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= 005425
(697 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1Q79|A Chain A, Crystal Structure Of Mammalian Poly(A) Polymerase
Length = 514
Score = 404 bits (1039), Expect = e-113, Method: Compositional matrix adjust.
Identities = 215/481 (44%), Positives = 304/481 (63%), Gaps = 15/481 (3%)
Query: 14 KQYGVTKPISMAGPTEADMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVK 73
K YG+T PIS+A P E D ++L + L G++E +EE ++R +LG++ + K+W++
Sbjct: 18 KHYGITSPISLAAPKETDXLLTQKLVETLKPFGVFEEEEELQRRILILGKLNNLVKEWIR 77
Query: 74 ELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNI 133
E++ + ++E+ IFTFGSYRLGVH GADIDALCV P +V R DFF ++
Sbjct: 78 EISESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRS-DFFTSFYDK 136
Query: 134 LAEMEEVTELQPVLDAHVPVMKFKFDGLSIDLLYASISRLVVREDLDISDMSVLNDVDEP 193
L EEV +L+ V +A VPV+K FDG+ ID+L+A ++ + EDLD+ D S+L ++D
Sbjct: 137 LKLQEEVKDLRAVEEAFVPVIKLXFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIR 196
Query: 194 TVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARV 253
+RSLNGCRV D+IL LVPN+++F TLR +K WAKR +YSN+ GFLGGV+WA+LVAR
Sbjct: 197 XIRSLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVART 256
Query: 254 CQLYPNAVPSMLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPII 313
CQLYPNA+ S LV +FF V++ W WPNPV+L +E L VWDPR N D+ H MPII
Sbjct: 257 CQLYPNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPII 316
Query: 314 TPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEVELNKAQWSALFEPYLFFESYRNYLQ 373
TPAYP NS+YNVS ST VM+++F+ G I +E+ L+KA+WS LFE FF+ Y++Y+
Sbjct: 317 TPAYPQQNSTYNVSVSTRMVMVEEFKQGLAITDEILLSKAEWSKLFEAPNFFQKYKHYIV 376
Query: 374 VDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKL-----QCHPYPHEYVDTSKPCAH 428
+ A L W G VES++R L +E++ + L Q P P E D K
Sbjct: 377 LLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAPKENPD--KEEFR 434
Query: 429 CAFFMGLQRKPGEVVQEGQQFDIRGSVEEF-----KLSINMYMFWKPGMEICVSHIRRKQ 483
+ +GL K E E D+ ++ F + +IN MF + M+I H++RKQ
Sbjct: 435 TMWVIGLVFKKTE-NSENLSVDLTYDIQSFTDTVYRQAINSKMF-EVDMKIAAMHVKRKQ 492
Query: 484 I 484
+
Sbjct: 493 L 493
>pdb|1Q78|A Chain A, Crystal Structure Of Poly(A) Polymerase In Complex With
3'- Datp And Magnesium Chloride
Length = 514
Score = 403 bits (1036), Expect = e-112, Method: Compositional matrix adjust.
Identities = 215/481 (44%), Positives = 304/481 (63%), Gaps = 15/481 (3%)
Query: 14 KQYGVTKPISMAGPTEADMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVK 73
K YG+T PIS+A P E D ++L + L G++E +EE ++R +LG++ + K+W++
Sbjct: 18 KHYGITSPISLAAPKETDXLLTQKLVETLKPFGVFEEEEELQRRILILGKLNNLVKEWIR 77
Query: 74 ELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNI 133
E++ + ++E+ IFTFGSYRLGVH GADIDALCV P +V R DFF ++
Sbjct: 78 EISESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRS-DFFTSFYDK 136
Query: 134 LAEMEEVTELQPVLDAHVPVMKFKFDGLSIDLLYASISRLVVREDLDISDMSVLNDVDEP 193
L EEV +L+ V +A VPV+K FDG+ ID+L+A ++ + EDLD+ D S+L ++D
Sbjct: 137 LKLQEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIR 196
Query: 194 TVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARV 253
+RSLNGCRV D+IL LVPN+++F TLR +K WAKR +YSN+ GFLGGV+WA+LVAR
Sbjct: 197 XIRSLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVART 256
Query: 254 CQLYPNAVPSMLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPII 313
CQLYPNA+ S LV +FF V++ W WPNPV+L +E L VWDPR N D+ H MPII
Sbjct: 257 CQLYPNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPII 316
Query: 314 TPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEVELNKAQWSALFEPYLFFESYRNYLQ 373
TPAYP NS+YNVS ST VM+++F+ G I +E+ L+KA+WS LFE FF+ Y++Y+
Sbjct: 317 TPAYPQQNSTYNVSVSTRMVMVEEFKQGLAITDEILLSKAEWSKLFEAPNFFQKYKHYIV 376
Query: 374 VDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKL-----QCHPYPHEYVDTSKPCAH 428
+ A L W G VES++R L +E++ + L Q P P E D K
Sbjct: 377 LLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAPKENPD--KEEFR 434
Query: 429 CAFFMGLQRKPGEVVQEGQQFDIRGSVEEF-----KLSINMYMFWKPGMEICVSHIRRKQ 483
+ +GL K E E D+ ++ F + +IN MF + M+I H++RKQ
Sbjct: 435 TMWVIGLVFKKTE-NSENLSVDLTYDIQSFTDTVYRQAINSKMF-EVDMKIAAMHVKRKQ 492
Query: 484 I 484
+
Sbjct: 493 L 493
>pdb|1F5A|A Chain A, Crystal Structure Of Mammalian Poly(A) Polymerase
Length = 513
Score = 381 bits (979), Expect = e-106, Method: Compositional matrix adjust.
Identities = 211/481 (43%), Positives = 299/481 (62%), Gaps = 15/481 (3%)
Query: 14 KQYGVTKPISMAGPTEADMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVK 73
K YG+T PIS+A P E D ++L + L G++E +EE ++R +LG++ + K+W++
Sbjct: 18 KHYGITSPISLAAPKETDCLLTQKLVETLKPFGVFEEEEELQRRILILGKLNNLVKEWIR 77
Query: 74 ELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNI 133
E++ + ++E+ IFTFGSYRLGVH GADIDALCV P +V R DFF ++
Sbjct: 78 EISESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRS-DFFTSFYDK 136
Query: 134 LAEMEEVTELQPVLDAHVPVMKFKFDGLSIDLLYASISRLVVREDLDISDMSVLNDVDEP 193
L EEV +L+ V +A VPV+K FDG+ ID+L+A ++ + EDLD+ D S+L ++D
Sbjct: 137 LKLQEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIR 196
Query: 194 TVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARV 253
+RSLNGCRV D+IL LVPN+++F TLR +K WAKR +YSN+ GFLGGV+WA LVAR
Sbjct: 197 CIRSLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAXLVART 256
Query: 254 CQLYPNAVPSMLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPII 313
CQLYPNA+ S LV +FF V++ W WPNPV+L +E L VWDPR N D+ H PII
Sbjct: 257 CQLYPNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLXPII 316
Query: 314 TPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEVELNKAQWSALFEPYLFFESYRNYLQ 373
TPAYP NS+YNVS ST V +++F+ G I +E+ L+KA+WS LFE FF+ Y++Y+
Sbjct: 317 TPAYPQQNSTYNVSVSTRXVXVEEFKQGLAITDEILLSKAEWSKLFEAPNFFQKYKHYIV 376
Query: 374 VDIVAANADDLLAWKGWVESRLRQLTLMIERDTYGKL-----QCHPYPHEYVDTSKPCAH 428
+ A L W G VES++R L +E++ + L Q P P E D K
Sbjct: 377 LLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAPKENPD--KEEFR 434
Query: 429 CAFFMGLQRKPGEVVQEGQQFDIRGSVEEF-----KLSINMYMFWKPGMEICVSHIRRKQ 483
+ +GL K E E D+ ++ F + +IN F + +I H++RKQ
Sbjct: 435 TXWVIGLVFKKTE-NSENLSVDLTYDIQSFTDTVYRQAINSKXF-EVDXKIAAXHVKRKQ 492
Query: 484 I 484
+
Sbjct: 493 L 493
>pdb|2HHP|A Chain A, Structure Of Yeast Poly(A) Polymerase In A Closed
Conformation
Length = 530
Score = 357 bits (917), Expect = 1e-98, Method: Compositional matrix adjust.
Identities = 175/407 (42%), Positives = 267/407 (65%), Gaps = 3/407 (0%)
Query: 14 KQYGVTKPISMAGPTEADMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVK 73
K +G+T P+S G T A+ + N L + L + G +E+++E R QVL ++++A+ +V
Sbjct: 5 KVFGITGPVSTVGATAAENKLNDSLIQELKKEGSFETEQETANRVQVLKILQELAQRFVY 64
Query: 74 ELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNI 133
E+++ + SD M DA IFT+GSYRLGVHGPG+DID L V P +V+RE DFF + ++
Sbjct: 65 EVSKKKNMSDGMARDAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVTRE-DFFTVFDSL 123
Query: 134 LAEMEEVTELQPVLDAHVPVMKFKFDGLSIDLLYASISRLVVREDLDISDMSVLNDVDEP 193
L E +E+ E+ PV DA VP++K KF G+SIDL+ A + + V L +SD ++L ++DE
Sbjct: 124 LRERKELDEIAPVPDAFVPIIKIKFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDEK 183
Query: 194 TVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARV 253
+R+LNG RV D+IL+LVP F LR +K WA+RR VY+N+ GF GGV WA+LVAR+
Sbjct: 184 DLRALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARI 243
Query: 254 CQLYPNAVPSMLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPII 313
CQLYPNA +++++RFF + + W WP PV+L I++ L VW+P+ +D++H MP+I
Sbjct: 244 CQLYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVI 303
Query: 314 TPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEVELNKAQWSALFEPYLFFESYRNYLQ 373
TPAYP M +++N++ ST +V++ +F G I ++ NK W+ LFE FF Y+ YL+
Sbjct: 304 TPAYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLE 363
Query: 374 VDIVAANADDL-LAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHEY 419
+ +D+ L W G VES++R L + +E K+ HP+ +
Sbjct: 364 ITAYTRGSDEQHLKWSGLVESKVRLLVMKLEVLAGIKI-AHPFTKPF 409
>pdb|2O1P|A Chain A, Structure Of Yeast Poly(A) Polymerase In A Somewhat Closed
State
pdb|2O1P|B Chain B, Structure Of Yeast Poly(A) Polymerase In A Somewhat Closed
State
Length = 546
Score = 357 bits (916), Expect = 1e-98, Method: Compositional matrix adjust.
Identities = 175/407 (42%), Positives = 267/407 (65%), Gaps = 3/407 (0%)
Query: 14 KQYGVTKPISMAGPTEADMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVK 73
K +G+T P+S G T A+ + N L + L + G +E+++E R QVL ++++A+ +V
Sbjct: 5 KVFGITGPVSTVGATAAENKLNDSLIQELKKEGSFETEQETANRVQVLKILQELAQRFVY 64
Query: 74 ELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNI 133
E+++ + SD M DA IFT+GSYRLGVHGPG+DID L V P +V+RE DFF + ++
Sbjct: 65 EVSKKKNMSDGMARDAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVTRE-DFFTVFDSL 123
Query: 134 LAEMEEVTELQPVLDAHVPVMKFKFDGLSIDLLYASISRLVVREDLDISDMSVLNDVDEP 193
L E +E+ E+ PV DA VP++K KF G+SIDL+ A + + V L +SD ++L ++DE
Sbjct: 124 LRERKELDEIAPVPDAFVPIIKIKFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDEK 183
Query: 194 TVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARV 253
+R+LNG RV D+IL+LVP F LR +K WA+RR VY+N+ GF GGV WA+LVAR+
Sbjct: 184 DLRALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARI 243
Query: 254 CQLYPNAVPSMLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPII 313
CQLYPNA +++++RFF + + W WP PV+L I++ L VW+P+ +D++H MP+I
Sbjct: 244 CQLYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVI 303
Query: 314 TPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEVELNKAQWSALFEPYLFFESYRNYLQ 373
TPAYP M +++N++ ST +V++ +F G I ++ NK W+ LFE FF Y+ YL+
Sbjct: 304 TPAYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLE 363
Query: 374 VDIVAANADDL-LAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHEY 419
+ +D+ L W G VES++R L + +E K+ HP+ +
Sbjct: 364 ITAYTRGSDEQHLKWSGLVESKVRLLVMKLEVLAGIKI-AHPFTKPF 409
>pdb|1FA0|A Chain A, Structure Of Yeast Poly(A) Polymerase Bound To Manganate
And 3'-Datp
pdb|1FA0|B Chain B, Structure Of Yeast Poly(A) Polymerase Bound To Manganate
And 3'-Datp
pdb|3C66|A Chain A, Yeast Poly(A) Polymerase In Complex With Fip1 Residues
80-105
pdb|3C66|B Chain B, Yeast Poly(A) Polymerase In Complex With Fip1 Residues
80-105
Length = 537
Score = 357 bits (916), Expect = 1e-98, Method: Compositional matrix adjust.
Identities = 175/407 (42%), Positives = 267/407 (65%), Gaps = 3/407 (0%)
Query: 14 KQYGVTKPISMAGPTEADMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVK 73
K +G+T P+S G T A+ + N L + L + G +E+++E R QVL ++++A+ +V
Sbjct: 5 KVFGITGPVSTVGATAAENKLNDSLIQELKKEGSFETEQETANRVQVLKILQELAQRFVY 64
Query: 74 ELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNI 133
E+++ + SD M DA IFT+GSYRLGVHGPG+DID L V P +V+RE DFF + ++
Sbjct: 65 EVSKKKNMSDGMARDAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVTRE-DFFTVFDSL 123
Query: 134 LAEMEEVTELQPVLDAHVPVMKFKFDGLSIDLLYASISRLVVREDLDISDMSVLNDVDEP 193
L E +E+ E+ PV DA VP++K KF G+SIDL+ A + + V L +SD ++L ++DE
Sbjct: 124 LRERKELDEIAPVPDAFVPIIKIKFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDEK 183
Query: 194 TVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARV 253
+R+LNG RV D+IL+LVP F LR +K WA+RR VY+N+ GF GGV WA+LVAR+
Sbjct: 184 DLRALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARI 243
Query: 254 CQLYPNAVPSMLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPII 313
CQLYPNA +++++RFF + + W WP PV+L I++ L VW+P+ +D++H MP+I
Sbjct: 244 CQLYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVI 303
Query: 314 TPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEVELNKAQWSALFEPYLFFESYRNYLQ 373
TPAYP M +++N++ ST +V++ +F G I ++ NK W+ LFE FF Y+ YL+
Sbjct: 304 TPAYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLE 363
Query: 374 VDIVAANADDL-LAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHEY 419
+ +D+ L W G VES++R L + +E K+ HP+ +
Sbjct: 364 ITAYTRGSDEQHLKWSGLVESKVRLLVMKLEVLAGIKI-AHPFTKPF 409
>pdb|2Q66|A Chain A, Structure Of Yeast Poly(A) Polymerase With Atp And
Oligo(A)
Length = 525
Score = 354 bits (908), Expect = 9e-98, Method: Compositional matrix adjust.
Identities = 174/407 (42%), Positives = 266/407 (65%), Gaps = 3/407 (0%)
Query: 14 KQYGVTKPISMAGPTEADMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVK 73
K +G+T P+S G T A+ + N L + L + G +E+++E R QVL ++++A+ +V
Sbjct: 1 KVFGITGPVSTVGATAAENKLNDSLIQELKKEGSFETEQETANRVQVLKILQELAQRFVY 60
Query: 74 ELTRLRGYSDQMVEDANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNI 133
E+++ + SD M DA IFT+GSYRLGVHGPG+DID L V P +V+RE DFF + ++
Sbjct: 61 EVSKKKNMSDGMARDAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVTRE-DFFTVFDSL 119
Query: 134 LAEMEEVTELQPVLDAHVPVMKFKFDGLSIDLLYASISRLVVREDLDISDMSVLNDVDEP 193
L E +E+ E+ PV DA VP++K KF G+SI L+ A + + V L +SD ++L ++DE
Sbjct: 120 LRERKELDEIAPVPDAFVPIIKIKFSGISIALICARLDQPQVPLSLTLSDKNLLRNLDEK 179
Query: 194 TVRSLNGCRVADQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVARV 253
+R+LNG RV D+IL+LVP F LR +K WA+RR VY+N+ GF GGV WA+LVAR+
Sbjct: 180 DLRALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARI 239
Query: 254 CQLYPNAVPSMLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPRKNRRDKTHHMPII 313
CQLYPNA +++++RFF + + W WP PV+L I++ L VW+P+ +D++H MP+I
Sbjct: 240 CQLYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVI 299
Query: 314 TPAYPCMNSSYNVSTSTLRVMMDQFQYGNTICEEVELNKAQWSALFEPYLFFESYRNYLQ 373
TPAYP M +++N++ ST +V++ +F G I ++ NK W+ LFE FF Y+ YL+
Sbjct: 300 TPAYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLE 359
Query: 374 VDIVAANADDL-LAWKGWVESRLRQLTLMIERDTYGKLQCHPYPHEY 419
+ +D+ L W G VES++R L + +E K+ HP+ +
Sbjct: 360 ITAYTRGSDEQHLKWSGLVESKVRLLVMKLEVLAGIKI-AHPFTKPF 405
>pdb|3NYB|A Chain A, Structure And Function Of The Polymerase Core Of Tramp, A
Rna Surveillance Complex
Length = 323
Score = 46.2 bits (108), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 72/282 (25%), Positives = 118/282 (41%), Gaps = 75/282 (26%)
Query: 37 ELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLRGYSDQMVEDANALIFTF 96
E++ F+ A + S+EE E R Q + IR+ K Q+ DA+ + F
Sbjct: 24 EIKDFV--AYISPSREEIEIRNQTISTIREAVK--------------QLWPDAD--LHVF 65
Query: 97 GSYRLGVHGPGADIDALCVGPSYVSREE--DFFFILHNILAEMEEVTELQPVLDAHVPVM 154
GSY ++ PG+DID CV S + +E + + L + L + TE++ V A VP++
Sbjct: 66 GSYSTDLYLPGSDID--CVVTSELGGKESRNNLYSLASHLKKKNLATEVEVVAKARVPII 123
Query: 155 KF--KFDGLSIDLLYASISRL----VVREDLDISDMSVLNDVDEPTVRSLNGCRVADQIL 208
KF G+ I + + + + ++RE LD D P +R L
Sbjct: 124 KFVEPHSGIHIAVSFERTNGIEAAKLIREWLD----------DTPGLREL---------- 163
Query: 209 KLVPNVEHFCTTLRCLKFWAKRRGVYSNV-TGFLGGVNWALLVARVCQLYPNAVPS---- 263
L +F RR +NV TG LGG + LV ++P + +
Sbjct: 164 -----------VLIVKQFLHARR--LNNVHTGGLGGFSIICLVFSFLHMHPRIITNEIDP 210
Query: 264 -----MLVSRFFRVYTMWRWPNPVMLCAIDEAELGFSVWDPR 300
+L+ FF +Y + V L + D G+ V+ P+
Sbjct: 211 KDNLGVLLIEFFELYGKNFGYDDVALGSSD----GYPVYFPK 248
>pdb|1HSL|A Chain A, Refined 1.89 Angstroms Structure Of The Histidine-Binding
Protein Complexed With Histidine And Its Relationship
With Many Other Active Transport(Slash)chemosensory
Receptors
pdb|1HSL|B Chain B, Refined 1.89 Angstroms Structure Of The Histidine-Binding
Protein Complexed With Histidine And Its Relationship
With Many Other Active Transport(Slash)chemosensory
Receptors
pdb|1HPB|P Chain P, The Bacterial Periplasmic Histidine-Binding Protein:
Structure(Slash)function Analysis Of The Ligand-Binding
Site And Comparison With Related Proteins
Length = 238
Score = 32.3 bits (72), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 34/74 (45%), Gaps = 26/74 (35%)
Query: 147 LDAHVPVMKFK-----FDGLSI-----------DLLYASISRLVVREDLDISDMSVLNDV 190
LDA +P +K K LSI D LYA+ SRLVV ++ DI
Sbjct: 52 LDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAKNSDI--------- 102
Query: 191 DEPTVRSLNGCRVA 204
+PTV SL G RV
Sbjct: 103 -QPTVASLKGKRVG 115
>pdb|3SEJ|A Chain A, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To Secretor Lewis Hbga (Leb)
pdb|3SEJ|B Chain B, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To Secretor Lewis Hbga (Leb)
pdb|3SEJ|C Chain C, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To Secretor Lewis Hbga (Leb)
pdb|3SEJ|D Chain D, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To Secretor Lewis Hbga (Leb)
pdb|3SEJ|E Chain E, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To Secretor Lewis Hbga (Leb)
pdb|3SEJ|F Chain F, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To Secretor Lewis Hbga (Leb)
pdb|3SEJ|G Chain G, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To Secretor Lewis Hbga (Leb)
pdb|3SEJ|H Chain H, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To Secretor Lewis Hbga (Leb)
pdb|3SEJ|I Chain I, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To Secretor Lewis Hbga (Leb)
pdb|3SEJ|J Chain J, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To Secretor Lewis Hbga (Leb)
pdb|3SJP|A Chain A, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05)
pdb|3SKB|A Chain A, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05)
pdb|3SKB|B Chain B, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05)
pdb|3SKB|C Chain C, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05)
pdb|3SKB|D Chain D, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05)
pdb|3SKB|E Chain E, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05)
pdb|3SKB|F Chain F, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05)
pdb|3SKB|G Chain G, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05)
pdb|3SKB|H Chain H, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05)
pdb|3SKB|I Chain I, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05)
pdb|3SKB|J Chain J, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05)
pdb|3SLD|A Chain A, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To A Trisaccharide
pdb|3SLD|B Chain B, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To A Trisaccharide
pdb|3SLD|C Chain C, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To A Trisaccharide
pdb|3SLD|D Chain D, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To A Trisaccharide
pdb|3SLD|E Chain E, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To A Trisaccharide
pdb|3SLD|F Chain F, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To A Trisaccharide
pdb|3SLD|G Chain G, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To A Trisaccharide
pdb|3SLD|H Chain H, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To A Trisaccharide
pdb|3SLD|I Chain I, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To A Trisaccharide
pdb|3SLD|J Chain J, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To A Trisaccharide
pdb|3SLN|A Chain A, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To H Pentasaccharide
pdb|3SLN|B Chain B, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To H Pentasaccharide
pdb|3SLN|C Chain C, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To H Pentasaccharide
pdb|3SLN|D Chain D, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To H Pentasaccharide
pdb|3SLN|E Chain E, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To H Pentasaccharide
pdb|3SLN|F Chain F, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To H Pentasaccharide
pdb|3SLN|G Chain G, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To H Pentasaccharide
pdb|3SLN|H Chain H, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To H Pentasaccharide
pdb|3SLN|I Chain I, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To H Pentasaccharide
pdb|3SLN|J Chain J, Structural Characterization Of A Gii.4 2004 Norovirus
Variant (Tch05) Bound To H Pentasaccharide
Length = 311
Score = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 5/78 (6%)
Query: 499 PRLASQQRSSENGNEYQTGSGLKRKKDPESVDQDGPEKRQSISPQKQDSLSPDHLAPSSV 558
P+L S Q S++ N+++TG + P V QDG Q+ + Q + PD+ S
Sbjct: 140 PKLGSVQFSTDTSNDFETGQ--NTRFTPVGVVQDGSTTHQN---EPQQWVLPDYSGRDSH 194
Query: 559 RSGTGSNVEPVIPDKRVL 576
V P P +++L
Sbjct: 195 NVHLAPAVAPTFPGEQLL 212
>pdb|4E7X|A Chain A, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E7X|B Chain B, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E7X|C Chain C, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E7X|D Chain D, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E80|A Chain A, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E80|B Chain B, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E80|C Chain C, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E80|D Chain D, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E8F|A Chain A, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
pdb|4E8F|B Chain B, Structural Basis For The Activity Of A Cytoplasmic Rna
Terminal U- Transferase
Length = 405
Score = 30.8 bits (68), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 41/185 (22%), Positives = 69/185 (37%), Gaps = 36/185 (19%)
Query: 90 NALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDA 149
+A + FGS G+ +D+D + S V + ++AE E LQ A
Sbjct: 82 DAELVAFGSLESGLALKNSDMDLCVLMDSRVQSDTIALQFYEELIAEGFEGKFLQ---RA 138
Query: 150 HVPVMKFKFD-----GLSIDLLYASISRLVVREDLDISDMSVLNDVDEPTVRSLNGCRVA 204
+P++K D G S +RL + L +S + L+ +P V
Sbjct: 139 RIPIIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVL-------- 190
Query: 205 DQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVAR--VCQLYPNAVP 262
+K WAKR+ + S G L + L+V + + P P
Sbjct: 191 ------------------LVKHWAKRKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFP 232
Query: 263 SMLVS 267
++L+S
Sbjct: 233 NLLLS 237
>pdb|3OGU|A Chain A, Dna Polymerase Beta Mutant 5p20 Complexed With 6bp Of Dna
Length = 335
Score = 30.0 bits (66), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 88 DANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEV 140
D+ + GS+R G G D+D L PS+ S +LH ++ ++++V
Sbjct: 170 DSEYIATVCGSFRRGAESSG-DMDVLLTHPSFTSESTKQPKLLHQVVEQLQKV 221
>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 = 30.0 bits (66), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 88 DANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEV 140
D+ + GS+R G G D+D L PS+ S +LH ++ ++++V
Sbjct: 170 DSEYIATVCGSFRRGAESSG-DMDVLLTHPSFTSESTKQPKLLHQVVEQLQKV 221
>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 = 30.0 bits (66), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 88 DANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEV 140
D+ + GS+R G G D+D L PS+ S +LH ++ ++++V
Sbjct: 170 DSEYIATVCGSFRRGAESSG-DMDVLLTHPSFTSESTKQPKLLHQVVEQLQKV 221
>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 = 30.0 bits (66), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 88 DANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEV 140
D+ + GS+R G G D+D L PS+ S +LH ++ ++++V
Sbjct: 170 DSEYIATVCGSFRRGAESSG-DMDVLLTHPSFTSESTKQPKLLHQVVEQLQKV 221
>pdb|4FHX|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity - H336n Mutant Bound
To Mgatp
Length = 349
Score = 29.6 bits (65), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 41/185 (22%), Positives = 69/185 (37%), Gaps = 36/185 (19%)
Query: 90 NALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDA 149
+A + FGS G+ +D+D + S V + ++AE E LQ A
Sbjct: 54 DAELVAFGSLESGLALKNSDMDLCVLMDSRVQSDTIALQFYEELIAEGFEGKFLQ---RA 110
Query: 150 HVPVMKFKFD-----GLSIDLLYASISRLVVREDLDISDMSVLNDVDEPTVRSLNGCRVA 204
+P++K D G S +RL + L +S + L+ +P V
Sbjct: 111 RIPIIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVL-------- 162
Query: 205 DQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVAR--VCQLYPNAVP 262
+K WAKR+ + S G L + L+V + + P P
Sbjct: 163 ------------------LVKHWAKRKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFP 204
Query: 263 SMLVS 267
++L+S
Sbjct: 205 NLLLS 209
>pdb|4FH3|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity
pdb|4FH5|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity - Mgutp Bound
pdb|4FHP|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity - Cautp Bound
pdb|4FHV|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity - Mgctp Bound
pdb|4FHW|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity - Mggtp Bound
pdb|4FHY|A Chain A, Crystal Structures Of The Cid1 Poly (U) Polymerase Reveal
The Mechanism For Utp Selectivity - Mg 3'-Datp Bound
Length = 349
Score = 29.6 bits (65), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 41/185 (22%), Positives = 69/185 (37%), Gaps = 36/185 (19%)
Query: 90 NALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDA 149
+A + FGS G+ +D+D + S V + ++AE E LQ A
Sbjct: 54 DAELVAFGSLESGLALKNSDMDLCVLMDSRVQSDTIALQFYEELIAEGFEGKFLQ---RA 110
Query: 150 HVPVMKFKFD-----GLSIDLLYASISRLVVREDLDISDMSVLNDVDEPTVRSLNGCRVA 204
+P++K D G S +RL + L +S + L+ +P V
Sbjct: 111 RIPIIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVL-------- 162
Query: 205 DQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVAR--VCQLYPNAVP 262
+K WAKR+ + S G L + L+V + + P P
Sbjct: 163 ------------------LVKHWAKRKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFP 204
Query: 263 SMLVS 267
++L+S
Sbjct: 205 NLLLS 209
>pdb|3GDX|A Chain A, Dna Polymerase Beta With A Gapped Dnd Substrate And
Dtmp(Cf2)pp
Length = 326
Score = 29.6 bits (65), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 88 DANALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEV 140
D+ + GS+R G G D+D L PS+ S +LH ++ ++++V
Sbjct: 161 DSEYIATVCGSFRRGAESSG-DMDVLLTHPSFTSESTKQPKLLHQVVEQLQKV 212
>pdb|4EP7|A Chain A, Functional Implications From The Cid1 Poly(U) Polymerase
Crystal Structure
pdb|4EP7|B Chain B, Functional Implications From The Cid1 Poly(U) Polymerase
Crystal Structure
Length = 340
Score = 29.6 bits (65), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 41/185 (22%), Positives = 69/185 (37%), Gaps = 36/185 (19%)
Query: 90 NALIFTFGSYRLGVHGPGADIDALCVGPSYVSREEDFFFILHNILAEMEEVTELQPVLDA 149
+A + FGS G+ +D+D + S V + ++AE E LQ A
Sbjct: 45 DAELVAFGSLESGLALKNSDMDLCVLMDSRVQSDTIALQFYEELIAEGFEGKFLQ---RA 101
Query: 150 HVPVMKFKFD-----GLSIDLLYASISRLVVREDLDISDMSVLNDVDEPTVRSLNGCRVA 204
+P++K D G S +RL + L +S + L+ +P V
Sbjct: 102 RIPIIKLTSDTKNGFGASFQCDIGFNNRLAIHNTLLLSSYTKLDARLKPMVL-------- 153
Query: 205 DQILKLVPNVEHFCTTLRCLKFWAKRRGVYSNVTGFLGGVNWALLVAR--VCQLYPNAVP 262
+K WAKR+ + S G L + L+V + + P P
Sbjct: 154 ------------------LVKHWAKRKQINSPYFGTLSSYGYVLMVLYYLIHVIKPPVFP 195
Query: 263 SMLVS 267
++L+S
Sbjct: 196 NLLLS 200
>pdb|3RJV|A Chain A, Crystal Structure Of A Putative Sel1 Repeat Protein
(Kpn_04481) From Klebsiella Pneumoniae Subsp. Pneumoniae
At 1.65 A Resolution
Length = 212
Score = 29.3 bits (64), Expect = 7.0, Method: Composition-based stats.
Identities = 29/96 (30%), Positives = 43/96 (44%), Gaps = 11/96 (11%)
Query: 22 ISMAGPTEADMQRNRELEKFLVEAGLYESKEEDEKREQVLGRIRQIAKDWVKELTRLR-- 79
+ + P +AD + R+L + VEAG SK + +VL + A D +T L+
Sbjct: 59 LKIRNPQQADYPQARQLAEKAVEAG---SKSGEIVLARVLVNRQAGATDVAHAITLLQDA 115
Query: 80 ---GYSDQMVEDANALIFTFGSYRLGVHGPGADIDA 112
SD V+ L + S GVHGP D+ A
Sbjct: 116 ARDSESDAAVDAQXLLGLIYAS---GVHGPEDDVKA 148
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
0.319 0.136 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,432,119
Number of Sequences: 62578
Number of extensions: 786797
Number of successful extensions: 1478
Number of sequences better than 100.0: 34
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 26
Number of HSP's that attempted gapping in prelim test: 1457
Number of HSP's gapped (non-prelim): 34
length of query: 697
length of database: 14,973,337
effective HSP length: 106
effective length of query: 591
effective length of database: 8,340,069
effective search space: 4928980779
effective search space used: 4928980779
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)