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Conserved domains on  [gi|1958664790|ref|XP_038943991|]
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DNA topoisomerase 3-beta-1 isoform X2 [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TOP1Ac super family cl30544
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
 29-163 1.72e-44

DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.


The actual alignment was detected with superfamily member cd00186:

Pssm-ID: 357420 [Multi-domain]  Cd Length: 381  Bit Score: 158.92  E-value: 1.72e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790  29 QSVPLEESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEnGRRLKPT 108
Cdd:cd00186   248 EKDDEEEEPPPLKEGDELKLEEVELEEKETQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKE-KKKLIPT 326

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958664790 109 NLGIVLVHGYHKIDAELVLPTIRSAVEKQLNLIAQGKANYHQVLGHTLDIFKRKF 163
Cdd:cd00186   327 ELGFAVIELLEKHFPELVDPEFTAKLEEKLDEIAEGKKDYQEVLEEFYEEFKKIV 381
 
Name Accession Description Interval E-value
TOP1Ac cd00186
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
 29-163 1.72e-44

DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.


Pssm-ID: 238110 [Multi-domain]  Cd Length: 381  Bit Score: 158.92  E-value: 1.72e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790  29 QSVPLEESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEnGRRLKPT 108
Cdd:cd00186   248 EKDDEEEEPPPLKEGDELKLEEVELEEKETQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKE-KKKLIPT 326

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958664790 109 NLGIVLVHGYHKIDAELVLPTIRSAVEKQLNLIAQGKANYHQVLGHTLDIFKRKF 163
Cdd:cd00186   327 ELGFAVIELLEKHFPELVDPEFTAKLEEKLDEIAEGKKDYQEVLEEFYEEFKKIV 381
Topoisom_bac pfam01131
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ...
 34-152 5.88e-40

DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes preferentially relax negatively supercoiled DNA, from a 5' phospho- tyrosine linkage in the enzyme-DNA covalent intermediate and has high affinity for single stranded DNA.


Pssm-ID: 426069 [Multi-domain]  Cd Length: 410  Bit Score: 147.39  E-value: 5.88e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790  34 EESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEnGRRLKPTNLGIV 113
Cdd:pfam01131 293 EEELPELKEGEELKVTQVEVEEKKTKPPPRYTEASLIKAMEKAGIGTPATRATIIETLLERGYVERK-KKSLVPTELGKA 371

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1958664790 114 LVHGYHKIDaELVLPTIRSAVEKQLNLIAQGKANYHQVL 152
Cdd:pfam01131 372 LVEALEKFP-DLVDPELTAELEEKLDEIAEGKLDWKDVL 409
TOP1Ac smart00437
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ...
 22-114 2.45e-34

Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit


Pssm-ID: 214663 [Multi-domain]  Cd Length: 259  Bit Score: 128.52  E-value: 2.45e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790   22 WERQLFPQSVPLEESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEn 101
Cdd:smart00437 168 WLKVYPEEKKEEEIELPTLKKGDELKVEEVEVEEKETKPPARYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVTKK- 246

                           90
                   ....*....|...
gi 1958664790  102 GRRLKPTNLGIVL 114
Cdd:smart00437 247 KKKLIPTELGIAV 259
PRK07219 PRK07219
DNA topoisomerase I; Validated
 25-261 5.03e-27

DNA topoisomerase I; Validated


Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 113.94  E-value: 5.03e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790  25 QLFPQSVPLEESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTveNGRR 104
Cdd:PRK07219  438 EVYPYEKFDEKELPDLEEGEKLKVNKIEIEAKETQPPKRYTQSSLIKEMEKRGLGTKATRHDIIEKLYKRGYVI--EGDP 515

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790 105 LKPTNLGIVLVHGYHKIDAELVLPTIRSAVEKQLNLIAQGKANYHQVLGHTLDIFKRKFHYFVDSIAGM-DELMEvSFSP 183
Cdd:PRK07219  516 PRPTDLGIAVIEALEKYAPEIVSEEMTAQLEADMQAIEDGKKKKEDVTEESREMLKEILSELKEKRKEIgDHLAG-SLKA 594

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790 184 LAATGKPLSRCGKCHRFMKYIQAKPSR--LHCS---HCDETYTLPQNGTIKLYKELrCPLDDFELVLWssgSRGKSYPL- 257
Cdd:PRK07219  595 ENRSLKTIGKCPECGGDLIIIRTDKGSrfVGCSgypDCRNTFPLPSTGRIKVLDEV-CEKCGLPVIKI---LRGKQTFVv 670


                  ....*
gi 1958664790 258 -CPYC 261
Cdd:PRK07219  671 gCPDC 675
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
34-164 1.40e-23

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 440316 [Multi-domain]  Cd Length: 541  Bit Score: 102.87  E-value: 1.40e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790  34 EESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIG---TDASIpvhINNICQRNYVTVEnGRRLKPTNL 110
Cdd:COG0550   412 EKRLPPLKEGEKLKLKKIEPEQHFTKPPPRYTEASLVKAMEELGIGrpsTYASI---IETLQDRGYVERE-GKRLVPTEL 487

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958664790 111 GIVLVHGYHKIDAELVLPTIRSAVEKQLNLIAQGKANYHQVLGHtldiFKRKFH 164
Cdd:COG0550   488 GFIVIDLLEEHFPDLVDYEFTAKMEEKLDEIAEGKLDWKDVLEE----FYKPFK 537
 
Name Accession Description Interval E-value
TOP1Ac cd00186
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
 29-163 1.72e-44

DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.


Pssm-ID: 238110 [Multi-domain]  Cd Length: 381  Bit Score: 158.92  E-value: 1.72e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790  29 QSVPLEESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEnGRRLKPT 108
Cdd:cd00186   248 EKDDEEEEPPPLKEGDELKLEEVELEEKETQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKE-KKKLIPT 326

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958664790 109 NLGIVLVHGYHKIDAELVLPTIRSAVEKQLNLIAQGKANYHQVLGHTLDIFKRKF 163
Cdd:cd00186   327 ELGFAVIELLEKHFPELVDPEFTAKLEEKLDEIAEGKKDYQEVLEEFYEEFKKIV 381
Topoisom_bac pfam01131
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ...
 34-152 5.88e-40

DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes preferentially relax negatively supercoiled DNA, from a 5' phospho- tyrosine linkage in the enzyme-DNA covalent intermediate and has high affinity for single stranded DNA.


Pssm-ID: 426069 [Multi-domain]  Cd Length: 410  Bit Score: 147.39  E-value: 5.88e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790  34 EESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEnGRRLKPTNLGIV 113
Cdd:pfam01131 293 EEELPELKEGEELKVTQVEVEEKKTKPPPRYTEASLIKAMEKAGIGTPATRATIIETLLERGYVERK-KKSLVPTELGKA 371

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1958664790 114 LVHGYHKIDaELVLPTIRSAVEKQLNLIAQGKANYHQVL 152
Cdd:pfam01131 372 LVEALEKFP-DLVDPELTAELEEKLDEIAEGKLDWKDVL 409
TOP1Ac smart00437
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ...
 22-114 2.45e-34

Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit


Pssm-ID: 214663 [Multi-domain]  Cd Length: 259  Bit Score: 128.52  E-value: 2.45e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790   22 WERQLFPQSVPLEESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEn 101
Cdd:smart00437 168 WLKVYPEEKKEEEIELPTLKKGDELKVEEVEVEEKETKPPARYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVTKK- 246

                           90
                   ....*....|...
gi 1958664790  102 GRRLKPTNLGIVL 114
Cdd:smart00437 247 KKKLIPTELGIAV 259
PRK07219 PRK07219
DNA topoisomerase I; Validated
 25-261 5.03e-27

DNA topoisomerase I; Validated


Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 113.94  E-value: 5.03e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790  25 QLFPQSVPLEESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTveNGRR 104
Cdd:PRK07219  438 EVYPYEKFDEKELPDLEEGEKLKVNKIEIEAKETQPPKRYTQSSLIKEMEKRGLGTKATRHDIIEKLYKRGYVI--EGDP 515

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790 105 LKPTNLGIVLVHGYHKIDAELVLPTIRSAVEKQLNLIAQGKANYHQVLGHTLDIFKRKFHYFVDSIAGM-DELMEvSFSP 183
Cdd:PRK07219  516 PRPTDLGIAVIEALEKYAPEIVSEEMTAQLEADMQAIEDGKKKKEDVTEESREMLKEILSELKEKRKEIgDHLAG-SLKA 594

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790 184 LAATGKPLSRCGKCHRFMKYIQAKPSR--LHCS---HCDETYTLPQNGTIKLYKELrCPLDDFELVLWssgSRGKSYPL- 257
Cdd:PRK07219  595 ENRSLKTIGKCPECGGDLIIIRTDKGSrfVGCSgypDCRNTFPLPSTGRIKVLDEV-CEKCGLPVIKI---LRGKQTFVv 670


                  ....*
gi 1958664790 258 -CPYC 261
Cdd:PRK07219  671 gCPDC 675
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
34-164 1.40e-23

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 440316 [Multi-domain]  Cd Length: 541  Bit Score: 102.87  E-value: 1.40e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790  34 EESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIG---TDASIpvhINNICQRNYVTVEnGRRLKPTNL 110
Cdd:COG0550   412 EKRLPPLKEGEKLKLKKIEPEQHFTKPPPRYTEASLVKAMEELGIGrpsTYASI---IETLQDRGYVERE-GKRLVPTEL 487

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958664790 111 GIVLVHGYHKIDAELVLPTIRSAVEKQLNLIAQGKANYHQVLGHtldiFKRKFH 164
Cdd:COG0550   488 GFIVIDLLEEHFPDLVDYEFTAKMEEKLDEIAEGKLDWKDVLEE----FYKPFK 537
PRK07220 PRK07220
DNA topoisomerase I; Validated
 22-228 4.67e-18

DNA topoisomerase I; Validated


Pssm-ID: 180892 [Multi-domain]  Cd Length: 740  Bit Score: 86.73  E-value: 4.67e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790  22 WeRQLFPQSVPLEESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVtveN 101
Cdd:PRK07220  428 W-RWYYPYNAPEDRLLPELSEGEELKVKKKEMLDKETQPPGRYGQGRLIKLMEDLGLGTKATRHEIISKLYSRAYI---H 503

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790 102 GRRLKPTNLGIVLVHGYHKIDAELVLPTIRSAVEKQLNLIAQGKANYHQVLGHTLDIFKRKFHYFVDSiagMDELMEVSF 181
Cdd:PRK07220  504 GNPIQPTNTAFAVVDALEKYAPTITKPDMTSRLEEDMDKIAEGKIKEDAVLEESREMLEQVFDELDKN---REKIRESLR 580

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958664790 182 SPLAATgKPLSRCGKC-HRFMKYIQAKPSR-LHCS---HCDETYTLPQNGTI 228
Cdd:PRK07220  581 EGLRED-KIIGKCPLCgSDLMVRRSKRGSRfIGCEgypECTFSLPLPKSGQI 631
PRK07726 PRK07726
DNA topoisomerase 3;
22-216 7.20e-17

DNA topoisomerase 3;


Pssm-ID: 236078 [Multi-domain]  Cd Length: 658  Bit Score: 82.90  E-value: 7.20e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790  22 WeRQLFPQSVPLEE---SLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLM-----------------EKHGIGTD 81
Cdd:PRK07726  437 W-KALLGKKEEDEEkeqPLPVLAKGDELKVEKGEVKEGQTQPPKRFTEGTLLSAMeniarfvqdkelkktlkETDGLGTE 515

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790  82 A---SIpvhINNICQRNYVTVeNGRRLKPTNLGIVLvhgyhkIDA---ELVLPTIRSAVEKQLNLIAQGKANYHQvlght 155
Cdd:PRK07726  516 AtraGI---IEKLFKRGYLEK-KGKYIHATDKGKQL------IDAlpeELTSPDMTAKWEQALDQISEGQLSYQD----- 580

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958664790 156 ldifkrkfhyFVDSIAG-MDELME---VSFSPLAATGKPLSRCGKCHRFMKyiQAKPSRLHCSHC 216
Cdd:PRK07726  581 ----------FMQPLKQwLKQLVEqakQSSEKYKFDNLTGPKCPDCGKPML--KVKGKNGKMLVC 633
PRK05776 PRK05776
DNA topoisomerase I; Provisional
 25-199 2.05e-14

DNA topoisomerase I; Provisional


Pssm-ID: 235602 [Multi-domain]  Cd Length: 670  Bit Score: 75.41  E-value: 2.05e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790  25 QLFPQSVPLEESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTvENGRR 104
Cdd:PRK05776  435 KYYPFHKFDEEELPLLKKGERVKIVDVKVRKSYTKPPSRYSKASLLKWMESVGIGTEATRARIIETLFKRGYLT-SNGKY 513

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790 105 LKPTNLGIVLVHGYHKIDAELVLPTIRSAVEKQLNLIAQGKANYHQVLGHT-------LDIFKRKFHYFVDSIAGMDELM 177
Cdd:PRK05776  514 IEVTPLGFGVAEVLEKYFPDIVSVELTRDFEEKLEMIRTGKATREEVIEEAketlnklLEEFKKNKDEIGEELAKALGLI 593

                         170       180
                  ....*....|....*....|..
gi 1958664790 178 evsfsplaatgKPLSRCGKCHR 199
Cdd:PRK05776  594 -----------KPVGKCKICGR 604
PRK06599 PRK06599
DNA topoisomerase I; Validated
 25-258 3.68e-14

DNA topoisomerase I; Validated


Pssm-ID: 235840 [Multi-domain]  Cd Length: 675  Bit Score: 74.51  E-value: 3.68e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790  25 QLFPQSVPLEES-----LPTCQKGDTFTVGEVkmLEKQ--TSPPDYLTEAELITLMEKHGIG---TDASIpvhINNICQR 94
Cdd:PRK06599  425 KVYGESKDDEEEddeklLPPLKEGEKLKLDEL--LPEQhfTEPPPRYSEASLVKKLEEYGIGrpsTYASI---ISTLQDR 499

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790  95 NYVTVENgRRLKPTNLG-IV---LVHGYHKI-----DAELvlptirsavEKQLNLIAQGKANYHQVLGHtldiFKRKFHY 165
Cdd:PRK06599  500 EYVELEK-KRFIPTDLGrIVndfLVEHFPKYvdydfTAGL---------EDELDEIAEGKKDWKPVLRE----FWEPFIS 565

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790 166 FVDSIAGMDELMEVSFSPLAAT-----GKPLS-RCGKCHRFmkyiqakpsrLHCSH---CDETYTLPQNG-----TIKLY 231
Cdd:PRK06599  566 NLEKVEEDVRTEKVTQEETDETcpkcgGGPLVlKLGKNGKF----------LGCSGypeCKYTKNITRDEdepieEEEIV 635

                         250       260       270
                  ....*....|....*....|....*....|..
gi 1958664790 232 KELRCPLDDFELVLwSSGSRGK-----SYPLC 258
Cdd:PRK06599  636 EEEKCPKCGGPLVL-KKGRYGKflacsGYPEC 666
PRK07561 PRK07561
DNA topoisomerase I subunit omega; Validated
 37-201 9.68e-13

DNA topoisomerase I subunit omega; Validated


Pssm-ID: 236048 [Multi-domain]  Cd Length: 859  Bit Score: 70.21  E-value: 9.68e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790  37 LPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIG---TDASIpvhINNICQRNYVTVENgRRLKPTNLG-I 112
Cdd:PRK07561  441 LPALKVGDALTLEKLDPTQHFTKPPARYSEASLVKELEKLGIGrpsTYASI---ISTIQDRGYVRLEN-RRFYPEKMGrI 516

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790 113 VlvhgyhkID------AELVLPTIRSAVEKQLNLIAQGKANYHQVlghtLDIFKRKFHYFVDSIA------GMDELMEVs 180
Cdd:PRK07561  517 V-------TDrleeffPRLVDYDFTARMEEELDDIANGEADWKPV----LDDFYKDFSQQLEKAEelreegGMRPNQMV- 584

                         170       180
                  ....*....|....*....|..
gi 1958664790 181 fsplaatgkPLSR-CGKCHRFM 201
Cdd:PRK07561  585 ---------ITDRdCPTCGRGM 597
PRK06319 PRK06319
DNA topoisomerase I/SWI domain fusion protein; Validated
 36-159 2.12e-10

DNA topoisomerase I/SWI domain fusion protein; Validated


Pssm-ID: 235778 [Multi-domain]  Cd Length: 860  Bit Score: 62.92  E-value: 2.12e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790  36 SLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVENGrRLKPTNLGIVLV 115
Cdd:PRK06319  451 HLPKLHEQDVLTKEELSAEQAFTKPLPRFTEASLVKELEKSGIGRPSTYATIMNKIQSREYTLKENQ-RLRPTELGKIIS 529

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1958664790 116 HGYhkidaELVLPTI-----RSAVEKQLNLIAQGKANYHQVLGHTLDIF 159
Cdd:PRK06319  530 QFL-----ETNFPRImdigfTALMEDELELIADNKKPWKLLLQEFWELF 573
PRK14973 PRK14973
DNA topoisomerase I; Provisional
 22-191 2.65e-10

DNA topoisomerase I; Provisional


Pssm-ID: 184936 [Multi-domain]  Cd Length: 936  Bit Score: 62.56  E-value: 2.65e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790  22 WeRQLFPQSVPLEESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVtveN 101
Cdd:PRK14973  427 W-RTVYPYSEAKENILPAFALGEKLPILAVNLEEKETQPPARYSQSRLIQRMEELGLGTKSTRHEVIGKLVSRKYI---E 502

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790 102 GRRLKPTNLGIVLVHGYHKIDAELVLPTIRSAVEKQLNLIAQGKANYHQVLGHTLDIFKRKFHYFVDSIAGM-DELM--- 177
Cdd:PRK14973  503 GNPLRPTLVGRAVTESLEEHAGTITEPDMTQTLEEHMQQIKERKRTRDDVVTESRKMLHRAFDELEANEAVIgRDIMert 582

                         170
                  ....*....|....*.
gi 1958664790 178 --EVSFSPLAATGKPL 191
Cdd:PRK14973  583 aeELTIGPCPVCGKDL 598
PRK08780 PRK08780
DNA topoisomerase I; Provisional
 37-205 2.97e-08

DNA topoisomerase I; Provisional


Pssm-ID: 181555 [Multi-domain]  Cd Length: 780  Bit Score: 55.92  E-value: 2.97e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790  37 LPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIG---TDASIpvhINNICQRNYVTVEnGRRLKPTNLGIV 113
Cdd:PRK08780  448 LPPMKEGDNVPLERIRAEQHFTEPPPRYTEASLVKALEEYGIGrpsTYASI---ISTLQFRKYVEME-GRRFRPTDVGRA 523

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790 114 LV-----HGYHKIDAELvlpTIRsaVEKQLNLIAQGKANYHQVLGHTLDIFKRKFHYFVDSIAGMDELMEVSFSPLAATG 188
Cdd:PRK08780  524 VNkfltgHFTRYVDYDF---TAR--LEDDLDAVSRGEKEWIPLMEKFWGPFKELVEEKKDSVDRTEAGQVRELGTDPKSG 598

                         170
                  ....*....|....*...
gi 1958664790 189 KPLS-RCGkchRFMKYIQ 205
Cdd:PRK08780  599 KPVSvRIG---RFGPMVQ 613
PRK08173 PRK08173
DNA topoisomerase III; Validated
 34-217 2.22e-05

DNA topoisomerase III; Validated


Pssm-ID: 236172 [Multi-domain]  Cd Length: 862  Bit Score: 46.97  E-value: 2.22e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790  34 EESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLME----------------KHGIGTDASIPVHINNICQRNYV 97
Cdd:PRK08173  460 DANLVPVQKGEKVKTDKIEAVALTTKPPARYNEATLLSAMEgagklveddelreamaEKGLGTPATRAAIIEGLLGEKYL 539

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790  98 tVENGRRLKPT----NLgIVLVHGYhKIDaELVLPTIRSAVEKQLNLIAQGK----ANYHQVLGHTLDIFKRKFHYFVDS 169
Cdd:PRK08173  540 -VREGRELIPTakafQL-MTLLRGL-GVE-ELTSPELTGEWEYKLSQIERGKlsrdAFMQEIAQMTQQIVKRAKEYDSDT 615

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1958664790 170 IAGmdelmevSFSPLAAtgkPLSRCGkchrfmKYIQAKPSRLHCSHCD 217
Cdd:PRK08173  616 IPG-------DYATLQT---PCPNCG------GVVKENYRRFACTKCD 647
PTZ00407 PTZ00407
DNA topoisomerase IA; Provisional
 55-143 5.57e-05

DNA topoisomerase IA; Provisional


Pssm-ID: 173597 [Multi-domain]  Cd Length: 805  Bit Score: 45.70  E-value: 5.57e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664790  55 EKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVENGRRLKPTNLGIVLVHgyhkiDAELVLPTI---- 130
Cdd:PTZ00407  570 ENRPVPPLPHSEGTLIEELKNNGVGRPSTYPMIVKTLLARGYIAVNPKGRCETTPVGRMLVE-----TAKSTFPSIvdig 644

                          90
                  ....*....|....
gi 1958664790 131 -RSAVEKQLNLIAQ 143
Cdd:PTZ00407  645 fTAAFEKKLDRIAK 658
 
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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