NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|957760154|gb|ALQ28067|]
View 

DNA topoisomerase 1, partial [Pseudomyrmex fortis]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Topoisom_I_N pfam02919
Eukaryotic DNA topoisomerase I, DNA binding fragment; Topoisomerase I promotes the relaxation ...
 1-200 9.23e-129

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: 364.88  E-value: 9.23e-129
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 957760154    1 PYEPLPPNVKFYYNGKEMKLSQDTEEVATFYARMLDHDYTTKTAFNNNFFTDWRDVMtdAERAKITDLSKCNFKEMHAYF 80
Cdd:pfam02919  16 PYEPLPHNVKLKYDGKPVDLPPEAEEVATFYAAMLETDYAQNPVFNKNFFNDFRKVL--KEKGGIKDFEKCDFSPIYEYF 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 957760154   81 VQKSEERKAMTKEEKQKIKEKNDEIQKEYGFCTIDGHKEKIGNFKIEPPGLFRGRGEHPKMGKLKKRVLPEDVLINCSKD 160
Cdd:pfam02919  94 EQEKEKKKAMSKEEKKALKEEKEKLEEPYGYCLVDGRKEKVGNFRVEPPGLFRGRGEHPKTGKLKKRVQPEDVTINIGKD 173

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 957760154  161 SNIPKPPPGHKWKEVRHDPTVTWLASWTENIQGQVKYVML 200
Cdd:pfam02919 174 APVPEPPPGHKWKEVVHDNTVTWLASWKENINGQFKYVML 213
TOPEUc super family cl42960
DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina ...
 131-284 5.72e-105

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


The actual alignment was detected with superfamily member smart00435:

Pssm-ID: 214661 [Multi-domain]  Cd Length: 391  Bit Score: 311.21  E-value: 5.72e-105
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 957760154   131 LFRGRGEHPKMGKLKKRVLPEDVLINCSKDSNIPKPPPGHKWKEVRHDPTVTWLASWTENIQGQVKYVMLNPSSKLKGEK 210
Cdd:smart00435   1 LFRGRGEHPKTGKLKRRIMPEDITINIGKDAPVPEPPPGHKWKEVRHDNTVTWLASWKENINGSIKYVFLAASSSLKGQS 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 957760154   211 DWQKYETARKLAKSIDKIRAEYREDWKSKEMRIRQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQL 284
Cdd:smart00435  81 DRKKYEKARKLKKHIDKIRKDYTKDLKSKEMKVRQRATALYLIDKLALRAGNEKGEDEADTVGCCSLRVEHVTL 154
 
Name Accession Description Interval E-value
Topoisom_I_N pfam02919
Eukaryotic DNA topoisomerase I, DNA binding fragment; Topoisomerase I promotes the relaxation ...
 1-200 9.23e-129

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: 364.88  E-value: 9.23e-129
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 957760154    1 PYEPLPPNVKFYYNGKEMKLSQDTEEVATFYARMLDHDYTTKTAFNNNFFTDWRDVMtdAERAKITDLSKCNFKEMHAYF 80
Cdd:pfam02919  16 PYEPLPHNVKLKYDGKPVDLPPEAEEVATFYAAMLETDYAQNPVFNKNFFNDFRKVL--KEKGGIKDFEKCDFSPIYEYF 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 957760154   81 VQKSEERKAMTKEEKQKIKEKNDEIQKEYGFCTIDGHKEKIGNFKIEPPGLFRGRGEHPKMGKLKKRVLPEDVLINCSKD 160
Cdd:pfam02919  94 EQEKEKKKAMSKEEKKALKEEKEKLEEPYGYCLVDGRKEKVGNFRVEPPGLFRGRGEHPKTGKLKKRVQPEDVTINIGKD 173

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 957760154  161 SNIPKPPPGHKWKEVRHDPTVTWLASWTENIQGQVKYVML 200
Cdd:pfam02919 174 APVPEPPPGHKWKEVVHDNTVTWLASWKENINGQFKYVML 213
Topoisomer_IB_N_htopoI_like cd03488
Topoisomer_IB_N_htopoI_like : N-terminal DNA binding fragment found in eukaryotic DNA ...
 1-201 2.49e-124

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: 353.57  E-value: 2.49e-124
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 957760154   1 PYEPLPPNVKFYYNGKEMKLSQDTEEVATFYARMLDHDYTTKTAFNNNFFTDWRDVMTDAERAKITDLSKCNFKEMHAYF 80
Cdd:cd03488   15 PYEPLPKNVKFYYDGKPVKLSPEAEEVATFYAKMLEHDYATKEIFQKNFFKDFKKVMTKEEKVIIKDFSKCDFTQMFAYF 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 957760154  81 VQKSEERKAMTKEEKQKIKEKNDEIQKEYGFCTIDGHKEKIGNFKIEPPGLFRGRGEHPKMGKLKKRVLPEDVLINCSKD 160
Cdd:cd03488   95 KAQKEEKKAMSKEEKKAIKAEKEKLEEEYGFCILDGHKEKVGNFRIEPPGLFRGRGAHPKTGKLKRRIMPEDIIINIGKD 174

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 957760154 161 SNIPKPPPGHKWKEVRHDPTVTWLASWTENIQGQVKYVMLN 201
Cdd:cd03488  175 AKVPEPPPGHKWKEVRHDNTVTWLASWTENINGSIKYVMLN 215
TOPEUc smart00435
DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina ...
 131-284 5.72e-105

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: 311.21  E-value: 5.72e-105
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 957760154   131 LFRGRGEHPKMGKLKKRVLPEDVLINCSKDSNIPKPPPGHKWKEVRHDPTVTWLASWTENIQGQVKYVMLNPSSKLKGEK 210
Cdd:smart00435   1 LFRGRGEHPKTGKLKRRIMPEDITINIGKDAPVPEPPPGHKWKEVRHDNTVTWLASWKENINGSIKYVFLAASSSLKGQS 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 957760154   211 DWQKYETARKLAKSIDKIRAEYREDWKSKEMRIRQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQL 284
Cdd:smart00435  81 DRKKYEKARKLKKHIDKIRKDYTKDLKSKEMKVRQRATALYLIDKLALRAGNEKGEDEADTVGCCSLRVEHVTL 154
Topoisom_I pfam01028
Eukaryotic DNA topoisomerase I, catalytic core; Topoisomerase I promotes the relaxation of DNA ...
 203-284 5.09e-55

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: 176.94  E-value: 5.09e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 957760154  203 SSKLKGEKDWQKYETARKLAKSIDKIRAEYREDWKSKEMRIRQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHI 282
Cdd:pfam01028   1 SSKLKGESDWKKYEKARKLKKHIDKIREDYTKDLKSKDMKERQRATAVYLIDKLALRVGNEKDEDEADTVGCCSLRVEHV 80


                  ..
gi 957760154  283 QL 284
Cdd:pfam01028  81 KL 82
Topo_IB_C cd00659
DNA topoisomerase IB, C-terminal catalytic domain; Topoisomerase I promotes the relaxation of ...
 209-286 6.08e-34

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: 122.77  E-value: 6.08e-34
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 957760154 209 EKDWQKYETARKLAKSIDKIRAEYREDWKSKE-MRIRQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLYD 286
Cdd:cd00659    1 ERDAKKFERARRLKKAIPKIRRRYRKDLKSKElMKERQLAVALYLIDKFALRVGNEKYEEENDTVGCCTLRKEHVTLEP 79
 
Name Accession Description Interval E-value
Topoisom_I_N pfam02919
Eukaryotic DNA topoisomerase I, DNA binding fragment; Topoisomerase I promotes the relaxation ...
 1-200 9.23e-129

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: 364.88  E-value: 9.23e-129
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 957760154    1 PYEPLPPNVKFYYNGKEMKLSQDTEEVATFYARMLDHDYTTKTAFNNNFFTDWRDVMtdAERAKITDLSKCNFKEMHAYF 80
Cdd:pfam02919  16 PYEPLPHNVKLKYDGKPVDLPPEAEEVATFYAAMLETDYAQNPVFNKNFFNDFRKVL--KEKGGIKDFEKCDFSPIYEYF 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 957760154   81 VQKSEERKAMTKEEKQKIKEKNDEIQKEYGFCTIDGHKEKIGNFKIEPPGLFRGRGEHPKMGKLKKRVLPEDVLINCSKD 160
Cdd:pfam02919  94 EQEKEKKKAMSKEEKKALKEEKEKLEEPYGYCLVDGRKEKVGNFRVEPPGLFRGRGEHPKTGKLKKRVQPEDVTINIGKD 173

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 957760154  161 SNIPKPPPGHKWKEVRHDPTVTWLASWTENIQGQVKYVML 200
Cdd:pfam02919 174 APVPEPPPGHKWKEVVHDNTVTWLASWKENINGQFKYVML 213
Topoisomer_IB_N_htopoI_like cd03488
Topoisomer_IB_N_htopoI_like : N-terminal DNA binding fragment found in eukaryotic DNA ...
 1-201 2.49e-124

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: 353.57  E-value: 2.49e-124
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 957760154   1 PYEPLPPNVKFYYNGKEMKLSQDTEEVATFYARMLDHDYTTKTAFNNNFFTDWRDVMTDAERAKITDLSKCNFKEMHAYF 80
Cdd:cd03488   15 PYEPLPKNVKFYYDGKPVKLSPEAEEVATFYAKMLEHDYATKEIFQKNFFKDFKKVMTKEEKVIIKDFSKCDFTQMFAYF 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 957760154  81 VQKSEERKAMTKEEKQKIKEKNDEIQKEYGFCTIDGHKEKIGNFKIEPPGLFRGRGEHPKMGKLKKRVLPEDVLINCSKD 160
Cdd:cd03488   95 KAQKEEKKAMSKEEKKAIKAEKEKLEEEYGFCILDGHKEKVGNFRIEPPGLFRGRGAHPKTGKLKRRIMPEDIIINIGKD 174

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 957760154 161 SNIPKPPPGHKWKEVRHDPTVTWLASWTENIQGQVKYVMLN 201
Cdd:cd03488  175 AKVPEPPPGHKWKEVRHDNTVTWLASWTENINGSIKYVMLN 215
Topoisomer_IB_N cd00660
Topoisomer_IB_N: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) ...
 1-201 2.67e-118

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: 338.47  E-value: 2.67e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 957760154   1 PYEPLPPNVKFYYNGKEMKLSQDTEEVATFYARMLDHDYTTKTAFNNNFFTDWRDVMTDAERAKITDLSKCNFKEMHAYF 80
Cdd:cd00660   15 PYEPLPKNVKFYYDGKPVKLPPEAEEVATFFAVMLETDYATKEVFRKNFFKDFRKILTKEEKHIIKKLSKCDFTPIYQYF 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 957760154  81 VQKSEERKAMTKEEKQKIKEKNDEIQKEYGFCTIDGHKEKIGNFKIEPPGLFRGRGEHPKMGKLKKRVLPEDVLINCSKD 160
Cdd:cd00660   95 EEEKEKKKAMSKEEKKAIKEEKEKLEEPYGYCLVDGHKEKVGNFRIEPPGLFRGRGEHPKMGKLKRRIMPEDITINIGKD 174

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 957760154 161 SNIPKPPPGHKWKEVRHDPTVTWLASWTENIQGQVKYVMLN 201
Cdd:cd00660  175 APVPEPPAGHKWKEVRHDNTVTWLASWKENINGQFKYVMLA 215
TOPEUc smart00435
DNA Topoisomerase I (eukaryota); DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina ...
 131-284 5.72e-105

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: 311.21  E-value: 5.72e-105
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 957760154   131 LFRGRGEHPKMGKLKKRVLPEDVLINCSKDSNIPKPPPGHKWKEVRHDPTVTWLASWTENIQGQVKYVMLNPSSKLKGEK 210
Cdd:smart00435   1 LFRGRGEHPKTGKLKRRIMPEDITINIGKDAPVPEPPPGHKWKEVRHDNTVTWLASWKENINGSIKYVFLAASSSLKGQS 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 957760154   211 DWQKYETARKLAKSIDKIRAEYREDWKSKEMRIRQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQL 284
Cdd:smart00435  81 DRKKYEKARKLKKHIDKIRKDYTKDLKSKEMKVRQRATALYLIDKLALRAGNEKGEDEADTVGCCSLRVEHVTL 154
Topoisomer_IB_N_LdtopoI_like cd03489
Topoisomer_IB_N_LdtopoI_like: N-terminal DNA binding fragment found in eukaryotic DNA ...
 1-200 2.99e-68

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: 211.27  E-value: 2.99e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 957760154   1 PYEPlpPNVKFYYNGKEMKLSQDTEEVATFYARMLDHDYTTKTAFNNNFFTDWRDVMtDAERAKITDLSKCNFKEMHAYF 80
Cdd:cd03489   15 PYKP--HGIPILYNGQPFDMTPEEEEVATMFAVMKEHDYYRKEVFRRNFFESWREIL-DKRHHPIRKLELCDFTPIYEWH 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 957760154  81 VQKSEERKAMTKEEKQKIKEKNDEIQKEYGFCTIDGHKEKIGNFKIEPPGLFRGRGEHPKMGKLKKRVLPEDVLINCSKD 160
Cdd:cd03489   92 LREKEKKKSRTKEEKKALKEEKDKEAEPYMWCVWDGVKEQVANFRVEPPGLFRGRGEHPKMGKLKKRIQPEDITINIGKG 171

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 957760154 161 SNIPKPPPGHKWKEVRHDPTVTWLASWTENIQGQVKYVML 200
Cdd:cd03489  172 APIPECPAGHKWKEVKHDNTVTWLAMWRDPIAGNFKYVML 211
Topoisom_I pfam01028
Eukaryotic DNA topoisomerase I, catalytic core; Topoisomerase I promotes the relaxation of DNA ...
 203-284 5.09e-55

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: 176.94  E-value: 5.09e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 957760154  203 SSKLKGEKDWQKYETARKLAKSIDKIRAEYREDWKSKEMRIRQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHI 282
Cdd:pfam01028   1 SSKLKGESDWKKYEKARKLKKHIDKIREDYTKDLKSKDMKERQRATAVYLIDKLALRVGNEKDEDEADTVGCCSLRVEHV 80


                  ..
gi 957760154  283 QL 284
Cdd:pfam01028  81 KL 82
Topoisomer_IB_N_1 cd03490
Topoisomer_IB_N_1: A subgroup of the N-terminal DNA binding fragment found in eukaryotic DNA ...
 1-201 4.53e-49

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: 162.38  E-value: 4.53e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 957760154   1 PYepLPPNVKFYYNGKEMKLSQDTEEVATFYARMLDHDYTTKTAFNNNFFTDW-RDVMTDAERAKITDLSKCNFKEMHAY 79
Cdd:cd03490   15 PY--VPHNVPIMYKGETIHLPPNLEEIATYWAQSMGTNYETKEKFCKNFWKVFvNSFEKDHKFIRRCKLSDADFSLIKNH 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 957760154  80 FVQKSEERKAMTKEEKQKIKEKNDEIQKEYGFCTIDGHKEKIGNFKIEPPGLFRGRGEHPKMGKLKKRVLPEDVLINCSK 159
Cdd:cd03490   93 LEEEKEKKKNLNKEEKEAKKKERAKREYPFNYALVDWIREKVSSNKLEPPGLFKGRGEHPKQGLLKSRIFPEDVILNISK 172

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 957760154 160 DSNIPKPP---PGHKWKEVRHDPTVTWLASWTENIQGQVKYVMLN 201
Cdd:cd03490  173 DAPVPKVTnfmEGHSWKDIYHDNSVTWLAYYKDSINDQFKYMFLS 217
Topo_IB_C cd00659
DNA topoisomerase IB, C-terminal catalytic domain; Topoisomerase I promotes the relaxation of ...
 209-286 6.08e-34

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: 122.77  E-value: 6.08e-34
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 957760154 209 EKDWQKYETARKLAKSIDKIRAEYREDWKSKE-MRIRQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLYD 286
Cdd:cd00659    1 ERDAKKFERARRLKKAIPKIRRRYRKDLKSKElMKERQLAVALYLIDKFALRVGNEKYEEENDTVGCCTLRKEHVTLEP 79
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH