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= 015933
(398 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1BPE|A Chain A, Crystal Structure Of Rat Dna Polymerase Beta; Evidence For
A Common Polymerase Mechanism
Length = 335
Score = 155 bits (392), Expect = 3e-38, Method: Compositional matrix adjust.
Identities = 81/189 (42%), Positives = 120/189 (63%), Gaps = 2/189 (1%)
Query: 209 LNKNITEIFGKLINIYRALGEDRRSF-SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 267
LN IT++ +L N + + + + +Y KA VI K P KI+S + K LPG+G +
Sbjct: 11 LNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIA 70
Query: 268 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNED 326
+ I E + TGKL KLE +D+ +I+ V GIGP+ A+KL ++G +TL+DL KNED
Sbjct: 71 EKIDEFLATGKLRKLEKIRRDDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNED 130
Query: 327 SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGD 386
L H QR+GLKYF+D + RIPR E+ QM+ ++ +++ PE I GS+RRG S GD
Sbjct: 131 KLNHHQRIGLKYFEDFEKRIPREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGD 190
Query: 387 LDVVIMHPD 395
+DV++ HP+
Sbjct: 191 MDVLLTHPN 199
>pdb|3V7K|A Chain A, Co-crystal Structure Of K72e Variant Of Rat Polymerase
Beta: Enzyme- Dna Binary Complex
pdb|3V7L|A Chain A, Apo Structure Of Rat Dna Polymerase Beta K72e Variant
Length = 340
Score = 155 bits (392), Expect = 4e-38, Method: Compositional matrix adjust.
Identities = 81/189 (42%), Positives = 120/189 (63%), Gaps = 2/189 (1%)
Query: 209 LNKNITEIFGKLINIYRALGEDRRSF-SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 267
LN IT++ +L N + + + + +Y KA VI K P KI+S + K LPG+G +
Sbjct: 16 LNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIA 75
Query: 268 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNED 326
+ I E + TGKL KLE +D+ +I+ V GIGP+ A+KL ++G +TL+DL KNED
Sbjct: 76 EEIDEFLATGKLRKLEKIRQDDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNED 135
Query: 327 SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGD 386
L H QR+GLKYF+D + RIPR E+ QM+ ++ +++ PE I GS+RRG S GD
Sbjct: 136 KLNHHQRIGLKYFEDFEKRIPREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGD 195
Query: 387 LDVVIMHPD 395
+DV++ HP+
Sbjct: 196 MDVLLTHPN 204
>pdb|3UXO|A Chain A, Crystal Structure Of Rat Dna Polymerase Beta Mutator I260q
Apoenzyme
pdb|3UXO|B Chain B, Crystal Structure Of Rat Dna Polymerase Beta Mutator I260q
Apoenzyme
pdb|3UXP|A Chain A, Co-Crystal Structure Of Rat Dna Polymerase Beta Mutator
I260q: Enzyme- Dna-Ddttp
pdb|3UXP|B Chain B, Co-Crystal Structure Of Rat Dna Polymerase Beta Mutator
I260q: Enzyme- Dna-Ddttp
Length = 335
Score = 155 bits (392), Expect = 4e-38, Method: Compositional matrix adjust.
Identities = 81/189 (42%), Positives = 120/189 (63%), Gaps = 2/189 (1%)
Query: 209 LNKNITEIFGKLINIYRALGEDRRSF-SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 267
LN IT++ +L N + + + + +Y KA VI K P KI+S + K LPG+G +
Sbjct: 11 LNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIA 70
Query: 268 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNED 326
+ I E + TGKL KLE +D+ +I+ V GIGP+ A+KL ++G +TL+DL KNED
Sbjct: 71 EKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNED 130
Query: 327 SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGD 386
L H QR+GLKYF+D + RIPR E+ QM+ ++ +++ PE I GS+RRG S GD
Sbjct: 131 KLNHHQRIGLKYFEDFEKRIPREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGD 190
Query: 387 LDVVIMHPD 395
+DV++ HP+
Sbjct: 191 MDVLLTHPN 199
>pdb|3V72|A Chain A, Crystal Structure Of Rat Dna Polymerase Beta Mutator
E295k: Enzyme- Dsdna
Length = 335
Score = 155 bits (392), Expect = 4e-38, Method: Compositional matrix adjust.
Identities = 81/189 (42%), Positives = 120/189 (63%), Gaps = 2/189 (1%)
Query: 209 LNKNITEIFGKLINIYRALGEDRRSF-SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 267
LN IT++ +L N + + + + +Y KA VI K P KI+S + K LPG+G +
Sbjct: 11 LNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIA 70
Query: 268 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNED 326
+ I E + TGKL KLE +D+ +I+ V GIGP+ A+KL ++G +TL+DL KNED
Sbjct: 71 EKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNED 130
Query: 327 SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGD 386
L H QR+GLKYF+D + RIPR E+ QM+ ++ +++ PE I GS+RRG S GD
Sbjct: 131 KLNHHQRIGLKYFEDFEKRIPREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGD 190
Query: 387 LDVVIMHPD 395
+DV++ HP+
Sbjct: 191 MDVLLTHPN 199
>pdb|3V7J|A Chain A, Co-crystal Structure Of Wild Type Rat Polymerase Beta:
Enzyme-dna Binary Complex
Length = 340
Score = 155 bits (391), Expect = 4e-38, Method: Compositional matrix adjust.
Identities = 81/189 (42%), Positives = 120/189 (63%), Gaps = 2/189 (1%)
Query: 209 LNKNITEIFGKLINIYRALGEDRRSF-SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 267
LN IT++ +L N + + + + +Y KA VI K P KI+S + K LPG+G +
Sbjct: 16 LNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIA 75
Query: 268 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNED 326
+ I E + TGKL KLE +D+ +I+ V GIGP+ A+KL ++G +TL+DL KNED
Sbjct: 76 EKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNED 135
Query: 327 SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGD 386
L H QR+GLKYF+D + RIPR E+ QM+ ++ +++ PE I GS+RRG S GD
Sbjct: 136 KLNHHQRIGLKYFEDFEKRIPREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGD 195
Query: 387 LDVVIMHPD 395
+DV++ HP+
Sbjct: 196 MDVLLTHPN 204
>pdb|2BPF|A Chain A, Structures Of Ternary Complexes Of Rat Dna Polymerase
Beta, A Dna Template-Primer, And Ddctp
pdb|2BPG|A Chain A, Structures Of Ternary Complexes Of Rat Dna Polymerase
Beta, A Dna Template-Primer, And Ddctp
pdb|2BPG|B Chain B, Structures Of Ternary Complexes Of Rat Dna Polymerase
Beta, A Dna Template-Primer, And Ddctp
pdb|1HUO|A Chain A, Crystal Structure Of Dna Polymerase Beta Complexed With
Dna And Cr-Tmppcp
pdb|1HUO|B Chain B, Crystal Structure Of Dna Polymerase Beta Complexed With
Dna And Cr-Tmppcp
pdb|1HUZ|A Chain A, Crystal Structure Of Dna Polymerase Complexed With Dna And
Cr-Pcp
pdb|1HUZ|B Chain B, Crystal Structure Of Dna Polymerase Complexed With Dna And
Cr-Pcp
pdb|1BPD|A Chain A, Crystal Structure Of Rat Dna Polymerase Beta: Evidence For
A Common Polymerase Mechanism
pdb|3UXN|A Chain A, Crystal Structure Of Rat Dna Polymerase Beta, Wild Type
Apoenzyme
pdb|3UXN|B Chain B, Crystal Structure Of Rat Dna Polymerase Beta, Wild Type
Apoenzyme
Length = 335
Score = 155 bits (391), Expect = 5e-38, Method: Compositional matrix adjust.
Identities = 81/189 (42%), Positives = 120/189 (63%), Gaps = 2/189 (1%)
Query: 209 LNKNITEIFGKLINIYRALGEDRRSF-SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 267
LN IT++ +L N + + + + +Y KA VI K P KI+S + K LPG+G +
Sbjct: 11 LNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIA 70
Query: 268 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNED 326
+ I E + TGKL KLE +D+ +I+ V GIGP+ A+KL ++G +TL+DL KNED
Sbjct: 71 EKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNED 130
Query: 327 SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGD 386
L H QR+GLKYF+D + RIPR E+ QM+ ++ +++ PE I GS+RRG S GD
Sbjct: 131 KLNHHQRIGLKYFEDFEKRIPREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGD 190
Query: 387 LDVVIMHPD 395
+DV++ HP+
Sbjct: 191 MDVLLTHPN 199
>pdb|1XSN|A Chain A, Crystal Structure Of Human Dna Polymerase Lambda In
Complex With A One Nucleotide Dna Gap And Ddttp
pdb|1XSP|A Chain A, Crystal Structure Of Human Dna Polymerase Lambda In
Complex With Nicked Dna And Pyrophosphate
pdb|2PFN|A Chain A, Na In The Active Site Of Dna Polymerase Lambda
pdb|2PFO|A Chain A, Dna Polymerase Lambda In Complex With Dna And Dupnpp
pdb|2PFP|A Chain A, Dna Polymerase Lambda In Complex With Dna And Dctp
pdb|2PFQ|A Chain A, Manganese Promotes Catalysis In A Dna Polymerase
Lambda-Dna Crystal
pdb|3HW8|A Chain A, Ternary Complex Of Dna Polymerase Lambda Of A Two
Nucleotide Gapped Dna Substrate With A C In The Scrunch
Site
pdb|3HWT|A Chain A, Ternary Complex Of Dna Polymerase Lambda Bound To A Two
Nucleotide Gapped Dna Substrate With A Scrunched Da
Length = 335
Score = 152 bits (384), Expect = 3e-37, Method: Compositional matrix adjust.
Identities = 75/186 (40%), Positives = 112/186 (60%), Gaps = 2/186 (1%)
Query: 210 NKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDH 269
N +ITE L Y G+ R+ Y KAI ++ + S + +PGIGK M +
Sbjct: 13 NLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEK 72
Query: 270 IQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLT 329
I EI+ +G L KL+H E V + LF +WG G TAQ Y++G R+L+D++++ SLT
Sbjct: 73 IIEILESGHLRKLDHI--SESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLT 130
Query: 330 HSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDV 389
Q +GLK++ D R+PR E ++E+ +QKA + ++ + GSYRRGKA+CGD+DV
Sbjct: 131 TQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDV 190
Query: 390 VIMHPD 395
+I HPD
Sbjct: 191 LITHPD 196
>pdb|3OGU|A Chain A, Dna Polymerase Beta Mutant 5p20 Complexed With 6bp Of Dna
Length = 335
Score = 152 bits (383), Expect = 4e-37, Method: Compositional matrix adjust.
Identities = 81/188 (43%), Positives = 117/188 (62%), Gaps = 2/188 (1%)
Query: 209 LNKNITEIFGKLINIYRALGEDRRSF-SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 267
LN IT++ +L N + + + + +Y KA VI K P KI+S + K LPG+G +
Sbjct: 11 LNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIA 70
Query: 268 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNED 326
+ I E + TGKL KLE +D+ +I+L V GIGP+ A+K ++G +TL+DL KNED
Sbjct: 71 EKIDEFLATGKLRKLEKIRQDDTSSSINLLTRVSGIGPSAARKFVDEGIKTLEDLRKNED 130
Query: 327 SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGD 386
L H QR+GLKYF D + RIPR E+ QM+ ++ ++V E I GS+RRG S GD
Sbjct: 131 KLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGD 190
Query: 387 LDVVIMHP 394
+DV++ HP
Sbjct: 191 MDVLLTHP 198
>pdb|3C5F|A Chain A, Structure Of A Binary Complex Of The R517a Pol Lambda
Mutant
pdb|3C5F|B Chain B, Structure Of A Binary Complex Of The R517a Pol Lambda
Mutant
Length = 335
Score = 152 bits (383), Expect = 4e-37, Method: Compositional matrix adjust.
Identities = 75/186 (40%), Positives = 112/186 (60%), Gaps = 2/186 (1%)
Query: 210 NKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDH 269
N +ITE L Y G+ R+ Y KAI ++ + S + +PGIGK M +
Sbjct: 13 NLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEK 72
Query: 270 IQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLT 329
I EI+ +G L KL+H E V + LF +WG G TAQ Y++G R+L+D++++ SLT
Sbjct: 73 IIEILESGHLRKLDHI--SESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLT 130
Query: 330 HSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDV 389
Q +GLK++ D R+PR E ++E+ +QKA + ++ + GSYRRGKA+CGD+DV
Sbjct: 131 TQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDV 190
Query: 390 VIMHPD 395
+I HPD
Sbjct: 191 LITHPD 196
>pdb|1RZT|A Chain A, Crystal Structure Of Dna Polymerase Lambda Complexed With
A Two Nucleotide Gap Dna Molecule
pdb|1RZT|E Chain E, Crystal Structure Of Dna Polymerase Lambda Complexed With
A Two Nucleotide Gap Dna Molecule
pdb|1RZT|I Chain I, Crystal Structure Of Dna Polymerase Lambda Complexed With
A Two Nucleotide Gap Dna Molecule
pdb|1RZT|M Chain M, Crystal Structure Of Dna Polymerase Lambda Complexed With
A Two Nucleotide Gap Dna Molecule
Length = 331
Score = 152 bits (383), Expect = 4e-37, Method: Compositional matrix adjust.
Identities = 75/186 (40%), Positives = 112/186 (60%), Gaps = 2/186 (1%)
Query: 210 NKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDH 269
N +ITE L Y G+ R+ Y KAI ++ + S + +PGIGK M +
Sbjct: 9 NLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEK 68
Query: 270 IQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLT 329
I EI+ +G L KL+H E V + LF +WG G TAQ Y++G R+L+D++++ SLT
Sbjct: 69 IIEILESGHLRKLDHI--SESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLT 126
Query: 330 HSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDV 389
Q +GLK++ D R+PR E ++E+ +QKA + ++ + GSYRRGKA+CGD+DV
Sbjct: 127 TQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDV 186
Query: 390 VIMHPD 395
+I HPD
Sbjct: 187 LITHPD 192
>pdb|3C5G|A Chain A, Structure Of A Ternary Complex Of The R517k Pol Lambda
Mutant
pdb|3C5G|B Chain B, Structure Of A Ternary Complex Of The R517k Pol Lambda
Mutant
Length = 335
Score = 152 bits (383), Expect = 4e-37, Method: Compositional matrix adjust.
Identities = 75/186 (40%), Positives = 112/186 (60%), Gaps = 2/186 (1%)
Query: 210 NKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDH 269
N +ITE L Y G+ R+ Y KAI ++ + S + +PGIGK M +
Sbjct: 13 NLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEK 72
Query: 270 IQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLT 329
I EI+ +G L KL+H E V + LF +WG G TAQ Y++G R+L+D++++ SLT
Sbjct: 73 IIEILESGHLRKLDHI--SESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLT 130
Query: 330 HSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDV 389
Q +GLK++ D R+PR E ++E+ +QKA + ++ + GSYRRGKA+CGD+DV
Sbjct: 131 TQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDV 190
Query: 390 VIMHPD 395
+I HPD
Sbjct: 191 LITHPD 196
>pdb|1XSL|A Chain A, Crystal Structure Of Human Dna Polymerase Lambda In
Complex With A One Nucleotide Dna Gap
pdb|1XSL|E Chain E, Crystal Structure Of Human Dna Polymerase Lambda In
Complex With A One Nucleotide Dna Gap
pdb|1XSL|I Chain I, Crystal Structure Of Human Dna Polymerase Lambda In
Complex With A One Nucleotide Dna Gap
pdb|1XSL|M Chain M, Crystal Structure Of Human Dna Polymerase Lambda In
Complex With A One Nucleotide Dna Gap
pdb|2BCQ|A Chain A, Dna Polymerase Lambda In Complex With A Dna Duplex
Containing An Unpaired Dtmp
pdb|2BCR|A Chain A, Dna Polymerase Lambda In Complex With A Dna Duplex
Containing An Unpaired Damp
pdb|2BCS|A Chain A, Dna Polymerase Lambda In Complex With A Dna Duplex
Containing An Unpaired Dcmp
pdb|2BCU|A Chain A, Dna Polymerase Lambda In Complex With A Dna Duplex
Containing An Unpaired Damp And A T:t Mismatch
pdb|2BCV|A Chain A, Dna Polymerase Lambda In Complex With Dttp And A Dna
Duplex Containing An Unpaired Dtmp
pdb|2GWS|A Chain A, Crystal Structure Of Human Dna Polymerase Lambda With A GG
MISMATCH In The Primer Terminus
pdb|2GWS|E Chain E, Crystal Structure Of Human Dna Polymerase Lambda With A GG
MISMATCH In The Primer Terminus
pdb|2GWS|I Chain I, Crystal Structure Of Human Dna Polymerase Lambda With A GG
MISMATCH In The Primer Terminus
pdb|2GWS|M Chain M, Crystal Structure Of Human Dna Polymerase Lambda With A GG
MISMATCH In The Primer Terminus
Length = 335
Score = 152 bits (383), Expect = 4e-37, Method: Compositional matrix adjust.
Identities = 75/186 (40%), Positives = 112/186 (60%), Gaps = 2/186 (1%)
Query: 210 NKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDH 269
N +ITE L Y G+ R+ Y KAI ++ + S + +PGIGK M +
Sbjct: 13 NLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEK 72
Query: 270 IQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLT 329
I EI+ +G L KL+H E V + LF +WG G TAQ Y++G R+L+D++++ SLT
Sbjct: 73 IIEILESGHLRKLDHI--SESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLT 130
Query: 330 HSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDV 389
Q +GLK++ D R+PR E ++E+ +QKA + ++ + GSYRRGKA+CGD+DV
Sbjct: 131 TQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDV 190
Query: 390 VIMHPD 395
+I HPD
Sbjct: 191 LITHPD 196
>pdb|3UQ2|A Chain A, Crystal Structure Of The Post-Catalytic Product Complex Of
Polymerase Lambda With An Rcmp Inserted Opposite A
Templating G And Damp Inserted Opposite A Templating T
At The Primer Terminus.
pdb|4FO6|A Chain A, Crystal Structure Of The Pre-Catalytic Ternary Complex Of
Polymerase Lambda With A Datp Analog Opposite A
Templating T And An Rcmp At The Primer Terminus
Length = 329
Score = 152 bits (383), Expect = 4e-37, Method: Compositional matrix adjust.
Identities = 75/186 (40%), Positives = 112/186 (60%), Gaps = 2/186 (1%)
Query: 210 NKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDH 269
N +ITE L Y G+ R+ Y KAI ++ + S + +PGIGK M +
Sbjct: 12 NLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEK 71
Query: 270 IQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLT 329
I EI+ +G L KL+H E V + LF +WG G TAQ Y++G R+L+D++++ SLT
Sbjct: 72 IIEILESGHLRKLDHI--SESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLT 129
Query: 330 HSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDV 389
Q +GLK++ D R+PR E ++E+ +QKA + ++ + GSYRRGKA+CGD+DV
Sbjct: 130 TQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDV 189
Query: 390 VIMHPD 395
+I HPD
Sbjct: 190 LITHPD 195
>pdb|3MGH|A Chain A, Binary Complex Of A Dna Polymerase Lambda Loop Mutant
pdb|3MGH|C Chain C, Binary Complex Of A Dna Polymerase Lambda Loop Mutant
pdb|3MGI|A Chain A, Ternary Complex Of A Dna Polymerase Lambda Loop Mutant
pdb|3PML|A Chain A, Crystal Structure Of A Polymerase Lambda Variant With A
Dgtp Analog Opposite A Templating T
pdb|3PML|B Chain B, Crystal Structure Of A Polymerase Lambda Variant With A
Dgtp Analog Opposite A Templating T
pdb|3PMN|A Chain A, Ternary Crystal Structure Of Polymerase Lambda Variant
With A Gt Mispair At The Primer Terminus With Mn2+ In
The Active Site
pdb|3PNC|A Chain A, Ternary Crystal Structure Of A Polymerase Lambda Variant
With A Gt Mispair At The Primer Terminus And Sodium At
Catalytic Metal Site
pdb|3UPQ|A Chain A, Crystal Structure Of The Pre-Catalytic Ternary Complex Of
Polymerase Lambda With An Ratp Analog Opposite A
Templating T.
pdb|3UQ0|A Chain A, Crystal Structure Of The Post-Catalytic Product Complex Of
Polymerase Lambda With An Ramp At The Primer Terminus
Length = 329
Score = 152 bits (383), Expect = 4e-37, Method: Compositional matrix adjust.
Identities = 75/186 (40%), Positives = 112/186 (60%), Gaps = 2/186 (1%)
Query: 210 NKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDH 269
N +ITE L Y G+ R+ Y KAI ++ + S + +PGIGK M +
Sbjct: 12 NLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEK 71
Query: 270 IQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLT 329
I EI+ +G L KL+H E V + LF +WG G TAQ Y++G R+L+D++++ SLT
Sbjct: 72 IIEILESGHLRKLDHI--SESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLT 129
Query: 330 HSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDV 389
Q +GLK++ D R+PR E ++E+ +QKA + ++ + GSYRRGKA+CGD+DV
Sbjct: 130 TQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDV 189
Query: 390 VIMHPD 395
+I HPD
Sbjct: 190 LITHPD 195
>pdb|3MDA|A Chain A, Dna Polymerase Lambda In Complex With Arac
pdb|3MDC|A Chain A, Dna Polymerase Lambda In Complex With Dfdctp
Length = 325
Score = 152 bits (383), Expect = 4e-37, Method: Compositional matrix adjust.
Identities = 75/186 (40%), Positives = 112/186 (60%), Gaps = 2/186 (1%)
Query: 210 NKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDH 269
N +ITE L Y G+ R+ Y KAI ++ + S + +PGIGK M +
Sbjct: 3 NLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEK 62
Query: 270 IQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLT 329
I EI+ +G L KL+H E V + LF +WG G TAQ Y++G R+L+D++++ SLT
Sbjct: 63 IIEILESGHLRKLDHI--SESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLT 120
Query: 330 HSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDV 389
Q +GLK++ D R+PR E ++E+ +QKA + ++ + GSYRRGKA+CGD+DV
Sbjct: 121 TQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDV 180
Query: 390 VIMHPD 395
+I HPD
Sbjct: 181 LITHPD 186
>pdb|3HX0|A Chain A, Ternary Complex Of L277a, H511a, R514 Mutant Pol Lambda
Bound To A 2 Nucleotide Gapped Dna Substrate With A
Scrunched Da
pdb|3HX0|F Chain F, Ternary Complex Of L277a, H511a, R514 Mutant Pol Lambda
Bound To A 2 Nucleotide Gapped Dna Substrate With A
Scrunched Da
pdb|3HX0|K Chain K, Ternary Complex Of L277a, H511a, R514 Mutant Pol Lambda
Bound To A 2 Nucleotide Gapped Dna Substrate With A
Scrunched Da
pdb|3HX0|P Chain P, Ternary Complex Of L277a, H511a, R514 Mutant Pol Lambda
Bound To A 2 Nucleotide Gapped Dna Substrate With A
Scrunched Da
Length = 335
Score = 151 bits (382), Expect = 5e-37, Method: Compositional matrix adjust.
Identities = 75/186 (40%), Positives = 112/186 (60%), Gaps = 2/186 (1%)
Query: 210 NKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDH 269
N +ITE L Y G+ R+ Y KAI ++ + S + +PGIGK M +
Sbjct: 13 NLHITEKLEVLAKAYSVQGDKWRAAGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEK 72
Query: 270 IQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLT 329
I EI+ +G L KL+H E V + LF +WG G TAQ Y++G R+L+D++++ SLT
Sbjct: 73 IIEILESGHLRKLDHI--SESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLT 130
Query: 330 HSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDV 389
Q +GLK++ D R+PR E ++E+ +QKA + ++ + GSYRRGKA+CGD+DV
Sbjct: 131 TQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDV 190
Query: 390 VIMHPD 395
+I HPD
Sbjct: 191 LITHPD 196
>pdb|3RH5|A Chain A, Dna Polymerase Beta Mutant (Y271) With A
Dideoxy-Terminated Primer With An Incoming
Deoxynucleotide (Dctp)
pdb|3RH6|A Chain A, Dna Polymerase Beta Mutant (Y271) With A
Dideoxy-Terminated Primer With An Incoming
Ribonucleotide (Rctp)
Length = 335
Score = 151 bits (381), Expect = 7e-37, Method: Compositional matrix adjust.
Identities = 80/188 (42%), Positives = 116/188 (61%), Gaps = 2/188 (1%)
Query: 209 LNKNITEIFGKLINIYRALGEDRRSF-SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 267
LN IT++ +L N + + + + +Y KA VI K P KI+S + K LPG+G +
Sbjct: 11 LNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIA 70
Query: 268 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNED 326
+ I E + TGKL KLE +D+ +I+ V GIGP+ A+K ++G +TL+DL KNED
Sbjct: 71 EKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNED 130
Query: 327 SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGD 386
L H QR+GLKYF D + RIPR E+ QM+ ++ ++V E I GS+RRG S GD
Sbjct: 131 KLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGD 190
Query: 387 LDVVIMHP 394
+DV++ HP
Sbjct: 191 MDVLLTHP 198
>pdb|4F5N|A Chain A, Open Ternary Complex Of R283k Dna Polymerase Beta With A
Metal Free Dctp Analog
pdb|4F5O|A Chain A, Open Ternary Complex Of R283k Dna Polymerase Beta With A
One Metal Bound Dctp Analog
pdb|4F5P|A Chain A, Open Ternary Mismatch Complex Of R283k Dna Polymerase Beta
With A Datp Analog
pdb|4F5Q|A Chain A, Closed Ternary Complex Of R283k Dna Polymerase Beta
pdb|4F5R|A Chain A, Open And Closed Ternary Complex Of R283k Dna Polymerase
Beta With A Dctp Analog In The Same Asymmetric Unit
pdb|4F5R|B Chain B, Open And Closed Ternary Complex Of R283k Dna Polymerase
Beta With A Dctp Analog In The Same Asymmetric Unit
pdb|4GXI|A Chain A, R283k Dna Polymerase Beta Binary Complex With A Templating
8og
pdb|4GXJ|A Chain A, R283k Dna Polymerase Beta Ternary Complex With A
Templating 8og And Incoming Dctp Analog
pdb|4GXK|A Chain A, R283k Dna Polymerase Beta Ternary Complex With A
Templating 8og And Incoming Datp Analog
Length = 335
Score = 150 bits (380), Expect = 8e-37, Method: Compositional matrix adjust.
Identities = 80/188 (42%), Positives = 116/188 (61%), Gaps = 2/188 (1%)
Query: 209 LNKNITEIFGKLINIYRALGEDRRSF-SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 267
LN IT++ +L N + + + + +Y KA VI K P KI+S + K LPG+G +
Sbjct: 11 LNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIA 70
Query: 268 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNED 326
+ I E + TGKL KLE +D+ +I+ V GIGP+ A+K ++G +TL+DL KNED
Sbjct: 71 EKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNED 130
Query: 327 SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGD 386
L H QR+GLKYF D + RIPR E+ QM+ ++ ++V E I GS+RRG S GD
Sbjct: 131 KLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGD 190
Query: 387 LDVVIMHP 394
+DV++ HP
Sbjct: 191 MDVLLTHP 198
>pdb|9ICG|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dctp
(1 Millimolar) And Zncl2 (1 Millimolar)
pdb|9ICH|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dgtp
(1 Millimolar) And Zncl2 (1 Millimolar)
pdb|9ICI|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dttp
(1 Millimolar) And Zncl2 (1 Millimolar)
pdb|9ICJ|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna
pdb|9ICK|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Artificial Mother Liquor
pdb|9ICL|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Pyrophosphate And Mncl2
pdb|9ICM|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Double Stranded Dna (No 5'-Phosphate)
pdb|9ICN|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + 2',3'-
Dideoxycytidine-5'-Triphosphate, Soaked In The Presence
Of Ddctp And Mgcl2
pdb|9ICO|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Dttp And Mgcl2
pdb|9ICP|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of
Pyrophosphate (1 Millimolar) And Mgcl2 (5 Millimolar)
pdb|9ICQ|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Datp (1
Millimolar) And Mncl2 (5 Millimolar)
pdb|9ICR|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + 2'-
Deoxycytidine-5'-Triphosphate, Soaked In The Presence Of
Dctp And Mncl2
pdb|9ICS|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + 2',3'-
Dideoxycytidine-5'-Triphosphate, Soaked In The Presence
Of Ddctp And Mncl2
pdb|9ICT|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + 2'-
Deoxyguanosine-5'-Triphosphate, Soaked In The Presence
Of Dgtp And Mncl2
pdb|9ICU|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Dttp (1
Millimolar) And Mncl2 (5 Millimolar)
pdb|9ICV|A Chain A, Dna Polymerase Beta (e.c.2.7.7.7)/dna Complex + 2'-
Deoxyadenosine-5'-triphosphate, Soaked In The Presence
Of Datp And Zncl2
pdb|9ICW|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Native Structure
pdb|9ICX|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Six Base Pairs Of Dna (non Gapped Dna Only)
pdb|9ICY|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7) Complexed With Seven
Base Pairs Of Dna (Non Gapped Dna Only)
pdb|8ICB|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of
Artificial Mother Liquor
pdb|8ICC|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna (no 5'-phosphate)
pdb|8ICE|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Cdcl2 (1 Millimolar)
pdb|8ICF|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(10 Millimolar) And Mgcl2 (50 Millimolar)
pdb|8ICG|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Mgcl2 (5 Millimolar)
pdb|8ICH|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dctp
(1 Millimolar) And Mgcl2 (5 Millimolar)
pdb|8ICI|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dgtp
(1 Millimolar) And Mgcl2 (5 Millimolar)
pdb|8ICJ|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + THYMIDINE-
5'-Triphosphate, Soaked In The Presence Of Dttp And
Mgcl2
pdb|8ICK|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar), Mgcl2 (5 Millimolar), And Mncl2 (5
Millimolar)
pdb|8ICL|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Nicl2 (5 Millimolar)
pdb|8ICM|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar), Mncl2 (5 Millimolar), And Ammonium
Sulfate (75 Millimolar)
pdb|8ICN|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Atp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICO|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of
Azt-Tp (1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICP|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICQ|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Of
Datp (0.1 Millimolar) And Mncl2 (0.5 Millimolar)
pdb|8ICR|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICS|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dctp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICT|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dctp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICU|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Ddatp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICV|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dgtp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICW|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dttp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICX|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Dttp
(1 Millimolar) And Mncl2 (5 Millimolar)
pdb|8ICY|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + THYMIDINE-
5'-Triphosphate, Soaked In The Presence Of Dttp And
Mncl2
pdb|8ICZ|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Of
Datp (1 Millimolar), Mncl2 (5 Millimolar), And Lithium
Sulfate (75 Millimolar)
pdb|9ICA|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + 2'-
Deoxyadenosine-5'-O-(1-Thiotriphosphate), Soaked In The
Presence Of Datp(Alpha)s And Mncl2
pdb|9ICB|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + 2'-
Deoxyadenosine-5'-Triphosphate, Soaked In The Presence
Of Datp And Cocl2
pdb|9ICC|A Chain A, Dna Polymerase Beta (e.c.2.7.7.7)/dna Complex + 2'-
Deoxyadenosine-5'-triphosphate, Soaked In The Presence
Of Datp And Crcl3
pdb|9ICE|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Cucl2 (0.1 Millimolar)
pdb|9ICF|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX + 2'-
Deoxyadenosine-5'-Triphosphate, Soaked In The Presence
Of Datp And Zncl2
pdb|1ZQQ|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Mncl2
(15 Millimolar) And Nacl (15 Millimolar)
pdb|1ZQR|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Nicl2
pdb|1ZQS|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Tlcl
(0.5 Millimolar)
pdb|1ZQT|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(0.01 Millimolar) And Zncl2 (0.02 Millimolar)
pdb|7ICE|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Cacl2
pdb|7ICF|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Cdcl2
(0.1 Millimolar) (Four-Day Soak)
pdb|7ICG|A Chain A, Dna Polymerase Beta (e.c.2.7.7.7)/dna Complex, Soaked In
The Presence Of Cdcl2
pdb|7ICH|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Cocl2
pdb|7ICI|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Crcl3
(0.1 Millimolar)
pdb|7ICJ|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Cucl2
(0.1 Millimolar)
pdb|7ICK|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Mgcl2
pdb|7ICL|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Mncl2
(0.1 Millimolar)
pdb|7ICM|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Mncl2
(1.0 Millimolar)
pdb|7ICN|A Chain A, Dna Polymerase Beta (e.c.2.7.7.7)/dna Complex, Soaked In
The Presence Of Nicl2
pdb|7ICO|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Zncl2
pdb|7ICP|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Zncl2
(0.01 Millimolar)
pdb|7ICQ|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Zncl2
pdb|7ICR|A Chain A, Dna Polymerase Beta (e.c.2.7.7.7)/dna Complex, Soaked In
The Presence Of Zncl2
pdb|7ICS|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Zncl2
pdb|7ICT|A Chain A, Dna Polymerase Beta (E.C.2.7.7.7)DNA COMPLEX, SOAKED IN
The Presence Of Zncl2 And Mgcl2
pdb|7ICU|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Cdcl2
(0.1 Millimolar)
pdb|7ICV|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Six Base Pairs Of Dna; Soaked In The Presence Of Mncl2
(0.1 Millimolar) And In The Absence Of Nacl
pdb|8ICA|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Datp
(1 Millimolar) And Cacl2 (5 Millimolar)
pdb|1ZQA|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Kcl
(150 Millimolar) At Ph 7.5
pdb|1ZQB|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Bacl2
(150 Millimolar)
pdb|1ZQC|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Cacl2
(15 Millimolar)
pdb|1ZQD|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Cacl2
(150 Millimolar)
pdb|1ZQE|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Crcl3
(saturated Solution)
pdb|1ZQF|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Cscl
(150 Millimolar)
pdb|1ZQG|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of A
Sodium-Free Artificial Mother Liquor At Ph 6.5
pdb|1ZQH|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of A
Sodium-Free Artificial Mother Liquor At Ph 7.5
pdb|1ZQI|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Kcl
(150 Millimolar)
pdb|1ZQJ|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Cacl2
(15 Millimolar) And Mgcl2 (15 Millimolar)
pdb|1ZQK|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Kcl
(75 Millimolar) And Mgcl2 (75 Millimolar)
pdb|1ZQL|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Mncl2
(15 Millimolar) And Mgcl2 (15 Millimolar)
pdb|1ZQM|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Mncl2
(15 Millimolar)
pdb|1ZQN|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Bacl2
(15 Millimolar) And Nacl (15 Millimolar)
pdb|1ZQO|A Chain A, Dna Polymerase Beta (pol B) (e.c.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Cacl2
(15 Millimolar) And Nacl (15 Millimolar)
pdb|1ZQP|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed With
Seven Base Pairs Of Dna; Soaked In The Presence Of Kcl
(75 Millimolar) And Nacl (75 Millimolar)
pdb|1BPX|A Chain A, Dna Polymerase BetaDNA COMPLEX
pdb|1BPY|A Chain A, Human Dna Polymerase Beta Complexed With Gapped Dna And
Ddctp
pdb|1BPZ|A Chain A, Human Dna Polymerase Beta Complexed With Nicked Dna
pdb|1MQ2|A Chain A, Human Dna Polymerase Beta Complexed With Gapped Dna
Containing An 8-Oxo-7,8-Dihydro-Guanine And Damp
pdb|1MQ3|A Chain A, Human Dna Polymerase Beta Complexed With Gapped Dna
Containing An 8-Oxo-7,8-Dihydro-Guanine Template Paired
With Dctp
pdb|1TV9|A Chain A, Human Dna Polymerase Beta Complexed With Nicked Dna
Containing A Mismatched Template Adenine And Incoming
Cytidine
pdb|1TVA|A Chain A, Human Dna Polymerase Beta Complexed With Nicked Dna
Containing A Mismatched Template Thymidine And Incoming
Cytidine
pdb|1ZJM|A Chain A, Human Dna Polymerase Beta Complexed With Dna Containing An
A-A Mismatched Primer Terminus
pdb|1ZJN|A Chain A, Human Dna Polymerase Beta Complexed With Dna Containing An
A-A Mismatched Primer Terminus With Dgtp
pdb|2FMP|A Chain A, Dna Polymerase Beta With A Terminated Gapped Dna Substrate
And Ddctp With Sodium In The Catalytic Site
pdb|2FMQ|A Chain A, Sodium In Active Site Of Dna Polymerase Beta
pdb|2FMS|A Chain A, Dna Polymerase Beta With A Gapped Dna Substrate And
Dumpnpp With Magnesium In The Catalytic Site
pdb|2I9G|A Chain A, Dna Polymerase Beta With A Benzo[c]phenanthrene Diol
Epoxide Adducted Guanine Base
pdb|2ISO|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Terminated Primer And 2'-Deoxyguanosine 5'-Beta, Gamma-
Difluoromethylene Triphosphate
pdb|2ISP|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Terminated Primer And 2'-Deoxyguanosine 5'-Beta, Gamma-
Methylene Triphosphate
pdb|2P66|A Chain A, Human Dna Polymerase Beta Complexed With Tetrahydrofuran
(abasic Site) Containing Dna
pdb|2PXI|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Terminated Primer And 2'-Deoxyguanosine 5'-Beta, Gamma-
Monofluoromethylene Triphosphate
pdb|3C2K|A Chain A, Dna Polymerase Beta With A Gapped Dna Substrate And
Dumpnpp With Manganese In The Active Site
pdb|3C2L|A Chain A, Ternary Complex Of Dna Polymerase Beta With A C:dapcpp
Mismatch In The Active Site
pdb|3C2M|A Chain A, Ternary Complex Of Dna Polymerase Beta With A G:dapcpp
Mismatch In The Active Site
pdb|3ISB|A Chain A, Binary Complex Of Human Dna Polymerase Beta With A Gapped
Dna
pdb|3ISC|A Chain A, Binary Complex Of Human Dna Polymerase Beta With An Abasic
Site (Thf) In The Gapped Dna
pdb|3ISD|A Chain A, Ternary Complex Of Human Dna Polymerase Beta With An
Abasic Site (Thf): Dapcpp Mismatch
pdb|3JPN|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Termin Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Dichloro Methyl Triphosphate
pdb|3JPO|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Termin Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Monochloromethy Triphosphate
pdb|3JPP|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Termin Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Monomethyl Meth Triphosphate
pdb|3JPQ|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Termin Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Monobromo Methy Triphosphate
pdb|3JPR|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Termin Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Dimethyl Methyl Triphosphate
pdb|3JPS|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Termin Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Fluoro Methyl M Triphosphate
pdb|3JPT|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Termin Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Fluoro Chloro M Triphosphate
pdb|3MBY|A Chain A, Ternary Complex Of Dna Polymerase Beta With Template Base
A And 8oxodgtp In The Active Site With A Dideoxy
Terminated Primer
pdb|3LK9|A Chain A, Dna Polymerase Beta With A Gapped Dna Substrate And
Dtmp(Cf2)p(Cf2)p
pdb|3RH4|A Chain A, Dna Polymerase Beta With A Dideoxy-Terminated Primer With
An Incoming Ribonucleotide (Rctp)
pdb|3RJE|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Gapped Dna
Containing 8odg At Template Position
pdb|3RJF|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Gapped Dna
Containing (Syn)8odg At Template Position Paired With
Non-Hydrolyzable Datp Analog (Dapcpp)
pdb|3RJG|A Chain A, Binary Complex Of Dna Polymerase Beta With A Gapped Dna
Containing 8odg:da Base-Pair At Primer Terminus
pdb|3RJH|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Gapped Dna
Containing (Syn)8odg:da At Primer Terminus And
Dg:dcmp(Cf2)ppin The Active Site
pdb|3RJI|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Gapped Dna
Containing 8odg At Template Position Paired With
Non-Hydrolyzable Dctp Analog (Dcmp(Cf2)pp)
pdb|3RJJ|A Chain A, Ternary Complex Crystal Structure Of Dna Polymerase Beta
With Template 8odg Provides Insight Into Mutagenic
Lesion Bypass
pdb|3RJK|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Gapped Dna
Containing 8odg:dc Base Pair At Primer Terminus And
Dg:dcmp(Cf2)pp In The Active Site
pdb|3TFR|A Chain A, Ternary Complex Structure Of Dna Polymerase Beta With A
Gapped Dna Substrate And A, B Damp(Cf2)pp In The Active
Site
pdb|3TFS|A Chain A, Ternary Complex Structure Of Dna Polymerase Beta With A
Gapped Dna Substrate And A, B Damp(Cfh)pp In The Active
Site: Stereoselective Binding Of (S) Isomer
pdb|4DO9|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Terminated Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Monofluoromethylene Triphosphate: Stereoselective
Binding Of R-Isomer
pdb|4DOA|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Terminated Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Monofluoromethylene Triphosphate: Non-Interactive
Binding Of S-Isomer
pdb|4DOB|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Terminated Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Monochlororomethylene Triphosphate:
Stereoselective Binding Of R-Isomer
pdb|4DOC|A Chain A, Ternary Complex Of Dna Polymerase Beta With A Dideoxy
Terminated Primer And 2'-Deoxyguanosine 5'-Beta,
Gamma-Monochlororomethylene Triphosphate:binding Of
S-Isomer
Length = 335
Score = 150 bits (380), Expect = 8e-37, Method: Compositional matrix adjust.
Identities = 80/188 (42%), Positives = 116/188 (61%), Gaps = 2/188 (1%)
Query: 209 LNKNITEIFGKLINIYRALGEDRRSF-SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 267
LN IT++ +L N + + + + +Y KA VI K P KI+S + K LPG+G +
Sbjct: 11 LNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIA 70
Query: 268 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNED 326
+ I E + TGKL KLE +D+ +I+ V GIGP+ A+K ++G +TL+DL KNED
Sbjct: 71 EKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNED 130
Query: 327 SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGD 386
L H QR+GLKYF D + RIPR E+ QM+ ++ ++V E I GS+RRG S GD
Sbjct: 131 KLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGD 190
Query: 387 LDVVIMHP 394
+DV++ HP
Sbjct: 191 MDVLLTHP 198
>pdb|3GDX|A Chain A, Dna Polymerase Beta With A Gapped Dnd Substrate And
Dtmp(Cf2)pp
Length = 326
Score = 150 bits (380), Expect = 1e-36, Method: Compositional matrix adjust.
Identities = 80/188 (42%), Positives = 116/188 (61%), Gaps = 2/188 (1%)
Query: 209 LNKNITEIFGKLINIYRALGEDRRSF-SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 267
LN IT++ +L N + + + + +Y KA VI K P KI+S + K LPG+G +
Sbjct: 2 LNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIA 61
Query: 268 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNED 326
+ I E + TGKL KLE +D+ +I+ V GIGP+ A+K ++G +TL+DL KNED
Sbjct: 62 EKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNED 121
Query: 327 SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGD 386
L H QR+GLKYF D + RIPR E+ QM+ ++ ++V E I GS+RRG S GD
Sbjct: 122 KLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGD 181
Query: 387 LDVVIMHP 394
+DV++ HP
Sbjct: 182 MDVLLTHP 189
>pdb|2IHM|A Chain A, Polymerase Mu In Ternary Complex With Gapped 11mer Dna
Duplex And Bound Incoming Nucleotide
pdb|2IHM|B Chain B, Polymerase Mu In Ternary Complex With Gapped 11mer Dna
Duplex And Bound Incoming Nucleotide
Length = 360
Score = 115 bits (287), Expect = 5e-26, Method: Compositional matrix adjust.
Identities = 56/165 (33%), Positives = 97/165 (58%), Gaps = 1/165 (0%)
Query: 232 RSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKV 291
R S+ +A V++ LP + S Q+ GLP G+ IQE++ G +++ E+
Sbjct: 39 RLLSFSRAASVLKSLPCPVASLSQLHGLPYFGEHSTRVIQELLEHGTCEEVKQVRCSERY 98
Query: 292 RTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE-DSLTHSQRLGLKYFDDIKTRIPRHE 350
+T+ LF +V+G+G TA + Y++G RTLD+L+ + LT Q+ GL+Y+ D+ T + R +
Sbjct: 99 QTMKLFTQVFGVGVKTANRWYQEGLRTLDELREQPQRLTQQQKAGLQYYQDLSTPVRRAD 158
Query: 351 VEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPD 395
E +++L++ A + LP + G +RRGK D+D +I HP+
Sbjct: 159 AEALQQLIEAAVRQTLPGATVTLTGGFRRGKLQGHDVDFLITHPE 203
>pdb|1RPL|A Chain A, 2.3 Angstroms Crystal Structure Of The Catalytic Domain Of
Dna Polymerase Beta
Length = 251
Score = 108 bits (271), Expect = 4e-24, Method: Compositional matrix adjust.
Identities = 53/115 (46%), Positives = 78/115 (67%), Gaps = 1/115 (0%)
Query: 282 LEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNEDSLTHSQRLGLKYFD 340
LE +D+ +I+ V GIGP+ A+KL ++G +TL+DL KNED L H QR+GLKYF+
Sbjct: 1 LEKIRQDDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNEDKLNHHQRIGLKYFE 60
Query: 341 DIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPD 395
D + RIPR E+ QM+ ++ +++ PE I GS+RRG S GD+DV++ HP+
Sbjct: 61 DFEKRIPREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGDMDVLLTHPN 115
>pdb|1JN3|A Chain A, Fidelity Properties And Structure Of M282l Mutator Mutant
Of Dna Polymerase: Subtle Structural Changes Influence
The Mechanism Of Nucleotide Discrimination
Length = 251
Score = 108 bits (270), Expect = 5e-24, Method: Compositional matrix adjust.
Identities = 53/115 (46%), Positives = 78/115 (67%), Gaps = 1/115 (0%)
Query: 282 LEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNEDSLTHSQRLGLKYFD 340
LE +D+ +I+ V GIGP+ A+KL ++G +TL+DL KNED L H QR+GLKYF+
Sbjct: 1 LEKIRQDDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNEDKLNHHQRIGLKYFE 60
Query: 341 DIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPD 395
D + RIPR E+ QM+ ++ +++ PE I GS+RRG S GD+DV++ HP+
Sbjct: 61 DFEKRIPREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGDMDVLLTHPN 115
>pdb|1BPB|A Chain A, Crystal Structure Of Rat Dna Polymerase Beta: Evidence For
A Common Polymerase Mechanism
pdb|1NOM|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7), 31-Kd Domain;
Soaked In The Presence Of Mncl2 (5 Millimolar)
pdb|1ZQU|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7), 31-Kd Domain;
Soaked In The Presence Of Artificial Mother Liquor
pdb|1ZQV|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7), 31-Kd Domain;
Soaked In The Presence Of Cacl2 (150 Millimolar)
pdb|1ZQW|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7), 31-Kd Domain;
Soaked In The Presence Of Cscl (150 Millimolar)
pdb|1ZQX|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7), 31-Kd Domain;
Soaked In The Presence Of Kcl (150 Millimolar)
pdb|1ZQY|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7), 31-Kd Domain;
Soaked In The Presence Of Mgcl2 (50 Millimolar)
pdb|1ZQZ|A Chain A, Dna Polymerase Beta (Pol B) (E.C.2.7.7.7), 31-Kd Domain;
Soaked In The Presence Of Mncl2 (50 Millimolar)
pdb|2BPC|A Chain A, Crystal Structure Of Rat Dna Polymerase Beta: Evidence For
A Common Polymerase Mechanism
Length = 248
Score = 105 bits (263), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 51/110 (46%), Positives = 76/110 (69%), Gaps = 1/110 (0%)
Query: 287 KDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNEDSLTHSQRLGLKYFDDIKTR 345
+D+ +I+ V GIGP+ A+KL ++G +TL+DL KNED L H QR+GLKYF+D + R
Sbjct: 3 QDDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNEDKLNHHQRIGLKYFEDFEKR 62
Query: 346 IPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPD 395
IPR E+ QM+ ++ +++ PE I GS+RRG S GD+DV++ HP+
Sbjct: 63 IPREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGDMDVLLTHPN 112
>pdb|3K75|D Chain D, X-Ray Crystal Structure Of Reduced Xrcc1 Bound To Dna Pol
Beta Catalytic Domain
pdb|3K75|E Chain E, X-Ray Crystal Structure Of Reduced Xrcc1 Bound To Dna Pol
Beta Catalytic Domain
Length = 252
Score = 105 bits (263), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 51/109 (46%), Positives = 75/109 (68%), Gaps = 1/109 (0%)
Query: 288 DEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNEDSLTHSQRLGLKYFDDIKTRI 346
D+ +I+ V GIGP+ A+KL ++G +TL+DL KNED L H QR+GLKYF+D + RI
Sbjct: 2 DDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNEDKLNHHQRIGLKYFEDFEKRI 61
Query: 347 PRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPD 395
PR E+ QM+ ++ +++ PE I GS+RRG S GD+DV++ HP+
Sbjct: 62 PREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGDMDVLLTHPN 110
>pdb|2VAN|A Chain A, Nucleotidyl Transfer Mechanism Of Mismatched Dntp
Incorporation By Dna Polymerase B By Structural And
Kinetic Analyses
Length = 245
Score = 105 bits (262), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 51/109 (46%), Positives = 75/109 (68%), Gaps = 1/109 (0%)
Query: 288 DEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNEDSLTHSQRLGLKYFDDIKTRI 346
D+ +I+ V GIGP+ A+KL ++G +TL+DL KNED L H QR+GLKYF+D + RI
Sbjct: 1 DDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNEDKLNHHQRIGLKYFEDFEKRI 60
Query: 347 PRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPD 395
PR E+ QM+ ++ +++ PE I GS+RRG S GD+DV++ HP+
Sbjct: 61 PREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGDMDVLLTHPN 109
>pdb|1JMS|A Chain A, Crystal Structure Of The Catalytic Core Of Murine Terminal
Deoxynucleotidyl Transferase
Length = 381
Score = 103 bits (256), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 56/190 (29%), Positives = 105/190 (55%), Gaps = 6/190 (3%)
Query: 212 NITEIFGKLINIYRALGEDRRS----FSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 267
N ++F ++I E R + ++ +A V++ LPF I S +G+P +G ++
Sbjct: 34 NYNQLFTDALDILAENDELRENEGSCLAFMRASSVLKSLPFPITSMKDTEGIPCLGDKVK 93
Query: 268 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDS 327
I+ I+ G+ S+ + DE+ ++ LF V+G+G TA+K + G RTL ++++ S
Sbjct: 94 SIIEGIIEDGESSEAKAVLNDERYKSFKLFTSVFGVGLKTAEKWFRMGFRTLSKIQSDKS 153
Query: 328 L--THSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCG 385
L T Q+ G Y++D+ + + R E E + L+++A LP+ ++ G +RRGK +
Sbjct: 154 LRFTQMQKAGFLYYEDLVSCVNRPEAEAVSMLVKEAVVTFLPDALVTMTGGFRRGKMTGH 213
Query: 386 DLDVVIMHPD 395
D+D +I P+
Sbjct: 214 DVDFLITSPE 223
>pdb|1KDH|A Chain A, Binary Complex Of Murine Terminal Deoxynucleotidyl
Transferase With A Primer Single Stranded Dna
pdb|1KEJ|A Chain A, Crystal Structure Of Murine Terminal Deoxynucleotidyl
Transferase Complexed With Ddatp
Length = 363
Score = 102 bits (254), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 56/190 (29%), Positives = 105/190 (55%), Gaps = 6/190 (3%)
Query: 212 NITEIFGKLINIYRALGEDRRS----FSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 267
N ++F ++I E R + ++ +A V++ LPF I S +G+P +G ++
Sbjct: 16 NYNQLFTDALDILAENDELRENEGSCLAFMRASSVLKSLPFPITSMKDTEGIPCLGDKVK 75
Query: 268 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDS 327
I+ I+ G+ S+ + DE+ ++ LF V+G+G TA+K + G RTL ++++ S
Sbjct: 76 SIIEGIIEDGESSEAKAVLNDERYKSFKLFTSVFGVGLKTAEKWFRMGFRTLSKIQSDKS 135
Query: 328 L--THSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCG 385
L T Q+ G Y++D+ + + R E E + L+++A LP+ ++ G +RRGK +
Sbjct: 136 LRFTQMQKAGFLYYEDLVSCVNRPEAEAVSMLVKEAVVTFLPDALVTMTGGFRRGKMTGH 195
Query: 386 DLDVVIMHPD 395
D+D +I P+
Sbjct: 196 DVDFLITSPE 205
>pdb|3LQC|B Chain B, X-Ray Crystal Structure Of Oxidized Xrcc1 Bound To Dna Pol
B Thumb Domain
Length = 200
Score = 57.4 bits (137), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 39/58 (67%)
Query: 338 YFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPD 395
YF+D + RIPR E+ QM+ ++ +++ PE I GS+RRG S GD+DV++ HP+
Sbjct: 1 YFEDFEKRIPREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGDMDVLLTHPN 58
>pdb|1DK3|A Chain A, Refined Solution Structure Of The N-Terminal Domain Of Dna
Polymerase Beta
pdb|1BNO|A Chain A, Nmr Solution Structure Of The N-Terminal Domain Of Dna
Polymerase Beta, Minimized Average Structure
pdb|1BNP|A Chain A, Nmr Solution Structure Of The N-Terminal Domain Of Dna
Polymerase Beta, 55 Structures
Length = 87
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 44/76 (57%), Gaps = 1/76 (1%)
Query: 209 LNKNITEIFGKLINIYRALGEDRRSF-SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 267
LN IT++ +L N + + + + +Y KA VI K P KI+S + K LPG+G +
Sbjct: 11 LNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIA 70
Query: 268 DHIQEIVTTGKLSKLE 283
+ I E + TGKL KLE
Sbjct: 71 EKIDEFLATGKLRKLE 86
>pdb|1DK2|A Chain A, Refined Solution Structure Of The N-Terminal Domain Of Dna
Polymerase Beta
Length = 86
Score = 53.9 bits (128), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 44/76 (57%), Gaps = 1/76 (1%)
Query: 209 LNKNITEIFGKLINIYRALGEDRRSF-SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 267
LN IT++ +L N + + + + +Y KA VI K P KI+S + K LPG+G +
Sbjct: 10 LNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIA 69
Query: 268 DHIQEIVTTGKLSKLE 283
+ I E + TGKL KLE
Sbjct: 70 EKIDEFLATGKLRKLE 85
>pdb|3B0Y|A Chain A, K263d Mutant Of Polx From Thermus Thermophilus Hb8
Complexed With Ca- Dgtp
Length = 575
Score = 53.1 bits (126), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 65/205 (31%), Positives = 97/205 (47%), Gaps = 27/205 (13%)
Query: 210 NKNITEIFGKLINIYRALGEDR-RSFSYYKAIPVIEKLPFKIE-----SADQVKGLPGIG 263
N+ + IF ++ + LG++ R +Y++A + L IE + + LPG+G
Sbjct: 3 NQELARIFEEIGLMSEFLGDNPFRVRAYHQAARTLYDLDTPIEEIAEKGKEALMELPGVG 62
Query: 264 KSMQDHIQEIVTTGKLSKLEHFEKDEKV-RTISLFGEVWGIGPATAQKLYEK-GHRTLDD 321
+ + I E + TGK+ K H E KV R + EV G+GP TA+ LYE G +L+
Sbjct: 63 PDLAEKILEFLRTGKVRK--HEELSRKVPRGVLEVMEVPGVGPKTARLLYEGLGIDSLEK 120
Query: 322 LK---NEDSLTHSQRLGLKYFDDIK----------TRIPRHEVEQMERLLQKAGEEVLPE 368
LK + LT + G K + I+ R P V + R L +A LP
Sbjct: 121 LKAALDRGDLTRLKGFGPKRAERIREGLALAQAAGKRRPLGAVLSLARSLLEA-IRALPG 179
Query: 369 V--IILCGGSYRRGKASCGDLDVVI 391
V LC GS RR K + GDLD ++
Sbjct: 180 VERAELC-GSARRYKDTVGDLDFLV 203
>pdb|3AU2|A Chain A, Dna Polymerase X From Thermus Thermophilus Hb8 Complexed
With Ca-Dgtp
pdb|3AU6|A Chain A, Dna Polymerase X From Thermus Thermophilus Hb8 Ternary
Complex With PrimerTEMPLATE DNA AND DDGTP
pdb|3AUO|A Chain A, Dna Polymerase X From Thermus Thermophilus Hb8 Ternary
Complex With 1- Nt Gapped Dna And Ddgtp
pdb|3AUO|B Chain B, Dna Polymerase X From Thermus Thermophilus Hb8 Ternary
Complex With 1- Nt Gapped Dna And Ddgtp
Length = 575
Score = 53.1 bits (126), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 65/205 (31%), Positives = 97/205 (47%), Gaps = 27/205 (13%)
Query: 210 NKNITEIFGKLINIYRALGEDR-RSFSYYKAIPVIEKLPFKIE-----SADQVKGLPGIG 263
N+ + IF ++ + LG++ R +Y++A + L IE + + LPG+G
Sbjct: 3 NQELARIFEEIGLMSEFLGDNPFRVRAYHQAARTLYDLDTPIEEIAEKGKEALMELPGVG 62
Query: 264 KSMQDHIQEIVTTGKLSKLEHFEKDEKV-RTISLFGEVWGIGPATAQKLYEK-GHRTLDD 321
+ + I E + TGK+ K H E KV R + EV G+GP TA+ LYE G +L+
Sbjct: 63 PDLAEKILEFLRTGKVRK--HEELSRKVPRGVLEVMEVPGVGPKTARLLYEGLGIDSLEK 120
Query: 322 LK---NEDSLTHSQRLGLKYFDDIK----------TRIPRHEVEQMERLLQKAGEEVLPE 368
LK + LT + G K + I+ R P V + R L +A LP
Sbjct: 121 LKAALDRGDLTRLKGFGPKRAERIREGLALAQAAGKRRPLGAVLSLARSLLEA-IRALPG 179
Query: 369 V--IILCGGSYRRGKASCGDLDVVI 391
V LC GS RR K + GDLD ++
Sbjct: 180 VERAELC-GSARRYKDTVGDLDFLV 203
>pdb|3B0X|A Chain A, K263a Mutant Of Polx From Thermus Thermophilus Hb8
Complexed With Ca- Dgtp
Length = 575
Score = 53.1 bits (126), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 65/205 (31%), Positives = 97/205 (47%), Gaps = 27/205 (13%)
Query: 210 NKNITEIFGKLINIYRALGEDR-RSFSYYKAIPVIEKLPFKIE-----SADQVKGLPGIG 263
N+ + IF ++ + LG++ R +Y++A + L IE + + LPG+G
Sbjct: 3 NQELARIFEEIGLMSEFLGDNPFRVRAYHQAARTLYDLDTPIEEIAEKGKEALMELPGVG 62
Query: 264 KSMQDHIQEIVTTGKLSKLEHFEKDEKV-RTISLFGEVWGIGPATAQKLYEK-GHRTLDD 321
+ + I E + TGK+ K H E KV R + EV G+GP TA+ LYE G +L+
Sbjct: 63 PDLAEKILEFLRTGKVRK--HEELSRKVPRGVLEVMEVPGVGPKTARLLYEGLGIDSLEK 120
Query: 322 LK---NEDSLTHSQRLGLKYFDDIK----------TRIPRHEVEQMERLLQKAGEEVLPE 368
LK + LT + G K + I+ R P V + R L +A LP
Sbjct: 121 LKAALDRGDLTRLKGFGPKRAERIREGLALAQAAGKRRPLGAVLSLARSLLEA-IRALPG 179
Query: 369 V--IILCGGSYRRGKASCGDLDVVI 391
V LC GS RR K + GDLD ++
Sbjct: 180 VERAELC-GSARRYKDTVGDLDFLV 203
>pdb|1NZP|A Chain A, Solution Structure Of The Lyase Domain Of Human Dna
Polymerase Lambda
Length = 87
Score = 49.3 bits (116), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 39/75 (52%)
Query: 210 NKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDH 269
N +ITE L Y G+ R+ Y KAI ++ + S + +PGIGK M +
Sbjct: 13 NLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEK 72
Query: 270 IQEIVTTGKLSKLEH 284
I EI+ +G L KL+H
Sbjct: 73 IIEILESGHLRKLDH 87
>pdb|1WF6|A Chain A, The Third Brca1 C-Terminus (Brct) Domain Of Similar To
S.Pombe Rad4+CUT5+ PRODUCT
Length = 132
Score = 34.7 bits (78), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 42/89 (47%), Gaps = 4/89 (4%)
Query: 18 IFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQH 77
+ G R++L G R+L R+ + G +L++ VTHV+ D + L+Q +
Sbjct: 40 LLDGCRIYLC--GFSGRKLDKLRRLINSGGGVRFNQLNEDVTHVIVGDYDDELKQFWNKS 97
Query: 78 LARFKGSVIRYQWLEDSLRLGEKVSEDLY 106
R V+ +WL + G +SE+ Y
Sbjct: 98 AHR--PHVVGAKWLLECFSKGYMLSEEPY 124
>pdb|2W9M|A Chain A, Structure Of Family X Dna Polymerase From Deinococcus
Radiodurans
pdb|2W9M|B Chain B, Structure Of Family X Dna Polymerase From Deinococcus
Radiodurans
Length = 578
Score = 32.7 bits (73), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 28/114 (24%), Positives = 52/114 (45%), Gaps = 5/114 (4%)
Query: 228 GEDRRSFSYYKAIPVIEKLPFKIES--ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHF 285
GED +S +Y A +E+L + A + G+P +GK + + + +G + LE
Sbjct: 29 GEDFKSRAYRSAARSLEELNEETPELLAREFTGIPKVGKGIAAELSDFARSGTFAPLEA- 87
Query: 286 EKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYF 339
+ + V G+GP + L+ G +L+ L+ ++ + GLK F
Sbjct: 88 AAGQLPPGLLDLLGVRGLGPKKIRSLWLAGIDSLERLR--EAAESGELAGLKGF 139
>pdb|1PZN|A Chain A, Rad51 (Rada)
pdb|1PZN|B Chain B, Rad51 (Rada)
pdb|1PZN|C Chain C, Rad51 (Rada)
pdb|1PZN|D Chain D, Rad51 (Rada)
pdb|1PZN|E Chain E, Rad51 (Rada)
pdb|1PZN|F Chain F, Rad51 (Rada)
pdb|1PZN|G Chain G, Rad51 (Rada)
Length = 349
Score = 29.6 bits (65), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 12/21 (57%), Positives = 17/21 (80%)
Query: 302 GIGPATAQKLYEKGHRTLDDL 322
G+GPATA+KL E G+ TL+ +
Sbjct: 42 GVGPATAEKLREAGYDTLEAI 62
>pdb|4DEZ|A Chain A, Structure Of Msdpo4
Length = 356
Score = 29.6 bits (65), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 18/36 (50%)
Query: 300 VWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLG 335
+WG+GP T +KL G T+ DL D + G
Sbjct: 183 LWGVGPKTTKKLAAMGITTVADLAVTDPSVLTTAFG 218
>pdb|2D8M|A Chain A, Solution Structure Of The First Brct Domain Of Dna-Repair
Protein Xrcc1
Length = 129
Score = 29.3 bits (64), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 18/83 (21%), Positives = 34/83 (40%), Gaps = 4/83 (4%)
Query: 24 VFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKG 83
V +V G QN R K +++GA ++ TH++ A + G
Sbjct: 26 VVVVLSGFQNPFRSELRDKALELGAKYRPDWTRDSTHLIC----AFANTPKYSQVLGLGG 81
Query: 84 SVIRYQWLEDSLRLGEKVSEDLY 106
++R +W+ D R+ ++ Y
Sbjct: 82 RIVRKEWVLDCHRMRRRLPSQRY 104
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
0.315 0.134 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,668,725
Number of Sequences: 62578
Number of extensions: 462269
Number of successful extensions: 1025
Number of sequences better than 100.0: 52
Number of HSP's better than 100.0 without gapping: 36
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 958
Number of HSP's gapped (non-prelim): 52
length of query: 398
length of database: 14,973,337
effective HSP length: 101
effective length of query: 297
effective length of database: 8,652,959
effective search space: 2569928823
effective search space used: 2569928823
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: 52 (24.6 bits)