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= 009742
(527 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 228 bits (581), Expect = 7e-60, Method: Compositional matrix adjust.
Identities = 125/329 (37%), Positives = 185/329 (56%), Gaps = 8/329 (2%)
Query: 199 NKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDH 258
N +ITE L Y G+ R+ Y KAI ++ + S + +PGIGK M +
Sbjct: 13 NLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEK 72
Query: 259 IQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLT 318
I EI+ +G L KL+H E V + LF +WG G TAQ Y++G R+L+D++++ SLT
Sbjct: 73 IIEILESGHLRKLDHI--SESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLT 130
Query: 319 HSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDV 378
Q +GLK++ D R+PR E ++E+ +QKA + ++ + GSYRRGKA+CGD+DV
Sbjct: 131 TQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDV 190
Query: 379 VIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCTYPGRELR 438
+I HPD +SH+G S+ + L++ FL +DL+ + E G Y G+C PG R
Sbjct: 191 LITHPDGRSHRGIFSRLLDSLRQEGFLTDDLV--SQEENGQQ---QKYLGVCRLPGPGRR 245
Query: 439 H-RIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGV 497
H R+D V P +A L+ +TG+ NR +R LA++KG L + L A + V
Sbjct: 246 HRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGAKV 305
Query: 498 RARTSLKFDTEKEVFDFLGFPWLEPHERN 526
L TEK+VF LG P+ EP ER+
Sbjct: 306 GPGRVLPTPTEKDVFRLLGLPYREPAERD 334
>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 = 228 bits (580), Expect = 9e-60, Method: Compositional matrix adjust.
Identities = 125/329 (37%), Positives = 185/329 (56%), Gaps = 8/329 (2%)
Query: 199 NKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDH 258
N +ITE L Y G+ R+ Y KAI ++ + S + +PGIGK M +
Sbjct: 13 NLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEK 72
Query: 259 IQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLT 318
I EI+ +G L KL+H E V + LF +WG G TAQ Y++G R+L+D++++ SLT
Sbjct: 73 IIEILESGHLRKLDHI--SESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLT 130
Query: 319 HSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDV 378
Q +GLK++ D R+PR E ++E+ +QKA + ++ + GSYRRGKA+CGD+DV
Sbjct: 131 TQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDV 190
Query: 379 VIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCTYPGRELR 438
+I HPD +SH+G S+ + L++ FL +DL+ + E G Y G+C PG R
Sbjct: 191 LITHPDGRSHRGIFSRLLDSLRQEGFLTDDLV--SQEENGQQ---QKYLGVCRLPGPGRR 245
Query: 439 H-RIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGV 497
H R+D V P +A L+ +TG+ NR +R LA++KG L + L A + V
Sbjct: 246 HRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKV 305
Query: 498 RARTSLKFDTEKEVFDFLGFPWLEPHERN 526
L TEK+VF LG P+ EP ER+
Sbjct: 306 GPGRVLPTPTEKDVFRLLGLPYREPAERD 334
>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 = 227 bits (579), Expect = 1e-59, Method: Compositional matrix adjust.
Identities = 125/329 (37%), Positives = 185/329 (56%), Gaps = 8/329 (2%)
Query: 199 NKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDH 258
N +ITE L Y G+ R+ Y KAI ++ + S + +PGIGK M +
Sbjct: 9 NLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEK 68
Query: 259 IQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLT 318
I EI+ +G L KL+H E V + LF +WG G TAQ Y++G R+L+D++++ SLT
Sbjct: 69 IIEILESGHLRKLDHI--SESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLT 126
Query: 319 HSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDV 378
Q +GLK++ D R+PR E ++E+ +QKA + ++ + GSYRRGKA+CGD+DV
Sbjct: 127 TQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDV 186
Query: 379 VIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCTYPGRELR 438
+I HPD +SH+G S+ + L++ FL +DL+ + E G Y G+C PG R
Sbjct: 187 LITHPDGRSHRGIFSRLLDSLRQEGFLTDDLV--SQEENGQQ---QKYLGVCRLPGPGRR 241
Query: 439 H-RIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGV 497
H R+D V P +A L+ +TG+ NR +R LA++KG L + L A + V
Sbjct: 242 HRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKV 301
Query: 498 RARTSLKFDTEKEVFDFLGFPWLEPHERN 526
L TEK+VF LG P+ EP ER+
Sbjct: 302 GPGRVLPTPTEKDVFRLLGLPYREPAERD 330
>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 = 226 bits (577), Expect = 2e-59, Method: Compositional matrix adjust.
Identities = 125/329 (37%), Positives = 185/329 (56%), Gaps = 8/329 (2%)
Query: 199 NKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDH 258
N +ITE L Y G+ R+ Y KAI ++ + S + +PGIGK M +
Sbjct: 3 NLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEK 62
Query: 259 IQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLT 318
I EI+ +G L KL+H E V + LF +WG G TAQ Y++G R+L+D++++ SLT
Sbjct: 63 IIEILESGHLRKLDHI--SESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLT 120
Query: 319 HSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDV 378
Q +GLK++ D R+PR E ++E+ +QKA + ++ + GSYRRGKA+CGD+DV
Sbjct: 121 TQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDV 180
Query: 379 VIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCTYPGRELR 438
+I HPD +SH+G S+ + L++ FL +DL+ + E G Y G+C PG R
Sbjct: 181 LITHPDGRSHRGIFSRLLDSLRQEGFLTDDLV--SQEENGQQ---QKYLGVCRLPGPGRR 235
Query: 439 H-RIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGV 497
H R+D V P +A L+ +TG+ NR +R LA++KG L + L A + V
Sbjct: 236 HRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKV 295
Query: 498 RARTSLKFDTEKEVFDFLGFPWLEPHERN 526
L TEK+VF LG P+ EP ER+
Sbjct: 296 GPGRVLPTPTEKDVFRLLGLPYREPAERD 324
>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 = 226 bits (576), Expect = 2e-59, Method: Compositional matrix adjust.
Identities = 124/329 (37%), Positives = 183/329 (55%), Gaps = 13/329 (3%)
Query: 199 NKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDH 258
N +ITE L Y G+ R+ Y KAI ++ + S + +PGIGK M +
Sbjct: 12 NLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEK 71
Query: 259 IQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLT 318
I EI+ +G L KL+H E V + LF +WG G TAQ Y++G R+L+D++++ SLT
Sbjct: 72 IIEILESGHLRKLDHI--SESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLT 129
Query: 319 HSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDV 378
Q +GLK++ D R+PR E ++E+ +QKA + ++ + GSYRRGKA+CGD+DV
Sbjct: 130 TQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDV 189
Query: 379 VIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCTYPGRELR 438
+I HPD +SH+G S+ + L++ FL +DL+ G Y G+C PG R
Sbjct: 190 LITHPDGRSHRGIFSRLLDSLRQEGFLTDDLV----------KGETKYLGVCRLPGPGRR 239
Query: 439 H-RIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGV 497
H R+D V P +A L+ +TG+ NR +R LA++KG L + L A + V
Sbjct: 240 HRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGAKV 299
Query: 498 RARTSLKFDTEKEVFDFLGFPWLEPHERN 526
L TEK+VF LG P+ EP ER+
Sbjct: 300 GPGRVLPTPTEKDVFRLLGLPYREPAERD 328
>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 = 226 bits (576), Expect = 2e-59, Method: Compositional matrix adjust.
Identities = 124/329 (37%), Positives = 184/329 (55%), Gaps = 8/329 (2%)
Query: 199 NKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDH 258
N +ITE L Y G+ R+ Y KAI ++ + S + +PGIGK M +
Sbjct: 13 NLHITEKLEVLAKAYSVQGDKWRAAGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEK 72
Query: 259 IQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLT 318
I EI+ +G L KL+H E V + LF +WG G TAQ Y++G R+L+D++++ SLT
Sbjct: 73 IIEILESGHLRKLDHI--SESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLT 130
Query: 319 HSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDV 378
Q +GLK++ D R+PR E ++E+ +QKA + ++ + GSYRRGKA+CGD+DV
Sbjct: 131 TQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDV 190
Query: 379 VIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCTYPGRELR 438
+I HPD +SH+G S+ + L++ FL +DL+ + E G Y G+C PG R
Sbjct: 191 LITHPDGRSHRGIFSRLLDSLRQEGFLTDDLV--SQEENGQQ---QKYLGVCRLPGPGRR 245
Query: 439 H-RIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGV 497
H R+D V P +A L+ +TG+ N +R LA++KG L + L A + V
Sbjct: 246 HRRLDIIVVPYSEFACALLYFTGSAAFNASMRALAKTKGMSLSEHALSTAVVRNTHGAKV 305
Query: 498 RARTSLKFDTEKEVFDFLGFPWLEPHERN 526
L TEK+VF LG P+ EP ER+
Sbjct: 306 GPGRVLPTPTEKDVFRLLGLPYREPAERD 334
>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 = 226 bits (576), Expect = 2e-59, Method: Compositional matrix adjust.
Identities = 124/329 (37%), Positives = 185/329 (56%), Gaps = 8/329 (2%)
Query: 199 NKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDH 258
N +ITE L Y G+ R+ Y KAI ++ + S + +PGIGK M +
Sbjct: 13 NLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEK 72
Query: 259 IQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLT 318
I EI+ +G L KL+H E V + LF +WG G TAQ Y++G R+L+D++++ SLT
Sbjct: 73 IIEILESGHLRKLDHI--SESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLT 130
Query: 319 HSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDV 378
Q +GLK++ D R+PR E ++E+ +QKA + ++ + GSYRRGKA+CGD+DV
Sbjct: 131 TQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDV 190
Query: 379 VIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCTYPGRELR 438
+I HPD +SH+G S+ + L++ FL +DL+ + E G Y G+C PG R
Sbjct: 191 LITHPDGRSHRGIFSRLLDSLRQEGFLTDDLV--SQEENGQQ---QKYLGVCRLPGPGRR 245
Query: 439 H-RIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGV 497
H R+D V P +A L+ +TG+ NR ++ LA++KG L + L A + V
Sbjct: 246 HRRLDIIVVPYSEFACALLYFTGSAHFNRSMKALAKTKGMSLSEHALSTAVVRNTHGCKV 305
Query: 498 RARTSLKFDTEKEVFDFLGFPWLEPHERN 526
L TEK+VF LG P+ EP ER+
Sbjct: 306 GPGRVLPTPTEKDVFRLLGLPYREPAERD 334
>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 = 226 bits (575), Expect = 3e-59, Method: Compositional matrix adjust.
Identities = 124/329 (37%), Positives = 183/329 (55%), Gaps = 13/329 (3%)
Query: 199 NKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDH 258
N +ITE L Y G+ R+ Y KAI ++ + S + +PGIGK M +
Sbjct: 12 NLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEK 71
Query: 259 IQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLT 318
I EI+ +G L KL+H E V + LF +WG G TAQ Y++G R+L+D++++ SLT
Sbjct: 72 IIEILESGHLRKLDHI--SESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLT 129
Query: 319 HSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDV 378
Q +GLK++ D R+PR E ++E+ +QKA + ++ + GSYRRGKA+CGD+DV
Sbjct: 130 TQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDV 189
Query: 379 VIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCTYPGRELR 438
+I HPD +SH+G S+ + L++ FL +DL+ G Y G+C PG R
Sbjct: 190 LITHPDGRSHRGIFSRLLDSLRQEGFLTDDLV----------KGETKYLGVCRLPGPGRR 239
Query: 439 H-RIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGV 497
H R+D V P +A L+ +TG+ NR +R LA++KG L + L A + V
Sbjct: 240 HRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKV 299
Query: 498 RARTSLKFDTEKEVFDFLGFPWLEPHERN 526
L TEK+VF LG P+ EP ER+
Sbjct: 300 GPGRVLPTPTEKDVFRLLGLPYREPAERD 328
>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 = 225 bits (573), Expect = 5e-59, Method: Compositional matrix adjust.
Identities = 124/329 (37%), Positives = 184/329 (55%), Gaps = 8/329 (2%)
Query: 199 NKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDH 258
N +ITE L Y G+ R+ Y KAI ++ + S + +PGIGK M +
Sbjct: 13 NLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEK 72
Query: 259 IQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLT 318
I EI+ +G L KL+H E V + LF +WG G TAQ Y++G R+L+D++++ SLT
Sbjct: 73 IIEILESGHLRKLDHI--SESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLT 130
Query: 319 HSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDV 378
Q +GLK++ D R+PR E ++E+ +QKA + ++ + GSYRRGKA+CGD+DV
Sbjct: 131 TQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDV 190
Query: 379 VIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCTYPGRELR 438
+I HPD +SH+G S+ + L++ FL +DL+ + E G Y G+C PG R
Sbjct: 191 LITHPDGRSHRGIFSRLLDSLRQEGFLTDDLV--SQEENGQQ---QKYLGVCRLPGPGRR 245
Query: 439 H-RIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGV 497
H R+D V P +A L+ +TG+ NR + LA++KG L + L A + V
Sbjct: 246 HRRLDIIVVPYSEFACALLYFTGSAHFNRSMAALAKTKGMSLSEHALSTAVVRNTHGCKV 305
Query: 498 RARTSLKFDTEKEVFDFLGFPWLEPHERN 526
L TEK+VF LG P+ EP ER+
Sbjct: 306 GPGRVLPTPTEKDVFRLLGLPYREPAERD 334
>pdb|1BPE|A Chain A, Crystal Structure Of Rat Dna Polymerase Beta; Evidence For
A Common Polymerase Mechanism
Length = 335
Score = 208 bits (530), Expect = 5e-54, Method: Compositional matrix adjust.
Identities = 121/340 (35%), Positives = 196/340 (57%), Gaps = 27/340 (7%)
Query: 198 LNKNITEIFGKLINIYRALGEDRRSF-SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 256
LN IT++ +L N + + + + +Y KA VI K P KI+S + K LPG+G +
Sbjct: 11 LNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIA 70
Query: 257 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNED 315
+ I E + TGKL KLE +D+ +I+ V GIGP+ A+KL ++G +TL+DL KNED
Sbjct: 71 EKIDEFLATGKLRKLEKIRRDDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNED 130
Query: 316 SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGD 375
L H QR+GLKYF+D + RIPR E+ QM+ ++ +++ PE I GS+RRG S GD
Sbjct: 131 KLNHHQRIGLKYFEDFEKRIPREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGD 190
Query: 376 LDVVIMHPDRKSHKG----FLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCT 431
+DV++ HP+ S L + V++L++++F+ + L G + G+C
Sbjct: 191 MDVLLTHPNFTSESSKQPKLLHRVVEQLQKVRFITDTL----------SKGETKFMGVCQ 240
Query: 432 YPG----RELRH-RIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFP 486
P E H RID ++ P+D Y G++ +TG+D+ N+ +R A KG+ +++ + P
Sbjct: 241 LPSENDENEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRP 300
Query: 487 ATYGSGGKQGVRARTSLKFDTEKEVFDFLGFPWLEPHERN 526
G GV A L D+E+++FD++ + + EP +R+
Sbjct: 301 L-----GVTGV-AGEPLPVDSEQDIFDYIQWRYREPKDRS 334
>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 = 208 bits (530), Expect = 5e-54, Method: Compositional matrix adjust.
Identities = 121/340 (35%), Positives = 196/340 (57%), Gaps = 27/340 (7%)
Query: 198 LNKNITEIFGKLINIYRALGEDRRSF-SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 256
LN IT++ +L N + + + + +Y KA VI K P KI+S + K LPG+G +
Sbjct: 16 LNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIA 75
Query: 257 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNED 315
+ I E + TGKL KLE +D+ +I+ V GIGP+ A+KL ++G +TL+DL KNED
Sbjct: 76 EEIDEFLATGKLRKLEKIRQDDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNED 135
Query: 316 SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGD 375
L H QR+GLKYF+D + RIPR E+ QM+ ++ +++ PE I GS+RRG S GD
Sbjct: 136 KLNHHQRIGLKYFEDFEKRIPREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGD 195
Query: 376 LDVVIMHPDRKSHKG----FLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCT 431
+DV++ HP+ S L + V++L++++F+ + L G + G+C
Sbjct: 196 MDVLLTHPNFTSESSKQPKLLHRVVEQLQKVRFITDTL----------SKGETKFMGVCQ 245
Query: 432 YPG----RELRH-RIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFP 486
P E H RID ++ P+D Y G++ +TG+D+ N+ +R A KG+ +++ + P
Sbjct: 246 LPSENDENEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRP 305
Query: 487 ATYGSGGKQGVRARTSLKFDTEKEVFDFLGFPWLEPHERN 526
G GV A L D+E+++FD++ + + EP +R+
Sbjct: 306 L-----GVTGV-AGEPLPVDSEQDIFDYIQWRYREPKDRS 339
>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 = 208 bits (530), Expect = 5e-54, Method: Compositional matrix adjust.
Identities = 121/340 (35%), Positives = 196/340 (57%), Gaps = 27/340 (7%)
Query: 198 LNKNITEIFGKLINIYRALGEDRRSF-SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 256
LN IT++ +L N + + + + +Y KA VI K P KI+S + K LPG+G +
Sbjct: 11 LNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIA 70
Query: 257 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNED 315
+ I E + TGKL KLE +D+ +I+ V GIGP+ A+KL ++G +TL+DL KNED
Sbjct: 71 EKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNED 130
Query: 316 SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGD 375
L H QR+GLKYF+D + RIPR E+ QM+ ++ +++ PE I GS+RRG S GD
Sbjct: 131 KLNHHQRIGLKYFEDFEKRIPREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGD 190
Query: 376 LDVVIMHPDRKSHKG----FLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCT 431
+DV++ HP+ S L + V++L++++F+ + L G + G+C
Sbjct: 191 MDVLLTHPNFTSESSKQPKLLHRVVEQLQKVRFITDTL----------SKGETKFMGVCQ 240
Query: 432 YPG----RELRH-RIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFP 486
P E H RID ++ P+D Y G++ +TG+D+ N+ +R A KG+ +++ + P
Sbjct: 241 LPSENDENEYPHRRIDIRLQPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRP 300
Query: 487 ATYGSGGKQGVRARTSLKFDTEKEVFDFLGFPWLEPHERN 526
G GV A L D+E+++FD++ + + EP +R+
Sbjct: 301 L-----GVTGV-AGEPLPVDSEQDIFDYIQWRYREPKDRS 334
>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 = 208 bits (530), Expect = 6e-54, Method: Compositional matrix adjust.
Identities = 121/340 (35%), Positives = 196/340 (57%), Gaps = 27/340 (7%)
Query: 198 LNKNITEIFGKLINIYRALGEDRRSF-SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 256
LN IT++ +L N + + + + +Y KA VI K P KI+S + K LPG+G +
Sbjct: 11 LNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIA 70
Query: 257 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNED 315
+ I E + TGKL KLE +D+ +I+ V GIGP+ A+KL ++G +TL+DL KNED
Sbjct: 71 EKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNED 130
Query: 316 SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGD 375
L H QR+GLKYF+D + RIPR E+ QM+ ++ +++ PE I GS+RRG S GD
Sbjct: 131 KLNHHQRIGLKYFEDFEKRIPREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGD 190
Query: 376 LDVVIMHPDRKSHKG----FLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCT 431
+DV++ HP+ S L + V++L++++F+ + L G + G+C
Sbjct: 191 MDVLLTHPNFTSESSKQPKLLHRVVEQLQKVRFITDTL----------SKGETKFMGVCQ 240
Query: 432 YPG----RELRH-RIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFP 486
P E H RID ++ P+D Y G++ +TG+D+ N+ +R A KG+ +++ + P
Sbjct: 241 LPSENDENEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRP 300
Query: 487 ATYGSGGKQGVRARTSLKFDTEKEVFDFLGFPWLEPHERN 526
G GV A L D+E+++FD++ + + EP +R+
Sbjct: 301 L-----GVTGV-AGEPLPVDSEQDIFDYIQWRYREPKDRS 334
>pdb|3V7J|A Chain A, Co-crystal Structure Of Wild Type Rat Polymerase Beta:
Enzyme-dna Binary Complex
Length = 340
Score = 208 bits (529), Expect = 7e-54, Method: Compositional matrix adjust.
Identities = 121/340 (35%), Positives = 196/340 (57%), Gaps = 27/340 (7%)
Query: 198 LNKNITEIFGKLINIYRALGEDRRSF-SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 256
LN IT++ +L N + + + + +Y KA VI K P KI+S + K LPG+G +
Sbjct: 16 LNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIA 75
Query: 257 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNED 315
+ I E + TGKL KLE +D+ +I+ V GIGP+ A+KL ++G +TL+DL KNED
Sbjct: 76 EKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNED 135
Query: 316 SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGD 375
L H QR+GLKYF+D + RIPR E+ QM+ ++ +++ PE I GS+RRG S GD
Sbjct: 136 KLNHHQRIGLKYFEDFEKRIPREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGD 195
Query: 376 LDVVIMHPDRKSHKG----FLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCT 431
+DV++ HP+ S L + V++L++++F+ + L G + G+C
Sbjct: 196 MDVLLTHPNFTSESSKQPKLLHRVVEQLQKVRFITDTL----------SKGETKFMGVCQ 245
Query: 432 YPG----RELRH-RIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFP 486
P E H RID ++ P+D Y G++ +TG+D+ N+ +R A KG+ +++ + P
Sbjct: 246 LPSENDENEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRP 305
Query: 487 ATYGSGGKQGVRARTSLKFDTEKEVFDFLGFPWLEPHERN 526
G GV A L D+E+++FD++ + + EP +R+
Sbjct: 306 L-----GVTGV-AGEPLPVDSEQDIFDYIQWRYREPKDRS 339
>pdb|3V72|A Chain A, Crystal Structure Of Rat Dna Polymerase Beta Mutator
E295k: Enzyme- Dsdna
Length = 335
Score = 207 bits (527), Expect = 1e-53, Method: Compositional matrix adjust.
Identities = 121/340 (35%), Positives = 195/340 (57%), Gaps = 27/340 (7%)
Query: 198 LNKNITEIFGKLINIYRALGEDRRSF-SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 256
LN IT++ +L N + + + + +Y KA VI K P KI+S + K LPG+G +
Sbjct: 11 LNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIA 70
Query: 257 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNED 315
+ I E + TGKL KLE +D+ +I+ V GIGP+ A+KL ++G +TL+DL KNED
Sbjct: 71 EKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNED 130
Query: 316 SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGD 375
L H QR+GLKYF+D + RIPR E+ QM+ ++ +++ PE I GS+RRG S GD
Sbjct: 131 KLNHHQRIGLKYFEDFEKRIPREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGD 190
Query: 376 LDVVIMHPDRKSHKG----FLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCT 431
+DV++ HP+ S L + V++L++++F+ + L G + G+C
Sbjct: 191 MDVLLTHPNFTSESSKQPKLLHRVVEQLQKVRFITDTL----------SKGETKFMGVCQ 240
Query: 432 YPG----RELRH-RIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFP 486
P E H RID ++ P+D Y G++ +TG+D+ N+ +R A KG+ ++ + P
Sbjct: 241 LPSENDENEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINKYTIRP 300
Query: 487 ATYGSGGKQGVRARTSLKFDTEKEVFDFLGFPWLEPHERN 526
G GV A L D+E+++FD++ + + EP +R+
Sbjct: 301 L-----GVTGV-AGEPLPVDSEQDIFDYIQWRYREPKDRS 334
>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 = 207 bits (527), Expect = 1e-53, Method: Compositional matrix adjust.
Identities = 122/340 (35%), Positives = 193/340 (56%), Gaps = 27/340 (7%)
Query: 198 LNKNITEIFGKLINIYRALGEDRRSF-SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 256
LN IT++ +L N + + + + +Y KA VI K P KI+S + K LPG+G +
Sbjct: 11 LNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIA 70
Query: 257 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNED 315
+ I E + TGKL KLE +D+ +I+ V GIGP+ A+K ++G +TL+DL KNED
Sbjct: 71 EKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNED 130
Query: 316 SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGD 375
L H QR+GLKYF D + RIPR E+ QM+ ++ ++V E I GS+RRG S GD
Sbjct: 131 KLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGD 190
Query: 376 LDVVIMHPDRKSHKG----FLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCT 431
+DV++ HP S L + V++L+++ F+ + L G + G+C
Sbjct: 191 MDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTL----------SKGETKFMGVCQ 240
Query: 432 YPG----RELRH-RIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFP 486
P +E H RID ++ P+D Y G++A+TG+D+ N+ +R A KG+ +++ + P
Sbjct: 241 LPSKNDEKEYPHRRIDIRLIPKDQYYCGVLAFTGSDIFNKNMRAHALEKGFTINEYTIRP 300
Query: 487 ATYGSGGKQGVRARTSLKFDTEKEVFDFLGFPWLEPHERN 526
G GV A L D+EK++FD++ + + EP +R+
Sbjct: 301 L-----GVTGV-AGEPLPVDSEKDIFDYIQWKYREPKDRS 334
>pdb|3OGU|A Chain A, Dna Polymerase Beta Mutant 5p20 Complexed With 6bp Of Dna
Length = 335
Score = 206 bits (523), Expect = 3e-53, Method: Compositional matrix adjust.
Identities = 122/340 (35%), Positives = 193/340 (56%), Gaps = 27/340 (7%)
Query: 198 LNKNITEIFGKLINIYRALGEDRRSF-SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 256
LN IT++ +L N + + + + +Y KA VI K P KI+S + K LPG+G +
Sbjct: 11 LNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIA 70
Query: 257 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNED 315
+ I E + TGKL KLE +D+ +I+L V GIGP+ A+K ++G +TL+DL KNED
Sbjct: 71 EKIDEFLATGKLRKLEKIRQDDTSSSINLLTRVSGIGPSAARKFVDEGIKTLEDLRKNED 130
Query: 316 SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGD 375
L H QR+GLKYF D + RIPR E+ QM+ ++ ++V E I GS+RRG S GD
Sbjct: 131 KLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGD 190
Query: 376 LDVVIMHPDRKSHKG----FLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCT 431
+DV++ HP S L + V++L+++ F+ + L G + G+C
Sbjct: 191 MDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTL----------SKGKTKFMGVCQ 240
Query: 432 YPG----RELRH-RIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFP 486
P +E H RID ++ P+D Y G++ +TG+D+ N+ +R A KG+ +++ + P
Sbjct: 241 LPSKNDEKEYPHRRIDIRLIPKDQYYCGMLYFTGSDIFNKNMRAHALEKGFTINEYTIRP 300
Query: 487 ATYGSGGKQGVRARTSLKFDTEKEVFDFLGFPWLEPHERN 526
G GV A L D+EK++FD++ + + EP +R+
Sbjct: 301 L-----GVTGV-AGEPLPVDSEKDIFDYIQWKYREPKDRS 334
>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 = 204 bits (519), Expect = 9e-53, Method: Compositional matrix adjust.
Identities = 121/340 (35%), Positives = 192/340 (56%), Gaps = 27/340 (7%)
Query: 198 LNKNITEIFGKLINIYRALGEDRRSF-SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 256
LN IT++ +L N + + + + +Y KA VI K P KI+S + K LPG+G +
Sbjct: 11 LNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIA 70
Query: 257 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNED 315
+ I E + TGKL KLE +D+ +I+ V GIGP+ A+K ++G +TL+DL KNED
Sbjct: 71 EKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNED 130
Query: 316 SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGD 375
L H QR+GLKYF D + RIPR E+ QM+ ++ ++V E I GS+RRG S GD
Sbjct: 131 KLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGD 190
Query: 376 LDVVIMHPDRKSHKG----FLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCT 431
+DV++ HP S L + V++L+++ F+ + L G + G+C
Sbjct: 191 MDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTL----------SKGETKFMGVCQ 240
Query: 432 YPG----RELRH-RIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFP 486
P +E H RID ++ P+D Y G++ +TG+D+ N+ +R A KG+ +++ + P
Sbjct: 241 LPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRP 300
Query: 487 ATYGSGGKQGVRARTSLKFDTEKEVFDFLGFPWLEPHERN 526
G GV A L D+EK++FD++ + + EP +R+
Sbjct: 301 L-----GVTGV-AGEPLPVDSEKDIFDYIQWKYREPKDRS 334
>pdb|3GDX|A Chain A, Dna Polymerase Beta With A Gapped Dnd Substrate And
Dtmp(Cf2)pp
Length = 326
Score = 204 bits (519), Expect = 1e-52, Method: Compositional matrix adjust.
Identities = 121/340 (35%), Positives = 192/340 (56%), Gaps = 27/340 (7%)
Query: 198 LNKNITEIFGKLINIYRALGEDRRSF-SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 256
LN IT++ +L N + + + + +Y KA VI K P KI+S + K LPG+G +
Sbjct: 2 LNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIA 61
Query: 257 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNED 315
+ I E + TGKL KLE +D+ +I+ V GIGP+ A+K ++G +TL+DL KNED
Sbjct: 62 EKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNED 121
Query: 316 SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGD 375
L H QR+GLKYF D + RIPR E+ QM+ ++ ++V E I GS+RRG S GD
Sbjct: 122 KLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGD 181
Query: 376 LDVVIMHPDRKSHKG----FLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCT 431
+DV++ HP S L + V++L+++ F+ + L G + G+C
Sbjct: 182 MDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTL----------SKGETKFMGVCQ 231
Query: 432 YPG----RELRH-RIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFP 486
P +E H RID ++ P+D Y G++ +TG+D+ N+ +R A KG+ +++ + P
Sbjct: 232 LPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRP 291
Query: 487 ATYGSGGKQGVRARTSLKFDTEKEVFDFLGFPWLEPHERN 526
G GV A L D+EK++FD++ + + EP +R+
Sbjct: 292 L-----GVTGV-AGEPLPVDSEKDIFDYIQWKYREPKDRS 325
>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 = 203 bits (516), Expect = 2e-52, Method: Compositional matrix adjust.
Identities = 120/340 (35%), Positives = 192/340 (56%), Gaps = 27/340 (7%)
Query: 198 LNKNITEIFGKLINIYRALGEDRRSF-SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 256
LN IT++ +L N + + + + +Y KA VI K P KI+S + K LPG+G +
Sbjct: 11 LNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIA 70
Query: 257 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNED 315
+ I E + TGKL KLE +D+ +I+ V GIGP+ A+K ++G +TL+DL KNED
Sbjct: 71 EKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNED 130
Query: 316 SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGD 375
L H QR+GLKYF D + RIPR E+ QM+ ++ ++V E I GS+RRG S GD
Sbjct: 131 KLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGD 190
Query: 376 LDVVIMHPDRKSHKG----FLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCT 431
+DV++ HP S L + V++L+++ F+ + L G + G+C
Sbjct: 191 MDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTL----------SKGETKFMGVCQ 240
Query: 432 YPG----RELRH-RIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFP 486
P +E H RID ++ P+D Y G++ +TG+D+ N+ ++ A KG+ +++ + P
Sbjct: 241 LPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMKAHALEKGFTINEYTIRP 300
Query: 487 ATYGSGGKQGVRARTSLKFDTEKEVFDFLGFPWLEPHERN 526
G GV A L D+EK++FD++ + + EP +R+
Sbjct: 301 L-----GVTGV-AGEPLPVDSEKDIFDYIQWKYREPKDRS 334
>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 = 162 bits (409), Expect = 6e-40, Method: Compositional matrix adjust.
Identities = 94/266 (35%), Positives = 154/266 (57%), Gaps = 26/266 (9%)
Query: 271 LEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNEDSLTHSQRLGLKYFD 329
LE +D+ +I+ V GIGP+ A+KL ++G +TL+DL KNED L H QR+GLKYF+
Sbjct: 1 LEKIRQDDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNEDKLNHHQRIGLKYFE 60
Query: 330 DIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSHK 389
D + RIPR E+ QM+ ++ +++ PE I GS+RRG S GD+DV++ HP+ S
Sbjct: 61 DFEKRIPREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGDMDVLLTHPNFTSES 120
Query: 390 G----FLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCTYPG----RELRH-R 440
L + V++L++++F+ + L G + G+C P E H R
Sbjct: 121 SKQPKLLHRVVEQLQKVRFITDTL----------SKGETKFMGVCQLPSENDENEYPHRR 170
Query: 441 IDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGVRAR 500
ID ++ P+D Y G++ +TG+D+ N+ LR A KG+ +++ + P G GV A
Sbjct: 171 IDIRLIPKDQYYCGVLYFTGSDIFNKNLRAHALEKGFTINEYTIRPL-----GVTGV-AG 224
Query: 501 TSLKFDTEKEVFDFLGFPWLEPHERN 526
L D+E+++FD++ + + EP +R+
Sbjct: 225 EPLPVDSEQDIFDYIQWRYREPKDRS 250
>pdb|1RPL|A Chain A, 2.3 Angstroms Crystal Structure Of The Catalytic Domain Of
Dna Polymerase Beta
Length = 251
Score = 161 bits (408), Expect = 8e-40, Method: Compositional matrix adjust.
Identities = 93/266 (34%), Positives = 154/266 (57%), Gaps = 26/266 (9%)
Query: 271 LEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNEDSLTHSQRLGLKYFD 329
LE +D+ +I+ V GIGP+ A+KL ++G +TL+DL KNED L H QR+GLKYF+
Sbjct: 1 LEKIRQDDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNEDKLNHHQRIGLKYFE 60
Query: 330 DIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSHK 389
D + RIPR E+ QM+ ++ +++ PE I GS+RRG S GD+DV++ HP+ S
Sbjct: 61 DFEKRIPREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGDMDVLLTHPNFTSES 120
Query: 390 G----FLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCTYPG----RELRH-R 440
L + V++L++++F+ + L G + G+C P E H R
Sbjct: 121 SKQPKLLHRVVEQLQKVRFITDTL----------SKGETKFMGVCQLPSENDENEYPHRR 170
Query: 441 IDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGVRAR 500
ID ++ P+D Y G++ +TG+D+ N+ +R A KG+ +++ + P G GV A
Sbjct: 171 IDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPL-----GVTGV-AG 224
Query: 501 TSLKFDTEKEVFDFLGFPWLEPHERN 526
L D+E+++FD++ + + EP +R+
Sbjct: 225 EPLPVDSEQDIFDYIQWRYREPKDRS 250
>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 = 158 bits (400), Expect = 6e-39, Method: Compositional matrix adjust.
Identities = 91/261 (34%), Positives = 152/261 (58%), Gaps = 26/261 (9%)
Query: 276 KDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNEDSLTHSQRLGLKYFDDIKTR 334
+D+ +I+ V GIGP+ A+KL ++G +TL+DL KNED L H QR+GLKYF+D + R
Sbjct: 3 QDDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNEDKLNHHQRIGLKYFEDFEKR 62
Query: 335 IPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSHKG---- 390
IPR E+ QM+ ++ +++ PE I GS+RRG S GD+DV++ HP+ S
Sbjct: 63 IPREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGDMDVLLTHPNFTSESSKQPK 122
Query: 391 FLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCTYPG----RELRH-RIDFKV 445
L + V++L++++F+ + L G + G+C P E H RID ++
Sbjct: 123 LLHRVVEQLQKVRFITDTL----------SKGETKFMGVCQLPSENDENEYPHRRIDIRL 172
Query: 446 YPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGVRARTSLKF 505
P+D Y G++ +TG+D+ N+ +R A KG+ +++ + P G GV A L
Sbjct: 173 IPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPL-----GVTGV-AGEPLPV 226
Query: 506 DTEKEVFDFLGFPWLEPHERN 526
D+E+++FD++ + + EP +R+
Sbjct: 227 DSEQDIFDYIQWRYREPKDRS 247
>pdb|2VAN|A Chain A, Nucleotidyl Transfer Mechanism Of Mismatched Dntp
Incorporation By Dna Polymerase B By Structural And
Kinetic Analyses
Length = 245
Score = 158 bits (399), Expect = 8e-39, Method: Compositional matrix adjust.
Identities = 91/260 (35%), Positives = 151/260 (58%), Gaps = 26/260 (10%)
Query: 277 DEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNEDSLTHSQRLGLKYFDDIKTRI 335
D+ +I+ V GIGP+ A+KL ++G +TL+DL KNED L H QR+GLKYF+D + RI
Sbjct: 1 DDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNEDKLNHHQRIGLKYFEDFEKRI 60
Query: 336 PRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSHKG----F 391
PR E+ QM+ ++ +++ PE I GS+RRG S GD+DV++ HP+ S
Sbjct: 61 PREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGDMDVLLTHPNFTSESSKQPKL 120
Query: 392 LSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCTYPG----RELRH-RIDFKVY 446
L + V++L++++F+ + L G + G+C P E H RID ++
Sbjct: 121 LHRVVEQLQKVRFITDTL----------SKGETKFMGVCQLPSENDENEYPHRRIDIRLQ 170
Query: 447 PRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGVRARTSLKFD 506
P+D Y G++ +TG+D+ N+ +R A KG+ +++ + P G GV A L D
Sbjct: 171 PKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPL-----GVTGV-AGEPLPVD 224
Query: 507 TEKEVFDFLGFPWLEPHERN 526
+E+++FD++ + + EP +R+
Sbjct: 225 SEQDIFDYIQWRYREPKDRS 244
>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 = 158 bits (399), Expect = 9e-39, Method: Compositional matrix adjust.
Identities = 91/260 (35%), Positives = 151/260 (58%), Gaps = 26/260 (10%)
Query: 277 DEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL-KNEDSLTHSQRLGLKYFDDIKTRI 335
D+ +I+ V GIGP+ A+KL ++G +TL+DL KNED L H QR+GLKYF+D + RI
Sbjct: 2 DDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNEDKLNHHQRIGLKYFEDFEKRI 61
Query: 336 PRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSHKG----F 391
PR E+ QM+ ++ +++ PE I GS+RRG S GD+DV++ HP+ S
Sbjct: 62 PREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGDMDVLLTHPNFTSESSKQPKL 121
Query: 392 LSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCTYPG----RELRH-RIDFKVY 446
L + V++L++++F+ + L G + G+C P E H RID ++
Sbjct: 122 LHRVVEQLQKVRFITDTL----------SKGETKFMGVCQLPSENDENEYPHRRIDIRLI 171
Query: 447 PRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGVRARTSLKFD 506
P+D Y G++ +TG+D+ N+ +R A KG+ +++ + P G GV A L D
Sbjct: 172 PKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPL-----GVTGV-AGEPLPVD 225
Query: 507 TEKEVFDFLGFPWLEPHERN 526
+E+++FD++ + + EP +R+
Sbjct: 226 SEQDIFDYIQWRYREPKDRS 245
>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 = 151 bits (381), Expect = 1e-36, Method: Compositional matrix adjust.
Identities = 101/360 (28%), Positives = 168/360 (46%), Gaps = 38/360 (10%)
Query: 195 PPDLNKNITEIFGKLINIYRALG---EDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGI 251
P L + T + L + A G + R S+ +A V++ LP + S Q+ GLP
Sbjct: 10 PSPLTHHNTLLSEALETLAEAAGFEANEGRLLSFSRAASVLKSLPCPVASLSQLHGLPYF 69
Query: 252 GKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL 311
G+ IQE++ G +++ E+ +T+ LF +V+G+G TA + Y++G RTLD+L
Sbjct: 70 GEHSTRVIQELLEHGTCEEVKQVRCSERYQTMKLFTQVFGVGVKTANRWYQEGLRTLDEL 129
Query: 312 KNE-DSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGK 370
+ + LT Q+ GL+Y+ D+ T + R + E +++L++ A + LP + G +RRGK
Sbjct: 130 REQPQRLTQQQKAGLQYYQDLSTPVRRADAEALQQLIEAAVRQTLPGATVTLTGGFRRGK 189
Query: 371 ASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEM------KFLREDLIFSTHSEEGTDSGVD 424
D+D +I HP+ G L K + L+ ++ R L S H+ S +D
Sbjct: 190 LQGHDVDFLITHPEEGQEVGLLPKVMSCLQSQGLVLYHQYHRSHLADSAHNLRQRSSTMD 249
Query: 425 TY---FGLCTYPGRELRH--------------RIDFKVYPRDIYAFGLIAWTGNDVLNRR 467
+ F + P + R+D V P + F L+ WTG+ R
Sbjct: 250 VFERSFCILGLPQPQQAALAGALPPCPTWKAVRVDLVVTPSSQFPFALLGWTGSQFFERE 309
Query: 468 LRLLA-ESKGYRLDDTGLFPATYGSGGKQGVRARTSLKFDTEKEVFDFLGFPWLEPHERN 526
LR + + KG L+ GLF + +E++VF LG +L P +RN
Sbjct: 310 LRRFSRQEKGLWLNSHGLFDP----------EQKRVFHATSEEDVFRLLGLKYLPPEQRN 359
>pdb|1JMS|A Chain A, Crystal Structure Of The Catalytic Core Of Murine Terminal
Deoxynucleotidyl Transferase
Length = 381
Score = 127 bits (319), Expect = 2e-29, Method: Compositional matrix adjust.
Identities = 100/358 (27%), Positives = 171/358 (47%), Gaps = 43/358 (12%)
Query: 201 NITEIFGKLINIYRALGEDRRS----FSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 256
N ++F ++I E R + ++ +A V++ LPF I S +G+P +G ++
Sbjct: 34 NYNQLFTDALDILAENDELRENEGSCLAFMRASSVLKSLPFPITSMKDTEGIPCLGDKVK 93
Query: 257 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDS 316
I+ I+ G+ S+ + DE+ ++ LF V+G+G TA+K + G RTL ++++ S
Sbjct: 94 SIIEGIIEDGESSEAKAVLNDERYKSFKLFTSVFGVGLKTAEKWFRMGFRTLSKIQSDKS 153
Query: 317 L--THSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCG 374
L T Q+ G Y++D+ + + R E E + L+++A LP+ ++ G +RRGK +
Sbjct: 154 LRFTQMQKAGFLYYEDLVSCVNRPEAEAVSMLVKEAVVTFLPDALVTMTGGFRRGKMTGH 213
Query: 375 DLDVVIMHPD--RKSHKGFLSKYVKKLKEMK-FLREDLIFSTHSEEGTDS-GVDT--YFG 428
D+D +I P+ + L K K+ L D++ ST + S VD +F
Sbjct: 214 DVDFLITSPEATEDEEQQLLHKVTDFWKQQGLLLYCDILESTFEKFKQPSRKVDALDHFQ 273
Query: 429 LCTYPGRELRH-------------------RIDFKVYPRDIYAFGLIAWTGNDVLNRRLR 469
C + +L H R+D + P D AF L+ WTG+ R LR
Sbjct: 274 KC-FLILKLDHGRVHSEKSGQQEGKGWKAIRVDLVMCPYDRRAFALLGWTGSRQFERDLR 332
Query: 470 LLA-ESKGYRLDDTGLFPATYGSGGKQGVRARTSLKFDTEKEVFDFLGFPWLEPHERN 526
A + LD+ L+ T R L+ ++E+E+F LG ++EP ERN
Sbjct: 333 RYATHERKMMLDNHALYDRT----------KRVFLEAESEEEIFAHLGLDYIEPWERN 380
>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 = 126 bits (317), Expect = 3e-29, Method: Compositional matrix adjust.
Identities = 100/358 (27%), Positives = 171/358 (47%), Gaps = 43/358 (12%)
Query: 201 NITEIFGKLINIYRALGEDRRS----FSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 256
N ++F ++I E R + ++ +A V++ LPF I S +G+P +G ++
Sbjct: 16 NYNQLFTDALDILAENDELRENEGSCLAFMRASSVLKSLPFPITSMKDTEGIPCLGDKVK 75
Query: 257 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDS 316
I+ I+ G+ S+ + DE+ ++ LF V+G+G TA+K + G RTL ++++ S
Sbjct: 76 SIIEGIIEDGESSEAKAVLNDERYKSFKLFTSVFGVGLKTAEKWFRMGFRTLSKIQSDKS 135
Query: 317 L--THSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCG 374
L T Q+ G Y++D+ + + R E E + L+++A LP+ ++ G +RRGK +
Sbjct: 136 LRFTQMQKAGFLYYEDLVSCVNRPEAEAVSMLVKEAVVTFLPDALVTMTGGFRRGKMTGH 195
Query: 375 DLDVVIMHPD--RKSHKGFLSKYVKKLKEMK-FLREDLIFSTHSEEGTDS-GVDT--YFG 428
D+D +I P+ + L K K+ L D++ ST + S VD +F
Sbjct: 196 DVDFLITSPEATEDEEQQLLHKVTDFWKQQGLLLYCDILESTFEKFKQPSRKVDALDHFQ 255
Query: 429 LCTYPGRELRH-------------------RIDFKVYPRDIYAFGLIAWTGNDVLNRRLR 469
C + +L H R+D + P D AF L+ WTG+ R LR
Sbjct: 256 KC-FLILKLDHGRVHSEKSGQQEGKGWKAIRVDLVMCPYDRRAFALLGWTGSRQFERDLR 314
Query: 470 LLA-ESKGYRLDDTGLFPATYGSGGKQGVRARTSLKFDTEKEVFDFLGFPWLEPHERN 526
A + LD+ L+ T R L+ ++E+E+F LG ++EP ERN
Sbjct: 315 RYATHERKMMLDNHALYDRT----------KRVFLEAESEEEIFAHLGLDYIEPWERN 362
>pdb|3LQC|B Chain B, X-Ray Crystal Structure Of Oxidized Xrcc1 Bound To Dna Pol
B Thumb Domain
Length = 200
Score = 109 bits (273), Expect = 4e-24, Method: Compositional matrix adjust.
Identities = 65/209 (31%), Positives = 115/209 (55%), Gaps = 25/209 (11%)
Query: 327 YFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDRK 386
YF+D + RIPR E+ QM+ ++ +++ PE I GS+RRG S GD+DV++ HP+
Sbjct: 1 YFEDFEKRIPREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGDMDVLLTHPNFT 60
Query: 387 SHKG----FLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCTYPG----RELR 438
S L + V++L++++F+ + L G + G+C P E
Sbjct: 61 SESSKQPKLLHRVVEQLQKVRFITDTL----------SKGETKFMGVCQLPSENDENEYP 110
Query: 439 H-RIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGV 497
H RID ++ P+D Y G++ +TG+D+ N+ +R A KG+ +++ + P G GV
Sbjct: 111 HRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPL-----GVTGV 165
Query: 498 RARTSLKFDTEKEVFDFLGFPWLEPHERN 526
A L D+E+++FD++ + + EP +R+
Sbjct: 166 -AGEPLPVDSEQDIFDYIQWRYREPKDRS 193
>pdb|3B0Y|A Chain A, K263d Mutant Of Polx From Thermus Thermophilus Hb8
Complexed With Ca- Dgtp
Length = 575
Score = 88.6 bits (218), Expect = 7e-18, Method: Compositional matrix adjust.
Identities = 104/352 (29%), Positives = 162/352 (46%), Gaps = 63/352 (17%)
Query: 199 NKNITEIFGKLINIYRALGEDR-RSFSYYKAIPVIEKLPFKIE-----SADQVKGLPGIG 252
N+ + IF ++ + LG++ R +Y++A + L IE + + LPG+G
Sbjct: 3 NQELARIFEEIGLMSEFLGDNPFRVRAYHQAARTLYDLDTPIEEIAEKGKEALMELPGVG 62
Query: 253 KSMQDHIQEIVTTGKLSKLEHFEKDEKV-RTISLFGEVWGIGPATAQKLYEK-GHRTLDD 310
+ + I E + TGK+ K H E KV R + EV G+GP TA+ LYE G +L+
Sbjct: 63 PDLAEKILEFLRTGKVRK--HEELSRKVPRGVLEVMEVPGVGPKTARLLYEGLGIDSLEK 120
Query: 311 LK---NEDSLTHSQRLGLKYFDDIK----------TRIPRHEVEQMERLLQKAGEEVLPE 357
LK + LT + G K + I+ R P V + R L +A LP
Sbjct: 121 LKAALDRGDLTRLKGFGPKRAERIREGLALAQAAGKRRPLGAVLSLARSLLEA-IRALPG 179
Query: 358 V--IILCGGSYRRGKASCGDLDVVIMHPD-RKSHKGFLSKYVKKLKEMKFLREDLIFSTH 414
V LCG S RR K + GDLD ++ + ++ +GF+ + ++KE +++
Sbjct: 180 VERAELCG-SARRYKDTVGDLDFLVASREGERAVEGFVR--LPQVKE--------VYAKG 228
Query: 415 SEEGTDSGVDTYFGLCTYPGRELRHRIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAES 474
E T V GL ++D +V P + Y GL TG+D + RLR LA+
Sbjct: 229 KERAT---VFLKNGL----------QVDLRVVPPESYGAGLQYLTGSDAHSIRLRALAQE 275
Query: 475 KGYRLDDTGLFPATYGSGGKQGVRARTSLKFDTEKEVFDFLGFPWLEPHERN 526
KG +L + G+F R + +TE+EV+ LG PW+ P R
Sbjct: 276 KGLKLSEYGVF------------RGEKRIAGETEEEVYAALGLPWIPPPLRE 315
>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 = 86.3 bits (212), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 103/352 (29%), Positives = 161/352 (45%), Gaps = 63/352 (17%)
Query: 199 NKNITEIFGKLINIYRALGEDR-RSFSYYKAIPVIEKLPFKIE-----SADQVKGLPGIG 252
N+ + IF ++ + LG++ R +Y++A + L IE + + LPG+G
Sbjct: 3 NQELARIFEEIGLMSEFLGDNPFRVRAYHQAARTLYDLDTPIEEIAEKGKEALMELPGVG 62
Query: 253 KSMQDHIQEIVTTGKLSKLEHFEKDEKV-RTISLFGEVWGIGPATAQKLYEK-GHRTLDD 310
+ + I E + TGK+ K H E KV R + EV G+GP TA+ LYE G +L+
Sbjct: 63 PDLAEKILEFLRTGKVRK--HEELSRKVPRGVLEVMEVPGVGPKTARLLYEGLGIDSLEK 120
Query: 311 LK---NEDSLTHSQRLGLKYFDDIK----------TRIPRHEVEQMERLLQKAGEEVLPE 357
LK + LT + G K + I+ R P V + R L +A LP
Sbjct: 121 LKAALDRGDLTRLKGFGPKRAERIREGLALAQAAGKRRPLGAVLSLARSLLEA-IRALPG 179
Query: 358 V--IILCGGSYRRGKASCGDLDVVIMHPD-RKSHKGFLSKYVKKLKEMKFLREDLIFSTH 414
V LCG S RR K + GDLD ++ + ++ +GF+ + ++KE +++
Sbjct: 180 VERAELCG-SARRYKDTVGDLDFLVASREGERAVEGFVR--LPQVKE--------VYAKG 228
Query: 415 SEEGTDSGVDTYFGLCTYPGRELRHRIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAES 474
E T V GL ++D +V P + Y GL TG+ + RLR LA+
Sbjct: 229 KERAT---VFLKNGL----------QVDLRVVPPESYGAGLQYLTGSKAHSIRLRALAQE 275
Query: 475 KGYRLDDTGLFPATYGSGGKQGVRARTSLKFDTEKEVFDFLGFPWLEPHERN 526
KG +L + G+F R + +TE+EV+ LG PW+ P R
Sbjct: 276 KGLKLSEYGVF------------RGEKRIAGETEEEVYAALGLPWIPPPLRE 315
>pdb|3B0X|A Chain A, K263a Mutant Of Polx From Thermus Thermophilus Hb8
Complexed With Ca- Dgtp
Length = 575
Score = 85.9 bits (211), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 103/352 (29%), Positives = 161/352 (45%), Gaps = 63/352 (17%)
Query: 199 NKNITEIFGKLINIYRALGEDR-RSFSYYKAIPVIEKLPFKIE-----SADQVKGLPGIG 252
N+ + IF ++ + LG++ R +Y++A + L IE + + LPG+G
Sbjct: 3 NQELARIFEEIGLMSEFLGDNPFRVRAYHQAARTLYDLDTPIEEIAEKGKEALMELPGVG 62
Query: 253 KSMQDHIQEIVTTGKLSKLEHFEKDEKV-RTISLFGEVWGIGPATAQKLYEK-GHRTLDD 310
+ + I E + TGK+ K H E KV R + EV G+GP TA+ LYE G +L+
Sbjct: 63 PDLAEKILEFLRTGKVRK--HEELSRKVPRGVLEVMEVPGVGPKTARLLYEGLGIDSLEK 120
Query: 311 LK---NEDSLTHSQRLGLKYFDDIK----------TRIPRHEVEQMERLLQKAGEEVLPE 357
LK + LT + G K + I+ R P V + R L +A LP
Sbjct: 121 LKAALDRGDLTRLKGFGPKRAERIREGLALAQAAGKRRPLGAVLSLARSLLEA-IRALPG 179
Query: 358 V--IILCGGSYRRGKASCGDLDVVIMHPD-RKSHKGFLSKYVKKLKEMKFLREDLIFSTH 414
V LCG S RR K + GDLD ++ + ++ +GF+ + ++KE +++
Sbjct: 180 VERAELCG-SARRYKDTVGDLDFLVASREGERAVEGFVR--LPQVKE--------VYAKG 228
Query: 415 SEEGTDSGVDTYFGLCTYPGRELRHRIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAES 474
E T V GL ++D +V P + Y GL TG+ + RLR LA+
Sbjct: 229 KERAT---VFLKNGL----------QVDLRVVPPESYGAGLQYLTGSAAHSIRLRALAQE 275
Query: 475 KGYRLDDTGLFPATYGSGGKQGVRARTSLKFDTEKEVFDFLGFPWLEPHERN 526
KG +L + G+F R + +TE+EV+ LG PW+ P R
Sbjct: 276 KGLKLSEYGVF------------RGEKRIAGETEEEVYAALGLPWIPPPLRE 315
>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 = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 44/76 (57%), Gaps = 1/76 (1%)
Query: 198 LNKNITEIFGKLINIYRALGEDRRSF-SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 256
LN IT++ +L N + + + + +Y KA VI K P KI+S + K LPG+G +
Sbjct: 11 LNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIA 70
Query: 257 DHIQEIVTTGKLSKLE 272
+ 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 = 52.8 bits (125), Expect = 5e-07, Method: Composition-based stats.
Identities = 30/76 (39%), Positives = 44/76 (57%), Gaps = 1/76 (1%)
Query: 198 LNKNITEIFGKLINIYRALGEDRRSF-SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQ 256
LN IT++ +L N + + + + +Y KA VI K P KI+S + K LPG+G +
Sbjct: 10 LNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIA 69
Query: 257 DHIQEIVTTGKLSKLE 272
+ I E + TGKL KLE
Sbjct: 70 EKIDEFLATGKLRKLE 85
>pdb|1NZP|A Chain A, Solution Structure Of The Lyase Domain Of Human Dna
Polymerase Lambda
Length = 87
Score = 48.5 bits (114), Expect = 8e-06, Method: Composition-based stats.
Identities = 27/75 (36%), Positives = 39/75 (52%)
Query: 199 NKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDH 258
N +ITE L Y G+ R+ Y KAI ++ + S + +PGIGK M +
Sbjct: 13 NLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEK 72
Query: 259 IQEIVTTGKLSKLEH 273
I EI+ +G L KL+H
Sbjct: 73 IIEILESGHLRKLDH 87
>pdb|1JAJ|A Chain A, Solution Structure Of Dna Polymerase X From The African
Swine Fever Virus
pdb|1JQR|A Chain A, Nmr Structure Of The African Swine Fever Virus Dna
Polymerase X
Length = 174
Score = 34.3 bits (77), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 40/173 (23%), Positives = 64/173 (36%), Gaps = 40/173 (23%)
Query: 360 ILCGGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEEGT 419
I+ GS RR + D+D++I+ P++K K L K
Sbjct: 34 IVAVGSLRREEKMLNDVDLLIIVPEKKLLKHVLPNIRIK--------------------- 72
Query: 420 DSGVDTYFGLCTYPGRELRHRIDFKVYPRDIYA-------FGLIAWTGNDVLNRRLRLLA 472
G+ +C L + K Y D++ + + +TG R+R
Sbjct: 73 --GLSFSVKVCGERKCVLFIEWEKKTYQLDLFTALAEEKPYAIFHFTGPVSYLIRIRAAL 130
Query: 473 ESKGYRLDDTGLFPATYGSGGKQGVRARTSLKFDTEKEVFDFLGFPWLEPHER 525
+ K Y+L+ GLF + LK TEKE+ LGF + P +R
Sbjct: 131 KKKNYKLNQYGLFKN----------QTLVPLKITTEKELIKELGFTYRIPKKR 173
>pdb|1WF6|A Chain A, The Third Brca1 C-Terminus (Brct) Domain Of Similar To
S.Pombe Rad4+CUT5+ PRODUCT
Length = 132
Score = 32.7 bits (73), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 40/87 (45%), Gaps = 11/87 (12%)
Query: 18 IFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQ----- 72
+ G R++L G R+L R+ + G +L++ VTHV+ D + L+Q
Sbjct: 40 LLDGCRIYLC--GFSGRKLDKLRRLINSGGGVRFNQLNEDVTHVIVGDYDDELKQFWNKS 97
Query: 73 ----SVIRYQWLEDSLRLGEKVSEDLY 95
V+ +WL + G +SE+ Y
Sbjct: 98 AHRPHVVGAKWLLECFSKGYMLSEEPY 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 = 0.56, Method: Compositional matrix adjust.
Identities = 28/114 (24%), Positives = 52/114 (45%), Gaps = 5/114 (4%)
Query: 217 GEDRRSFSYYKAIPVIEKLPFKIES--ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHF 274
GED +S +Y A +E+L + A + G+P +GK + + + +G + LE
Sbjct: 29 GEDFKSRAYRSAARSLEELNEETPELLAREFTGIPKVGKGIAAELSDFARSGTFAPLEA- 87
Query: 275 EKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYF 328
+ + V G+GP + L+ G +L+ L+ ++ + GLK F
Sbjct: 88 AAGQLPPGLLDLLGVRGLGPKKIRSLWLAGIDSLERLR--EAAESGELAGLKGF 139
>pdb|3SQD|A Chain A, Crystal Structure Of Human Ptip Brct56-Gamma H2ax Complex
pdb|3SQD|B Chain B, Crystal Structure Of Human Ptip Brct56-Gamma H2ax Complex
Length = 219
Score = 32.0 bits (71), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 47/88 (53%), Gaps = 10/88 (11%)
Query: 25 FLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAM----DLEALLQQSVIRY--- 77
F++ G + ++Q + +KL +G V E ++K TH++A ++ L SV+++
Sbjct: 18 FVLFTGFEPVQVQQYIKKLYILGGEVAES-AQKCTHLIASKVTRTVKFLTAISVVKHIVT 76
Query: 78 -QWLEDSLRLGEKVSEDLYRIKLDPEGE 104
+WLE+ R + + E Y ++ D E E
Sbjct: 77 PEWLEECFRCQKFIDEQNYILR-DAEAE 103
>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 = 4.5, Method: Compositional matrix adjust.
Identities = 12/21 (57%), Positives = 17/21 (80%)
Query: 291 GIGPATAQKLYEKGHRTLDDL 311
G+GPATA+KL E G+ TL+ +
Sbjct: 42 GVGPATAEKLREAGYDTLEAI 62
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
0.317 0.136 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,219,668
Number of Sequences: 62578
Number of extensions: 692600
Number of successful extensions: 2061
Number of sequences better than 100.0: 44
Number of HSP's better than 100.0 without gapping: 38
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1921
Number of HSP's gapped (non-prelim): 47
length of query: 527
length of database: 14,973,337
effective HSP length: 103
effective length of query: 424
effective length of database: 8,527,803
effective search space: 3615788472
effective search space used: 3615788472
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)