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Conserved domains on  [gi|386764449|ref|NP_001245679|]
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topoisomerase 1, isoform D [Drosophila melanogaster]

Protein Classification

Topoisomer_IB_N_htopoI_like and Topo_IB_C domain-containing protein( domain architecture ID 11556523)

Topoisomer_IB_N_htopoI_like and Topo_IB_C domain-containing protein

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
TOPEUc smart00435
DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina ...
581-942 0e+00

DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras


:

Pssm-ID: 214661 [Multi-domain]  Cd Length: 391  Bit Score: 642.09  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449   581 LFRGRGEHPKMGMIKRRIQASDVSINCGKDSKVPSPPPGSRWKEVRHDNTVTWLASWIENVQGQVKYIMLNPSSKLKGEK 660
Cdd:smart00435   1 LFRGRGEHPKTGKLKRRIMPEDITINIGKDAPVPEPPPGHKWKEVRHDNTVTWLASWKENINGSIKYVFLAASSSLKGQS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449   661 DHIKYETARRLDKVIDKIRATYRDEWKSKEMRVRQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHVQLHkelng 740
Cdd:smart00435  81 DRKKYEKARKLKKHIDKIRKDYTKDLKSKEMKVRQRATALYLIDKLALRAGNEKGEDEADTVGCCSLRVEHVTLK----- 155
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449   741 KENVVVFDFPGKDSIRYYNEVEVEKRVFKNLELFMEHKKEGDDLFDRLNTQVLNEHLKELMEGLTAKVFRTYNASKTLQS 820
Cdd:smart00435 156 PPNKVIFDFLGKDSIRYYNEVEVDKQVFKNLKIFMKPKKPGDDLFDRLNTSKLNKHLKELMPGLTAKVFRTYNASITLQE 235
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449   821 QLDLLTDPSATVPEKLLAYNRANRAVAILCNHQRSVPKSHEKSMENLKEKIKAKREAIEKC-------------ESEYHS 887
Cdd:smart00435 236 QLKELTAKDGNVAEKILAYNRANREVAILCNHQRTVSKTHEKSMEKLQEKIKALKYQLKRLkkmillfemisdlKRKLKS 315
                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 386764449   888 RD---------------------EKKGKQLERLRDQLKKLELQETDRDENKTIALGTSKLNYLDPRISVAWCKKHD 942
Cdd:smart00435 316 KFerdnekldaevkekkkekkkeEKKKKQIERLEERIEKLEVQATDKEENKTVALGTSKINYIDPRITVAWCKKFD 391
Topoisomer_IB_N_htopoI_like cd03488
Topoisomer_IB_N_htopoI_like : N-terminal DNA binding fragment found in eukaryotic DNA ...
437-651 2.13e-139

Topoisomer_IB_N_htopoI_like : N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit religation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. This family may represent more than one structural domain.


:

Pssm-ID: 239570  Cd Length: 215  Bit Score: 415.20  E-value: 2.13e-139
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449 437 KWSTLEHKGPVFAPRYERVPRNVRFYYDGKPLELSEETEEAATFYAKMLNHDYCTKEVFNNNFFKDFRKSMTPREREIIK 516
Cdd:cd03488    1 KWTTLEHNGPVFAPPYEPLPKNVKFYYDGKPVKLSPEAEEVATFYAKMLEHDYATKEIFQKNFFKDFKKVMTKEEKVIIK 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449 517 DFRKCNFQEMFNYFQAESEKRKAASKEEKLIKKNENEALMKEFGFCMIDGHKEKIGNFRLEPPGLFRGRGEHPKMGMIKR 596
Cdd:cd03488   81 DFSKCDFTQMFAYFKAQKEEKKAMSKEEKKAIKAEKEKLEEEYGFCILDGHKEKVGNFRIEPPGLFRGRGAHPKTGKLKR 160
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 386764449 597 RIQASDVSINCGKDSKVPSPPPGSRWKEVRHDNTVTWLASWIENVQGQVKYIMLN 651
Cdd:cd03488  161 RIMPEDIIINIGKDAKVPEPPPGHKWKEVRHDNTVTWLASWTENINGSIKYVMLN 215
 
Name Accession Description Interval E-value
TOPEUc smart00435
DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina ...
581-942 0e+00

DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras


Pssm-ID: 214661 [Multi-domain]  Cd Length: 391  Bit Score: 642.09  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449   581 LFRGRGEHPKMGMIKRRIQASDVSINCGKDSKVPSPPPGSRWKEVRHDNTVTWLASWIENVQGQVKYIMLNPSSKLKGEK 660
Cdd:smart00435   1 LFRGRGEHPKTGKLKRRIMPEDITINIGKDAPVPEPPPGHKWKEVRHDNTVTWLASWKENINGSIKYVFLAASSSLKGQS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449   661 DHIKYETARRLDKVIDKIRATYRDEWKSKEMRVRQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHVQLHkelng 740
Cdd:smart00435  81 DRKKYEKARKLKKHIDKIRKDYTKDLKSKEMKVRQRATALYLIDKLALRAGNEKGEDEADTVGCCSLRVEHVTLK----- 155
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449   741 KENVVVFDFPGKDSIRYYNEVEVEKRVFKNLELFMEHKKEGDDLFDRLNTQVLNEHLKELMEGLTAKVFRTYNASKTLQS 820
Cdd:smart00435 156 PPNKVIFDFLGKDSIRYYNEVEVDKQVFKNLKIFMKPKKPGDDLFDRLNTSKLNKHLKELMPGLTAKVFRTYNASITLQE 235
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449   821 QLDLLTDPSATVPEKLLAYNRANRAVAILCNHQRSVPKSHEKSMENLKEKIKAKREAIEKC-------------ESEYHS 887
Cdd:smart00435 236 QLKELTAKDGNVAEKILAYNRANREVAILCNHQRTVSKTHEKSMEKLQEKIKALKYQLKRLkkmillfemisdlKRKLKS 315
                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 386764449   888 RD---------------------EKKGKQLERLRDQLKKLELQETDRDENKTIALGTSKLNYLDPRISVAWCKKHD 942
Cdd:smart00435 316 KFerdnekldaevkekkkekkkeEKKKKQIERLEERIEKLEVQATDKEENKTVALGTSKINYIDPRITVAWCKKFD 391
Topoisomer_IB_N_htopoI_like cd03488
Topoisomer_IB_N_htopoI_like : N-terminal DNA binding fragment found in eukaryotic DNA ...
437-651 2.13e-139

Topoisomer_IB_N_htopoI_like : N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit religation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. This family may represent more than one structural domain.


Pssm-ID: 239570  Cd Length: 215  Bit Score: 415.20  E-value: 2.13e-139
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449 437 KWSTLEHKGPVFAPRYERVPRNVRFYYDGKPLELSEETEEAATFYAKMLNHDYCTKEVFNNNFFKDFRKSMTPREREIIK 516
Cdd:cd03488    1 KWTTLEHNGPVFAPPYEPLPKNVKFYYDGKPVKLSPEAEEVATFYAKMLEHDYATKEIFQKNFFKDFKKVMTKEEKVIIK 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449 517 DFRKCNFQEMFNYFQAESEKRKAASKEEKLIKKNENEALMKEFGFCMIDGHKEKIGNFRLEPPGLFRGRGEHPKMGMIKR 596
Cdd:cd03488   81 DFSKCDFTQMFAYFKAQKEEKKAMSKEEKKAIKAEKEKLEEEYGFCILDGHKEKVGNFRIEPPGLFRGRGAHPKTGKLKR 160
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 386764449 597 RIQASDVSINCGKDSKVPSPPPGSRWKEVRHDNTVTWLASWIENVQGQVKYIMLN 651
Cdd:cd03488  161 RIMPEDIIINIGKDAKVPEPPPGHKWKEVRHDNTVTWLASWTENINGSIKYVMLN 215
Topoisom_I_N pfam02919
Eukaryotic DNA topoisomerase I, DNA binding fragment; Topoisomerase I promotes the relaxation ...
436-650 1.85e-135

Eukaryotic DNA topoisomerase I, DNA binding fragment; Topoisomerase I promotes the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination. This family may be more than one structural domain.


Pssm-ID: 460746  Cd Length: 213  Bit Score: 404.94  E-value: 1.85e-135
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449  436 VKWSTLEHKGPVFAPRYERVPRNVRFYYDGKPLELSEETEEAATFYAKMLNHDYCTKEVFNNNFFKDFRKSMtpREREII 515
Cdd:pfam02919   1 IKWTTLEHNGVLFPPPYEPLPHNVKLKYDGKPVDLPPEAEEVATFYAAMLETDYAQNPVFNKNFFNDFRKVL--KEKGGI 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449  516 KDFRKCNFQEMFNYFQAESEKRKAASKEEKLIKKNENEALMKEFGFCMIDGHKEKIGNFRLEPPGLFRGRGEHPKMGMIK 595
Cdd:pfam02919  79 KDFEKCDFSPIYEYFEQEKEKKKAMSKEEKKALKEEKEKLEEPYGYCLVDGRKEKVGNFRVEPPGLFRGRGEHPKTGKLK 158
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 386764449  596 RRIQASDVSINCGKDSKVPSPPPGSRWKEVRHDNTVTWLASWIENVQGQVKYIML 650
Cdd:pfam02919 159 KRVQPEDVTINIGKDAPVPEPPPGHKWKEVVHDNTVTWLASWKENINGQFKYVML 213
Topoisom_I pfam01028
Eukaryotic DNA topoisomerase I, catalytic core; Topoisomerase I promotes the relaxation of DNA ...
653-855 3.40e-124

Eukaryotic DNA topoisomerase I, catalytic core; Topoisomerase I promotes the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination.


Pssm-ID: 460030 [Multi-domain]  Cd Length: 198  Bit Score: 374.93  E-value: 3.40e-124
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449  653 SSKLKGEKDHIKYETARRLDKVIDKIRATYRDEWKSKEMRVRQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHV 732
Cdd:pfam01028   1 SSKLKGESDWKKYEKARKLKKHIDKIREDYTKDLKSKDMKERQRATAVYLIDKLALRVGNEKDEDEADTVGCCSLRVEHV 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449  733 QLHKElngkeNVVVFDFPGKDSIRYYNEVEVEKRVFKNLELFMEHKKEGDDLFDRLNTQVLNEHLKELMEGLTAKVFRTY 812
Cdd:pfam01028  81 KLHPP-----NTVEFDFLGKDSIRYYNTVEVDLQVFKNLKIFKKNKKPGDDLFDRLNTSKLNKYLKELMPGLTAKVFRTY 155
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 386764449  813 NASKTLQSQLDLLTDPSATVPEKLLAYNRANRAVAILCNHQRS 855
Cdd:pfam01028 156 NASITLQEQLKELVPKEGSVAEKLLAYNRANREVAILCNHQRS 198
Topo_IB_C cd00659
DNA topoisomerase IB, C-terminal catalytic domain; Topoisomerase I promotes the relaxation of ...
659-858 1.59e-88

DNA topoisomerase IB, C-terminal catalytic domain; Topoisomerase I promotes the relaxation of both positive and negative DNA superhelical tension by introducing a transient single-stranded break in duplex DNA. This function is vital for the processes of replication, transcription, and recombination. Unlike Topo IA enzymes, Topo IB enzymes do not require a single-stranded region of DNA or metal ions for their function. The type IB family of DNA topoisomerases includes eukaryotic nuclear topoisomerase I, topoisomerases of poxviruses, and bacterial versions of Topo IB. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their C-terminal catalytic domain and the overall reaction mechanism with tyrosine recombinases. The C-terminal catalytic domain in topoisomerases is linked to a divergent N-terminal domain that shows no sequence or structure similarity to the N-terminal domains of tyrosine recombinases.


Pssm-ID: 271176 [Multi-domain]  Cd Length: 210  Bit Score: 281.47  E-value: 1.59e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449 659 EKDHIKYETARRLDKVIDKIRATYRDEWKSKE-MRVRQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHVQLHKe 737
Cdd:cd00659    1 ERDAKKFERARRLKKAIPKIRRRYRKDLKSKElMKERQLAVALYLIDKFALRVGNEKYEEENDTVGCCTLRKEHVTLEP- 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449 738 lngkeNVVVFDFPGKDSIRYYNEVEVEKRVFKNLELFMehKKEGDDLFD-----RLNTQVLNEHLKELMEGLTAKVFRTY 812
Cdd:cd00659   80 -----NVVEFDFLGKDSIRYYNEVPVDPRVFKNLKIFM--KLPGDDLFDyvdvrRLNTSKLNAYLRELMGGLTAKDFRTY 152
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 386764449 813 NASKTLQSQLDLLTDPSATVPEKLLAYNRANRAVAILCNHQRSVPK 858
Cdd:cd00659  153 GASLTLQQQLKELTAPDSNIPAKKKVYNRANRAVAILCNHTPAVSK 198
Top1 COG3569
DNA topoisomerase IB [Replication, recombination and repair];
661-815 1.06e-09

DNA topoisomerase IB [Replication, recombination and repair];


Pssm-ID: 442790  Cd Length: 345  Bit Score: 61.34  E-value: 1.06e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449 661 DHIKYETARRLDKVIDKIRATYRDEWKSKEMRvRQRAVALYF--IDKLALRAGNEKDEDQADTVGCCSLRVEHVQLHKel 738
Cdd:COG3569   95 DETKFDRLLAFGRALPRIRRRVARDLRRRGLP-REKVLAAVVrlLDRTLIRVGNEEYARENGSYGLTTLRKRHVKVDG-- 171
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449 739 ngkeNVVVFDFPGKDSIRyyNEVEVE-KRVFKNLELFMEHKkeGDDLFD---------RLNTQVLNEHLKELM-EGLTAK 807
Cdd:COG3569  172 ----DTVRFRFRGKSGKE--HEVTLRdRRLARLVRRLQDLP--GQELFQyrdedgerhPVDSGDVNAYLREITgEDFTAK 243

                 ....*...
gi 386764449 808 VFRTYNAS 815
Cdd:COG3569  244 DFRTWAGT 251
PHA03101 PHA03101
DNA topoisomerase type I; Provisional
660-818 1.31e-03

DNA topoisomerase type I; Provisional


Pssm-ID: 222985 [Multi-domain]  Cd Length: 314  Bit Score: 41.89  E-value: 1.31e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449 660 KDHIKYETARR------LDKVIDKIRATYRDEWKSKEMRV--RQRAVAL-----YFIdklalRAGNEKDEDQADTVGCCS 726
Cdd:PHA03101  74 KLHVKNRNANRdkifvrVHNVIKKINCFIDKNIKIKKKNDvnFQLAVFLlmetsFFI-----RTGKMKYLKENETVGLLT 148
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449 727 LRVEHVQLhkelngKENVVVFDFPGKDSIRYYNEVEVEKRVFKNLELFMEHKKEGDDLFDRLNTQVLNEHLKelMEGLTA 806
Cdd:PHA03101 149 LKNKHITI------SNDKILIKFVGKDKVSHEFVVHKSNRLYKPLLKLIDKTNPDDFLFNKLSERKVYKFMK--QFGIRL 220
                        170
                 ....*....|..
gi 386764449 807 KVFRTYNASKTL 818
Cdd:PHA03101 221 KDLRTYGVNYTF 232
 
Name Accession Description Interval E-value
TOPEUc smart00435
DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina ...
581-942 0e+00

DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras


Pssm-ID: 214661 [Multi-domain]  Cd Length: 391  Bit Score: 642.09  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449   581 LFRGRGEHPKMGMIKRRIQASDVSINCGKDSKVPSPPPGSRWKEVRHDNTVTWLASWIENVQGQVKYIMLNPSSKLKGEK 660
Cdd:smart00435   1 LFRGRGEHPKTGKLKRRIMPEDITINIGKDAPVPEPPPGHKWKEVRHDNTVTWLASWKENINGSIKYVFLAASSSLKGQS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449   661 DHIKYETARRLDKVIDKIRATYRDEWKSKEMRVRQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHVQLHkelng 740
Cdd:smart00435  81 DRKKYEKARKLKKHIDKIRKDYTKDLKSKEMKVRQRATALYLIDKLALRAGNEKGEDEADTVGCCSLRVEHVTLK----- 155
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449   741 KENVVVFDFPGKDSIRYYNEVEVEKRVFKNLELFMEHKKEGDDLFDRLNTQVLNEHLKELMEGLTAKVFRTYNASKTLQS 820
Cdd:smart00435 156 PPNKVIFDFLGKDSIRYYNEVEVDKQVFKNLKIFMKPKKPGDDLFDRLNTSKLNKHLKELMPGLTAKVFRTYNASITLQE 235
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449   821 QLDLLTDPSATVPEKLLAYNRANRAVAILCNHQRSVPKSHEKSMENLKEKIKAKREAIEKC-------------ESEYHS 887
Cdd:smart00435 236 QLKELTAKDGNVAEKILAYNRANREVAILCNHQRTVSKTHEKSMEKLQEKIKALKYQLKRLkkmillfemisdlKRKLKS 315
                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 386764449   888 RD---------------------EKKGKQLERLRDQLKKLELQETDRDENKTIALGTSKLNYLDPRISVAWCKKHD 942
Cdd:smart00435 316 KFerdnekldaevkekkkekkkeEKKKKQIERLEERIEKLEVQATDKEENKTVALGTSKINYIDPRITVAWCKKFD 391
Topoisomer_IB_N_htopoI_like cd03488
Topoisomer_IB_N_htopoI_like : N-terminal DNA binding fragment found in eukaryotic DNA ...
437-651 2.13e-139

Topoisomer_IB_N_htopoI_like : N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit religation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. This family may represent more than one structural domain.


Pssm-ID: 239570  Cd Length: 215  Bit Score: 415.20  E-value: 2.13e-139
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449 437 KWSTLEHKGPVFAPRYERVPRNVRFYYDGKPLELSEETEEAATFYAKMLNHDYCTKEVFNNNFFKDFRKSMTPREREIIK 516
Cdd:cd03488    1 KWTTLEHNGPVFAPPYEPLPKNVKFYYDGKPVKLSPEAEEVATFYAKMLEHDYATKEIFQKNFFKDFKKVMTKEEKVIIK 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449 517 DFRKCNFQEMFNYFQAESEKRKAASKEEKLIKKNENEALMKEFGFCMIDGHKEKIGNFRLEPPGLFRGRGEHPKMGMIKR 596
Cdd:cd03488   81 DFSKCDFTQMFAYFKAQKEEKKAMSKEEKKAIKAEKEKLEEEYGFCILDGHKEKVGNFRIEPPGLFRGRGAHPKTGKLKR 160
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 386764449 597 RIQASDVSINCGKDSKVPSPPPGSRWKEVRHDNTVTWLASWIENVQGQVKYIMLN 651
Cdd:cd03488  161 RIMPEDIIINIGKDAKVPEPPPGHKWKEVRHDNTVTWLASWTENINGSIKYVMLN 215
Topoisom_I_N pfam02919
Eukaryotic DNA topoisomerase I, DNA binding fragment; Topoisomerase I promotes the relaxation ...
436-650 1.85e-135

Eukaryotic DNA topoisomerase I, DNA binding fragment; Topoisomerase I promotes the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination. This family may be more than one structural domain.


Pssm-ID: 460746  Cd Length: 213  Bit Score: 404.94  E-value: 1.85e-135
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449  436 VKWSTLEHKGPVFAPRYERVPRNVRFYYDGKPLELSEETEEAATFYAKMLNHDYCTKEVFNNNFFKDFRKSMtpREREII 515
Cdd:pfam02919   1 IKWTTLEHNGVLFPPPYEPLPHNVKLKYDGKPVDLPPEAEEVATFYAAMLETDYAQNPVFNKNFFNDFRKVL--KEKGGI 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449  516 KDFRKCNFQEMFNYFQAESEKRKAASKEEKLIKKNENEALMKEFGFCMIDGHKEKIGNFRLEPPGLFRGRGEHPKMGMIK 595
Cdd:pfam02919  79 KDFEKCDFSPIYEYFEQEKEKKKAMSKEEKKALKEEKEKLEEPYGYCLVDGRKEKVGNFRVEPPGLFRGRGEHPKTGKLK 158
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 386764449  596 RRIQASDVSINCGKDSKVPSPPPGSRWKEVRHDNTVTWLASWIENVQGQVKYIML 650
Cdd:pfam02919 159 KRVQPEDVTINIGKDAPVPEPPPGHKWKEVVHDNTVTWLASWKENINGQFKYVML 213
Topoisomer_IB_N cd00660
Topoisomer_IB_N: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) ...
437-651 9.84e-133

Topoisomer_IB_N: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit re-ligation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanosomatid parasite topo I differ from human topo I in their sensitivity to CPTs and other classical topo I inhibitors. Trypanosomatid topos I play putative roles in organizing the kinetoplast DNA network unique to these parasites. This family may represent more than one structural domain.


Pssm-ID: 238356  Cd Length: 215  Bit Score: 397.79  E-value: 9.84e-133
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449 437 KWSTLEHKGPVFAPRYERVPRNVRFYYDGKPLELSEETEEAATFYAKMLNHDYCTKEVFNNNFFKDFRKSMTPREREIIK 516
Cdd:cd00660    1 KWTTLEHNGVIFPPPYEPLPKNVKFYYDGKPVKLPPEAEEVATFFAVMLETDYATKEVFRKNFFKDFRKILTKEEKHIIK 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449 517 DFRKCNFQEMFNYFQAESEKRKAASKEEKLIKKNENEALMKEFGFCMIDGHKEKIGNFRLEPPGLFRGRGEHPKMGMIKR 596
Cdd:cd00660   81 KLSKCDFTPIYQYFEEEKEKKKAMSKEEKKAIKEEKEKLEEPYGYCLVDGHKEKVGNFRIEPPGLFRGRGEHPKMGKLKR 160
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 386764449 597 RIQASDVSINCGKDSKVPSPPPGSRWKEVRHDNTVTWLASWIENVQGQVKYIMLN 651
Cdd:cd00660  161 RIMPEDITINIGKDAPVPEPPAGHKWKEVRHDNTVTWLASWKENINGQFKYVMLA 215
Topoisom_I pfam01028
Eukaryotic DNA topoisomerase I, catalytic core; Topoisomerase I promotes the relaxation of DNA ...
653-855 3.40e-124

Eukaryotic DNA topoisomerase I, catalytic core; Topoisomerase I promotes the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination.


Pssm-ID: 460030 [Multi-domain]  Cd Length: 198  Bit Score: 374.93  E-value: 3.40e-124
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449  653 SSKLKGEKDHIKYETARRLDKVIDKIRATYRDEWKSKEMRVRQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHV 732
Cdd:pfam01028   1 SSKLKGESDWKKYEKARKLKKHIDKIREDYTKDLKSKDMKERQRATAVYLIDKLALRVGNEKDEDEADTVGCCSLRVEHV 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449  733 QLHKElngkeNVVVFDFPGKDSIRYYNEVEVEKRVFKNLELFMEHKKEGDDLFDRLNTQVLNEHLKELMEGLTAKVFRTY 812
Cdd:pfam01028  81 KLHPP-----NTVEFDFLGKDSIRYYNTVEVDLQVFKNLKIFKKNKKPGDDLFDRLNTSKLNKYLKELMPGLTAKVFRTY 155
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 386764449  813 NASKTLQSQLDLLTDPSATVPEKLLAYNRANRAVAILCNHQRS 855
Cdd:pfam01028 156 NASITLQEQLKELVPKEGSVAEKLLAYNRANREVAILCNHQRS 198
Topo_IB_C cd00659
DNA topoisomerase IB, C-terminal catalytic domain; Topoisomerase I promotes the relaxation of ...
659-858 1.59e-88

DNA topoisomerase IB, C-terminal catalytic domain; Topoisomerase I promotes the relaxation of both positive and negative DNA superhelical tension by introducing a transient single-stranded break in duplex DNA. This function is vital for the processes of replication, transcription, and recombination. Unlike Topo IA enzymes, Topo IB enzymes do not require a single-stranded region of DNA or metal ions for their function. The type IB family of DNA topoisomerases includes eukaryotic nuclear topoisomerase I, topoisomerases of poxviruses, and bacterial versions of Topo IB. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their C-terminal catalytic domain and the overall reaction mechanism with tyrosine recombinases. The C-terminal catalytic domain in topoisomerases is linked to a divergent N-terminal domain that shows no sequence or structure similarity to the N-terminal domains of tyrosine recombinases.


Pssm-ID: 271176 [Multi-domain]  Cd Length: 210  Bit Score: 281.47  E-value: 1.59e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449 659 EKDHIKYETARRLDKVIDKIRATYRDEWKSKE-MRVRQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHVQLHKe 737
Cdd:cd00659    1 ERDAKKFERARRLKKAIPKIRRRYRKDLKSKElMKERQLAVALYLIDKFALRVGNEKYEEENDTVGCCTLRKEHVTLEP- 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449 738 lngkeNVVVFDFPGKDSIRYYNEVEVEKRVFKNLELFMehKKEGDDLFD-----RLNTQVLNEHLKELMEGLTAKVFRTY 812
Cdd:cd00659   80 -----NVVEFDFLGKDSIRYYNEVPVDPRVFKNLKIFM--KLPGDDLFDyvdvrRLNTSKLNAYLRELMGGLTAKDFRTY 152
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 386764449 813 NASKTLQSQLDLLTDPSATVPEKLLAYNRANRAVAILCNHQRSVPK 858
Cdd:cd00659  153 GASLTLQQQLKELTAPDSNIPAKKKVYNRANRAVAILCNHTPAVSK 198
Topoisomer_IB_N_LdtopoI_like cd03489
Topoisomer_IB_N_LdtopoI_like: N-terminal DNA binding fragment found in eukaryotic DNA ...
437-650 4.27e-70

Topoisomer_IB_N_LdtopoI_like: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit re-ligation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanosomatid parasite topo I differ from human topo I in their sensitivity to CPTs and other classical topo I inhibitors. Trypanosomatid topo I play putative roles in organizing the kinetoplast DNA network unique to these parasites. This family may represent more than one structural domain.


Pssm-ID: 239571  Cd Length: 212  Bit Score: 231.69  E-value: 4.27e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449 437 KWSTLEHKGPVFAPRYErvPRNVRFYYDGKPLELSEETEEAATFYAKMLNHDYCTKEVFNNNFFKDFRKSMTPReREIIK 516
Cdd:cd03489    1 RWTTLVHNGVLFPPPYK--PHGIPILYNGQPFDMTPEEEEVATMFAVMKEHDYYRKEVFRRNFFESWREILDKR-HHPIR 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449 517 DFRKCNFQEMFNYFQAESEKRKAASKEEKLIKKNENEALMKEFGFCMIDGHKEKIGNFRLEPPGLFRGRGEHPKMGMIKR 596
Cdd:cd03489   78 KLELCDFTPIYEWHLREKEKKKSRTKEEKKALKEEKDKEAEPYMWCVWDGVKEQVANFRVEPPGLFRGRGEHPKMGKLKK 157
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 386764449 597 RIQASDVSINCGKDSKVPSPPPGSRWKEVRHDNTVTWLASWIENVQGQVKYIML 650
Cdd:cd03489  158 RIQPEDITINIGKGAPIPECPAGHKWKEVKHDNTVTWLAMWRDPIAGNFKYVML 211
Topoisomer_IB_N_1 cd03490
Topoisomer_IB_N_1: A subgroup of the N-terminal DNA binding fragment found in eukaryotic DNA ...
437-651 1.10e-56

Topoisomer_IB_N_1: A subgroup of the N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB. Topo IB proteins include the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit religation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanosomatid parasite topos I differ from human topo I in their sensitivity to CPTs and other classical topo I inhibitors. Trypanosomatid topos I have putative roles in organizing the kinetoplast DNA network unique to these parasites. This family may represent more than one structural domain.


Pssm-ID: 239572  Cd Length: 217  Bit Score: 194.74  E-value: 1.10e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449 437 KWSTLEHKGPVFAPRYerVPRNVRFYYDGKPLELSEETEEAATFYAKMLNHDYCTKEVFNNNFFKDFRKSMTPREREI-I 515
Cdd:cd03490    1 QWKYLEHNGMIFTPPY--VPHNVPIMYKGETIHLPPNLEEIATYWAQSMGTNYETKEKFCKNFWKVFVNSFEKDHKFIrR 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449 516 KDFRKCNFQEMFNYFQAESEKRKAASKEEKLIKKNENEALMKEFGFCMIDGHKEKIGNFRLEPPGLFRGRGEHPKMGMIK 595
Cdd:cd03490   79 CKLSDADFSLIKNHLEEEKEKKKNLNKEEKEAKKKERAKREYPFNYALVDWIREKVSSNKLEPPGLFKGRGEHPKQGLLK 158
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 386764449 596 RRIQASDVSINCGKDSKVPSPP---PGSRWKEVRHDNTVTWLASWIENVQGQVKYIMLN 651
Cdd:cd03490  159 SRIFPEDVILNISKDAPVPKVTnfmEGHSWKDIYHDNSVTWLAYYKDSINDQFKYMFLS 217
Topo_C_assoc pfam14370
C-terminal topoisomerase domain; This domain is found at the C-terminal of topoisomerase and ...
900-968 6.26e-36

C-terminal topoisomerase domain; This domain is found at the C-terminal of topoisomerase and other similar enzymes.


Pssm-ID: 464154 [Multi-domain]  Cd Length: 68  Bit Score: 129.99  E-value: 6.26e-36
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 386764449  900 RDQLKKLELQETDRDENKTIALGTSKLNYLDPRISVAWCKKHDVPIEKIFNKTQRTKFLWAVHmADENY 968
Cdd:pfam14370   1 KERIKKLELQLKDKEENKTVALGTSKINYIDPRITVAWCKKHDVPIEKIFSKTLREKFPWAMD-VDPDW 68
Top1 COG3569
DNA topoisomerase IB [Replication, recombination and repair];
661-815 1.06e-09

DNA topoisomerase IB [Replication, recombination and repair];


Pssm-ID: 442790  Cd Length: 345  Bit Score: 61.34  E-value: 1.06e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449 661 DHIKYETARRLDKVIDKIRATYRDEWKSKEMRvRQRAVALYF--IDKLALRAGNEKDEDQADTVGCCSLRVEHVQLHKel 738
Cdd:COG3569   95 DETKFDRLLAFGRALPRIRRRVARDLRRRGLP-REKVLAAVVrlLDRTLIRVGNEEYARENGSYGLTTLRKRHVKVDG-- 171
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449 739 ngkeNVVVFDFPGKDSIRyyNEVEVE-KRVFKNLELFMEHKkeGDDLFD---------RLNTQVLNEHLKELM-EGLTAK 807
Cdd:COG3569  172 ----DTVRFRFRGKSGKE--HEVTLRdRRLARLVRRLQDLP--GQELFQyrdedgerhPVDSGDVNAYLREITgEDFTAK 243

                 ....*...
gi 386764449 808 VFRTYNAS 815
Cdd:COG3569  244 DFRTWAGT 251
PHA03101 PHA03101
DNA topoisomerase type I; Provisional
660-818 1.31e-03

DNA topoisomerase type I; Provisional


Pssm-ID: 222985 [Multi-domain]  Cd Length: 314  Bit Score: 41.89  E-value: 1.31e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449 660 KDHIKYETARR------LDKVIDKIRATYRDEWKSKEMRV--RQRAVAL-----YFIdklalRAGNEKDEDQADTVGCCS 726
Cdd:PHA03101  74 KLHVKNRNANRdkifvrVHNVIKKINCFIDKNIKIKKKNDvnFQLAVFLlmetsFFI-----RTGKMKYLKENETVGLLT 148
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386764449 727 LRVEHVQLhkelngKENVVVFDFPGKDSIRYYNEVEVEKRVFKNLELFMEHKKEGDDLFDRLNTQVLNEHLKelMEGLTA 806
Cdd:PHA03101 149 LKNKHITI------SNDKILIKFVGKDKVSHEFVVHKSNRLYKPLLKLIDKTNPDDFLFNKLSERKVYKFMK--QFGIRL 220
                        170
                 ....*....|..
gi 386764449 807 KVFRTYNASKTL 818
Cdd:PHA03101 221 KDLRTYGVNYTF 232
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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