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= 002293
(940 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1BGX|T Chain T, Taq Polymerase In Complex With Tp7, An Inhibitory Fab
pdb|1TAU|A Chain A, Taq Polymerase (E.C.2.7.7.7)DNAB-Octylglucoside Complex
Length = 832
Score = 90.5 bits (223), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 53/140 (37%), Positives = 77/140 (55%), Gaps = 2/140 (1%)
Query: 780 ATEQEAREACDAISALCEVCSIDSLISNFILPLQGSNVSGKNGRVHCSLN-INTETGRLS 838
A + REA + + + + L S +I PL + + GR+H N T TGRLS
Sbjct: 517 AVLEALREAHPIVEKILQYRELTKLKSTYIDPLP-DLIHPRTGRLHTRFNQTATATGRLS 575
Query: 839 ARRPNLQNQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAG 898
+ PNLQN P +IR+AFIA G L+ DY Q+ELR+LAHL+ ++++ F+ G
Sbjct: 576 SSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEG 635
Query: 899 GDFHSRTAMNMYPHIRNAVE 918
D H+ TA M+ R AV+
Sbjct: 636 RDIHTETASWMFGVPREAVD 655
>pdb|2KTQ|A Chain A, Open Ternary Complex Of The Large Fragment Of Dna
Polymerase I From Thermus Aquaticus
Length = 538
Score = 90.5 bits (223), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 53/140 (37%), Positives = 77/140 (55%), Gaps = 2/140 (1%)
Query: 780 ATEQEAREACDAISALCEVCSIDSLISNFILPLQGSNVSGKNGRVHCSLN-INTETGRLS 838
A + REA + + + + L S +I PL + + GR+H N T TGRLS
Sbjct: 223 AVLEALREAHPIVEKILQYRELTKLKSTYIDPLP-DLIHPRTGRLHTRFNQTATATGRLS 281
Query: 839 ARRPNLQNQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAG 898
+ PNLQN P +IR+AFIA G L+ DY Q+ELR+LAHL+ ++++ F+ G
Sbjct: 282 SSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEG 341
Query: 899 GDFHSRTAMNMYPHIRNAVE 918
D H+ TA M+ R AV+
Sbjct: 342 RDIHTETASWMFGVPREAVD 361
>pdb|5KTQ|A Chain A, Large Fragment Of Taq Dna Polymerase Bound To Dctp
pdb|1KTQ|A Chain A, Dna Polymerase
Length = 543
Score = 90.1 bits (222), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 53/140 (37%), Positives = 77/140 (55%), Gaps = 2/140 (1%)
Query: 780 ATEQEAREACDAISALCEVCSIDSLISNFILPLQGSNVSGKNGRVHCSLN-INTETGRLS 838
A + REA + + + + L S +I PL + + GR+H N T TGRLS
Sbjct: 228 AVLEALREAHPIVEKILQYRELTKLKSTYIDPLP-DLIHPRTGRLHTRFNQTATATGRLS 286
Query: 839 ARRPNLQNQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAG 898
+ PNLQN P +IR+AFIA G L+ DY Q+ELR+LAHL+ ++++ F+ G
Sbjct: 287 SSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEG 346
Query: 899 GDFHSRTAMNMYPHIRNAVE 918
D H+ TA M+ R AV+
Sbjct: 347 RDIHTETASWMFGVPREAVD 366
>pdb|1QSS|A Chain A, Ddgtp-Trapped Closed Ternary Complex Of The Large Fragment
Of Dna Polymerase I From Thermus Aquaticus
pdb|1QSY|A Chain A, Ddatp-Trapped Closed Ternary Complex Of The Large Fragment
Of Dna Polymerase I From Thermus Aquaticus
Length = 539
Score = 90.1 bits (222), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 53/140 (37%), Positives = 77/140 (55%), Gaps = 2/140 (1%)
Query: 780 ATEQEAREACDAISALCEVCSIDSLISNFILPLQGSNVSGKNGRVHCSLN-INTETGRLS 838
A + REA + + + + L S +I PL + + GR+H N T TGRLS
Sbjct: 225 AVLEALREAHPIVEKILQYRELTKLKSTYIDPLP-DLIHPRTGRLHTRFNQTATATGRLS 283
Query: 839 ARRPNLQNQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAG 898
+ PNLQN P +IR+AFIA G L+ DY Q+ELR+LAHL+ ++++ F+ G
Sbjct: 284 SSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEG 343
Query: 899 GDFHSRTAMNMYPHIRNAVE 918
D H+ TA M+ R AV+
Sbjct: 344 RDIHTETASWMFGVPREAVD 363
>pdb|4KTQ|A Chain A, Binary Complex Of The Large Fragment Of Dna Polymerase I
From T. Aquaticus Bound To A PrimerTEMPLATE DNA
Length = 539
Score = 90.1 bits (222), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 53/140 (37%), Positives = 77/140 (55%), Gaps = 2/140 (1%)
Query: 780 ATEQEAREACDAISALCEVCSIDSLISNFILPLQGSNVSGKNGRVHCSLN-INTETGRLS 838
A + REA + + + + L S +I PL + + GR+H N T TGRLS
Sbjct: 224 AVLEALREAHPIVEKILQYRELTKLKSTYIDPLP-DLIHPRTGRLHTRFNQTATATGRLS 282
Query: 839 ARRPNLQNQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAG 898
+ PNLQN P +IR+AFIA G L+ DY Q+ELR+LAHL+ ++++ F+ G
Sbjct: 283 SSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEG 342
Query: 899 GDFHSRTAMNMYPHIRNAVE 918
D H+ TA M+ R AV+
Sbjct: 343 RDIHTETASWMFGVPREAVD 362
>pdb|3KTQ|A Chain A, Crystal Structure Of An Active Ternary Complex Of The
Large Fragment Of Dna Polymerase I From Thermus
Aquaticus
pdb|1JXE|A Chain A, Stoffel Fragment Of Taq Dna Polymerase I
pdb|3LWL|A Chain A, Structure Of Klenow Fragment Of Taq Polymerase In Complex
Wi Abasic Site
pdb|3LWM|A Chain A, Structure Of The Large Fragment Of Thermus Aquaticus Dna
Pol In Complex With A Blunt-Ended Dna And Ddatp
pdb|3M8R|A Chain A, Crystal Structure Of The Large Fragment Of Dna Polymerase
I From Thermus Aquaticus In A Closed Ternary Complex
With Trapped 4'- Ethylated Dttp
pdb|3M8S|A Chain A, Crystal Structure Of The Large Fragment Of Dna Polymerase
I From Thermus Aquaticus In A Closed Ternary Complex
With Trapped 4'- Methylated Dttp
pdb|3OJS|A Chain A, Snapshots Of The Large Fragment Of Dna Polymerase I From
Thermus Aquaticus Processing C5 Modified Thymidines
pdb|3OJU|A Chain A, Snapshot Of The Large Fragment Of Dna Polymerase I From
Thermus Aquaticus Processing C5 Modified Thymidies
pdb|3RR7|A Chain A, Binary Structure Of The Large Fragment Of Taq Dna
Polymerase Bound To An Abasic Site
pdb|3RR8|A Chain A, Ternary Structure Of The Large Fragment Of Taq Dna
Polymerase Bound To An Abasic Site And A Ddgtp
pdb|3RRG|A Chain A, Ternary Structure Of The Large Fragment Of Taq Dna
Polymerase Bound To An Abasic Site And A Ddgtp
pdb|3RRH|A Chain A, Ternary Structure Of The Large Fragment Of Taq Dna
Polymerase Bound To An Abasic Site And A Ddttp
pdb|3T3F|A Chain A, Ternary Structure Of The Large Fragment Of Taq Dna
Polymerase Bound To An Abasic Site And Dnitp
pdb|4DF4|A Chain A, Crystal Structure Of The Large Fragment Of Dna Polymerase
I From Thermus Aquaticus In A Closed Ternary Complex
With 7-(N-(10- Hydroxydecanoyl)-Aminopentinyl)-7-Deaza-2
-Datp
pdb|4DF8|A Chain A, Crystal Structure Of The Large Fragment Of Dna Polymerase
I From Thermus Aquaticus In A Closed Ternary Complex
With Aminopentinyl-7- Deaza-2-Datp
pdb|4DFJ|A Chain A, Crystal Structure Of The Large Fragment Of Dna Polymerase
I From Thermus Aquaticus In A Closed Ternary Complex
With 5-(Aminopentinyl)- Dttp
pdb|4DFK|A Chain A, Large Fragment Of Dna Polymerase I From Thermus Aquaticus
In A Closed Ternary Complex With
5-(N-(10-Hydroxydecanoyl)-Aminopentinyl)-2-Dutp
pdb|4DFM|A Chain A, Crystal Structure Of The Large Fragment Of Dna Polymerase
I From Thermus Aquaticus In Ternary Complex With
5-(Aminopentinyl)-2-Dctp
pdb|4DFP|A Chain A, Crystal Structure Of The Large Fragment Of Dna Polymerase
I From Thermus Aqauticus In A Ternary Complex With
7-(Aminopentinyl)-7- Deaza-Dgtp
pdb|3RTV|A Chain A, Crystal Structure Of The Large Fragment Of Dna Polymerase
I From Thermus Aquaticus In A Closed Ternary Complex
With Natural PrimerTEMPLATE DNA
pdb|3SV3|A Chain A, Crystal Structure Of The Large Fragment Of Dna Polymerase
I From Thermus Aquaticus In A Closed Ternary Complex
With The Artificial Base Pair Dnam-D5sicstp
pdb|3SV4|A Chain A, Crystal Structure Of The Large Fragment Of Dna Polymerase
I From Thermus Aquaticus In An Open Binary Complex With
Dt As Templating Nucleobase
pdb|3SYZ|A Chain A, Crystal Structure Of The Large Fragment Of Dna Polymerase
I From Thermus Aquaticus In An Open Binary Complex With
Dnam As Templating Nucleobase
pdb|3SZ2|A Chain A, Crystal Structure Of The Large Fragment Of Dna Polymerase
I From Thermus Aquaticus In An Open Binary Complex With
Dg As Templating Nucleobase
pdb|4DLG|A Chain A, Ternary Structure Of The Large Fragment Of Taq Dna
Polymerase
Length = 540
Score = 90.1 bits (222), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 53/140 (37%), Positives = 77/140 (55%), Gaps = 2/140 (1%)
Query: 780 ATEQEAREACDAISALCEVCSIDSLISNFILPLQGSNVSGKNGRVHCSLN-INTETGRLS 838
A + REA + + + + L S +I PL + + GR+H N T TGRLS
Sbjct: 225 AVLEALREAHPIVEKILQYRELTKLKSTYIDPLP-DLIHPRTGRLHTRFNQTATATGRLS 283
Query: 839 ARRPNLQNQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAG 898
+ PNLQN P +IR+AFIA G L+ DY Q+ELR+LAHL+ ++++ F+ G
Sbjct: 284 SSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEG 343
Query: 899 GDFHSRTAMNMYPHIRNAVE 918
D H+ TA M+ R AV+
Sbjct: 344 RDIHTETASWMFGVPREAVD 363
>pdb|1QTM|A Chain A, Ddttp-trapped Closed Ternary Complex Of The Large Fragment
Of Dna Polymerase I From Thermus Aquaticus
Length = 539
Score = 90.1 bits (222), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 53/140 (37%), Positives = 77/140 (55%), Gaps = 2/140 (1%)
Query: 780 ATEQEAREACDAISALCEVCSIDSLISNFILPLQGSNVSGKNGRVHCSLN-INTETGRLS 838
A + REA + + + + L S +I PL + + GR+H N T TGRLS
Sbjct: 225 AVLEALREAHPIVEKILQYRELTKLKSTYIDPLP-DLIHPRTGRLHTRFNQTATATGRLS 283
Query: 839 ARRPNLQNQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAG 898
+ PNLQN P +IR+AFIA G L+ DY Q+ELR+LAHL+ ++++ F+ G
Sbjct: 284 SSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEG 343
Query: 899 GDFHSRTAMNMYPHIRNAVE 918
D H+ TA M+ R AV+
Sbjct: 344 RDIHTETASWMFGVPREAVD 363
>pdb|3PO4|A Chain A, Structure Of A Mutant Of The Large Fragment Of Dna
Polymerase I From Thermus Aquaticus In Complex With A
Blunt-Ended Dna And Ddatp
pdb|3PO5|A Chain A, Structure Of A Mutant Of The Large Fragment Of Dna
Polymerase I From Thermus Auqaticus In Complex With An
Abasic Site And Ddatp
pdb|3PY8|A Chain A, Crystal Structure Of A Mutant Of The Large Fragment Of Dna
Polymerase I From Thermus Aquaticus In A Closed Ternary
Complex With Dna And Ddctp
Length = 540
Score = 88.2 bits (217), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 53/140 (37%), Positives = 76/140 (54%), Gaps = 2/140 (1%)
Query: 780 ATEQEAREACDAISALCEVCSIDSLISNFILPLQGSNVSGKNGRVHCSLN-INTETGRLS 838
A + REA + + + + L S +I PL + + GR+H N T TGRLS
Sbjct: 225 AVLEALREAHPIVEKILQYRELTKLKSTYIDPLP-DLIHPRTGRLHTRFNQTATATGRLS 283
Query: 839 ARRPNLQNQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAG 898
+ PNLQN P +IR+AFIA G L+ DY Q ELR+LAHL+ ++++ F+ G
Sbjct: 284 SSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYSQKELRVLAHLSGDENLIRVFQEG 343
Query: 899 GDFHSRTAMNMYPHIRNAVE 918
D H+ TA M+ R AV+
Sbjct: 344 RDIHTETASWMFGVPREAVD 363
>pdb|1DPI|A Chain A, Structure Of Large Fragment Of Escherichia Coli Dna
Polymerase I Complexed With DTMP
pdb|1KFD|A Chain A, Crystal Structures Of The Klenow Fragment Of Dna
Polymerase I Complexed With Deoxynucleoside Triphosphate
And Pyrophosphate
Length = 605
Score = 87.4 bits (215), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 48/102 (47%), Positives = 63/102 (61%), Gaps = 4/102 (3%)
Query: 810 LPLQGSNVSGKNGRVHCSLN-INTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNS 868
LPL ++ K GRVH S + T TGRLS+ PNLQN P ++ +IRQAFIA
Sbjct: 321 LPLM---INPKTGRVHTSYHQAVTATGRLSSTDPNLQNIPVRNEEGRRIRQAFIAPEDYV 377
Query: 869 LIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMY 910
++ ADY Q+ELRI+AHL+ K +L AF G D H TA ++
Sbjct: 378 IVSADYSQIELRIMAHLSRDKGLLTAFAEGKDIHRATAAEVF 419
Score = 36.6 bits (83), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 20/39 (51%)
Query: 428 FAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTM 466
P ED KV N +D +L NYG+++ G DTM
Sbjct: 82 LKPLLEDEKALKVGQNLKYDRGILANYGIELRGIAFDTM 120
>pdb|1KLN|A Chain A, Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) MutantDNA
Complex
Length = 605
Score = 87.4 bits (215), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 48/102 (47%), Positives = 63/102 (61%), Gaps = 4/102 (3%)
Query: 810 LPLQGSNVSGKNGRVHCSLN-INTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNS 868
LPL ++ K GRVH S + T TGRLS+ PNLQN P ++ +IRQAFIA
Sbjct: 321 LPLM---INPKTGRVHTSYHQAVTATGRLSSTDPNLQNIPVRNEEGRRIRQAFIAPEDYV 377
Query: 869 LIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMY 910
++ ADY Q+ELRI+AHL+ K +L AF G D H TA ++
Sbjct: 378 IVSADYSQIELRIMAHLSRDKGLLTAFAEGKDIHRATAAEVF 419
Score = 36.6 bits (83), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 20/39 (51%)
Query: 428 FAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTM 466
P ED KV N +D +L NYG+++ G DTM
Sbjct: 82 LKPLLEDEKALKVGQNLKYDRGILANYGIELRGIAFDTM 120
>pdb|1KFS|A Chain A, Dna Polymerase I Klenow Fragment (e.c.2.7.7.7) Mutant/dna
Complex
pdb|1KRP|A Chain A, Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) MutantDNA
Complex
pdb|1KSP|A Chain A, Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) MutantDNA
Complex
pdb|2KFN|A Chain A, Klenow Fragment With Bridging-Sulfur Substrate And
Manganese
pdb|2KFZ|A Chain A, Klenow Fragment With Bridging-Sulfur Substrate And Zinc
Only
pdb|2KZM|A Chain A, Klenow Fragment With Normal Substrate And Zinc And
Manganese
pdb|2KZZ|A Chain A, Klenow Fragment With Normal Substrate And Zinc Only
pdb|1QSL|A Chain A, Klenow Fragment Complexed With Single-Stranded Substrate
And Europium (Iii) Ion
pdb|1D9D|A Chain A, Crystall Structure Of The Complex Of Dna Polymerase I
Klenow Fragment With Short Dna Fragment Carrying 2'-0-
Aminopropyl-Rna Modifications 5'-D(Tcg)-Ap(Auc)-3'
pdb|1D9F|A Chain A, Crystal Structure Of The Complex Of Dna Polymerase I
Klenow Fragment With Dna Tetramer Carrying
2'-O-(3-Aminopropyl)- Rna Modification
5'-D(Tt)-Ap(U)-D(T)-3'
Length = 605
Score = 87.4 bits (215), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 48/102 (47%), Positives = 63/102 (61%), Gaps = 4/102 (3%)
Query: 810 LPLQGSNVSGKNGRVHCSLN-INTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNS 868
LPL ++ K GRVH S + T TGRLS+ PNLQN P ++ +IRQAFIA
Sbjct: 321 LPLM---INPKTGRVHTSYHQAVTATGRLSSTDPNLQNIPVRNEEGRRIRQAFIAPEDYV 377
Query: 869 LIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMY 910
++ ADY Q+ELRI+AHL+ K +L AF G D H TA ++
Sbjct: 378 IVSADYSQIELRIMAHLSRDKGLLTAFAEGKDIHRATAAEVF 419
Score = 36.6 bits (83), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 20/39 (51%)
Query: 428 FAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTM 466
P ED KV N +D +L NYG+++ G DTM
Sbjct: 82 LKPLLEDEKALKVGQNLKYDRGILANYGIELRGIAFDTM 120
>pdb|1D8Y|A Chain A, Crystal Structure Of The Complex Of Dna Polymerase I
Klenow Fragment With Dna
Length = 605
Score = 87.0 bits (214), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 48/102 (47%), Positives = 63/102 (61%), Gaps = 4/102 (3%)
Query: 810 LPLQGSNVSGKNGRVHCSLN-INTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNS 868
LPL ++ K GRVH S + T TGRLS+ PNLQN P ++ +IRQAFIA
Sbjct: 321 LPLM---INPKTGRVHTSYHQAVTATGRLSSTDPNLQNIPVRNEEGRRIRQAFIAPEDYV 377
Query: 869 LIVADYGQLELRILAHLANCKSMLDAFKAGGDFHSRTAMNMY 910
++ ADY Q+ELRI+AHL+ K +L AF G D H TA ++
Sbjct: 378 IVSADYSQIELRIMAHLSRDKGLLTAFAEGKDIHRATAAEVF 419
Score = 36.6 bits (83), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 20/39 (51%)
Query: 428 FAPFFEDPSIKKVWHNYSFDNHVLENYGLKVSGFHADTM 466
P ED KV N +D +L NYG+++ G DTM
Sbjct: 82 LKPLLEDEKALKVGQNLKYDRGILANYGIELRGIAFDTM 120
>pdb|1TAQ|A Chain A, Structure Of Taq Dna Polymerase
Length = 832
Score = 85.1 bits (209), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 51/140 (36%), Positives = 74/140 (52%), Gaps = 2/140 (1%)
Query: 780 ATEQEAREACDAISALCEVCSIDSLISNFILPLQGSNVSGKNGRVHCSLN-INTETGRLS 838
A + REA + + + + L S +I PL + + GR+H N T TGRL
Sbjct: 517 AVLEALREAHPIVEKILQYRELTKLKSTYIDPLP-DLIHPRTGRLHTRFNQTATATGRLC 575
Query: 839 ARRPNLQNQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAG 898
PNLQN P +IR+ FIA G L+ DY Q+ELR+LAHL+ ++++ F+ G
Sbjct: 576 CCDPNLQNIPVRTPLGQRIRRGFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEG 635
Query: 899 GDFHSRTAMNMYPHIRNAVE 918
D H+ TA M+ R AV+
Sbjct: 636 RDIHTETASWMFGVPREAVD 655
>pdb|4DLE|A Chain A, Ternary Structure Of The Large Fragment Of Taq Dna
Polymerase: 4- Fluoroproline Variant
Length = 540
Score = 81.6 bits (200), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 50/140 (35%), Positives = 74/140 (52%), Gaps = 2/140 (1%)
Query: 780 ATEQEAREACDAISALCEVCSIDSLISNFILPLQGSNVSGKNGRVHCSLN-INTETGRLS 838
A + REA + + + + L S +I L + + GR+H N T TGRLS
Sbjct: 225 AVLEALREAHXIVEKILQYRELTKLKSTYIDXLX-DLIHXRTGRLHTRFNQTATATGRLS 283
Query: 839 ARRPNLQNQPALEKDRYKIRQAFIAVPGNSLIVADYGQLELRILAHLANCKSMLDAFKAG 898
+ NLQN +IR+AFIA G L+ DY Q+ELR+LAHL+ ++++ F+ G
Sbjct: 284 SSDXNLQNIXVRTXLGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEG 343
Query: 899 GDFHSRTAMNMYPHIRNAVE 918
D H+ TA M+ R AV+
Sbjct: 344 RDIHTETASWMFGVXREAVD 363
>pdb|3TAN|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Duplex Dna With Cytosine-Adenine
Mismatch At (N-1) Position
pdb|3TAP|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Duplex Dna With Cytosine-Adenine
Mismatch At (N-3) Position
pdb|3TAQ|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Duplex Dna With Cytosine-Adenine
Mismatch At (N-4) Position
pdb|3TAR|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Duplex Dna With Cytosine-Adenine
Mismatch At (N-6) Position
pdb|4DQS|A Chain A, Binary Complex Of Bacillus Dna Polymerase I Large Fragment
And Duplex Dna With Rc In Primer Terminus Paired With Dg
Of Template
Length = 592
Score = 80.9 bits (198), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 41/90 (45%), Positives = 61/90 (67%), Gaps = 2/90 (2%)
Query: 823 RVHCSLN-INTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLI-VADYGQLELR 880
+VH N T+TGRLS+ PNLQN P ++ KIRQAF+ + LI ADY Q+ELR
Sbjct: 317 KVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELR 376
Query: 881 ILAHLANCKSMLDAFKAGGDFHSRTAMNMY 910
+LAH+A ++++AF+ D H++TAM+++
Sbjct: 377 VLAHIAEDDNLMEAFRRDLDIHTKTAMDIF 406
>pdb|4DQI|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Dctp (Paired With Dg Of
Template)
pdb|4DQI|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Dctp (Paired With Dg Of
Template)
pdb|4DQP|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Ddctp (Paired With Dg Of
Template)
pdb|4DQP|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Ddctp (Paired With Dg Of
Template)
pdb|4DS4|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Rctp In Presence Of Mn2+
pdb|4DS4|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Rctp In Presence Of Mn2+
pdb|4DS5|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Rctp In Presence Of Mg2+
pdb|4DS5|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment, Dna Duplex, And Rctp In Presence Of Mg2+
Length = 592
Score = 80.9 bits (198), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 41/90 (45%), Positives = 61/90 (67%), Gaps = 2/90 (2%)
Query: 823 RVHCSLN-INTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLI-VADYGQLELR 880
+VH N T+TGRLS+ PNLQN P ++ KIRQAF+ + LI ADY Q+ELR
Sbjct: 317 KVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELR 376
Query: 881 ILAHLANCKSMLDAFKAGGDFHSRTAMNMY 910
+LAH+A ++++AF+ D H++TAM+++
Sbjct: 377 VLAHIAEDDNLMEAFRRDLDIHTKTAMDIF 406
>pdb|3HPO|A Chain A, Crystal Structure Of Fragment Dna Polymerase I From
Bacillus Stearothermophilus Y714s Mutant Bound To G:t
Mismatch
Length = 580
Score = 80.9 bits (198), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 41/90 (45%), Positives = 61/90 (67%), Gaps = 2/90 (2%)
Query: 823 RVHCSLN-INTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLI-VADYGQLELR 880
+VH N T+TGRLS+ PNLQN P ++ KIRQAF+ + LI ADY Q+ELR
Sbjct: 305 KVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELR 364
Query: 881 ILAHLANCKSMLDAFKAGGDFHSRTAMNMY 910
+LAH+A ++++AF+ D H++TAM+++
Sbjct: 365 VLAHIAEDDNLMEAFRRDLDIHTKTAMDIF 394
>pdb|3PV8|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddttp-Da In Closed
Conformation
pdb|3PV8|D Chain D, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddttp-Da In Closed
Conformation
pdb|3PX0|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Dctp-Da Mismatch (Tautomer) In
Closed Conformation
pdb|3PX0|D Chain D, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Dctp-Da Mismatch (Tautomer) In
Closed Conformation
pdb|3PX4|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddctp-Da Mismatch (Wobble) In
Ajar Conformation
pdb|3PX4|D Chain D, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddctp-Da Mismatch (Wobble) In
Ajar Conformation
pdb|3PX6|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddctp-Da Mismatch (Tautomer)
In Closed Conformation
pdb|3PX6|D Chain D, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddctp-Da Mismatch (Tautomer)
In Closed Conformation
pdb|3THV|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddatp-Dt In Closed
Conformation
pdb|3THV|D Chain D, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddatp-Dt In Closed
Conformation
pdb|3TI0|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddgtp-Dc In Closed
Conformation
pdb|3TI0|D Chain D, Crystal Structure Of Bacillus Dna Polymerase I Large
Fragment Bound To Dna And Ddgtp-Dc In Closed
Conformation
pdb|4DSE|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment F710y, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mg2+
pdb|4DSE|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment F710y, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mg2+
pdb|4DSF|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment F710y, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mn2+
pdb|4DSF|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment F710y, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mn2+
Length = 592
Score = 80.9 bits (198), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 41/90 (45%), Positives = 61/90 (67%), Gaps = 2/90 (2%)
Query: 823 RVHCSLN-INTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLI-VADYGQLELR 880
+VH N T+TGRLS+ PNLQN P ++ KIRQAF+ + LI ADY Q+ELR
Sbjct: 317 KVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELR 376
Query: 881 ILAHLANCKSMLDAFKAGGDFHSRTAMNMY 910
+LAH+A ++++AF+ D H++TAM+++
Sbjct: 377 VLAHIAEDDNLMEAFRRDLDIHTKTAMDIF 406
>pdb|3HP6|A Chain A, Crystal Structure Of Fragment Dna Polymerase I From
Bacillus Stearothermophilus F710y Mutant Bound To G:t
Mismatch
pdb|3HP6|D Chain D, Crystal Structure Of Fragment Dna Polymerase I From
Bacillus Stearothermophilus F710y Mutant Bound To G:t
Mismatch
Length = 580
Score = 80.9 bits (198), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 41/90 (45%), Positives = 61/90 (67%), Gaps = 2/90 (2%)
Query: 823 RVHCSLN-INTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLI-VADYGQLELR 880
+VH N T+TGRLS+ PNLQN P ++ KIRQAF+ + LI ADY Q+ELR
Sbjct: 305 KVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELR 364
Query: 881 ILAHLANCKSMLDAFKAGGDFHSRTAMNMY 910
+LAH+A ++++AF+ D H++TAM+++
Sbjct: 365 VLAHIAEDDNLMEAFRRDLDIHTKTAMDIF 394
>pdb|2XY6|A Chain A, Crystal Structure Of A Salicylic Aldehyde Basepair In
Complex With Fragment Dna Polymerase I From Bacillus
Stearothermophilus
Length = 581
Score = 80.9 bits (198), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 41/90 (45%), Positives = 61/90 (67%), Gaps = 2/90 (2%)
Query: 823 RVHCSLN-INTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLI-VADYGQLELR 880
+VH N T+TGRLS+ PNLQN P ++ KIRQAF+ + LI ADY Q+ELR
Sbjct: 306 KVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELR 365
Query: 881 ILAHLANCKSMLDAFKAGGDFHSRTAMNMY 910
+LAH+A ++++AF+ D H++TAM+++
Sbjct: 366 VLAHIAEDDNLMEAFRRDLDIHTKTAMDIF 395
>pdb|2Y1I|A Chain A, Crystal Structure Of A S-Diastereomer Analogue Of The
Spore Photoproduct In Complex With Fragment Dna
Polymerase I From Bacillus Stearothermophilus
pdb|2Y1J|A Chain A, Crystal Structure Of A R-Diastereomer Analogue Of The
Spore Photoproduct In Complex With Fragment Dna
Polymerase I From Bacillus Stearothermophilus
Length = 580
Score = 80.9 bits (198), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 41/90 (45%), Positives = 61/90 (67%), Gaps = 2/90 (2%)
Query: 823 RVHCSLN-INTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLI-VADYGQLELR 880
+VH N T+TGRLS+ PNLQN P ++ KIRQAF+ + LI ADY Q+ELR
Sbjct: 305 KVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELR 364
Query: 881 ILAHLANCKSMLDAFKAGGDFHSRTAMNMY 910
+LAH+A ++++AF+ D H++TAM+++
Sbjct: 365 VLAHIAEDDNLMEAFRRDLDIHTKTAMDIF 394
>pdb|2XO7|A Chain A, Crystal Structure Of A Da:o-Allylhydroxylamine-Dc Basepair
In Complex With Fragment Dna Polymerase I From Bacillus
Stearothermophilus
Length = 580
Score = 80.9 bits (198), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 41/90 (45%), Positives = 61/90 (67%), Gaps = 2/90 (2%)
Query: 823 RVHCSLN-INTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLI-VADYGQLELR 880
+VH N T+TGRLS+ PNLQN P ++ KIRQAF+ + LI ADY Q+ELR
Sbjct: 305 KVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELR 364
Query: 881 ILAHLANCKSMLDAFKAGGDFHSRTAMNMY 910
+LAH+A ++++AF+ D H++TAM+++
Sbjct: 365 VLAHIAEDDNLMEAFRRDLDIHTKTAMDIF 394
>pdb|3EYZ|A Chain A, Cocrystal Structure Of Bacillus Fragment Dna Polymerase I
With Duplex Dna (Open Form)
Length = 580
Score = 80.9 bits (198), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 41/90 (45%), Positives = 61/90 (67%), Gaps = 2/90 (2%)
Query: 823 RVHCSLN-INTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLI-VADYGQLELR 880
+VH N T+TGRLS+ PNLQN P ++ KIRQAF+ + LI ADY Q+ELR
Sbjct: 305 KVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELR 364
Query: 881 ILAHLANCKSMLDAFKAGGDFHSRTAMNMY 910
+LAH+A ++++AF+ D H++TAM+++
Sbjct: 365 VLAHIAEDDNLMEAFRRDLDIHTKTAMDIF 394
>pdb|2HHQ|A Chain A, O6-Methyl-Guanine:t Pair In The Polymerase-10 Basepair
Position
pdb|2HHS|A Chain A, O6-Methyl:c Pair In The Polymerase-10 Basepair Position
pdb|2HHT|A Chain A, C:o6-Methyl-Guanine Pair In The Polymerase-2 Basepair
Position
pdb|2HHU|A Chain A, C:o6-Methyl-Guanine In The Polymerase Postinsertion Site
(- 1 Basepair Position)
pdb|2HHV|A Chain A, T:o6-Methyl-Guanine In The Polymerase-2 Basepair Position
pdb|2HHX|A Chain A, O6-Methyl-Guanine In The Polymerase Template Preinsertion
Site
pdb|2HW3|A Chain A, T:o6-Methyl-Guanine Pair In The Polymerase Postinsertion
Site (-1 Basepair Position)
Length = 580
Score = 80.9 bits (198), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 41/90 (45%), Positives = 61/90 (67%), Gaps = 2/90 (2%)
Query: 823 RVHCSLN-INTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLI-VADYGQLELR 880
+VH N T+TGRLS+ PNLQN P ++ KIRQAF+ + LI ADY Q+ELR
Sbjct: 305 KVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELR 364
Query: 881 ILAHLANCKSMLDAFKAGGDFHSRTAMNMY 910
+LAH+A ++++AF+ D H++TAM+++
Sbjct: 365 VLAHIAEDDNLMEAFRRDLDIHTKTAMDIF 394
>pdb|1L3S|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Fragment
Complexed To 9 Base Pairs Of Duplex Dna.
pdb|1L3T|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Fragment
Product Complex With 10 Base Pairs Of Duplex Dna
Following Addition Of A Single Dttp Residue
pdb|1L3U|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Fragment
Product Complex With 11 Base Pairs Of Duplex Dna
Following Addition Of A Dttp And A Datp Residue.
pdb|1L3V|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Fragment
Product Complex With 15 Base Pairs Of Duplex Dna
Following Addition Of Dttp, Datp, Dctp, And Dgtp
Residues.
pdb|1L5U|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Fragment
Product Complex With 12 Base Pairs Of Duplex Dna
Following Addition Of A Dttp, A Datp, And A Dctp
Residue.
pdb|1NJW|A Chain A, Guanine-Thymine Mismatch At The Polymerase Active Site
pdb|1NJX|A Chain A, Thymine-Guanine Mismatch At The Polymerase Active Site
pdb|1NJY|A Chain A, Thymine-Thymine Mismatch At The Polymerase Active Site
pdb|1NJZ|A Chain A, Cytosine-thymine Mismatch At The Polymerase Active Site
pdb|1NK0|A Chain A, Adenine-Guanine Mismatch At The Polymerase Active Site
pdb|1NK4|A Chain A, Guanine-Guanine Mismatch At The Polymerase Active Site
pdb|1NK5|A Chain A, Adenine-Adenine Mismatch At The Polymerase Active Site
pdb|1NK6|A Chain A, Cytosine-Cytosine Mismatch At The Polymerase Active Site
pdb|1NK7|A Chain A, Guanine-Adenine Mismatch At The Polymerase Active Site
pdb|1NK8|A Chain A, A Bacillus Dna Polymerase I Product Complex Bound To A
Guanine-Thymine Mismatch After A Single Round Of Primer
Extension, Following Incorporation Of Dctp.
pdb|1NK9|A Chain A, A Bacillus Dna Polymerase I Product Complex Bound To A
Guanine-Thymine Mismatch After Two Rounds Of Primer
Extension, Following Incorporation Of Dctp And Dgtp.
pdb|1NKB|A Chain A, A Bacillus Dna Polymerase I Product Complex Bound To A
Guanine-Thymine Mismatch After Three Rounds Of Primer
Extension, Following Incorporation Of Dctp, Dgtp, And
Dttp.
pdb|1NKC|A Chain A, A Bacillus Dna Polymerase I Product Complex Bound To A
Guanine-Thymine Mismatch After Five Rounds Of Primer
Extension, Following Incorporation Of Dctp, Dgtp, Dttp,
And Datp.
pdb|1NKE|A Chain A, A Bacillus Dna Polymerase I Product Complex Bound To A
Cytosine-Thymine Mismatch After A Single Round Of Primer
Extension, Following Incorporation Of Dctp.
pdb|1XC9|A Chain A, Structure Of A High-Fidelity Polymerase Bound To A
Benzo[a]pyrene Adduct That Blocks Replication
pdb|1XWL|A Chain A, Bacillus Stearothermophilus (Newly Identified Strain As
Yet Unnamed) Dna Polymerase Fragment
Length = 580
Score = 80.9 bits (198), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 41/90 (45%), Positives = 61/90 (67%), Gaps = 2/90 (2%)
Query: 823 RVHCSLN-INTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLI-VADYGQLELR 880
+VH N T+TGRLS+ PNLQN P ++ KIRQAF+ + LI ADY Q+ELR
Sbjct: 305 KVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELR 364
Query: 881 ILAHLANCKSMLDAFKAGGDFHSRTAMNMY 910
+LAH+A ++++AF+ D H++TAM+++
Sbjct: 365 VLAHIAEDDNLMEAFRRDLDIHTKTAMDIF 394
>pdb|1U45|A Chain A, 8oxoguanine At The Pre-Insertion Site Of The Polymerase
Active Site
pdb|1U47|A Chain A, Cytosine-8-Oxoguanine Base Pair At The Polymerase Active
Site
pdb|1U48|A Chain A, Extension Of A Cytosine-8-Oxoguanine Base Pair
pdb|1U49|A Chain A, Adenine-8oxoguanine Mismatch At The Polymerase Active Site
pdb|1U4B|A Chain A, Extension Of An Adenine-8oxoguanine Mismatch
pdb|1UA0|A Chain A, Aminofluorene Dna Adduct At The Pre-Insertion Site Of A
Dna Polymerase
pdb|1UA1|A Chain A, Structure Of Aminofluorene Adduct Paired Opposite Cytosine
At The Polymerase Active Site
Length = 580
Score = 80.9 bits (198), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 41/90 (45%), Positives = 61/90 (67%), Gaps = 2/90 (2%)
Query: 823 RVHCSLN-INTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLI-VADYGQLELR 880
+VH N T+TGRLS+ PNLQN P ++ KIRQAF+ + LI ADY Q+ELR
Sbjct: 305 KVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELR 364
Query: 881 ILAHLANCKSMLDAFKAGGDFHSRTAMNMY 910
+LAH+A ++++AF+ D H++TAM+++
Sbjct: 365 VLAHIAEDDNLMEAFRRDLDIHTKTAMDIF 394
>pdb|3HT3|A Chain A, Crystal Structure Of Fragment Dna Polymerase I From
Bacillus Stearothermophilus V713p Mutant Bound To G:dctp
pdb|3HT3|D Chain D, Crystal Structure Of Fragment Dna Polymerase I From
Bacillus Stearothermophilus V713p Mutant Bound To G:dctp
Length = 579
Score = 80.9 bits (198), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 41/90 (45%), Positives = 61/90 (67%), Gaps = 2/90 (2%)
Query: 823 RVHCSLN-INTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLI-VADYGQLELR 880
+VH N T+TGRLS+ PNLQN P ++ KIRQAF+ + LI ADY Q+ELR
Sbjct: 304 KVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELR 363
Query: 881 ILAHLANCKSMLDAFKAGGDFHSRTAMNMY 910
+LAH+A ++++AF+ D H++TAM+++
Sbjct: 364 VLAHIAEDDNLMEAFRRDLDIHTKTAMDIF 393
>pdb|2HVH|A Chain A, Ddctp:o6meg Pair In The Polymerase Active Site (0
Position)
pdb|2HVH|D Chain D, Ddctp:o6meg Pair In The Polymerase Active Site (0
Position)
pdb|2HVI|A Chain A, Ddctp:g Pair In The Polymerase Active Site (0 Position)
pdb|2HVI|D Chain D, Ddctp:g Pair In The Polymerase Active Site (0 Position)
pdb|3EZ5|A Chain A, Cocrystal Structure Of Bacillus Fragment Dna Polymerase I
With Duplex Dna , Dctp, And Zinc (Closed Form).
pdb|3EZ5|D Chain D, Cocrystal Structure Of Bacillus Fragment Dna Polymerase I
With Duplex Dna , Dctp, And Zinc (Closed Form)
Length = 580
Score = 80.9 bits (198), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 41/90 (45%), Positives = 61/90 (67%), Gaps = 2/90 (2%)
Query: 823 RVHCSLN-INTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLI-VADYGQLELR 880
+VH N T+TGRLS+ PNLQN P ++ KIRQAF+ + LI ADY Q+ELR
Sbjct: 305 KVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELR 364
Query: 881 ILAHLANCKSMLDAFKAGGDFHSRTAMNMY 910
+LAH+A ++++AF+ D H++TAM+++
Sbjct: 365 VLAHIAEDDNLMEAFRRDLDIHTKTAMDIF 394
>pdb|1LV5|A Chain A, Crystal Structure Of The Closed Conformation Of Bacillus
Dna Polymerase I Fragment Bound To Dna And Dctp
pdb|1LV5|B Chain B, Crystal Structure Of The Closed Conformation Of Bacillus
Dna Polymerase I Fragment Bound To Dna And Dctp
Length = 580
Score = 80.9 bits (198), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 41/90 (45%), Positives = 61/90 (67%), Gaps = 2/90 (2%)
Query: 823 RVHCSLN-INTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLI-VADYGQLELR 880
+VH N T+TGRLS+ PNLQN P ++ KIRQAF+ + LI ADY Q+ELR
Sbjct: 305 KVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELR 364
Query: 881 ILAHLANCKSMLDAFKAGGDFHSRTAMNMY 910
+LAH+A ++++AF+ D H++TAM+++
Sbjct: 365 VLAHIAEDDNLMEAFRRDLDIHTKTAMDIF 394
>pdb|3BDP|A Chain A, Dna Polymerase IDNA COMPLEX
pdb|4BDP|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Fragment
Complexed To 11 Base Pairs Of Duplex Dna After Addition
Of Two Datp Residues
pdb|2BDP|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Fragment
Complexed To 9 Base Pairs Of Duplex Dna
Length = 580
Score = 80.9 bits (198), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 41/90 (45%), Positives = 61/90 (67%), Gaps = 2/90 (2%)
Query: 823 RVHCSLN-INTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLI-VADYGQLELR 880
+VH N T+TGRLS+ PNLQN P ++ KIRQAF+ + LI ADY Q+ELR
Sbjct: 305 KVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELR 364
Query: 881 ILAHLANCKSMLDAFKAGGDFHSRTAMNMY 910
+LAH+A ++++AF+ D H++TAM+++
Sbjct: 365 VLAHIAEDDNLMEAFRRDLDIHTKTAMDIF 394
>pdb|2XY5|A Chain A, Crystal Structure Of An Artificial Salen-Copper Basepair
In Complex With Fragment Dna Polymerase I From Bacillus
Stearothermophilus
Length = 581
Score = 80.9 bits (198), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 41/90 (45%), Positives = 61/90 (67%), Gaps = 2/90 (2%)
Query: 823 RVHCSLN-INTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLI-VADYGQLELR 880
+VH N T+TGRLS+ PNLQN P ++ KIRQAF+ + LI ADY Q+ELR
Sbjct: 306 KVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELR 365
Query: 881 ILAHLANCKSMLDAFKAGGDFHSRTAMNMY 910
+LAH+A ++++AF+ D H++TAM+++
Sbjct: 366 VLAHIAEDDNLMEAFRRDLDIHTKTAMDIF 395
>pdb|2HHW|A Chain A, Ddttp:o6-Methyl-Guanine Pair In The Polymerase Active
Site, In The Closed Conformation
pdb|2HHW|D Chain D, Ddttp:o6-Methyl-Guanine Pair In The Polymerase Active
Site, In The Closed Conformation
Length = 580
Score = 80.9 bits (198), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 41/90 (45%), Positives = 61/90 (67%), Gaps = 2/90 (2%)
Query: 823 RVHCSLN-INTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLI-VADYGQLELR 880
+VH N T+TGRLS+ PNLQN P ++ KIRQAF+ + LI ADY Q+ELR
Sbjct: 305 KVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELR 364
Query: 881 ILAHLANCKSMLDAFKAGGDFHSRTAMNMY 910
+LAH+A ++++AF+ D H++TAM+++
Sbjct: 365 VLAHIAEDDNLMEAFRRDLDIHTKTAMDIF 394
>pdb|2XY7|A Chain A, Crystal Structure Of A Salicylic Aldehyde Base In The
Pre-Insertion Site Of Fragment Dna Polymerase I From
Bacillus Stearothermophilus
Length = 580
Score = 80.5 bits (197), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 41/90 (45%), Positives = 61/90 (67%), Gaps = 2/90 (2%)
Query: 823 RVHCSLN-INTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLI-VADYGQLELR 880
+VH N T+TGRLS+ PNLQN P ++ KIRQAF+ + LI ADY Q+ELR
Sbjct: 305 KVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELR 364
Query: 881 ILAHLANCKSMLDAFKAGGDFHSRTAMNMY 910
+LAH+A ++++AF+ D H++TAM+++
Sbjct: 365 VLAHIAEDDNLMEAFRRDLDIHTKTAMDIF 394
>pdb|4DQQ|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment E658a, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mg2+
pdb|4DQQ|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment E658a, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mg2+
pdb|4DQR|A Chain A, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment E658a, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mn2+
pdb|4DQR|D Chain D, Ternary Complex Of Bacillus Dna Polymerase I Large
Fragment E658a, Dna Duplex, And Rctp (Paired With Dg Of
Template) In Presence Of Mn2+
pdb|4E0D|A Chain A, Binary Complex Of Bacillus Dna Polymerase I Large Fragment
E658a And Duplex Dna
Length = 592
Score = 78.6 bits (192), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 40/90 (44%), Positives = 60/90 (66%), Gaps = 2/90 (2%)
Query: 823 RVHCSLN-INTETGRLSARRPNLQNQPALEKDRYKIRQAFIAVPGNSLI-VADYGQLELR 880
+VH N T+TGRLS+ PNLQN P ++ KIRQAF+ + LI ADY Q+ LR
Sbjct: 317 KVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIALR 376
Query: 881 ILAHLANCKSMLDAFKAGGDFHSRTAMNMY 910
+LAH+A ++++AF+ D H++TAM+++
Sbjct: 377 VLAHIAEDDNLMEAFRRDLDIHTKTAMDIF 406
>pdb|1UG9|A Chain A, Crystal Structure Of Glucodextranase From Arthrobacter
Globiformis I42
pdb|1ULV|A Chain A, Crystal Structure Of Glucodextranase Complexed With
Acarbose
Length = 1020
Score = 30.0 bits (66), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 5/46 (10%)
Query: 439 KVWHNYSFDNHVLENYGLKVSGFHADTMHMARLWDSSRRTEGGYSL 484
++WH Y++D YG K G D + RLW G Y+L
Sbjct: 563 RMWHRYTYDG-----YGEKADGSPWDGTGIGRLWPLLSGERGEYAL 603
>pdb|1SP9|A Chain A, 4-hydroxyphenylpyruvate Dioxygenase
pdb|1SP9|B Chain B, 4-hydroxyphenylpyruvate Dioxygenase
Length = 445
Score = 29.3 bits (64), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 22/32 (68%)
Query: 280 SEIECFEDGSSYTPPPKLVSFKRSNQKNPKND 311
SE + +DG++ +P KLV F + +KNPK+D
Sbjct: 9 SENQNHDDGAASSPGFKLVGFSKFVRKNPKSD 40
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
0.314 0.130 0.380
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 27,635,529
Number of Sequences: 62578
Number of extensions: 1141789
Number of successful extensions: 1913
Number of sequences better than 100.0: 46
Number of HSP's better than 100.0 without gapping: 35
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1828
Number of HSP's gapped (non-prelim): 76
length of query: 940
length of database: 14,973,337
effective HSP length: 108
effective length of query: 832
effective length of database: 8,214,913
effective search space: 6834807616
effective search space used: 6834807616
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 56 (26.2 bits)