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= 010783
(501 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3UMV|A Chain A, Eukaryotic Class Ii Cpd Photolyase Structure Reveals A
Basis For Improved Uv-Tolerance In Plants
pdb|3UMV|B Chain B, Eukaryotic Class Ii Cpd Photolyase Structure Reveals A
Basis For Improved Uv-Tolerance In Plants
Length = 506
Score = 611 bits (1575), Expect = e-175, Method: Compositional matrix adjust.
Identities = 313/500 (62%), Positives = 371/500 (74%), Gaps = 25/500 (5%)
Query: 3 SLTPPSTA--------VQPGRIRVLKQGSLDKKRGPVVYWMFRDQRVRDNWALIHAVDQA 54
S++PP TA P R+RV+ G VVYWM RDQR+ DNWAL+HA A
Sbjct: 5 SVSPPRTAPGPANPSPAHPSRVRVIHPGGGKPGGP-VVYWMLRDQRLADNWALLHAAGLA 63
Query: 55 NKNNVPVAVAFNLFDQ--FLGAKARQLGFMLRGLRLLQRNIEETFQILFFLFQGEAEDNI 112
+ P+AVAF LF + L A+ RQLGF+LRGLR L + F G AE I
Sbjct: 64 AASASPLAVAFALFPRPFLLSARRRQLGFLLRGLRRLAADAAARHLPFFLFTGGPAE--I 121
Query: 113 PNFVRECGASLLVTDFSPLREIRRCKDKICN---RVSDSVTIHEVDAHNVVPVWVASEKL 169
P V+ GAS LV DFSPLR +R D + R + V +H+VDAHNVVPVW AS K+
Sbjct: 122 PALVQRLGASTLVADFSPLRPVREALDAVVGDLRREAPGVAVHQVDAHNVVPVWTASAKM 181
Query: 170 EYSAKTLRGKINKLLPEYLIDYPMLEQPIEKWTGTRQSIDWDSIIAAVLRKGAEVPEIGW 229
EYSAKT RGK++K++ EYL+++P L + + +DWD++IA V + VPEI W
Sbjct: 182 EYSAKTFRGKVSKVMDEYLVEFPELPAVVPWDREQPEGVDWDALIARVCSEAENVPEIDW 241
Query: 230 CESGEDAAMEVLKGSKDGFLTKRLKNYPTDRNNPLKPRALSGLSPYLHFGQISAQRCALE 289
CE GE+AA+E L GSKDGFLTKR+K+Y TDRN+P KPRALSGLSPYLHFG ISAQRCALE
Sbjct: 242 CEPGEEAAIEALLGSKDGFLTKRIKSYETDRNDPTKPRALSGLSPYLHFGHISAQRCALE 301
Query: 290 ARKARKLCPELLYLPATLKAIDTFLEELIVRRELADNFCFYQPNYDSLKGAWEWARKSLK 349
A+K R L P K++D FLEEL+VRRELADNFC+YQP YDSL GAWEWARK+L
Sbjct: 302 AKKCRHLSP---------KSVDAFLEELVVRRELADNFCYYQPQYDSLSGAWEWARKTLM 352
Query: 350 DHASDKREHIYTKEQFEKAQTADPLWNASQMEMVYNGKMHGFMRMYWAKKILEWTTGPEE 409
DHA+DKREHIYT+EQ E A+T DPLWNASQ+EMV++GKMHGFMRMYWAKKILEWT+GPEE
Sbjct: 353 DHAADKREHIYTREQLENAKTHDPLWNASQLEMVHHGKMHGFMRMYWAKKILEWTSGPEE 412
Query: 410 ALAIAIYLNDKYEIDGRDPNGYVGCMWSICGVHDQGWKERPVFGKIRYMNYSGCKRKFDV 469
AL+ AIYLNDKYEIDGRDP+GYVGCMWSICG+HDQGWKERPVFGKIRYMNY+GCKRKFDV
Sbjct: 413 ALSTAIYLNDKYEIDGRDPSGYVGCMWSICGLHDQGWKERPVFGKIRYMNYAGCKRKFDV 472
Query: 470 DGYIAYVKRIVGGTKKRRAD 489
D YI+YVKR+ G +KKR A+
Sbjct: 473 DAYISYVKRLAGQSKKRNAE 492
>pdb|2XRY|A Chain A, X-Ray Structure Of Archaeal Class Ii Cpd Photolyase From
Methanosarcina Mazei
pdb|2XRZ|A Chain A, X-Ray Structure Of Archaeal Class Ii Cpd Photolyase From
Methanosarcina Mazei In Complex With Intact Cpd-Lesion
pdb|2XRZ|B Chain B, X-Ray Structure Of Archaeal Class Ii Cpd Photolyase From
Methanosarcina Mazei In Complex With Intact Cpd-Lesion
Length = 482
Score = 408 bits (1048), Expect = e-114, Method: Compositional matrix adjust.
Identities = 230/487 (47%), Positives = 296/487 (60%), Gaps = 41/487 (8%)
Query: 4 LTPPSTAVQPGRIRVLKQGSLDKKRGPVVYWMFRDQRVRDNWALIHAVDQANKNNVPVAV 63
L P + + P RIR LK G + GPVVYWM RDQR DNWAL+ + A + NVPV V
Sbjct: 14 LVPRGSHMNPKRIRALKSGK--QGDGPVVYWMSRDQRAEDNWALLFSRAIAKEANVPVVV 71
Query: 64 AFNLFDQFLGAKARQLGFMLRGLRLLQRNIEETFQILFFLFQGEAEDNIPNFVRECGASL 123
F L D+FL A RQ FML+GL+ L+ ++ +I F +G+ + I FV++ A
Sbjct: 72 VFCLTDEFLEAGIRQYEFMLKGLQELEVSLSRK-KIPSFFLRGDPGEKISRFVKDYNAGT 130
Query: 124 LVTDFSPLREIRRCKDKICNRVSDSVTIHEVDAHNVVPVWVASEKLEYSAKTLRGKI--- 180
LVTDFSPLR + +K+ + +S + EVDAHNVVP W AS+K EY+A T R K+
Sbjct: 131 LVTDFSPLRIKNQWIEKVISGIS--IPFFEVDAHNVVPCWEASQKHEYAAHTFRPKLYAL 188
Query: 181 -------------NKLLPEYLIDYPMLEQPIEKW-TGTRQSIDWDSIIAAVLRKGAEVPE 226
N + PE M+E + TG + + A+L+ + E
Sbjct: 189 LPEFLEEFPELEPNSVTPELSAGAGMVETLSDVLETGVKALLP----ERALLKNKDPLFE 244
Query: 227 IGWCESGEDAAMEVLKGSKDGFLTKRLKNYPTDRNNPLKPRALSGLSPYLHFGQISAQRC 286
E GE AA +V+ + F+ RL +Y RN+P K LS LSPYLHFGQIS+QR
Sbjct: 245 PWHFEPGEKAAKKVM----ESFIADRLDSYGALRNDPTK-NMLSNLSPYLHFGQISSQRV 299
Query: 287 ALEARKARKLCPELLYLPATLKAIDTFLEELIVRRELADNFCFYQPNYDSLKGAWEWARK 346
LE KA P + KA FL+E+++ +E++DNFC+Y P YD + WA++
Sbjct: 300 VLEVEKAESN-------PGSKKA---FLDEILIWKEISDNFCYYNPGYDGFESFPSWAKE 349
Query: 347 SLKDHASDKREHIYTKEQFEKAQTADPLWNASQMEMVYNGKMHGFMRMYWAKKILEWTTG 406
SL H +D R HIYT E+FE +T DPLWNASQME++ GKMHG+ RMYWAKKILEW+
Sbjct: 350 SLNAHRNDVRSHIYTLEEFEAGKTHDPLWNASQMELLSTGKMHGYTRMYWAKKILEWSES 409
Query: 407 PEEALAIAIYLNDKYEIDGRDPNGYVGCMWSICGVHDQGWKERPVFGKIRYMNYSGCKRK 466
PE+AL IAI LND+YE+DGRDPNGY G WSI GVHD+ W ER V GKIRYM+Y GCKRK
Sbjct: 410 PEKALEIAICLNDRYELDGRDPNGYAGIAWSIGGVHDRAWGEREVTGKIRYMSYEGCKRK 469
Query: 467 FDVDGYI 473
FDV YI
Sbjct: 470 FDVKLYI 476
>pdb|1OWL|A Chain A, Structure Of Apophotolyase From Anacystis Nidulans
pdb|1OWM|A Chain A, Data1:dna Photolyase RECEIVED X-Rays Dose 1.2 Exp15
PhotonsMM2
pdb|1OWN|A Chain A, Data3:dna Photolyase RECEIVED X-Rays Dose 4.8 Exp15
PhotonsMM2
pdb|1OWO|A Chain A, Data4:photoreduced Dna Photolyase RECEIVED X-Rays Dose
1.2 Exp15 PhotonsMM2
pdb|1OWP|A Chain A, Data6:photoreduced Dna Pholyase RECEIVED X-Rays Dose 4.8
Exp15 PhotonsMM2
pdb|1QNF|A Chain A, Structure Of Photolyase
Length = 484
Score = 52.0 bits (123), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 114/512 (22%), Positives = 191/512 (37%), Gaps = 118/512 (23%)
Query: 29 GPVVYWMFRDQRVRDNWALIHAVDQANKNNVPVAVAFNLFDQFLG----AKARQLGFMLR 84
P+++W RD R+ DN L A Q+ + + F L Q L A AR + ++
Sbjct: 3 APILFWHRRDLRLSDNIGLAAARAQSAQ----LIGLFCLDPQILQSADMAPAR-VAYLQG 57
Query: 85 GLRLLQRNIEETFQILFFLFQGEAEDNIPNFVRECGASLLV--TDFSP------------ 130
L+ LQ+ ++ L L QG+ + IP ++ A + D P
Sbjct: 58 CLQELQQRYQQAGSRLLLL-QGDPQHLIPQLAQQLQAEAVYWNQDIEPYGRDRDGQVAAA 116
Query: 131 -----LREIR------RCKDKICNRVSDSVTIHEVDAHN------VVPVWVASEKLEYSA 173
+R ++ D+I + + +++ N PV +E ++ S
Sbjct: 117 LKTAGIRAVQLWDQLLHSPDQILSGSGNPYSVYGPFWKNWQAQPKPTPVATPTELVDLSP 176
Query: 174 KTLRGKINKLLPEYLIDYPMLEQPIEKWTGTRQSIDWDSIIAAVLRKGAEVPEIGWCESG 233
+ L + P L + P L+Q DWD E G
Sbjct: 177 EQL----TAIAPLLLSELPTLKQ---------LGFDWDGGFP--------------VEPG 209
Query: 234 EDAAMEVLKGSKDGFLTKRLKNYPTDRNNPLKPRALSGLSPYLHFGQISAQRCALEARKA 293
E AA+ L+ F + + +Y RN P + SGLSP L FG I ++ A A
Sbjct: 210 ETAAIARLQE----FCDRAIADYDPQRNFPAE-AGTSGLSPALKFGAIGIRQAWQAASAA 264
Query: 294 RKLCPELLYLPATLKAIDTFLEELIVRRELADNFCFYQPN-----YDSLKGAWEWARKSL 348
L +I + +EL RE + ++ P+ Y SL + W
Sbjct: 265 HALSRS----DEARNSIRVWQQEL-AWREFYQHALYHFPSLADGPYRSLWQQFPW----- 314
Query: 349 KDHASDKREHIYTKEQFEKAQTADPLWNASQMEMVYNGKMHGFMRMYWAK-----KILEW 403
+ RE ++T + +AQT P+ +A+ ++ G MH RM A I++W
Sbjct: 315 -----ENREALFTA--WTQAQTGYPIVDAAMRQLTETGWMHNRCRMIVASFLTKDLIIDW 367
Query: 404 TTGPEEALAIAIYLNDKYEIDGRDPNGYVGCMWSICGVHDQGWKERPVFGKIRYMNYSGC 463
G + + ++ +DG G WS G +P +R N +
Sbjct: 368 RRGEQFFM--------QHLVDGDLAANNGGWQWSASS----GMDPKP----LRIFNPASQ 411
Query: 464 KRKFDVDGYIAYVKRIVGGTKKRRADSLVSGK 495
+KFD Y+KR + + L+SG+
Sbjct: 412 AKKFDATA--TYIKRWLPELRHVHPKDLISGE 441
>pdb|1TEZ|A Chain A, Complex Between Dna And The Dna Photolyase From Anacystis
Nidulans
pdb|1TEZ|B Chain B, Complex Between Dna And The Dna Photolyase From Anacystis
Nidulans
pdb|1TEZ|C Chain C, Complex Between Dna And The Dna Photolyase From Anacystis
Nidulans
pdb|1TEZ|D Chain D, Complex Between Dna And The Dna Photolyase From Anacystis
Nidulans
Length = 474
Score = 51.6 bits (122), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 114/512 (22%), Positives = 191/512 (37%), Gaps = 118/512 (23%)
Query: 29 GPVVYWMFRDQRVRDNWALIHAVDQANKNNVPVAVAFNLFDQFLG----AKARQLGFMLR 84
P+++W RD R+ DN L A Q+ + + F L Q L A AR + ++
Sbjct: 2 APILFWHRRDLRLSDNIGLAAARAQSAQ----LIGLFCLDPQILQSADMAPAR-VAYLQG 56
Query: 85 GLRLLQRNIEETFQILFFLFQGEAEDNIPNFVRECGASLLV--TDFSP------------ 130
L+ LQ+ ++ L L QG+ + IP ++ A + D P
Sbjct: 57 CLQELQQRYQQAGSRLLLL-QGDPQHLIPQLAQQLQAEAVYWNQDIEPYGRDRDGQVAAA 115
Query: 131 -----LREIR------RCKDKICNRVSDSVTIHEVDAHN------VVPVWVASEKLEYSA 173
+R ++ D+I + + +++ N PV +E ++ S
Sbjct: 116 LKTAGIRAVQLWDQLLHSPDQILSGSGNPYSVYGPFWKNWQAQPKPTPVATPTELVDLSP 175
Query: 174 KTLRGKINKLLPEYLIDYPMLEQPIEKWTGTRQSIDWDSIIAAVLRKGAEVPEIGWCESG 233
+ L + P L + P L+Q DWD E G
Sbjct: 176 EQL----TAIAPLLLSELPTLKQ---------LGFDWDGGFP--------------VEPG 208
Query: 234 EDAAMEVLKGSKDGFLTKRLKNYPTDRNNPLKPRALSGLSPYLHFGQISAQRCALEARKA 293
E AA+ L+ F + + +Y RN P + SGLSP L FG I ++ A A
Sbjct: 209 ETAAIARLQE----FCDRAIADYDPQRNFPAE-AGTSGLSPALKFGAIGIRQAWQAASAA 263
Query: 294 RKLCPELLYLPATLKAIDTFLEELIVRRELADNFCFYQPN-----YDSLKGAWEWARKSL 348
L +I + +EL RE + ++ P+ Y SL + W
Sbjct: 264 HALSRS----DEARNSIRVWQQEL-AWREFYQHALYHFPSLADGPYRSLWQQFPW----- 313
Query: 349 KDHASDKREHIYTKEQFEKAQTADPLWNASQMEMVYNGKMHGFMRMYWAK-----KILEW 403
+ RE ++T + +AQT P+ +A+ ++ G MH RM A I++W
Sbjct: 314 -----ENREALFTA--WTQAQTGYPIVDAAMRQLTETGWMHNRCRMIVASFLTKDLIIDW 366
Query: 404 TTGPEEALAIAIYLNDKYEIDGRDPNGYVGCMWSICGVHDQGWKERPVFGKIRYMNYSGC 463
G + + ++ +DG G WS G +P +R N +
Sbjct: 367 RRGEQFFM--------QHLVDGDLAANNGGWQWSASS----GMDPKP----LRIFNPASQ 410
Query: 464 KRKFDVDGYIAYVKRIVGGTKKRRADSLVSGK 495
+KFD Y+KR + + L+SG+
Sbjct: 411 AKKFDATA--TYIKRWLPELRHVHPKDLISGE 440
>pdb|3CVX|A Chain A, Drosophila Melanogaster (6-4) Photolyase H369m Mutant
Bound To Ds Dna With A T-T (6-4) Photolesion
Length = 543
Score = 48.5 bits (114), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 91/413 (22%), Positives = 160/413 (38%), Gaps = 40/413 (9%)
Query: 1 MASLTPPSTAVQPGRIRVLKQGSLDKKRGPVVYWMFRDQRVRDNWALIHAVDQANKNN-- 58
MAS + P K G +D +R +V+W + R+ DN AL H AN
Sbjct: 1 MASWSHPQFEKGASTSLYKKAGLMDSQRSTLVHWFRKGLRLHDNPALSHIFTAANAAPGR 60
Query: 59 ---VPVAVAFNLFDQFLGAKARQLGFMLRGLRLLQRNIEETFQILFFLFQGEAEDNIPNF 115
P+ + ++ A + F+ + L L + + L F+ +G+ + P
Sbjct: 61 YFVRPIFILDPGILDWMQVGANRWRFLQQTLEDLDNQLRKLNSRL-FVVRGKPAEVFPRI 119
Query: 116 VRECGASLLV--TDFSPLREIRRCKDKICNRVSDSVTIHEVDAHNVV-PVWVASEKLEYS 172
+ +L TD P R + + ++ V + +H + P V ++ L +
Sbjct: 120 FKSWRVEMLTFETDIEPYSVTRDAAVQKLAK-AEGVRVETHCSHTIYNPELVIAKNLGKA 178
Query: 173 AKTLRG--------KINKLL--PEYLIDYPMLEQPIEKWTGTRQSIDWDSIIAAVLRKGA 222
T + K+ K+L PE L + P P + + S +D L K
Sbjct: 179 PITYQKFLGIVEQLKVPKVLGVPEKLKNMPT---PPKDEVEQKDSAAYDCPTMKQLVKRP 235
Query: 223 EVPEIGWCESGEDAAMEVLKGS-KDGFLTKRLKNYPTDRNNPLKPRALSGLSPYLHFGQI 281
E GE A+ ++ S KD R + P N L+P + + LSPYL FG +
Sbjct: 236 EELGPNKFPGGETEALRRMEESLKDEIWVARFEK-PNTAPNSLEP-STTVLSPYLKFGCL 293
Query: 282 SAQRCALEARKARKLCPELLYLPATLKAIDTFLEELIVRRELADNFCFYQPNYDSLKGAW 341
SA+ + ++ K P+ P +L ++ RE +PN+D + G
Sbjct: 294 SARLFNQKLKEIIKRQPKHSQPPVSLIG-------QLMWREFYYTVAAAEPNFDRMLGNV 346
Query: 342 EWARKSLKDHASDKREHIYTKEQFEKAQTADPLWNASQMEMVYNGKMHGFMRM 394
+ ++H +H+ E + +T P +A ++ G +H RM
Sbjct: 347 YCMQIPWQEHP----DHL---EAWTHGRTGYPFIDAIMRQLRQEGWIHHLARM 392
>pdb|3CVW|A Chain A, Drosophila Melanogaster (6-4) Photolyase H365n Mutant
Bound To Ds Dna With A T-T (6-4) Photolesion And
Cofactor F0
Length = 543
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 90/412 (21%), Positives = 159/412 (38%), Gaps = 40/412 (9%)
Query: 1 MASLTPPSTAVQPGRIRVLKQGSLDKKRGPVVYWMFRDQRVRDNWALIHAVDQANKNN-- 58
MAS + P K G +D +R +V+W + R+ DN AL H AN
Sbjct: 1 MASWSHPQFEKGASTSLYKKAGLMDSQRSTLVHWFRKGLRLHDNPALSHIFTAANAAPGR 60
Query: 59 ---VPVAVAFNLFDQFLGAKARQLGFMLRGLRLLQRNIEETFQILFFLFQGEAEDNIPNF 115
P+ + ++ A + F+ + L L + + L F+ +G+ + P
Sbjct: 61 YFVRPIFILDPGILDWMQVGANRWRFLQQTLEDLDNQLRKLNSRL-FVVRGKPAEVFPRI 119
Query: 116 VRECGASLLV--TDFSPLREIRRCKDKICNRVSDSVTIHEVDAHNVV-PVWVASEKLEYS 172
+ +L TD P R + + ++ V + +H + P V ++ L +
Sbjct: 120 FKSWRVEMLTFETDIEPYSVTRDAAVQKLAK-AEGVRVETHCSHTIYNPELVIAKNLGKA 178
Query: 173 AKTLRG--------KINKLL--PEYLIDYPMLEQPIEKWTGTRQSIDWDSIIAAVLRKGA 222
T + K+ K+L PE L + P P + + S +D L K
Sbjct: 179 PITYQKFLGIVEQLKVPKVLGVPEKLKNMPT---PPKDEVEQKDSAAYDCPTMKQLVKRP 235
Query: 223 EVPEIGWCESGEDAAMEVLKGS-KDGFLTKRLKNYPTDRNNPLKPRALSGLSPYLHFGQI 281
E GE A+ ++ S KD R + P N L+P + + LSPYL FG +
Sbjct: 236 EELGPNKFPGGETEALRRMEESLKDEIWVARFEK-PNTAPNSLEP-STTVLSPYLKFGCL 293
Query: 282 SAQRCALEARKARKLCPELLYLPATLKAIDTFLEELIVRRELADNFCFYQPNYDSLKGAW 341
SA+ + ++ K P+ P +L ++ RE +PN+D + G
Sbjct: 294 SARLFNQKLKEIIKRQPKHSQPPVSLIG-------QLMWREFYYTVAAAEPNFDRMLGNV 346
Query: 342 EWARKSLKDHASDKREHIYTKEQFEKAQTADPLWNASQMEMVYNGKMHGFMR 393
+ ++H +H+ E + +T P +A ++ G +H R
Sbjct: 347 YCMQIPWQEHP----DHL---EAWTHGRTGYPFIDAIMRQLRQEGWIHNLAR 391
>pdb|3CVU|A Chain A, Drosophila Melanogaster (6-4) Photolyase Bound To Ds Dna
With A T-T (6-4) Photolesion
pdb|3CVY|A Chain A, Drosophila Melanogaster (6-4) Photolyase Bound To Repaired
Ds Dna
pdb|2WB2|A Chain A, Drosophila Melanogaster (6-4) Photolyase Bound To Double
Stranded Dna Containing A T(6-4)c Photolesion
pdb|3CVV|A Chain A, Drosophila Melanogaster (6-4) Photolyase Bound To Ds Dna
With A T-T (6-4) Photolesion And F0 Cofactor
pdb|2WQ6|A Chain A, Structure Of The 6-4 Photolyase Of D. Melanogaster In
Complex With The Non-Natural N4-Methyl T(Dewar)c Lesion
pdb|2WQ7|A Chain A, Structure Of The 6-4 Photolyase Of D. Melanogaster In
Complex With The Non-Natural N4-Methyl T(6-4)c Lesion
Length = 543
Score = 46.2 bits (108), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 90/412 (21%), Positives = 159/412 (38%), Gaps = 40/412 (9%)
Query: 1 MASLTPPSTAVQPGRIRVLKQGSLDKKRGPVVYWMFRDQRVRDNWALIHAVDQANKNN-- 58
MAS + P K G +D +R +V+W + R+ DN AL H AN
Sbjct: 1 MASWSHPQFEKGASTSLYKKAGLMDSQRSTLVHWFRKGLRLHDNPALSHIFTAANAAPGR 60
Query: 59 ---VPVAVAFNLFDQFLGAKARQLGFMLRGLRLLQRNIEETFQILFFLFQGEAEDNIPNF 115
P+ + ++ A + F+ + L L + + L F+ +G+ + P
Sbjct: 61 YFVRPIFILDPGILDWMQVGANRWRFLQQTLEDLDNQLRKLNSRL-FVVRGKPAEVFPRI 119
Query: 116 VRECGASLLV--TDFSPLREIRRCKDKICNRVSDSVTIHEVDAHNVV-PVWVASEKLEYS 172
+ +L TD P R + + ++ V + +H + P V ++ L +
Sbjct: 120 FKSWRVEMLTFETDIEPYSVTRDAAVQKLAK-AEGVRVETHCSHTIYNPELVIAKNLGKA 178
Query: 173 AKTLRG--------KINKLL--PEYLIDYPMLEQPIEKWTGTRQSIDWDSIIAAVLRKGA 222
T + K+ K+L PE L + P P + + S +D L K
Sbjct: 179 PITYQKFLGIVEQLKVPKVLGVPEKLKNMPT---PPKDEVEQKDSAAYDCPTMKQLVKRP 235
Query: 223 EVPEIGWCESGEDAAMEVLKGS-KDGFLTKRLKNYPTDRNNPLKPRALSGLSPYLHFGQI 281
E GE A+ ++ S KD R + P N L+P + + LSPYL FG +
Sbjct: 236 EELGPNKFPGGETEALRRMEESLKDEIWVARFEK-PNTAPNSLEP-STTVLSPYLKFGCL 293
Query: 282 SAQRCALEARKARKLCPELLYLPATLKAIDTFLEELIVRRELADNFCFYQPNYDSLKGAW 341
SA+ + ++ K P+ P +L ++ RE +PN+D + G
Sbjct: 294 SARLFNQKLKEIIKRQPKHSQPPVSLIG-------QLMWREFYYTVAAAEPNFDRMLGNV 346
Query: 342 EWARKSLKDHASDKREHIYTKEQFEKAQTADPLWNASQMEMVYNGKMHGFMR 393
+ ++H +H+ E + +T P +A ++ G +H R
Sbjct: 347 YCMQIPWQEHP----DHL---EAWTHGRTGYPFIDAIMRQLRQEGWIHHLAR 391
>pdb|3PZP|A Chain A, Human Dna Polymerase Kappa Extending Opposite A Cis-Syn
Thymine Dimer
pdb|3PZP|B Chain B, Human Dna Polymerase Kappa Extending Opposite A Cis-Syn
Thymine Dimer
Length = 517
Score = 32.0 bits (71), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 27/111 (24%), Positives = 53/111 (47%), Gaps = 11/111 (9%)
Query: 253 LKNYPTDRNNPLKPRALSGLSPYLHFGQISAQRCALEARKARKLCPELLYLPATLKAIDT 312
+++ P ++ P+ ++S LS + + R A+ A++LCP+L+ +P
Sbjct: 106 MRDNPELKDKPIAVGSMSMLSTSNYHARRFGVRAAMPGFIAKRLCPQLIIVPP------N 159
Query: 313 FLEELIVRRELADNFCFYQPNY--DSLKGAWEWARKSLKDHAS---DKREH 358
F + V +E+ + Y PN+ SL A+ K L++ + DKR +
Sbjct: 160 FDKYRAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRY 210
>pdb|2OH2|A Chain A, Ternary Complex Of Human Dna Polymerase
pdb|2OH2|B Chain B, Ternary Complex Of Human Dna Polymerase
pdb|2W7O|A Chain A, Structure And Activity Of Bypass Synthesis By Human Dna
Polymerase Kappa Opposite The 7,8-Dihydro-8-
Oxodeoxyguanosine Adduct
pdb|2W7O|B Chain B, Structure And Activity Of Bypass Synthesis By Human Dna
Polymerase Kappa Opposite The 7,8-Dihydro-8-
Oxodeoxyguanosine Adduct
pdb|2W7P|A Chain A, Structure And Activity Of Bypass Synthesis By Human Dna
Polymerase Kappa Opposite The 7,8-Dihydro-8-
Oxodeoxyguanosine Adduct
pdb|2W7P|B Chain B, Structure And Activity Of Bypass Synthesis By Human Dna
Polymerase Kappa Opposite The 7,8-Dihydro-8-
Oxodeoxyguanosine Adduct
pdb|3IN5|A Chain A, Structure Of Human Dna Polymerase Kappa Inserting Datp
Opposite An 8-Oxog Dna Lesion
pdb|3IN5|B Chain B, Structure Of Human Dna Polymerase Kappa Inserting Datp
Opposite An 8-Oxog Dna Lesion
Length = 508
Score = 32.0 bits (71), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 29/111 (26%), Positives = 53/111 (47%), Gaps = 11/111 (9%)
Query: 253 LKNYPTDRNNPLKPRALSGLSPYLHFGQISAQRCALEARKARKLCPELLYLPATLKAIDT 312
+++ P ++ P+ ++S LS + + R A+ A++LCP+L+ +P
Sbjct: 99 MRDNPELKDKPIAVGSMSMLSTSNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRA 158
Query: 313 FLEELIVRRELADNFCFYQPNY--DSLKGAWEWARKSLKDHAS---DKREH 358
+E V+ LAD Y PN+ SL A+ K L++ + DKR +
Sbjct: 159 VSKE--VKEILAD----YDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRY 203
>pdb|1T94|A Chain A, Crystal Structure Of The Catalytic Core Of Human Dna
Polymerase Kappa
pdb|1T94|B Chain B, Crystal Structure Of The Catalytic Core Of Human Dna
Polymerase Kappa
Length = 459
Score = 31.6 bits (70), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 29/111 (26%), Positives = 53/111 (47%), Gaps = 11/111 (9%)
Query: 253 LKNYPTDRNNPLKPRALSGLSPYLHFGQISAQRCALEARKARKLCPELLYLPATLKAIDT 312
+++ P ++ P+ ++S LS + + R A+ A++LCP+L+ +P
Sbjct: 50 MRDNPELKDKPIAVGSMSMLSTSNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRA 109
Query: 313 FLEELIVRRELADNFCFYQPNY--DSLKGAWEWARKSLKDHAS---DKREH 358
+E V+ LAD Y PN+ SL A+ K L++ + DKR +
Sbjct: 110 VSKE--VKEILAD----YDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRY 154
>pdb|1YVG|A Chain A, Structural Analysis Of The Catalytic Domain Of Tetanus
Neurotoxin
Length = 468
Score = 30.4 bits (67), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 354 DKREHIYT-KEQFEKAQTADPLWNASQMEMVYNGKMHGFMRMYWAKK 399
D + IY K QF+K + N + +++YN M+GF + KK
Sbjct: 319 DSYKQIYQQKYQFDKDSNGQYIVNEDKFQILYNSIMYGFTEIELGKK 365
>pdb|1Z7H|A Chain A, 2.3 Angstrom Crystal Structure Of Tetanus Neurotoxin Light
Chain
Length = 447
Score = 30.0 bits (66), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 354 DKREHIYT-KEQFEKAQTADPLWNASQMEMVYNGKMHGFMRMYWAKK 399
D + IY K QF+K + N + +++YN M+GF + KK
Sbjct: 324 DSYKQIYQQKYQFDKDSNGQYIVNEDKFQILYNSIMYGFTEVELGKK 370
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
0.321 0.137 0.428
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,746,610
Number of Sequences: 62578
Number of extensions: 684994
Number of successful extensions: 1461
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1438
Number of HSP's gapped (non-prelim): 21
length of query: 501
length of database: 14,973,337
effective HSP length: 103
effective length of query: 398
effective length of database: 8,527,803
effective search space: 3394065594
effective search space used: 3394065594
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: 53 (25.0 bits)