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= psy5925
(696 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 = 118 bits (296), Expect = 9e-27, Method: Compositional matrix adjust.
Identities = 96/339 (28%), Positives = 161/339 (47%), Gaps = 46/339 (13%)
Query: 353 SNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLN----------LNQEL 402
+ E+E+ S + + + DPD++IGY YLL R L +N + QE+
Sbjct: 311 ATEEEMLSNWRNFIIKVDPDVIIGYNTTNFDIPYLLNRAKALKVNDFPYFGRLKTVKQEI 370
Query: 403 SRITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPL 462
K +R E KN + GR+ ++L + ++ E L+SYT + H L E+
Sbjct: 371 KESVFSSKAYGTR-ETKNVNID--GRLQLDLLQFIQREYKLRSYTLNAVSAHFLGEQKED 427
Query: 463 HSWKLLTCWW----EHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQF 518
+ +++ E R L + + YL +RL+E+L + +EMAR+ G+ F
Sbjct: 428 VHYSIISDLQNGDSETRRRLAVYCLKDAYLP-----LRLMEKLMALVNYTEMARVTGVPF 482
Query: 519 YEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPLILEPESRLYTDPII 578
+L+RG Q +V S + R + V P+++ +A E +I EP Y PI
Sbjct: 483 SYLLARGQQIKVVSQLFR--KCLEIDTVIPNMQSQASDDQYEGATVI-EPIRGYYDVPIA 539
Query: 579 VLDFQSLYPSVIIAYNYCFSTCLGR--VEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTI 636
LDF SLYPS+++A+N C++T + VE L + K+ ++ I
Sbjct: 540 TLDFNSLYPSIMMAHNLCYTTLCNKATVERLNL-------------------KIDEDYVI 580
Query: 637 SPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMKEYK 675
+P+G FV R GILP +L E++ R K+ +++ K
Sbjct: 581 TPNGDYFVTTKRRRGILPIILDELISARKRAKKDLRDEK 619
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 15/27 (55%), Positives = 21/27 (77%)
Query: 111 YTDPIIVLDFQSLYPSVIIAYNYCFST 137
Y PI LDF SLYPS+++A+N C++T
Sbjct: 534 YDVPIATLDFNSLYPSIMMAHNLCYTT 560
>pdb|1WNS|A Chain A, Crystal Structure Of Family B Dna Polymerase From
Hyperthermophilic Archaeon Pyrococcus Kodakaraensis Kod1
Length = 774
Score = 89.7 bits (221), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 84/322 (26%), Positives = 148/322 (45%), Gaps = 38/322 (11%)
Query: 352 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKR 411
VS E+E+ F+ V++ DPD+LI Y + + YL +R LG+N L R K
Sbjct: 184 VSTEREMIKRFLRVVKEKDPDVLITYNGDNFDFAYLKKRCEKLGINFA--LGRDGSEPKI 241
Query: 412 NSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCW 471
D +++ GRI +L+ ++R +NL +YT E + V + + +T
Sbjct: 242 QRMGDRF---AVEVKGRIHFDLYPVIRRTINLPTYTLEAVYEAVFGQPKEKVYAEEITTA 298
Query: 472 WEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQFRVE 531
WE +L + V Y + + + + +F+ ++++RL G ++V + VE
Sbjct: 299 WETGENLER---VARYSMEDAKVTYELGK-EFLPMEAQLSRLIGQSLWDVSRSSTGNLVE 354
Query: 532 SIMLRLSRLNNFVAVS-PSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQSLYPSVI 590
+LR + N +A + P K+ A R + EPE L+ + I+ LDF+SLYPS+I
Sbjct: 355 WFLLRKAYERNELAPNKPDEKELARRRQSYEGGYVKEPERGLWEN-IVYLDFRSLYPSII 413
Query: 591 IAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTISPSGVAFVDKSIRC 650
I +N T L R GC + +V+ + + ++
Sbjct: 414 ITHNVSPDT-LNRE-----------GCKEYDVAPQVGHRFCKDFP--------------- 446
Query: 651 GILPKMLQEILDTRLMVKQSMK 672
G +P +L ++L+ R +K+ MK
Sbjct: 447 GFIPSLLGDLLEERQKIKKKMK 468
Score = 31.2 bits (69), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 115 IIVLDFQSLYPSVIIAYNYCFST 137
I+ LDF+SLYPS+II +N T
Sbjct: 400 IVYLDFRSLYPSIIITHNVSPDT 422
>pdb|1WN7|A Chain A, Crystal Structure Of Archaeal Family B Dna Polymerase
Mutant
Length = 774
Score = 89.7 bits (221), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 84/322 (26%), Positives = 148/322 (45%), Gaps = 38/322 (11%)
Query: 352 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKR 411
VS E+E+ F+ V++ DPD+LI Y + + YL +R LG+N L R K
Sbjct: 184 VSTEREMIKRFLRVVKEKDPDVLITYNGDNFDFAYLKKRCEKLGINFA--LGRDGSEPKI 241
Query: 412 NSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCW 471
D +++ GRI +L+ ++R +NL +YT E + V + + +T
Sbjct: 242 QRMGDRF---AVEVKGRIHFDLYPVIRRTINLPTYTLEAVYEAVFGQPKEKVYAEEITTA 298
Query: 472 WEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQFRVE 531
WE +L + V Y + + + + +F+ ++++RL G ++V + VE
Sbjct: 299 WETGENLER---VARYSMEDAKVTYELGK-EFLPMEAQLSRLIGQSLWDVSRSSTGNLVE 354
Query: 532 SIMLRLSRLNNFVAVS-PSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQSLYPSVI 590
+LR + N +A + P K+ A R + EPE L+ + I+ LDF+SLYPS+I
Sbjct: 355 WFLLRKAYERNELAPNKPDEKELARRRQSYEGGYVKEPERGLWEN-IVYLDFRSLYPSII 413
Query: 591 IAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTISPSGVAFVDKSIRC 650
I +N T L R GC + +V+ + + ++
Sbjct: 414 ITHNVSPDT-LNRE-----------GCKEYDVAPQVGHRFCKDFP--------------- 446
Query: 651 GILPKMLQEILDTRLMVKQSMK 672
G +P +L ++L+ R +K+ MK
Sbjct: 447 GFIPSLLGDLLEERQKIKKKMK 468
Score = 31.2 bits (69), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 115 IIVLDFQSLYPSVIIAYNYCFST 137
I+ LDF+SLYPS+II +N T
Sbjct: 400 IVYLDFRSLYPSIIITHNVSPDT 422
>pdb|1QHT|A Chain A, Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon
Length = 775
Score = 88.6 bits (218), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 84/322 (26%), Positives = 142/322 (44%), Gaps = 38/322 (11%)
Query: 352 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKR 411
VS EKE+ F+ VR+ DPD+LI Y + + YL +R LG+ L R K
Sbjct: 184 VSTEKEMIKRFLRVVREKDPDVLITYNGDNFDFAYLKKRCEELGIKFT--LGRDGSEPKI 241
Query: 412 NSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCW 471
D +++ GRI +L+ ++R +NL +YT E + V + + +
Sbjct: 242 QRMGDRF---AVEVKGRIHFDLYPVIRRTINLPTYTLEAVYEAVFGKPKEKVYAEEIAQA 298
Query: 472 WEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQFRVE 531
WE L + V Y + + + + +F ++++RL G ++V + VE
Sbjct: 299 WESGEGLER---VARYSMEDAKVTYELGR-EFFPMEAQLSRLIGQSLWDVSRSSTGNLVE 354
Query: 532 SIMLRLS-RLNNFVAVSPSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQSLYPSVI 590
+LR + + N P ++ A R + + EPE L+ D I+ LDF+SLYPS+I
Sbjct: 355 WFLLRKAYKRNELAPNKPDERELARRRGGYAGGYVKEPERGLW-DNIVYLDFRSLYPSII 413
Query: 591 IAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTISPSGVAFVDKSIRC 650
I +N T L R GC + +V+ K ++
Sbjct: 414 ITHNVSPDT-LNRE-----------GCKEYDVAPEVGHKFCKDFP--------------- 446
Query: 651 GILPKMLQEILDTRLMVKQSMK 672
G +P +L ++L+ R +K+ MK
Sbjct: 447 GFIPSLLGDLLEERQKIKRKMK 468
Score = 32.7 bits (73), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 13/20 (65%), Positives = 17/20 (85%)
Query: 113 DPIIVLDFQSLYPSVIIAYN 132
D I+ LDF+SLYPS+II +N
Sbjct: 398 DNIVYLDFRSLYPSIIITHN 417
>pdb|2VWK|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography. V93q Polymerase Variant
Length = 773
Score = 86.7 bits (213), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 81/326 (24%), Positives = 149/326 (45%), Gaps = 46/326 (14%)
Query: 352 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKR 411
VS EKE+ F++ V++ DPD+LI Y + ++ YL +R LG+ + R
Sbjct: 184 VSTEKEMIKRFLKVVKEKDPDVLITYNGDNFAFAYLKKRSEKLGVKF---------ILGR 234
Query: 412 NSSRDEVKNT----QLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKL 467
S +++ +++ GRI +L+ ++R +NL +YT E + + + +
Sbjct: 235 EGSEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTINLPTYTLEAVYEAIFGQPKEKVYAEE 294
Query: 468 LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQ 527
+ WE L + V Y + + + + +F ++++RL G ++V +
Sbjct: 295 IAQAWETGEGLER---VARYSMEDAKVTYELGK-EFFPMEAQLSRLVGQSLWDVSRSSTG 350
Query: 528 FRVESIMLRLSRLNNFVAVS-PSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQSLY 586
VE +LR + N +A + P ++ A R + + EPE L+ + I+ LDF+SLY
Sbjct: 351 NLVEWFLLRKAYERNELAPNKPDERELARRRESYAGGYVKEPERGLWEN-IVYLDFRSLY 409
Query: 587 PSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTISPSGVAFVDK 646
PS+II +N T L R GC + +V+ + K ++
Sbjct: 410 PSIIITHNVSPDT-LNRE-----------GCEEYDVAPQVGHKFCKDFP----------- 446
Query: 647 SIRCGILPKMLQEILDTRLMVKQSMK 672
G +P +L ++L+ R VK+ MK
Sbjct: 447 ----GFIPSLLGDLLEERQKVKKKMK 468
Score = 31.2 bits (69), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 12/18 (66%), Positives = 16/18 (88%)
Query: 115 IIVLDFQSLYPSVIIAYN 132
I+ LDF+SLYPS+II +N
Sbjct: 400 IVYLDFRSLYPSIIITHN 417
>pdb|2XHB|A Chain A, Crystal Structure Of Dna Polymerase From Thermococcus
Gorgonarius In Complex With Hypoxanthine-Containing Dna
Length = 773
Score = 86.7 bits (213), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 81/326 (24%), Positives = 149/326 (45%), Gaps = 46/326 (14%)
Query: 352 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKR 411
VS EKE+ F++ V++ DPD+LI Y + ++ YL +R LG+ + R
Sbjct: 184 VSTEKEMIKRFLKVVKEKDPDVLITYNGDNFAFAYLKKRSEKLGVKF---------ILGR 234
Query: 412 NSSRDEVKNT----QLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKL 467
S +++ +++ GRI +L+ ++R +NL +YT E + + + +
Sbjct: 235 EGSEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTINLPTYTLEAVYEAIFGQPKEKVYAEE 294
Query: 468 LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQ 527
+ WE L + V Y + + + + +F ++++RL G ++V +
Sbjct: 295 IAQAWETGEGLER---VARYSMEDAKVTYELGK-EFFPMEAQLSRLVGQSLWDVSRSSTG 350
Query: 528 FRVESIMLRLSRLNNFVAVS-PSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQSLY 586
VE +LR + N +A + P ++ A R + + EPE L+ + I+ LDF+SLY
Sbjct: 351 NLVEWFLLRKAYERNELAPNKPDERELARRRESYAGGYVKEPERGLWEN-IVYLDFRSLY 409
Query: 587 PSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTISPSGVAFVDK 646
PS+II +N T L R GC + +V+ + K ++
Sbjct: 410 PSIIITHNVSPDT-LNRE-----------GCEEYDVAPQVGHKFCKDFP----------- 446
Query: 647 SIRCGILPKMLQEILDTRLMVKQSMK 672
G +P +L ++L+ R VK+ MK
Sbjct: 447 ----GFIPSLLGDLLEERQKVKKKMK 468
Score = 31.2 bits (69), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 12/18 (66%), Positives = 16/18 (88%)
Query: 115 IIVLDFQSLYPSVIIAYN 132
I+ LDF+SLYPS+II +N
Sbjct: 400 IVYLDFRSLYPSIIITHN 417
>pdb|2VWJ|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography
Length = 773
Score = 86.7 bits (213), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 81/326 (24%), Positives = 149/326 (45%), Gaps = 46/326 (14%)
Query: 352 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKR 411
VS EKE+ F++ V++ DPD+LI Y + ++ YL +R LG+ + R
Sbjct: 184 VSTEKEMIKRFLKVVKEKDPDVLITYNGDNFAFAYLKKRSEKLGVKF---------ILGR 234
Query: 412 NSSRDEVKNT----QLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKL 467
S +++ +++ GRI +L+ ++R +NL +YT E + + + +
Sbjct: 235 EGSEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTINLPTYTLEAVYEAIFGQPKEKVYAEE 294
Query: 468 LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQ 527
+ WE L + V Y + + + + +F ++++RL G ++V +
Sbjct: 295 IAQAWETGEGLER---VARYSMEDAKVTYELGK-EFFPMEAQLSRLVGQSLWDVSRSSTG 350
Query: 528 FRVESIMLRLSRLNNFVAVS-PSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQSLY 586
VE +LR + N +A + P ++ A R + + EPE L+ + I+ LDF+SLY
Sbjct: 351 NLVEWFLLRKAYERNELAPNKPDERELARRRESYAGGYVKEPERGLWEN-IVYLDFRSLY 409
Query: 587 PSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTISPSGVAFVDK 646
PS+II +N T L R GC + +V+ + K ++
Sbjct: 410 PSIIITHNVSPDT-LNRE-----------GCEEYDVAPQVGHKFCKDFP----------- 446
Query: 647 SIRCGILPKMLQEILDTRLMVKQSMK 672
G +P +L ++L+ R VK+ MK
Sbjct: 447 ----GFIPSLLGDLLEERQKVKKKMK 468
Score = 31.2 bits (69), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 12/18 (66%), Positives = 16/18 (88%)
Query: 115 IIVLDFQSLYPSVIIAYN 132
I+ LDF+SLYPS+II +N
Sbjct: 400 IVYLDFRSLYPSIIITHN 417
>pdb|1TGO|A Chain A, Thermostable B Type Dna Polymerase From Thermococcus
Gorgonarius
Length = 773
Score = 85.9 bits (211), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 84/326 (25%), Positives = 151/326 (46%), Gaps = 46/326 (14%)
Query: 352 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLN--LNQELS--RITE 407
VS EKE+ F++ V++ DPD+LI Y + + YL +R LG+ L +E S +I
Sbjct: 184 VSTEKEMIKRFLKVVKEKDPDVLITYNGDNFDFAYLKKRSEKLGVKFILGREGSEPKIQR 243
Query: 408 VEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKL 467
+ R + +++ GRI +L+ ++R +NL +YT E + + + +
Sbjct: 244 MGDRFA---------VEVKGRIHFDLYPVIRRTINLPTYTLEAVYEAIFGQPKEKVYAEE 294
Query: 468 LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQ 527
+ WE L + V Y + + + + +F ++++RL G ++V +
Sbjct: 295 IAQAWETGEGLER---VARYSMEDAKVTYELGK-EFFPMEAQLSRLVGQSLWDVSRSSTG 350
Query: 528 FRVESIMLRLSRLNNFVAVS-PSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQSLY 586
VE +LR + N +A + P ++ A R + + EPE L+ + I+ LDF+SLY
Sbjct: 351 NLVEWFLLRKAYERNELAPNKPDERELARRRESYAGGYVKEPERGLWEN-IVYLDFRSLY 409
Query: 587 PSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTISPSGVAFVDK 646
PS+II +N T L R GC + +V+ + K ++
Sbjct: 410 PSIIITHNVSPDT-LNRE-----------GCEEYDVAPQVGHKFCKDFP----------- 446
Query: 647 SIRCGILPKMLQEILDTRLMVKQSMK 672
G +P +L ++L+ R VK+ MK
Sbjct: 447 ----GFIPSLLGDLLEERQKVKKKMK 468
Score = 31.2 bits (69), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 12/18 (66%), Positives = 16/18 (88%)
Query: 115 IIVLDFQSLYPSVIIAYN 132
I+ LDF+SLYPS+II +N
Sbjct: 400 IVYLDFRSLYPSIIITHN 417
>pdb|1QQC|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
D.Tok
Length = 773
Score = 82.8 bits (203), Expect = 6e-16, Method: Compositional matrix adjust.
Identities = 79/326 (24%), Positives = 148/326 (45%), Gaps = 46/326 (14%)
Query: 352 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKR 411
VS EKE+ F++ +++ DPD+LI Y + + YL +R +LG+ + R
Sbjct: 184 VSTEKEMIKRFLKVIQEKDPDVLITYNGDNFDFAYLKKRSEMLGVKF---------ILGR 234
Query: 412 NSSRDEVKNT----QLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKL 467
+ S +++ +++ GRI +L+ ++R +NL +YT E + V + +
Sbjct: 235 DGSEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTINLPTYTLETVYEPVFGQPKEKVYAEE 294
Query: 468 LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQ 527
+ WE L + V Y + + + +F ++++RL G ++V +
Sbjct: 295 IARAWESGEGLER---VARYSMEDAKATYELGK-EFFPMEAQLSRLVGQSLWDVSRSSTG 350
Query: 528 FRVESIMLRLSRLNNFVAVS-PSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQSLY 586
VE +LR + N VA + P ++ A + + EPE L+ + I+ LD++SLY
Sbjct: 351 NLVEWFLLRKAYERNDVAPNKPDERELARRTESYAGGYVKEPEKGLWEN-IVYLDYKSLY 409
Query: 587 PSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTISPSGVAFVDK 646
PS+II +N T L R GC + +V+ + + ++
Sbjct: 410 PSIIITHNVSPDT-LNRE-----------GCREYDVAPQVGHRFCKDFP----------- 446
Query: 647 SIRCGILPKMLQEILDTRLMVKQSMK 672
G +P +L ++L+ R VK+ MK
Sbjct: 447 ----GFIPSLLGDLLEERQKVKKKMK 468
Score = 30.0 bits (66), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 115 IIVLDFQSLYPSVIIAYNYCFSTC 138
I+ LD++SLYPS+II +N T
Sbjct: 400 IVYLDYKSLYPSIIITHNVSPDTL 423
>pdb|2JGU|A Chain A, Crystal Structure Of Dna-directed Dna Polymerase
Length = 775
Score = 82.4 bits (202), Expect = 7e-16, Method: Compositional matrix adjust.
Identities = 81/324 (25%), Positives = 146/324 (45%), Gaps = 39/324 (12%)
Query: 352 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKR 411
VS EKE+ F+ +R+ DPDI++ Y ++ + YL +R LG+ L + R K
Sbjct: 184 VSTEKEMIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKRAEKLGIKLT--IGRDGSEPKM 241
Query: 412 NSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCW 471
D T +++ GRI +L+ ++R +NL +YT E + + + +
Sbjct: 242 QRIGD---MTAVEVKGRIHFDLYHVIRTTINLPTYTLEAVYEAIFGKPKEKVYADEIAKA 298
Query: 472 WEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQFRVE 531
WE +L + V Y + + + +F+ +++RL G ++V + VE
Sbjct: 299 WESGENLER---VAKYSMEDAKATYELGK-EFLPMEIQLSRLVGQPLWDVSRSSTGNLVE 354
Query: 532 SIMLRLSRLNNFVAVSPSIKQRAHMRAPESLP--LILEPESRLYTDPIIVLDFQSLYPSV 589
+LR + N VA + ++ R ES + EPE L+ + I+ LD++SLYPS+
Sbjct: 355 WFLLRKAYERNEVAPNKPSEEEYQRRLRESYTGGFVKEPEKGLWEN-IVYLDYKSLYPSI 413
Query: 590 IIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTISPSGVAFVDKSIR 649
II +N T +E GC + +++ + K +++
Sbjct: 414 IITHNVSPDTL--NLE----------GCKNYDIAPQVGHKFCKDIP-------------- 447
Query: 650 CGILPKMLQEILDTRLMVKQSMKE 673
G +P +L +L+ R +K MKE
Sbjct: 448 -GFIPSLLGHLLEERQKIKTKMKE 470
Score = 30.0 bits (66), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 115 IIVLDFQSLYPSVIIAYNYCFSTC 138
I+ LD++SLYPS+II +N T
Sbjct: 401 IVYLDYKSLYPSIIITHNVSPDTL 424
>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 = 81.3 bits (199), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 78/326 (23%), Positives = 147/326 (45%), Gaps = 46/326 (14%)
Query: 352 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKR 411
VS EKE+ F++ +++ DPD+LI Y + + YL +R +LG+ + R
Sbjct: 184 VSTEKEMIKRFLKVIQEKDPDVLITYNGDNFDFAYLKKRSEMLGVKF---------ILGR 234
Query: 412 NSSRDEVKNT----QLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKL 467
+ S +++ +++ GRI +L+ ++R +NL +YT E + V + +
Sbjct: 235 DGSEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTINLPTYTLETVYEPVFGQPAEKVYAEE 294
Query: 468 LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQ 527
+ W L + V Y + + + +F ++++RL G ++V +
Sbjct: 295 IAEAWASGEGLER---VARYSMEDAKATYELGK-EFFPMEAQLSRLVGQSLWDVSRSSTG 350
Query: 528 FRVESIMLRLSRLNNFVAVS-PSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQSLY 586
VE +LR + N VA + P ++ A + + EPE L+ + I+ LD++SLY
Sbjct: 351 NLVEWFLLRKAYERNDVAPNKPDERELARRTESYAGGYVKEPEKGLWEN-IVYLDYKSLY 409
Query: 587 PSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTISPSGVAFVDK 646
PS+II +N T L R GC + +V+ + + ++
Sbjct: 410 PSIIITHNVSPDT-LNRE-----------GCREYDVAPQVGHRFCKDFP----------- 446
Query: 647 SIRCGILPKMLQEILDTRLMVKQSMK 672
G +P +L ++L+ R VK+ MK
Sbjct: 447 ----GFIPSLLGDLLEERQKVKKKMK 468
Score = 30.0 bits (66), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 115 IIVLDFQSLYPSVIIAYNYCFST 137
I+ LD++SLYPS+II +N T
Sbjct: 400 IVYLDYKSLYPSIIITHNVSPDT 422
>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 = 80.5 bits (197), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 80/324 (24%), Positives = 145/324 (44%), Gaps = 39/324 (12%)
Query: 352 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKR 411
VS+E+E+ F+ +R+ DPDI++ Y ++ + YL +R LG+ L + R K
Sbjct: 184 VSSEREMIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKRAEKLGIKLT--IGRDGSEPKM 241
Query: 412 NSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLHSWKLLTCW 471
D T +++ GRI +L+ ++ +NL +YT E + + + +
Sbjct: 242 QRIGD---MTAVEVKGRIHFDLYHVITRTINLPTYTLEAVYEAIFGKPKEKVYADEIAKA 298
Query: 472 WEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQFRVE 531
WE +L + V Y + + + +F+ +++RL G ++V + VE
Sbjct: 299 WESGENLER---VAKYSMEDAKATYELGK-EFLPMEIQLSRLIGQPLWDVSRSSTGNLVE 354
Query: 532 SIMLRLSRLNNFVAVSPSIKQRAHMRAPESLP--LILEPESRLYTDPIIVLDFQSLYPSV 589
+LR + N VA + ++ R ES + EPE L+ D I+ LDF +LYPS+
Sbjct: 355 WFLLRKAYERNEVAPNKPSEEEYQRRLRESYTGGFVKEPEKGLWDD-IVYLDFIALYPSI 413
Query: 590 IIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTISPSGVAFVDKSIR 649
II +N T +E GC + +++ + K +++
Sbjct: 414 IITHNVSPDTL--NLE----------GCKNYDIAPQVGHKFCKDIP-------------- 447
Query: 650 CGILPKMLQEILDTRLMVKQSMKE 673
G +P +L +L+ R +K MKE
Sbjct: 448 -GFIPSLLGHLLEERQKIKTKMKE 470
Score = 30.4 bits (67), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 113 DPIIVLDFQSLYPSVIIAYNYCFSTC 138
D I+ LDF +LYPS+II +N T
Sbjct: 399 DDIVYLDFIALYPSIIITHNVSPDTL 424
>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 = 77.8 bits (190), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 84/329 (25%), Positives = 151/329 (45%), Gaps = 45/329 (13%)
Query: 352 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKR 411
VS+E+E+ ++ +R+ DPD++I Y + ++ YLL+R LG+ L L R K
Sbjct: 206 VSSEREMIKRLVKVIREKDPDVIITYNGDNFAFPYLLKRAEKLGIKLP--LGRDNSEPKM 263
Query: 412 NSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVL---HERIPLHSWKLL 468
D + +++ GRI +L+ ++R +NL +YT E + + E++ H +
Sbjct: 264 QRMGD---SLAVEIKGRIHFDLFPVIRRTINLPTYTLEAVYEAIFGKSKEKVYAHE---I 317
Query: 469 TCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQF 528
WE L + V Y + + + + +F +++ARL G ++V +
Sbjct: 318 AEAWETGKGLER---VAKYSMEDAKVTFELGK-EFFPMEAQLARLVGQPVWDVSRSSTGN 373
Query: 529 RVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLP--LILEPESRLYTDPIIVLDFQSLY 586
VE +LR + N +A + ++ R ES + EPE L+ + I+ LDF+SLY
Sbjct: 374 LVEWFLLRKAYERNELAPNKPDEREYERRLRESYEGGYVKEPEKGLW-EGIVSLDFRSLY 432
Query: 587 PSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTISPSGVAFVDK 646
PS+II +N T L R C + +V+ + + ++
Sbjct: 433 PSIIITHNVSPDT-LNRE-----------NCKEYDVAPQVGHRFCKDFP----------- 469
Query: 647 SIRCGILPKMLQEILDTRLMVKQSMKEYK 675
G +P +L +L+ R +K+ MKE K
Sbjct: 470 ----GFIPSLLGNLLEERQKIKKRMKESK 494
Score = 31.2 bits (69), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/24 (54%), Positives = 17/24 (70%)
Query: 115 IIVLDFQSLYPSVIIAYNYCFSTC 138
I+ LDF+SLYPS+II +N T
Sbjct: 423 IVSLDFRSLYPSIIITHNVSPDTL 446
>pdb|3A2F|A Chain A, Crystal Structure Of Pyrococcus Furiosus Dna
PolymerasePCNA Monomer Mutant Complex
Length = 775
Score = 77.4 bits (189), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 77/327 (23%), Positives = 147/327 (44%), Gaps = 45/327 (13%)
Query: 352 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKR 411
VS+E+E F+ +R+ DPDI++ Y ++ + YL +R LG+ L + R K
Sbjct: 184 VSSEREXIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKRAEKLGIKLT--IGRDGSEPKX 241
Query: 412 NSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHE-RIPLHSWKLLTC 470
D T +++ GRI +L+ ++ +NL +YT E + + + + +++ ++
Sbjct: 242 QRIGD---XTAVEVKGRIHFDLYHVITRTINLPTYTLEAVYEAIFGKPKEKVYADEIAKA 298
Query: 471 W--WEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQF 528
W E+ + K+ + G +F+ +++RL G ++V +
Sbjct: 299 WESGENLERVAKYSXEDAKATYELG-------KEFLPXEIQLSRLVGQPLWDVSRSSTGN 351
Query: 529 RVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLP--LILEPESRLYTDPIIVLDFQSLY 586
VE +LR + N VA + ++ R ES + EPE L+ + I+ LDF++LY
Sbjct: 352 LVEWFLLRKAYERNEVAPNKPSEEEYQRRLRESYTGGFVKEPEKGLWEN-IVYLDFRALY 410
Query: 587 PSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTISPSGVAFVDK 646
PS+II +N T +E GC + +++ + K +++
Sbjct: 411 PSIIITHNVSPDTL--NLE----------GCKNYDIAPQVGHKFCKDIP----------- 447
Query: 647 SIRCGILPKMLQEILDTRLMVKQSMKE 673
G +P +L +L+ R +K KE
Sbjct: 448 ----GFIPSLLGHLLEERQKIKTKXKE 470
Score = 30.0 bits (66), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 115 IIVLDFQSLYPSVIIAYNYCFSTC 138
I+ LDF++LYPS+II +N T
Sbjct: 401 IVYLDFRALYPSIIITHNVSPDTL 424
>pdb|4FM2|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase (Triple Mutant)
Bound To A Dsdna, In Edition Mode
Length = 793
Score = 75.5 bits (184), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 84/329 (25%), Positives = 149/329 (45%), Gaps = 45/329 (13%)
Query: 352 VSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKR 411
VS+E+E+ ++ +R+ DPD++I Y + ++ YLL+R LG+ L L R K
Sbjct: 206 VSSEREMIKRLVKVIREKDPDVIITYNGDNFAFPYLLKRAEKLGIKLP--LGRDNSEPKM 263
Query: 412 NSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVL---HERIPLHSWKLL 468
D + + + GRI +L+ ++R +NL +YT E + + E++ H +
Sbjct: 264 QRMGD---SLAVAIKGRIHFDLFPVIRRTINLPTYTLEAVYEAIFGKSKEKVYAHE---I 317
Query: 469 TCWWEHRTHLYKWMTVEHYLIRVTGIIRLIEQLDFIGRTSEMARLFGIQFYEVLSRGSQF 528
WE L + V Y + + + + +F +++ARL G + V +
Sbjct: 318 AEAWETGKGLER---VAKYSMEDAKVTFELGK-EFFPMEAQLARLVGQPVWAVSRSSTGN 373
Query: 529 RVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLP--LILEPESRLYTDPIIVLDFQSLY 586
VE +LR + N +A + ++ R ES + EPE L+ + I+ LDF+SLY
Sbjct: 374 LVEWFLLRKAYERNELAPNKPDEREYERRLRESYEGGYVKEPEKGLW-EGIVSLDFRSLY 432
Query: 587 PSVIIAYNYCFSTCLGRVEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTISPSGVAFVDK 646
PS+II +N T L R C + +V+ + + ++
Sbjct: 433 PSIIITHNVSPDT-LNRE-----------NCKEYDVAPQVGHRFCKDFP----------- 469
Query: 647 SIRCGILPKMLQEILDTRLMVKQSMKEYK 675
G +P +L +L+ R +K+ MKE K
Sbjct: 470 ----GFIPSLLGNLLEERQKIKKRMKESK 494
Score = 31.2 bits (69), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 13/24 (54%), Positives = 17/24 (70%)
Query: 115 IIVLDFQSLYPSVIIAYNYCFSTC 138
I+ LDF+SLYPS+II +N T
Sbjct: 423 IVSLDFRSLYPSIIITHNVSPDTL 446
>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 = 73.2 bits (178), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 82/392 (20%), Positives = 159/392 (40%), Gaps = 97/392 (24%)
Query: 354 NEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLER----------GYVLGLNLNQELS 403
+E E+ F+ V+Q+ P+ + GY I W +LL + GY G + +
Sbjct: 400 SEFEMLLAFMTLVKQYGPEFVTGYNIINFDWPFLLAKLTDIYKVPLDGY--GRMNGRGVF 457
Query: 404 RITEVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIPLH 463
R+ ++ + + K +++++ G + I+++ ++ ++ L SY + VL ++
Sbjct: 458 RVWDIGQSHFQ----KRSKIKVNGMVNIDMYGIITDKIKLSSYKLNAVAEAVLKDKKKDL 513
Query: 464 SWKLLTCWWEHRTHLYKWMTVEHYLIRVTGII-----RLIEQLDFIGRTSEMARLFGIQF 518
S++ + ++ T + + Y I+ + ++ + + L+ S +ARL GI
Sbjct: 514 SYRDIPAYYA--TGPAQRGVIGEYCIQDSLLVGQLFFKFLPHLEL----SAVARLAGINI 567
Query: 519 YEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQR---AHMRAPESLPL----------- 564
+ G Q RV + +LRL+ F+ P + R A AP+
Sbjct: 568 TRTIYDGQQIRVFTCLLRLADQKGFIL--PDTQGRFRGAGGEAPKRPAAAREDEERPEEE 625
Query: 565 ---------------------------------ILEPESRLYTDPIIVLDFQSLYPSVII 591
+L+P S + +P++V DF SLYPS+I
Sbjct: 626 GEDEDEREEGGGEREPEGARETAGRHVGYQGAKVLDPTSGFHVNPVVVFDFASLYPSIIQ 685
Query: 592 AYNYCFSTCLGR---VEHLGVSDSFPFGCIDLNVSIRSLKKLQQNLTISPSGVAFVDKSI 648
A+N CFST R V HL + +++ V R L FV +
Sbjct: 686 AHNLCFSTLSLRADAVAHLEAGKDY----LEIEVGGRRL--------------FFVKAHV 727
Query: 649 RCGILPKMLQEILDTRLMVKQSMKEYKFSESL 680
R +L +L++ L R ++ + + E++
Sbjct: 728 RESLLSILLRDWLAMRKQIRSRIPQSSPEEAV 759
Score = 42.7 bits (99), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 16/28 (57%), Positives = 22/28 (78%)
Query: 110 LYTDPIIVLDFQSLYPSVIIAYNYCFST 137
+ +P++V DF SLYPS+I A+N CFST
Sbjct: 666 FHVNPVVVFDFASLYPSIIQAHNLCFST 693
>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 = 60.8 bits (146), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 75/356 (21%), Positives = 144/356 (40%), Gaps = 80/356 (22%)
Query: 353 SNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGL----NLNQELSRI--T 406
+NEK + S F ++ DPD++IG+ ++ + L R + L + ++ + L R
Sbjct: 266 NNEKAMLSCFCAMLKVEDPDVIIGHRLQNVYLDVLAHRMHDLNIPTFSSIGRRLRRTWPE 325
Query: 407 EVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFE-NIMYHVLHERIPLHSW 465
+ + NS+ + + + GR++ ++ + + + +++ + MY V
Sbjct: 326 KFGRGNSNMNHFFISDI-CSGRLICDIANEMGQSLTPKCQSWDLSEMYQV---------- 374
Query: 466 KLLTCWWEHRTHLYKW-------------MTVEHYLIRVTGIIRLIEQLDFIGRTSEMAR 512
TC EH+ + M ++ + + ++ + T ++
Sbjct: 375 ---TCEKEHKPLDIDYQNPQYQNDVNSMTMALQENITNCMISAEVSYRIQLLTLTKQLTN 431
Query: 513 LFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAV------SPSIKQRAH----------M 556
L G + + L R E I+L N F+ S + KQR +
Sbjct: 432 LAGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDKEGNRSRAQKQRQNEENADAPVNSK 491
Query: 557 RAPESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFG 616
+A L+ EPE L+ + ++V+DF SLYPS+I +N CF+T E + D P
Sbjct: 492 KAKYQGGLVFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVDRNKEDI---DELP-- 546
Query: 617 CIDLNVSIRSLKKLQQNLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMK 672
++ PS + G+LP++L ++D R VK+ MK
Sbjct: 547 ------------------SVPPS-------EVDQGVLPRLLANLVDRRREVKKVMK 577
Score = 37.4 bits (85), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 22/28 (78%)
Query: 110 LYTDPIIVLDFQSLYPSVIIAYNYCFST 137
L+ + ++V+DF SLYPS+I +N CF+T
Sbjct: 507 LHKNYVLVMDFNSLYPSIIQEFNICFTT 534
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 29/65 (44%)
Query: 305 PIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIE 364
P ++ +NEK + S F ++ DPD++IG+ ++ L R N SI
Sbjct: 259 PGRVRLFNNEKAMLSCFCAMLKVEDPDVIIGHRLQNVYLDVLAHRMHDLNIPTFSSIGRR 318
Query: 365 NVRQW 369
R W
Sbjct: 319 LRRTW 323
>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 = 60.8 bits (146), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 75/356 (21%), Positives = 144/356 (40%), Gaps = 80/356 (22%)
Query: 353 SNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGL----NLNQELSRI--T 406
+NEK + S F ++ DPD++IG+ ++ + L R + L + ++ + L R
Sbjct: 266 NNEKAMLSCFCAMLKVEDPDVIIGHRLQNVYLDVLAHRMHDLNIPTFSSIGRRLRRTWPE 325
Query: 407 EVEKRNSSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFE-NIMYHVLHERIPLHSW 465
+ + NS+ + + + GR++ ++ + + + +++ + MY V
Sbjct: 326 KFGRGNSNMNHFFISDI-CSGRLICDIANEMGQSLTPKCQSWDLSEMYQV---------- 374
Query: 466 KLLTCWWEHRTHLYKW-------------MTVEHYLIRVTGIIRLIEQLDFIGRTSEMAR 512
TC EH+ + M ++ + + ++ + T ++
Sbjct: 375 ---TCEKEHKPLDIDYQNPQYQNDVNSMTMALQENITNCMISAEVSYRIQLLTLTKQLTN 431
Query: 513 LFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAV------SPSIKQRAH----------M 556
L G + + L R E I+L N F+ S + KQR +
Sbjct: 432 LAGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDKEGNRSRAQKQRQNEENADAPVNSK 491
Query: 557 RAPESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFG 616
+A L+ EPE L+ + ++V+DF SLYPS+I +N CF+T E + D P
Sbjct: 492 KAKYQGGLVFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVDRNKEDI---DELP-- 546
Query: 617 CIDLNVSIRSLKKLQQNLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMK 672
++ PS + G+LP++L ++D R VK+ MK
Sbjct: 547 ------------------SVPPS-------EVDQGVLPRLLANLVDRRREVKKVMK 577
Score = 37.4 bits (85), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 22/28 (78%)
Query: 110 LYTDPIIVLDFQSLYPSVIIAYNYCFST 137
L+ + ++V+DF SLYPS+I +N CF+T
Sbjct: 507 LHKNYVLVMDFNSLYPSIIQEFNICFTT 534
Score = 31.6 bits (70), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 29/65 (44%)
Query: 305 PIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIE 364
P ++ +NEK + S F ++ DPD++IG+ ++ L R N SI
Sbjct: 259 PGRVRLFNNEKAMLSCFCAMLKVEDPDVIIGHRLQNVYLDVLAHRMHDLNIPTFSSIGRR 318
Query: 365 NVRQW 369
R W
Sbjct: 319 LRRTW 323
>pdb|4B08|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha,
Selenomethionine Protein
Length = 910
Score = 55.5 bits (132), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 76/355 (21%), Positives = 130/355 (36%), Gaps = 78/355 (21%)
Query: 353 SNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERGYVLGLNLNQELSRITEVEKRN 412
+NEK S F ++ DPD++IG+ ++ + L R + L + + R
Sbjct: 266 NNEKAXLSCFCAXLKVEDPDVIIGHRLQNVYLDVLAHRXHDLNIPTFSSIGR-------- 317
Query: 413 SSRDEVKNTQLQMPGRIVINLWRLLRHEVNLQSYTFENIMYHVLHERIP-LHSWKL---- 467
++ T + GR N ++ +I P SW L
Sbjct: 318 ----RLRRTWPEKFGRGNSNXNHFFISDI-CSGRLICDIANEXGQSLTPKCQSWDLSEXY 372
Query: 468 -LTCWWEHRTHLYKWMTVEHYLIRVTGIIRLIE-------------QLDFIGRTSEMARL 513
+TC EH+ + ++ + L E ++ + T ++ L
Sbjct: 373 QVTCEKEHKPLDIDYQNPQYQNDVNSXTXALQENITNCXISAEVSYRIQLLTLTKQLTNL 432
Query: 514 FGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAV------SPSIKQRAH----------MR 557
G + + L R E I+L N F+ S + KQR + +
Sbjct: 433 AGNAWAQTLGGTRAGRNEYILLHEFSRNGFIVPDKEGNRSRAQKQRQNEENADAPVNSKK 492
Query: 558 APESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTCLGRVEHLGVSDSFPFGC 617
A L+ EPE L+ + ++V DF SLYPS+I +N CF+T E + D P
Sbjct: 493 AKYQGGLVFEPEKGLHKNYVLVXDFNSLYPSIIQEFNICFTTVDRNKEDI---DELP--- 546
Query: 618 IDLNVSIRSLKKLQQNLTISPSGVAFVDKSIRCGILPKMLQEILDTRLMVKQSMK 672
++ PS + G+LP++L ++D R VK+ K
Sbjct: 547 -----------------SVPPS-------EVDQGVLPRLLANLVDRRREVKKVXK 577
Score = 36.2 bits (82), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 21/28 (75%)
Query: 110 LYTDPIIVLDFQSLYPSVIIAYNYCFST 137
L+ + ++V DF SLYPS+I +N CF+T
Sbjct: 507 LHKNYVLVXDFNSLYPSIIQEFNICFTT 534
Score = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 28/65 (43%)
Query: 305 PIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLERHFVSNEKELFSIFIE 364
P ++ +NEK S F ++ DPD++IG+ ++ L R N SI
Sbjct: 259 PGRVRLFNNEKAXLSCFCAXLKVEDPDVIIGHRLQNVYLDVLAHRXHDLNIPTFSSIGRR 318
Query: 365 NVRQW 369
R W
Sbjct: 319 LRRTW 323
>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 = 33.1 bits (74), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 57/258 (22%), Positives = 104/258 (40%), Gaps = 36/258 (13%)
Query: 347 LERHFVSNEKELFSIFIENVRQWDPDILIGYEIETLSWGYLLERG--YVLGLNLNQELSR 404
E +V++ +L +DPD++IG+ + L + Y L L L ++ S
Sbjct: 196 FELEYVASRPQLLEKLNAWFANYDPDVIIGWNVVQFDLRMLQKHAERYRLPLRLGRDNS- 254
Query: 405 ITEVEKRNSSRDEVKNTQL--QMPGRIVINLWRLLRHEV-NLQSYTFENIMYHVLHERIP 461
E+E R KN Q GR++I+ L+ N S++ E + +L E
Sbjct: 255 --ELEWREHG---FKNGVFFAQAKGRLIIDGIEALKSAFWNFSSFSLETVAQELLGEG-- 307
Query: 462 LHSWKLLTCWWEHRTHLYKWMTVEHYLIR---------VTGIIRLIEQLDFIGRTSEMAR 512
K + W+ + + + + VT I E + F+ E A
Sbjct: 308 ----KSIDNPWDRMDEIDRRFAEDKPALATYNLKNCELVTQIFHKTEIMPFL---LERAT 360
Query: 513 LFGIQFYEVLSRGSQFRVESIMLRLSRLNNFVAVSPSIKQRAHMRAPESLPLILEPESRL 572
+ G+ + R L R++ V+P++ + +P +++ L
Sbjct: 361 VNGLP----VDRHGGSVAAFGHLYFPRMHRAGYVAPNLGEVPPHASPGGY--VMDSRPGL 414
Query: 573 YTDPIIVLDFQSLYPSVI 590
Y D ++VLD++SLYPS+I
Sbjct: 415 Y-DSVLVLDYKSLYPSII 431
>pdb|1S5J|A Chain A, Insight In Dna Replication: The Crystal Structure Of Dna
Polymerase B1 From The Archaeon Sulfolobus Solfataricus
Length = 847
Score = 33.1 bits (74), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 6/57 (10%)
Query: 544 VAVSPSIKQRAHMRAPESLPLILEPESRLYTDPIIVLDFQSLYPSVIIAYNYCFSTC 600
+ S IK + + A ++++P + ++ + I VLDF SLYPS+I +N + T
Sbjct: 448 IRTSALIKGKGYKGA-----VVIDPPAGIFFN-ITVLDFASLYPSIIRTWNLSYETV 498
Score = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 115 IIVLDFQSLYPSVIIAYNYCFSTC 138
I VLDF SLYPS+I +N + T
Sbjct: 475 ITVLDFASLYPSIIRTWNLSYETV 498
>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 = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 297 ELP-EVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER 349
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+F+ Y+ R
Sbjct: 177 EVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
>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 = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 297 ELP-EVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER 349
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+F+ Y+ R
Sbjct: 177 EVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
>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 = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 297 ELP-EVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER 349
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+F+ Y+ R
Sbjct: 177 EVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
>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 = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 297 ELP-EVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER 349
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+F+ Y+ R
Sbjct: 177 EVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
>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 = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 297 ELP-EVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER 349
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+F+ Y+ R
Sbjct: 177 EVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
>pdb|3SUN|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dttp
Opposite 2ap (At Rich Sequence)
Length = 895
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 297 ELP-EVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER 349
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+F+ Y+ R
Sbjct: 177 EVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
>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 = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 297 ELP-EVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER 349
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+F+ Y+ R
Sbjct: 177 EVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
>pdb|3SUQ|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dctp
Opposite 2ap (At Rich Sequence)
Length = 897
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 297 ELP-EVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER 349
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+F+ Y+ R
Sbjct: 177 EVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
>pdb|3SQ1|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dupcpp Opposite
Da
Length = 901
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 297 ELP-EVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER 349
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+F+ Y+ R
Sbjct: 177 EVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
>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 = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 297 ELP-EVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER 349
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+F+ Y+ R
Sbjct: 177 EVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
>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 = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 297 ELP-EVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER 349
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+F+ Y+ R
Sbjct: 177 EVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
>pdb|1Q9Y|A Chain A, Crystal Structure Of Enterobacteria Phage Rb69 Gp43 Dna
Polymerase Complexed With 8-Oxoguanosine Containing Dna
Length = 906
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 297 ELP-EVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER 349
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+F+ Y+ R
Sbjct: 180 EVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 232
>pdb|3CQ8|A Chain A, Ternary Complex Of The L415f Mutant Rb69 Exo(-)polymerase
Length = 903
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 297 ELP-EVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER 349
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+F+ Y+ R
Sbjct: 177 EVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
>pdb|3SUO|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dttp
Opposite 2ap (Gc Rich Sequence)
Length = 900
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 297 ELP-EVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER 349
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+F+ Y+ R
Sbjct: 177 EVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 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 = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 297 ELP-EVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER 349
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+F+ Y+ R
Sbjct: 177 EVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
>pdb|3LDS|A Chain A, Crystal Structure Of Rb69 Gp43 With Dna And Datp Opposite
8-
Length = 903
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 297 ELP-EVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER 349
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+F+ Y+ R
Sbjct: 177 EVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
>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 = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 297 ELP-EVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER 349
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+F+ Y+ R
Sbjct: 177 EVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
>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 = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 297 ELP-EVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER 349
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+F+ Y+ R
Sbjct: 177 EVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
>pdb|3SPY|A Chain A, Rb69 Dna Polymerase(L415aL561AS565GY567A) TERNARY COMPLEX
WITH Dupcpp Opposite Da
Length = 901
Score = 31.6 bits (70), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 297 ELP-EVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER 349
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+F+ Y+ R
Sbjct: 177 EVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
>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 = 31.6 bits (70), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 297 ELP-EVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER 349
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+F+ Y+ R
Sbjct: 177 EVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
>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 = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 30/54 (55%), Gaps = 2/54 (3%)
Query: 297 ELP-EVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER 349
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+F Y+ R
Sbjct: 177 EVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFDIPYVYNR 229
>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 = 30.8 bits (68), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 30/54 (55%), Gaps = 2/54 (3%)
Query: 297 ELP-EVRTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER 349
E+P E+ K I M F NEKEL ++ +Q P IL G+ +E+F Y+ R
Sbjct: 177 EVPSEIIDKIIYMPF-DNEKELLMEYLNFWQQKTPVILTGWNVESFDIPYVYNR 229
>pdb|2LRI|C Chain C, Nmr Structure Of The Second Phd Finger Of Aire
(aire-phd2)
Length = 66
Score = 30.4 bits (67), Expect = 3.5, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 22/56 (39%), Gaps = 17/56 (30%)
Query: 3 LARGFICELCNSEEVIFPWQLSSVHRCNQCGACFHTKCH---------SQLPCKRC 49
LA G C +C + V RC C A FH +CH + L C+ C
Sbjct: 9 LAPGARCGVCGDG--------TDVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSC 56
>pdb|2DMD|A Chain A, Solution Structure Of The N-Terminal C2h2 Type
Zinc-Binding Domain Of The Zinc Finger Protein 64,
Isoforms 1 And 2
Length = 96
Score = 30.4 bits (67), Expect = 3.5, Method: Composition-based stats.
Identities = 20/73 (27%), Positives = 29/73 (39%), Gaps = 27/73 (36%)
Query: 24 SSVHRCNQCGACF--------HTKCHSQL---PCKRCIRMRIRRDSMKGIVDVKCFEESS 72
S H+C CG CF H +CH+ + CK C D + SS
Sbjct: 6 SGPHKCEVCGKCFSRKDKLKTHMRCHTGVKPYKCKTC--------------DYAAADSSS 51
Query: 73 LERSMK--PDDRP 83
L + ++ D+RP
Sbjct: 52 LNKHLRIHSDERP 64
>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
Length = 523
Score = 30.0 bits (66), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 302 RTKPIQMNFVSNEKELFSTFIENVRQWDPDILIGYEIETFS-WGY 345
RT I++ +++ E+ + F+E++ W+P +L E S WG+
Sbjct: 112 RTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGH 156
>pdb|1GA2|A Chain A, The Crystal Structure Of Endoglucanase 9g From Clostridium
Cellulolyticum Complexed With Cellobiose
pdb|1GA2|B Chain B, The Crystal Structure Of Endoglucanase 9g From Clostridium
Cellulolyticum Complexed With Cellobiose
pdb|1G87|A Chain A, The Crystal Structure Of Endoglucanase 9g From Clostridium
Cellulolyticum
pdb|1G87|B Chain B, The Crystal Structure Of Endoglucanase 9g From Clostridium
Cellulolyticum
pdb|1KFG|A Chain A, The X-Ray Crystal Structure Of Cel9g From Clostridium
Cellulolyticum Complexed With A Thio-Oligosaccharide
Inhibitor
pdb|1KFG|B Chain B, The X-Ray Crystal Structure Of Cel9g From Clostridium
Cellulolyticum Complexed With A Thio-Oligosaccharide
Inhibitor
Length = 614
Score = 29.6 bits (65), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 28/75 (37%)
Query: 255 ISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNE 314
I L P Y E+KA+ Y P K+ SE+ P+ + SN
Sbjct: 461 IKAGLNSTGPNYTEIKAVVYNQTGWPARVTDKISFKYFMDLSEIVAAGIDPLSLVTSSNY 520
Query: 315 KELFSTFIENVRQWD 329
E +T + V WD
Sbjct: 521 SEGKNTKVSGVLPWD 535
>pdb|1K72|A Chain A, The X-ray Crystal Structure Of Cel9g Complexed With
Cellotriose
pdb|1K72|B Chain B, The X-ray Crystal Structure Of Cel9g Complexed With
Cellotriose
Length = 614
Score = 29.6 bits (65), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 28/75 (37%)
Query: 255 ISRALLKPDPAYDEVKAIFYYLYTCPPEEDRKVGIILIGQESELPEVRTKPIQMNFVSNE 314
I L P Y E+KA+ Y P K+ SE+ P+ + SN
Sbjct: 461 IKAGLNSTGPNYTEIKAVVYNQTGWPARVTDKISFKYFMDLSEIVAAGIDPLSLVTSSNY 520
Query: 315 KELFSTFIENVRQWD 329
E +T + V WD
Sbjct: 521 SEGKNTKVSGVLPWD 535
>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 = 29.3 bits (64), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 313 NEKELFSTFIENVRQWDPDILIGYEIETFSWGYLLER 349
NEKEL ++ +Q P IL G+ +E+F+ Y+ R
Sbjct: 193 NEKELLXEYLNFWQQKTPVILTGWNVESFAIPYVYNR 229
>pdb|2RO1|A Chain A, Nmr Solution Structures Of Human Kap1 Phd
Finger-Bromodomain
Length = 189
Score = 29.3 bits (64), Expect = 7.9, Method: Composition-based stats.
Identities = 9/13 (69%), Positives = 9/13 (69%)
Query: 29 CNQCGACFHTKCH 41
CNQC CFH CH
Sbjct: 17 CNQCEFCFHLDCH 29
>pdb|1FP0|A Chain A, Solution Structure Of The Phd Domain From The Kap-1
Corepressor
Length = 88
Score = 29.3 bits (64), Expect = 7.9, Method: Composition-based stats.
Identities = 9/13 (69%), Positives = 9/13 (69%)
Query: 29 CNQCGACFHTKCH 41
CNQC CFH CH
Sbjct: 40 CNQCEFCFHLDCH 52
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
0.323 0.138 0.424
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,701,775
Number of Sequences: 62578
Number of extensions: 798004
Number of successful extensions: 1586
Number of sequences better than 100.0: 52
Number of HSP's better than 100.0 without gapping: 48
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1387
Number of HSP's gapped (non-prelim): 170
length of query: 696
length of database: 14,973,337
effective HSP length: 106
effective length of query: 590
effective length of database: 8,340,069
effective search space: 4920640710
effective search space used: 4920640710
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (25.8 bits)