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= psy12450
(168 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 = 135 bits (341), Expect = 8e-33, Method: Compositional matrix adjust.
Identities = 65/113 (57%), Positives = 83/113 (73%), Gaps = 1/113 (0%)
Query: 49 IIPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTI 108
+IP +DQ+EGATVIEP +GYY PIATLDF+SLYPSIMMAHNLCYTTL T+
Sbjct: 508 VIPNMQSQASDDQYEGATVIEPIRGYYDVPIATLDFNSLYPSIMMAHNLCYTTLCNKATV 567
Query: 109 TKLELTPDQ-YSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETD 160
+L L D+ Y TP G++F+ + R+G+LP IL+ L+SARK+AK DL+ E D
Sbjct: 568 ERLNLKIDEDYVITPNGDYFVTTKRRRGILPIILDELISARKRAKKDLRDEKD 620
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/35 (48%), Positives = 26/35 (74%)
Query: 10 GLETVRRDNSPLVANMINTCLQKLLINRDPDGAVT 44
GL +VRRD+ LV+ ++N L+K+LI R+ DGA+
Sbjct: 768 GLASVRRDSCSLVSIVMNKVLKKILIERNVDGALA 802
>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 = 79.7 bits (195), Expect = 7e-16, Method: Compositional matrix adjust.
Identities = 40/109 (36%), Positives = 67/109 (61%), Gaps = 5/109 (4%)
Query: 62 FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTL-LTPQTITKLELTPDQYSK 120
++GA V++P G++ +P+ DF+SLYPSI+ AHNLC++TL L + LE D Y +
Sbjct: 654 YQGAKVLDPTSGFHVNPVVVFDFASLYPSIIQAHNLCFSTLSLRADAVAHLEAGKD-YLE 712
Query: 121 TPCGN---FFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVL 166
G FF+K+ +R+ LL +L + L+ RKQ ++ + + + E +L
Sbjct: 713 IEVGGRRLFFVKAHVRESLLSILLRDWLAMRKQIRSRIPQSSPEEAVLL 761
>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 = 65.5 bits (158), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 40/142 (28%), Positives = 67/142 (47%), Gaps = 33/142 (23%)
Query: 44 TQKNFIIPTYHGGQGEDQ-------------------FEGATVIEPKKGYYADPIATLDF 84
++ FI+P G + Q ++G V EP+KG + + + +DF
Sbjct: 458 SRNGFIVPDKEGNRSRAQKQRQNEENADAPVNSKKAKYQGGLVFEPEKGLHKNYVLVMDF 517
Query: 85 SSLYPSIMMAHNLCYTTL-LTPQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEILEN 143
+SLYPSI+ N+C+TT+ + I +L P S + +G+LP +L N
Sbjct: 518 NSLYPSIIQEFNICFTTVDRNKEDIDELPSVP-------------PSEVDQGVLPRLLAN 564
Query: 144 LLSARKQAKNDLKKETDELTQV 165
L+ R++ K +K ETD +V
Sbjct: 565 LVDRRREVKKVMKTETDPHKRV 586
>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 = 65.1 bits (157), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 40/142 (28%), Positives = 67/142 (47%), Gaps = 33/142 (23%)
Query: 44 TQKNFIIPTYHGGQGEDQ-------------------FEGATVIEPKKGYYADPIATLDF 84
++ FI+P G + Q ++G V EP+KG + + + +DF
Sbjct: 458 SRNGFIVPDKEGNRSRAQKQRQNEENADAPVNSKKAKYQGGLVFEPEKGLHKNYVLVMDF 517
Query: 85 SSLYPSIMMAHNLCYTTL-LTPQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEILEN 143
+SLYPSI+ N+C+TT+ + I +L P S + +G+LP +L N
Sbjct: 518 NSLYPSIIQEFNICFTTVDRNKEDIDELPSVP-------------PSEVDQGVLPRLLAN 564
Query: 144 LLSARKQAKNDLKKETDELTQV 165
L+ R++ K +K ETD +V
Sbjct: 565 LVDRRREVKKVMKTETDPHKRV 586
>pdb|4B08|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha,
Selenomethionine Protein
Length = 910
Score = 62.8 bits (151), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 40/142 (28%), Positives = 65/142 (45%), Gaps = 33/142 (23%)
Query: 44 TQKNFIIPTYHGGQGEDQ-------------------FEGATVIEPKKGYYADPIATLDF 84
++ FI+P G + Q ++G V EP+KG + + + DF
Sbjct: 458 SRNGFIVPDKEGNRSRAQKQRQNEENADAPVNSKKAKYQGGLVFEPEKGLHKNYVLVXDF 517
Query: 85 SSLYPSIMMAHNLCYTTL-LTPQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEILEN 143
+SLYPSI+ N+C+TT+ + I +L P S + +G+LP +L N
Sbjct: 518 NSLYPSIIQEFNICFTTVDRNKEDIDELPSVP-------------PSEVDQGVLPRLLAN 564
Query: 144 LLSARKQAKNDLKKETDELTQV 165
L+ R++ K K ETD +V
Sbjct: 565 LVDRRREVKKVXKTETDPHKRV 586
>pdb|4FM2|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase (Triple Mutant)
Bound To A Dsdna, In Edition Mode
Length = 793
Score = 58.5 bits (140), Expect = 2e-09, Method: Composition-based stats.
Identities = 36/105 (34%), Positives = 57/105 (54%), Gaps = 10/105 (9%)
Query: 62 FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKT 121
+EG V EP+KG + + I +LDF SLYPSI++ HN+ T L + + ++ P Q
Sbjct: 407 YEGGYVKEPEKGLW-EGIVSLDFRSLYPSIIITHNVSPDT-LNRENCKEYDVAP-QVGHR 463
Query: 122 PCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVL 166
C +F G +P +L NLL R++ K +K+ D + + L
Sbjct: 464 FCKDF-------PGFIPSLLGNLLEERQKIKKRMKESKDPVEKKL 501
>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 = 58.2 bits (139), Expect = 2e-09, Method: Composition-based stats.
Identities = 36/105 (34%), Positives = 57/105 (54%), Gaps = 10/105 (9%)
Query: 62 FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKT 121
+EG V EP+KG + + I +LDF SLYPSI++ HN+ T L + + ++ P Q
Sbjct: 407 YEGGYVKEPEKGLW-EGIVSLDFRSLYPSIIITHNVSPDT-LNRENCKEYDVAP-QVGHR 463
Query: 122 PCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVL 166
C +F G +P +L NLL R++ K +K+ D + + L
Sbjct: 464 FCKDF-------PGFIPSLLGNLLEERQKIKKRMKESKDPVEKKL 501
>pdb|1QHT|A Chain A, Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon
Length = 775
Score = 53.5 bits (127), Expect = 5e-08, Method: Composition-based stats.
Identities = 35/105 (33%), Positives = 55/105 (52%), Gaps = 10/105 (9%)
Query: 62 FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKT 121
+ G V EP++G + D I LDF SLYPSI++ HN+ T L + + ++ P+ K
Sbjct: 384 YAGGYVKEPERGLW-DNIVYLDFRSLYPSIIITHNVSPDT-LNREGCKEYDVAPEVGHKF 441
Query: 122 PCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVL 166
C +F G +P +L +LL R++ K +K D L + L
Sbjct: 442 -CKDF-------PGFIPSLLGDLLEERQKIKRKMKATVDPLEKKL 478
>pdb|1WNS|A Chain A, Crystal Structure Of Family B Dna Polymerase From
Hyperthermophilic Archaeon Pyrococcus Kodakaraensis Kod1
Length = 774
Score = 53.1 bits (126), Expect = 8e-08, Method: Composition-based stats.
Identities = 34/105 (32%), Positives = 55/105 (52%), Gaps = 10/105 (9%)
Query: 62 FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKT 121
+EG V EP++G + + I LDF SLYPSI++ HN+ T L + + ++ P Q
Sbjct: 384 YEGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVSPDT-LNREGCKEYDVAP-QVGHR 440
Query: 122 PCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVL 166
C +F G +P +L +LL R++ K +K D + + L
Sbjct: 441 FCKDF-------PGFIPSLLGDLLEERQKIKKKMKATIDPIERKL 478
>pdb|1WN7|A Chain A, Crystal Structure Of Archaeal Family B Dna Polymerase
Mutant
Length = 774
Score = 53.1 bits (126), Expect = 8e-08, Method: Composition-based stats.
Identities = 34/105 (32%), Positives = 55/105 (52%), Gaps = 10/105 (9%)
Query: 62 FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKT 121
+EG V EP++G + + I LDF SLYPSI++ HN+ T L + + ++ P Q
Sbjct: 384 YEGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVSPDT-LNREGCKEYDVAP-QVGHR 440
Query: 122 PCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVL 166
C +F G +P +L +LL R++ K +K D + + L
Sbjct: 441 FCKDF-------PGFIPSLLGDLLEERQKIKKKMKATIDPIERKL 478
>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 = 52.8 bits (125), Expect = 8e-08, Method: Composition-based stats.
Identities = 35/107 (32%), Positives = 57/107 (53%), Gaps = 10/107 (9%)
Query: 60 DQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYS 119
+ + G V EP+KG + D I LDF +LYPSI++ HN ++P T+ LE +
Sbjct: 383 ESYTGGFVKEPEKGLW-DDIVYLDFIALYPSIIITHN------VSPDTLN-LEGCKNYDI 434
Query: 120 KTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVL 166
G+ F K G +P +L +LL R++ K +K+ D + ++L
Sbjct: 435 APQVGHKFCKDI--PGFIPSLLGHLLEERQKIKTKMKETQDPIEKIL 479
>pdb|2XHB|A Chain A, Crystal Structure Of Dna Polymerase From Thermococcus
Gorgonarius In Complex With Hypoxanthine-Containing Dna
Length = 773
Score = 52.4 bits (124), Expect = 1e-07, Method: Composition-based stats.
Identities = 33/107 (30%), Positives = 55/107 (51%), Gaps = 10/107 (9%)
Query: 60 DQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYS 119
+ + G V EP++G + + I LDF SLYPSI++ HN+ T L + + ++ P Q
Sbjct: 382 ESYAGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVSPDT-LNREGCEEYDVAP-QVG 438
Query: 120 KTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVL 166
C +F G +P +L +LL R++ K +K D + + L
Sbjct: 439 HKFCKDF-------PGFIPSLLGDLLEERQKVKKKMKATIDPIEKKL 478
>pdb|2VWJ|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography
Length = 773
Score = 52.4 bits (124), Expect = 1e-07, Method: Composition-based stats.
Identities = 33/107 (30%), Positives = 55/107 (51%), Gaps = 10/107 (9%)
Query: 60 DQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYS 119
+ + G V EP++G + + I LDF SLYPSI++ HN+ T L + + ++ P Q
Sbjct: 382 ESYAGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVSPDT-LNREGCEEYDVAP-QVG 438
Query: 120 KTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVL 166
C +F G +P +L +LL R++ K +K D + + L
Sbjct: 439 HKFCKDF-------PGFIPSLLGDLLEERQKVKKKMKATIDPIEKKL 478
>pdb|2VWK|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography. V93q Polymerase Variant
Length = 773
Score = 52.4 bits (124), Expect = 1e-07, Method: Composition-based stats.
Identities = 33/107 (30%), Positives = 55/107 (51%), Gaps = 10/107 (9%)
Query: 60 DQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYS 119
+ + G V EP++G + + I LDF SLYPSI++ HN+ T L + + ++ P Q
Sbjct: 382 ESYAGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVSPDT-LNREGCEEYDVAP-QVG 438
Query: 120 KTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVL 166
C +F G +P +L +LL R++ K +K D + + L
Sbjct: 439 HKFCKDF-------PGFIPSLLGDLLEERQKVKKKMKATIDPIEKKL 478
>pdb|1TGO|A Chain A, Thermostable B Type Dna Polymerase From Thermococcus
Gorgonarius
Length = 773
Score = 52.4 bits (124), Expect = 1e-07, Method: Composition-based stats.
Identities = 33/107 (30%), Positives = 55/107 (51%), Gaps = 10/107 (9%)
Query: 60 DQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYS 119
+ + G V EP++G + + I LDF SLYPSI++ HN+ T L + + ++ P Q
Sbjct: 382 ESYAGGYVKEPERGLWEN-IVYLDFRSLYPSIIITHNVSPDT-LNREGCEEYDVAP-QVG 438
Query: 120 KTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVL 166
C +F G +P +L +LL R++ K +K D + + L
Sbjct: 439 HKFCKDF-------PGFIPSLLGDLLEERQKVKKKMKATIDPIEKKL 478
>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 = 52.0 bits (123), Expect = 2e-07, Method: Composition-based stats.
Identities = 33/107 (30%), Positives = 55/107 (51%), Gaps = 10/107 (9%)
Query: 60 DQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYS 119
+ + G V EP+KG + + I LD+ SLYPSI++ HN+ T L + + ++ P Q
Sbjct: 382 ESYAGGYVKEPEKGLWEN-IVYLDYKSLYPSIIITHNVSPDT-LNREGCREYDVAP-QVG 438
Query: 120 KTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVL 166
C +F G +P +L +LL R++ K +K D + + L
Sbjct: 439 HRFCKDF-------PGFIPSLLGDLLEERQKVKKKMKATVDPIERKL 478
>pdb|1QQC|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
D.Tok
Length = 773
Score = 52.0 bits (123), Expect = 2e-07, Method: Composition-based stats.
Identities = 33/107 (30%), Positives = 55/107 (51%), Gaps = 10/107 (9%)
Query: 60 DQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYS 119
+ + G V EP+KG + + I LD+ SLYPSI++ HN+ T L + + ++ P Q
Sbjct: 382 ESYAGGYVKEPEKGLWEN-IVYLDYKSLYPSIIITHNVSPDT-LNREGCREYDVAP-QVG 438
Query: 120 KTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVL 166
C +F G +P +L +LL R++ K +K D + + L
Sbjct: 439 HRFCKDF-------PGFIPSLLGDLLEERQKVKKKMKATVDPIERKL 478
>pdb|2JGU|A Chain A, Crystal Structure Of Dna-directed Dna Polymerase
Length = 775
Score = 52.0 bits (123), Expect = 2e-07, Method: Composition-based stats.
Identities = 34/107 (31%), Positives = 57/107 (53%), Gaps = 10/107 (9%)
Query: 60 DQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYS 119
+ + G V EP+KG + + I LD+ SLYPSI++ HN ++P T+ LE +
Sbjct: 383 ESYTGGFVKEPEKGLWEN-IVYLDYKSLYPSIIITHN------VSPDTLN-LEGCKNYDI 434
Query: 120 KTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVL 166
G+ F K G +P +L +LL R++ K +K+ D + ++L
Sbjct: 435 APQVGHKFCKDI--PGFIPSLLGHLLEERQKIKTKMKETQDPIEKIL 479
>pdb|3A2F|A Chain A, Crystal Structure Of Pyrococcus Furiosus Dna
PolymerasePCNA Monomer Mutant Complex
Length = 775
Score = 50.8 bits (120), Expect = 4e-07, Method: Composition-based stats.
Identities = 34/107 (31%), Positives = 56/107 (52%), Gaps = 10/107 (9%)
Query: 60 DQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYS 119
+ + G V EP+KG + + I LDF +LYPSI++ HN ++P T+ LE +
Sbjct: 383 ESYTGGFVKEPEKGLWEN-IVYLDFRALYPSIIITHN------VSPDTLN-LEGCKNYDI 434
Query: 120 KTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKETDELTQVL 166
G+ F K G +P +L +LL R++ K K+ D + ++L
Sbjct: 435 APQVGHKFCKDI--PGFIPSLLGHLLEERQKIKTKXKETQDPIEKIL 479
>pdb|1S5J|A Chain A, Insight In Dna Replication: The Crystal Structure Of Dna
Polymerase B1 From The Archaeon Sulfolobus Solfataricus
Length = 847
Score = 42.0 bits (97), Expect = 2e-04, Method: Composition-based stats.
Identities = 20/41 (48%), Positives = 28/41 (68%), Gaps = 1/41 (2%)
Query: 62 FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTL 102
++GA VI+P G + + I LDF+SLYPSI+ NL Y T+
Sbjct: 459 YKGAVVIDPPAGIFFN-ITVLDFASLYPSIIRTWNLSYETV 498
>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 = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 32/105 (30%), Positives = 49/105 (46%), Gaps = 12/105 (11%)
Query: 64 GATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPC 123
G V++ + G Y D + LD+ SLYPSI+ T L+ P + + PD T
Sbjct: 404 GGYVMDSRPGLY-DSVLVLDYKSLYPSIIR------TFLIDPVGLVEGMAQPDPEHSTEG 456
Query: 124 GNFFLKS--SLRKGLLPEILENLLSARKQAKNDLKKETDELTQVL 166
FL + S K LPEI+ N+ R +AK K + +++
Sbjct: 457 ---FLDAWFSREKHCLPEIVTNIWHGRDEAKRQGNKPLSQALKII 498
>pdb|1Q8I|A Chain A, Crystal Structure Of Escherichia Coli Dna Polymerase Ii
Length = 783
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 32/105 (30%), Positives = 49/105 (46%), Gaps = 12/105 (11%)
Query: 64 GATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPC 123
G V++ + G Y D + LD+ SLYPSI+ T L+ P + + PD T
Sbjct: 401 GGYVMDSRPGLY-DSVLVLDYKSLYPSIVR------TFLIDPVGLVEGMAQPDPEHSTEG 453
Query: 124 GNFFLKS--SLRKGLLPEILENLLSARKQAKNDLKKETDELTQVL 166
FL + S K LPEI+ N+ R +AK K + +++
Sbjct: 454 ---FLDAWFSREKHCLPEIVTNIWHGRDEAKRQGNKPLSQALKII 495
>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 = 38.9 bits (89), Expect = 0.001, Method: Composition-based stats.
Identities = 34/123 (27%), Positives = 55/123 (44%), Gaps = 20/123 (16%)
Query: 42 AVTQKNFIIPTYHGGQGEDQ----FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNL 97
++ ++N +IP QG + GA V EP Y + + D +SLYPSI+ N+
Sbjct: 372 SLKEQNKVIP-----QGRSHPVQPYPGAFVKEPIPNRY-KYVXSFDLTSLYPSIIRQVNI 425
Query: 98 CYTTLLTPQTITKL--------ELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARK 149
T+ + L E D YS +P G + K R G++P + + + RK
Sbjct: 426 SPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGXXYYKD--RDGVVPTEITKVFNQRK 483
Query: 150 QAK 152
+ K
Sbjct: 484 EHK 486
>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 = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 35/123 (28%), Positives = 55/123 (44%), Gaps = 20/123 (16%)
Query: 42 AVTQKNFIIPTYHGGQGEDQ----FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNL 97
++ ++N +IP QG + GA V EP Y + + D +SLYPSI+ N+
Sbjct: 372 SLKEQNKVIP-----QGRSHPVQPYPGAFVKEPIPNRYK-YVMSFDLTSLYPSIIRQVNI 425
Query: 98 CYTTLLTPQTITKL--------ELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARK 149
T+ + L E D YS +P G + K R G++P + +S RK
Sbjct: 426 SPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKWVSQRK 483
Query: 150 QAK 152
+ K
Sbjct: 484 EHK 486
>pdb|3CFO|A Chain A, Triple Mutant Apo Structure
pdb|3CFP|A Chain A, Structure Of The Replicating Complex Of A Pol Alpha Family
Dna Polymerase, Ternary Complex 1
pdb|3CFR|A Chain A, Structure Of The Replicating Complex Of A Pol Alpha Family
Dna Polymerase, Ternary Complex 2
Length = 909
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 34/123 (27%), Positives = 55/123 (44%), Gaps = 20/123 (16%)
Query: 42 AVTQKNFIIPTYHGGQGEDQ----FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNL 97
++ ++N +IP QG + GA V EP Y + + D +SLYPSI+ N+
Sbjct: 372 SLKEQNKVIP-----QGRSHPVQPYPGAFVKEPIPNRYK-YVMSFDLTSLYPSIIRQVNI 425
Query: 98 CYTTLLTPQTITKL--------ELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARK 149
T+ + L E D YS +P G + K R G++P + + + RK
Sbjct: 426 SPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRK 483
Query: 150 QAK 152
+ K
Sbjct: 484 EHK 486
>pdb|3SUN|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dttp
Opposite 2ap (At Rich Sequence)
Length = 895
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 34/123 (27%), Positives = 55/123 (44%), Gaps = 20/123 (16%)
Query: 42 AVTQKNFIIPTYHGGQGEDQ----FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNL 97
++ ++N +IP QG + GA V EP Y + + D +SLYPSI+ N+
Sbjct: 372 SLKEQNKVIP-----QGRSHPVQPYPGAFVKEPIPNRYK-YVMSFDLTSLYPSIIRQVNI 425
Query: 98 CYTTLLTPQTITKL--------ELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARK 149
T+ + L E D YS +P G + K R G++P + + + RK
Sbjct: 426 SPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRK 483
Query: 150 QAK 152
+ K
Sbjct: 484 EHK 486
>pdb|3SUQ|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dctp
Opposite 2ap (At Rich Sequence)
Length = 897
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 34/123 (27%), Positives = 55/123 (44%), Gaps = 20/123 (16%)
Query: 42 AVTQKNFIIPTYHGGQGEDQ----FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNL 97
++ ++N +IP QG + GA V EP Y + + D +SLYPSI+ N+
Sbjct: 372 SLKEQNKVIP-----QGRSHPVQPYPGAFVKEPIPNRYK-YVMSFDLTSLYPSIIRQVNI 425
Query: 98 CYTTLLTPQTITKL--------ELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARK 149
T+ + L E D YS +P G + K R G++P + + + RK
Sbjct: 426 SPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRK 483
Query: 150 QAK 152
+ K
Sbjct: 484 EHK 486
>pdb|4DTJ|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp Opposite An
Abasic Site And DdtDA AS THE PENULTIMATE BASE-Pair
pdb|4DTM|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp Opposite An
Abasic Site And DdgDC AS THE PENULTIMATE BASE-Pair
Length = 901
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 34/123 (27%), Positives = 55/123 (44%), Gaps = 20/123 (16%)
Query: 42 AVTQKNFIIPTYHGGQGEDQ----FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNL 97
++ ++N +IP QG + GA V EP Y + + D +SLYPSI+ N+
Sbjct: 372 SLKEQNKVIP-----QGRSHPVQPYPGAFVKEPIPNRYK-YVMSFDLTSLYPSIIRQVNI 425
Query: 98 CYTTLLTPQTITKL--------ELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARK 149
T+ + L E D YS +P G + K R G++P + + + RK
Sbjct: 426 SPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRK 483
Query: 150 QAK 152
+ K
Sbjct: 484 EHK 486
>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 = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 34/123 (27%), Positives = 55/123 (44%), Gaps = 20/123 (16%)
Query: 42 AVTQKNFIIPTYHGGQGEDQ----FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNL 97
++ ++N +IP QG + GA V EP Y + + D +SLYPSI+ N+
Sbjct: 372 SLKEQNKVIP-----QGRSHPVQPYPGAFVKEPIPNRYK-YVMSFDLTSLYPSIIRQVNI 425
Query: 98 CYTTLLTPQTITKL--------ELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARK 149
T+ + L E D YS +P G + K R G++P + + + RK
Sbjct: 426 SPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRK 483
Query: 150 QAK 152
+ K
Sbjct: 484 EHK 486
>pdb|3SUO|A Chain A, Rb69 Dna Polymerase (Y567a) Ternary Complex With Dttp
Opposite 2ap (Gc Rich Sequence)
Length = 900
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 34/123 (27%), Positives = 55/123 (44%), Gaps = 20/123 (16%)
Query: 42 AVTQKNFIIPTYHGGQGEDQ----FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNL 97
++ ++N +IP QG + GA V EP Y + + D +SLYPSI+ N+
Sbjct: 372 SLKEQNKVIP-----QGRSHPVQPYPGAFVKEPIPNRYK-YVMSFDLTSLYPSIIRQVNI 425
Query: 98 CYTTLLTPQTITKL--------ELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARK 149
T+ + L E D YS +P G + K R G++P + + + RK
Sbjct: 426 SPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRK 483
Query: 150 QAK 152
+ K
Sbjct: 484 EHK 486
>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 = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 34/123 (27%), Positives = 55/123 (44%), Gaps = 20/123 (16%)
Query: 42 AVTQKNFIIPTYHGGQGEDQ----FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNL 97
++ ++N +IP QG + GA V EP Y + + D +SLYPSI+ N+
Sbjct: 372 SLKEQNKVIP-----QGRSHPVQPYPGAFVKEPIPNRYK-YVMSFDLTSLYPSIIRQVNI 425
Query: 98 CYTTLLTPQTITKL--------ELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARK 149
T+ + L E D YS +P G + K R G++P + + + RK
Sbjct: 426 SPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRK 483
Query: 150 QAK 152
+ K
Sbjct: 484 EHK 486
>pdb|3LDS|A Chain A, Crystal Structure Of Rb69 Gp43 With Dna And Datp Opposite
8-
Length = 903
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 34/123 (27%), Positives = 55/123 (44%), Gaps = 20/123 (16%)
Query: 42 AVTQKNFIIPTYHGGQGEDQ----FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNL 97
++ ++N +IP QG + GA V EP Y + + D +SLYPSI+ N+
Sbjct: 372 SLKEQNKVIP-----QGRSHPVQPYPGAFVKEPIPNRYK-YVMSFDLTSLYPSIIRQVNI 425
Query: 98 CYTTLLTPQTITKL--------ELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARK 149
T+ + L E D YS +P G + K R G++P + + + RK
Sbjct: 426 SPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRK 483
Query: 150 QAK 152
+ K
Sbjct: 484 EHK 486
>pdb|3SQ1|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dupcpp Opposite
Da
Length = 901
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 34/123 (27%), Positives = 55/123 (44%), Gaps = 20/123 (16%)
Query: 42 AVTQKNFIIPTYHGGQGEDQ----FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNL 97
++ ++N +IP QG + GA V EP Y + + D +SLYPSI+ N+
Sbjct: 372 SLKEQNKVIP-----QGRSHPVQPYPGAFVKEPIPNRYK-YVMSFDLTSLYPSIIRQVNI 425
Query: 98 CYTTLLTPQTITKL--------ELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARK 149
T+ + L E D YS +P G + K R G++P + + + RK
Sbjct: 426 SPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRK 483
Query: 150 QAK 152
+ K
Sbjct: 484 EHK 486
>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 = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 34/123 (27%), Positives = 55/123 (44%), Gaps = 20/123 (16%)
Query: 42 AVTQKNFIIPTYHGGQGEDQ----FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNL 97
++ ++N +IP QG + GA V EP Y + + D +SLYPSI+ N+
Sbjct: 372 SLKEQNKVIP-----QGRSHPVQPYPGAFVKEPIPNRYK-YVMSFDLTSLYPSIIRQVNI 425
Query: 98 CYTTLLTPQTITKL--------ELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARK 149
T+ + L E D YS +P G + K R G++P + + + RK
Sbjct: 426 SPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRK 483
Query: 150 QAK 152
+ K
Sbjct: 484 EHK 486
>pdb|3QEP|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DTTP Opposite Difluorotoluene Nucleoside
pdb|3S9H|A Chain A, Rb69 Dna Polymerase Triple Mutant(L561aS565GY567A) TERNARY
COMPLEX With Dupnpp And A Dideoxy-Terminated Primer In
The Presence Of Ca2+
pdb|3SQ0|A Chain A, Dna Polymerase(L561aS565GY567A) TERNARY COMPLEX WITH
DUPNPP OPPOSITE Da (Mn2+)
pdb|3QEI|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DCTP Opposite Difluorotoluene Nucleoside
pdb|3QER|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DATP Opposite Difluorotoluene Nucleoside
pdb|3QES|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DGTP Opposite Difluorotoluene Nucleoside
pdb|3QET|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DTTP Opposite Dt
pdb|3QEV|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DCTP Opposite Dt
pdb|3QEW|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DDTP Opposite Dt
pdb|3QEX|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DGTP Opposite Dt
pdb|4E3S|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dqtp Opposite Dt
pdb|4DTN|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp Opposite An
Abasic Site And DdaDT AS THE PENULTIMATE BASE-Pair
pdb|4DTO|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp Opposite An
Abasic Site And DdaDT AS THE PENULTIMATE BASE-Pair
pdb|4DTP|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dgtp Opposite An
Abasic Site And DdaDT AS THE PENULTIMATE BASE-Pair
pdb|4DTR|A Chain A, Rb69 Dna Polymerase Ternary Complex With Datp Opposite An
Abasic Site And DdcDG AS THE PENULTIMATE BASE-Pair
pdb|4DTS|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp Opposite An
Abasic Site And DdcDG AS THE PENULTIMATE BASE-Pair
pdb|4DTU|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dgtp Opposite An
Abasic Site And DdcDG AS THE PENULTIMATE BASE-Pair
pdb|4DTX|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dttp Opposite An
Abasic Site And DdcDG AS THE PENULTIMATE BASE-Pair
pdb|4FJM|A Chain A, Rb69 Dna Polymerase Ternary Complex With Dctp/da
Length = 903
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 34/123 (27%), Positives = 55/123 (44%), Gaps = 20/123 (16%)
Query: 42 AVTQKNFIIPTYHGGQGEDQ----FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNL 97
++ ++N +IP QG + GA V EP Y + + D +SLYPSI+ N+
Sbjct: 372 SLKEQNKVIP-----QGRSHPVQPYPGAFVKEPIPNRYK-YVMSFDLTSLYPSIIRQVNI 425
Query: 98 CYTTLLTPQTITKL--------ELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARK 149
T+ + L E D YS +P G + K R G++P + + + RK
Sbjct: 426 SPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRK 483
Query: 150 QAK 152
+ K
Sbjct: 484 EHK 486
>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 = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 34/123 (27%), Positives = 55/123 (44%), Gaps = 20/123 (16%)
Query: 42 AVTQKNFIIPTYHGGQGEDQ----FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNL 97
++ ++N +IP QG + GA V EP Y + + D +SLYPSI+ N+
Sbjct: 372 SLKEQNKVIP-----QGRSHPVQPYPGAFVKEPIPNRYK-YVMSFDLTSLYPSIIRQVNI 425
Query: 98 CYTTLLTPQTITKL--------ELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARK 149
T+ + L E D YS +P G + K R G++P + + + RK
Sbjct: 426 SPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRK 483
Query: 150 QAK 152
+ K
Sbjct: 484 EHK 486
>pdb|3SCX|A Chain A, Rb69 Dna Polymerase Triple Mutant(L561aS565GY567A) TERNARY
COMPLEX With Dupnpp And A Deoxy-Terminated Primer In The
Presence Of Ca2+
pdb|3SI6|A Chain A, Rb69 Dna Polymerase Triple Mutant (L561aS565GY567A)
TERNARY COMPLEX With Dupnpp And A Deoxy-Terminated
Primer In The Presence Of Mg2+
pdb|3SJJ|A Chain A, Rb69 Dna Polymerase Triple Mutant (L561aS565GY567A)
TERNARY COMPLEX With Dupnpp And A Deoxy-Terminated
Primer In The Presence Of Mn2+
pdb|3SNN|A Chain A, Rb69 Dna Polymerase (L561aS565GY567A) TERNARY COMPLEX WITH
DCTP Opposite Dg In The Presence Of Mg2+
Length = 903
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 34/123 (27%), Positives = 55/123 (44%), Gaps = 20/123 (16%)
Query: 42 AVTQKNFIIPTYHGGQGEDQ----FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNL 97
++ ++N +IP QG + GA V EP Y + + D +SLYPSI+ N+
Sbjct: 372 SLKEQNKVIP-----QGRSHPVQPYPGAFVKEPIPNRYK-YVMSFDLTSLYPSIIRQVNI 425
Query: 98 CYTTLLTPQTITKL--------ELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARK 149
T+ + L E D YS +P G + K R G++P + + + RK
Sbjct: 426 SPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRK 483
Query: 150 QAK 152
+ K
Sbjct: 484 EHK 486
>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 = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 34/123 (27%), Positives = 55/123 (44%), Gaps = 20/123 (16%)
Query: 42 AVTQKNFIIPTYHGGQGEDQ----FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNL 97
++ ++N +IP QG + GA V EP Y + + D +SLYPSI+ N+
Sbjct: 372 SLKEQNKVIP-----QGRSHPVQPYPGAFVKEPIPNRYK-YVMSFDLTSLYPSIIRQVNI 425
Query: 98 CYTTLLTPQTITKL--------ELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARK 149
T+ + L E D YS +P G + K R G++P + + + RK
Sbjct: 426 SPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRK 483
Query: 150 QAK 152
+ K
Sbjct: 484 EHK 486
>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 = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 34/123 (27%), Positives = 55/123 (44%), Gaps = 20/123 (16%)
Query: 42 AVTQKNFIIPTYHGGQGEDQ----FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNL 97
++ ++N +IP QG + GA V EP Y + + D +SLYPSI+ N+
Sbjct: 372 SLKEQNKVIP-----QGRSHPVQPYPGAFVKEPIPNRYK-YVMSFDLTSLYPSIIRQVNI 425
Query: 98 CYTTLLTPQTITKL--------ELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARK 149
T+ + L E D YS +P G + K R G++P + + + RK
Sbjct: 426 SPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRK 483
Query: 150 QAK 152
+ K
Sbjct: 484 EHK 486
>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 = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 34/123 (27%), Positives = 55/123 (44%), Gaps = 20/123 (16%)
Query: 42 AVTQKNFIIPTYHGGQGEDQ----FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNL 97
++ ++N +IP QG + GA V EP Y + + D +SLYPSI+ N+
Sbjct: 372 SLKEQNKVIP-----QGRSHPVQPYPGAFVKEPIPNRYK-YVMSFDLTSLYPSIIRQVNI 425
Query: 98 CYTTLLTPQTITKL--------ELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARK 149
T+ + L E D YS +P G + K R G++P + + + RK
Sbjct: 426 SPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRK 483
Query: 150 QAK 152
+ K
Sbjct: 484 EHK 486
>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 = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 34/123 (27%), Positives = 55/123 (44%), Gaps = 20/123 (16%)
Query: 42 AVTQKNFIIPTYHGGQGEDQ----FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNL 97
++ ++N +IP QG + GA V EP Y + + D +SLYPSI+ N+
Sbjct: 365 SLKEQNKVIP-----QGRSHPVQPYPGAFVKEPIPNRYK-YVMSFDLTSLYPSIIRQVNI 418
Query: 98 CYTTLLTPQTITKL--------ELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARK 149
T+ + L E D YS +P G + K R G++P + + + RK
Sbjct: 419 SPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRK 476
Query: 150 QAK 152
+ K
Sbjct: 477 EHK 479
>pdb|1Q9Y|A Chain A, Crystal Structure Of Enterobacteria Phage Rb69 Gp43 Dna
Polymerase Complexed With 8-Oxoguanosine Containing Dna
Length = 906
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 34/123 (27%), Positives = 55/123 (44%), Gaps = 20/123 (16%)
Query: 42 AVTQKNFIIPTYHGGQGEDQ----FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNL 97
++ ++N +IP QG + GA V EP Y + + D +SLYPSI+ N+
Sbjct: 375 SLKEQNKVIP-----QGRSHPVQPYPGAFVKEPIPNRYK-YVMSFDLTSLYPSIIRQVNI 428
Query: 98 CYTTLLTPQTITKL--------ELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARK 149
T+ + L E D YS +P G + K R G++P + + + RK
Sbjct: 429 SPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRK 486
Query: 150 QAK 152
+ K
Sbjct: 487 EHK 489
>pdb|3CQ8|A Chain A, Ternary Complex Of The L415f Mutant Rb69 Exo(-)polymerase
Length = 903
Score = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 33/123 (26%), Positives = 54/123 (43%), Gaps = 20/123 (16%)
Query: 42 AVTQKNFIIPTYHGGQGEDQ----FEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNL 97
++ ++N +IP QG + GA V EP Y + + D +S YPSI+ N+
Sbjct: 372 SLKEQNKVIP-----QGRSHPVQPYPGAFVKEPIPNRYK-YVMSFDLTSFYPSIIRQVNI 425
Query: 98 CYTTLLTPQTITKL--------ELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARK 149
T+ + L E D YS +P G + K R G++P + + + RK
Sbjct: 426 SPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKD--RDGVVPTEITKVFNQRK 483
Query: 150 QAK 152
+ K
Sbjct: 484 EHK 486
>pdb|3B9X|A Chain A, Crystal Structure Of The E. Coli Pyrimidine Nucleoside
Hydrolase Yeik In Complex With Inosine
pdb|3B9X|B Chain B, Crystal Structure Of The E. Coli Pyrimidine Nucleoside
Hydrolase Yeik In Complex With Inosine
pdb|3B9X|C Chain C, Crystal Structure Of The E. Coli Pyrimidine Nucleoside
Hydrolase Yeik In Complex With Inosine
pdb|3B9X|D Chain D, Crystal Structure Of The E. Coli Pyrimidine Nucleoside
Hydrolase Yeik In Complex With Inosine
Length = 333
Score = 30.8 bits (68), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 75 YADP-IATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPCGNFF 127
+ADP A + F+S P +MM +L T+ TP I ++E + P G F
Sbjct: 188 FADPEAARVVFTSGVPLVMMGLDLTNQTVCTPDVIARME-----RAGGPAGELF 236
>pdb|3MKM|A Chain A, Crystal Structure Of The E. Coli Pyrimidine Nucleoside
Hydrolase Yeik (Apo-Form)
pdb|3MKM|B Chain B, Crystal Structure Of The E. Coli Pyrimidine Nucleoside
Hydrolase Yeik (Apo-Form)
pdb|3MKM|C Chain C, Crystal Structure Of The E. Coli Pyrimidine Nucleoside
Hydrolase Yeik (Apo-Form)
pdb|3MKM|D Chain D, Crystal Structure Of The E. Coli Pyrimidine Nucleoside
Hydrolase Yeik (Apo-Form)
pdb|3MKN|A Chain A, Crystal Structure Of The E. Coli Pyrimidine Nucleosidase
Yeik Bound To A Competitive Inhibitor
pdb|3MKN|B Chain B, Crystal Structure Of The E. Coli Pyrimidine Nucleosidase
Yeik Bound To A Competitive Inhibitor
pdb|3MKN|C Chain C, Crystal Structure Of The E. Coli Pyrimidine Nucleosidase
Yeik Bound To A Competitive Inhibitor
pdb|3MKN|D Chain D, Crystal Structure Of The E. Coli Pyrimidine Nucleosidase
Yeik Bound To A Competitive Inhibitor
Length = 316
Score = 30.8 bits (68), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 75 YADP-IATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPCGNFF 127
+ADP A + F+S P +MM +L T+ TP I ++E + P G F
Sbjct: 171 FADPEAARVVFTSGVPLVMMGLDLTNQTVCTPDVIARME-----RAGGPAGELF 219
>pdb|1Q8F|A Chain A, Crystal Structure Of The E.Coli Pyrimidine Nucleoside
Hydrolase Yeik
pdb|1Q8F|B Chain B, Crystal Structure Of The E.Coli Pyrimidine Nucleoside
Hydrolase Yeik
pdb|1Q8F|C Chain C, Crystal Structure Of The E.Coli Pyrimidine Nucleoside
Hydrolase Yeik
pdb|1Q8F|D Chain D, Crystal Structure Of The E.Coli Pyrimidine Nucleoside
Hydrolase Yeik
Length = 313
Score = 30.8 bits (68), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 75 YADP-IATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPCGNFF 127
+ADP A + F+S P +MM +L T+ TP I ++E + P G F
Sbjct: 168 FADPEAARVVFTSGVPLVMMGLDLTNQTVCTPDVIARME-----RAGGPAGELF 216
>pdb|3VX8|B Chain B, Crystal Structure Of Arabidopsis Thaliana Atg7ntd-Atg3
Complex
pdb|3VX8|C Chain C, Crystal Structure Of Arabidopsis Thaliana Atg7ntd-Atg3
Complex
Length = 292
Score = 30.0 bits (66), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 32/112 (28%), Positives = 51/112 (45%), Gaps = 11/112 (9%)
Query: 43 VTQKNFI--IPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYT 100
+ +KN I IPTY GG+ +D + AD + D ++L + ++AH
Sbjct: 112 INEKNTIQSIPTYFGGEEDDDIPDMEEFDE-----ADNVVENDPATLQSTYLVAHEPDDD 166
Query: 101 TLLTPQTITKLELTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLS---ARK 149
+L +T L +T D+Y +TP R L PE++ +S ARK
Sbjct: 167 NILRTRTY-DLSITYDKYYQTPRVWLTGYDESRMLLQPELVMEDVSQDHARK 217
>pdb|1R0N|B Chain B, Crystal Structure Of Heterodimeric Ecdsyone Receptor Dna
Binding Complex
pdb|1R0O|B Chain B, Crystal Structure Of The Heterodimeric Ecdysone Receptor
Dna-Binding Complex
Length = 109
Score = 26.9 bits (58), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 116 DQYSKTPCGNFFLKSSLRKGLLPEIL--ENLLSARKQAKNDLKKETDELT 163
D Y + C LK L G+ PE + EN + +++ K +KE D++T
Sbjct: 54 DMYMRRKCQECRLKKCLAVGMRPECVVPENQCAMKRREKK-AQKEKDKMT 102
>pdb|2HAN|B Chain B, Structural Basis Of Heterodimeric Ecdysteroid Receptor
Interaction With Natural Response Element Hsp27 Gene
Promoter
Length = 119
Score = 26.6 bits (57), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 116 DQYSKTPCGNFFLKSSLRKGLLPEIL--ENLLSARKQAKNDLKKETDELT 163
D Y + C LK L G+ PE + EN + +++ K +KE D++T
Sbjct: 56 DMYMRRKCQECRLKKCLAVGMRPECVVPENQCAMKRREKK-AQKEKDKMT 104
>pdb|3CG1|A Chain A, Crystal Structure Of P. Furiosus Periplasmic Binding
Protein ModaWTPA WITH BOUND TUNGSTATE
pdb|3CG1|B Chain B, Crystal Structure Of P. Furiosus Periplasmic Binding
Protein ModaWTPA WITH BOUND TUNGSTATE
Length = 296
Score = 26.2 bits (56), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 64 GATVIEPKKGYYADPI--ATLDFSSLYPSIMMAHNLCYTTL 102
G VI PK+ + ++D+ +Y S+ HNL Y TL
Sbjct: 182 GKIVIRPKETDLLGLVESGSIDYIFIYKSVAKQHNLSYITL 222
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 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,145,128
Number of Sequences: 62578
Number of extensions: 203620
Number of successful extensions: 447
Number of sequences better than 100.0: 56
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 35
Number of HSP's that attempted gapping in prelim test: 399
Number of HSP's gapped (non-prelim): 76
length of query: 168
length of database: 14,973,337
effective HSP length: 92
effective length of query: 76
effective length of database: 9,216,161
effective search space: 700428236
effective search space used: 700428236
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: 48 (23.1 bits)