEKLGLKVHRLKSG----PLGGDQQIGAMI-AEGKIDVLIFFWDPLEPQ 112
Query: 461 ATDTEALGLLKW-------LATSQAAEDLNSDDELLHETILSPLLPETTIDKVLEKANTD 513
A D + L++ +A +++ D I SPL+ + V EK D
Sbjct: 113 AHDVDVKALIRIATVYNIPVAITRSTADF---------LISSPLM-----NDVYEKIQID 158
Query: 514 YERESQKECQDILDSIEDE 532
YE E ++ + +++ E+E
Sbjct: 159 YEEELERRIRKVVEGEEEE 177
>pdb|1PGV|A Chain A, Structural Genomics Of Caenorhabditis Elegans:
Tropomodulin C-Terminal Domain
Length = 197
Score = 30.8 bits (68), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 34/65 (52%)
Query: 454 FGIDIPQATDTEALGLLKWLATSQAAEDLNSDDELLHETILSPLLPETTIDKVLEKANTD 513
F + +D+EA GL++ + TS + LN + L +L+ LL T + + + + D
Sbjct: 75 FSLANTAISDSEARGLIELIETSPSLRVLNVESNFLTPELLARLLRSTLVTQSIVEFKAD 134
Query: 514 YERES 518
+R+S
Sbjct: 135 NQRQS 139
>pdb|2AHN|A Chain A, High Resolution Structure Of A Cherry Allergen Pru Av 2
Length = 222
Score = 30.4 bits (67), Expect = 8.2, Method: Composition-based stats.
Identities = 16/43 (37%), Positives = 28/43 (65%), Gaps = 3/43 (6%)
Query: 620 SLPFSVSEQFNK-DIETVSC--NISSLCVTEVKDHGATGSLVG 659
+LP SV+ Q D +T SC N++++C +E++ G+ GS+V
Sbjct: 113 NLPMSVTPQGGTGDCKTASCPANVNAVCPSELQKKGSDGSVVA 155
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
0.318 0.135 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 43,830,375
Number of Sequences: 62578
Number of extensions: 1847920
Number of successful extensions: 3821
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 3714
Number of HSP's gapped (non-prelim): 58
length of query: 1459
length of database: 14,973,337
effective HSP length: 111
effective length of query: 1348
effective length of database: 8,027,179
effective search space: 10820637292
effective search space used: 10820637292
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.9 bits)