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Conserved domains on  [gi|1720386791|ref|XP_030104905|]
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DNA topoisomerase 3-beta-1 isoform X2 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TOP1Ac cd00186
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
 75-496 1.74e-149

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: 441.66  E-value: 1.74e-149
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  75 HNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGdldsslISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQakvhtdk 154
Cdd:cd00186     1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRRKGV------LSAGRVQSPTLGLIVEREREIKAFVPEDYWEIK------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 155 eesllldwdrvrvfdweiaqmflnmtklekEAWVEATSRKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAERLYTQ 234
Cdd:cd00186    68 ------------------------------EAVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEA 117

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 235 GYISYPRTETTHYPENFDLKGSLRQQANHPYWADSVKQLLAeGINRPRKGHDAGDHPPITPMK----SATEAELGGDAWR 310
Cdd:cd00186   118 GLITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPLLG-RRNPKRGKKEQGAHEAIRPTKvaptPELEANLSEDEFK 196

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 311 LYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCMGKTVISPGFTEIMPWQSVPLEESLPTCQKGDTFTVGEVKMLEKQ 390
Cdd:cd00186   197 LYELIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEEEPPPLKEGDELKLEEVELEEKE 276

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 391 TSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEsGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVEKQ 470
Cdd:cd00186   277 TQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKE-KKKLIPTELGFAVIELLEKHFPELVDPEFTAKLEEK 355

                         410       420
                  ....*....|....*....|....*.
gi 1720386791 471 LNLIAQGKADYHQVLGHTLDIFKRKF 496
Cdd:cd00186   356 LDEIAEGKKDYQEVLEEFYEEFKKIV 381
TOPRIM super family cl00718
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 1-70 9.12e-22

Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


The actual alignment was detected with superfamily member cd03362:

Pssm-ID: 469888 [Multi-domain]  Cd Length: 151  Bit Score: 92.30  E-value: 9.12e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791   1 MVKFLQVEGRGCDYVVLWLDCDKEGENICFEVLDAVLPVMNnahngeKTVFRARFSSITDTDICNAMTRL 70
Cdd:cd03362    88 QFKVLKKLAKRADEIVIATDADREGELIGREILEYAKCVKR------KPVKRAWFSSLTPKAIRRAFKNL 151
 
Name Accession Description Interval E-value
TOP1Ac cd00186
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
 75-496 1.74e-149

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: 441.66  E-value: 1.74e-149
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  75 HNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGdldsslISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQakvhtdk 154
Cdd:cd00186     1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRRKGV------LSAGRVQSPTLGLIVEREREIKAFVPEDYWEIK------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 155 eesllldwdrvrvfdweiaqmflnmtklekEAWVEATSRKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAERLYTQ 234
Cdd:cd00186    68 ------------------------------EAVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEA 117

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 235 GYISYPRTETTHYPENFDLKGSLRQQANHPYWADSVKQLLAeGINRPRKGHDAGDHPPITPMK----SATEAELGGDAWR 310
Cdd:cd00186   118 GLITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPLLG-RRNPKRGKKEQGAHEAIRPTKvaptPELEANLSEDEFK 196

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 311 LYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCMGKTVISPGFTEIMPWQSVPLEESLPTCQKGDTFTVGEVKMLEKQ 390
Cdd:cd00186   197 LYELIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEEEPPPLKEGDELKLEEVELEEKE 276

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 391 TSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEsGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVEKQ 470
Cdd:cd00186   277 TQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKE-KKKLIPTELGFAVIELLEKHFPELVDPEFTAKLEEK 355

                         410       420
                  ....*....|....*....|....*.
gi 1720386791 471 LNLIAQGKADYHQVLGHTLDIFKRKF 496
Cdd:cd00186   356 LDEIAEGKKDYQEVLEEFYEEFKKIV 381
Topoisom_bac pfam01131
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ...
 72-485 1.08e-139

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: 417.41  E-value: 1.08e-139
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  72 EPDHNEALSVDARQELDLRIGCAFTRFQTKYFQGKygdldsSLISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVH 151
Cdd:pfam01131   1 EIDENLVDAQLARRELDWLIGFNLSRLLTLKLKGN------KLLSAGRVQTPTLALIVEREREIENFVPEPYWTIEATLK 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 152 TDKEESLLLDWDRVRVFDWEIAQMFLNmtKLEK-EAWVEATSRKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAER 230
Cdd:pfam01131  75 DGGGVFANAKWKRGRIFDKEEAEAILE--KLKKgTAVVTSVESKEKKKPPPLPFNTTTLQKEASRKLGFSAKKTMSIAQK 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 231 LYTQ-GYISYPRTETTHYPENFDLKGSLR-QQANHPYWADSVKQLLAEG-INRPRKGHDAGDHPPITPMKSAT-EAELGG 306
Cdd:pfam01131 153 LYEKhGLITYPRTDSTYLSDDATLKAILEyLTKNYGKYLPYAPRLLKKTkGKLTVGNAKVTAHEAIRPTGDIPvLPELSD 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 307 DAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCMGKTVISPGFTEIMPWQSVPLEESLPTCQKGDTFTVGEVKM 386
Cdd:pfam01131 233 DERKLYELIVRRFLASQMPPAVYETTTVVLEVGGEEFRASGKVILEDGWLKVYPYEKKEDEEELPELKEGEELKVTQVEV 312

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 387 LEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEsGRRLKPTNLGIVLVHGYYKIDaELVLPTIRSA 466
Cdd:pfam01131 313 EEKKTKPPPRYTEASLIKAMEKAGIGTPATRATIIETLLERGYVERK-KKSLVPTELGKALVEALEKFP-DLVDPELTAE 390

                         410
                  ....*....|....*....
gi 1720386791 467 VEKQLNLIAQGKADYHQVL 485
Cdd:pfam01131 391 LEEKLDEIAEGKLDWKDVL 409
PRK07219 PRK07219
DNA topoisomerase I; Validated
 10-594 1.02e-123

DNA topoisomerase I; Validated


Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 389.75  E-value: 1.02e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  10 RGCDYVVLWLDCDKEGENICFEVLDAVLPVmnnahnGEKTVFRARFSSITDTDICNAMTRLSEPDHNEALSVDARQELDL 89
Cdd:PRK07219   96 KDADEIIIATDYDREGELIGKEAYHILREV------CQVPVKRARFSSLTKKEIRKAFENPDEIDFNLADAGEARQIIDL 169

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  90 RIGCAFTRFQTKYFqGKYGDLDssLISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAkVHTDKEESLLLDWDRV---- 165
Cdd:PRK07219  170 YWGAALTRFLSLSV-RQLGRWD--FLSVGRVQTPTLAFIVDREREIRAFDPEDYWKIEA-LLDKEAQYFYRDLIGGheae 245

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 166 RVFDWEIAQMFLNMTKLEKEAWVEATSRKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAERLYTQGYISYPRTETT 245
Cdd:PRK07219  246 KFWDEEEAEEIYEKLKGAKEATVSSVKKRERTISPPAPFNTTEFLREASKIFGISPKRAMEIAEKLYTAGYISYPRTDNT 325

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 246 HYPENFDLKGSLRQQANHPYWADSVKQLLAEGINRPRKG-HDAGDHPPITPMKSATEAELGGDAWRLYEYITRHFIATVS 324
Cdd:PRK07219  326 VYPDDLDPKELLKKLSKKKEYGPYAESILEQENIKPTEGkKETTDHPPIHPVDVPKREELSDDEWKVYELIVRRFLATLA 405

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 325 HDCKYLQSTISFRIGPEHFTCMGKTVISPGFTEIMPWQSvPLEESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELIT 404
Cdd:PRK07219  406 DPAEWEYLKVELDVNGEIFKASGSRLVEEGWHEVYPYEK-FDEKELPDLEEGEKLKVNKIEIEAKETQPPKRYTQSSLIK 484

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 405 LMEKHGIGTDASIPVHINNICQRNYVtVESGrRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVEKQLNLIAQGKADYHQV 484
Cdd:PRK07219  485 EMEKRGLGTKATRHDIIEKLYKRGYV-IEGD-PPRPTDLGIAVIEALEKYAPEIVSEEMTAQLEADMQAIEDGKKKKEDV 562

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 485 LGHTLDIFKRKFHYFVDSIAGM-DELMEvSFSPLAATGKPLSRCGKCHRFMKYIQAKPSR--LHCS---HCDETYTLPQN 558
Cdd:PRK07219  563 TEESREMLKEILSELKEKRKEIgDHLAG-SLKAENRSLKTIGKCPECGGDLIIIRTDKGSrfVGCSgypDCRNTFPLPST 641

                         570       580       590
                  ....*....|....*....|....*....|....*...
gi 1720386791 559 GTIKLYKELrCPLDDFELVLWssgSRGKSYPL--CPYC 594
Cdd:PRK07219  642 GRIKVLDEV-CEKCGLPVIKI---LRGKQTFVvgCPDC 675
TOP1Ac smart00437
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ...
 193-447 1.10e-107

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: 329.21  E-value: 1.10e-107
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  193 RKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAERLYTQGYISYPRTETTHYPENFDLKGSLRQQANHP-YWADSVK 271
Cdd:smart00437   2 EKEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYIQKLYGkEYLDLAV 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  272 QLLAEGInrPRKGHDA-GDHPPITPMKSAT----EAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCM 346
Cdd:smart00437  82 VLLKPRK--PRKGKKAqGAHEAIRPTKPIFtpelEKELSEDEFKLYELIWRRFLASQMPDAKYEETKVTIKIGGEKFKAK 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  347 GKTVISPGFTEIMPWQSVPLEESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQ 426
Cdd:smart00437 160 GKTLLFDGWLKVYPEEKKEEEIELPTLKKGDELKVEEVEVEEKETKPPARYTEASLIKLMEKRGIGRPSTYASIIETLLD 239

                          250       260
                   ....*....|....*....|.
gi 1720386791  427 RNYVTVEsGRRLKPTNLGIVL 447
Cdd:smart00437 240 RGYVTKK-KKKLIPTELGIAV 259
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
10-497 9.25e-89

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 440316 [Multi-domain]  Cd Length: 541  Bit Score: 289.69  E-value: 9.25e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  10 RGCDYVVLWLDCDKEGENICFEVLDAVlpvmnnahNGEKTVFRARFSSITDTDICNAMTRLSEPDHNeaLsVDA---RQE 86
Cdd:COG0550    70 KKADEVILATDPDREGEAIAWHLLELL--------GDKKPVKRVVFNEITKKAIKEAFKNPRDIDMN--L-VDAqqaRRI 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  87 LDLRIGCAFTRFQTKYFQGKygdldsslISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVHTDKE--ESLLLDWDR 164
Cdd:COG0550   139 LDRLVGYNLSPLLWKKVKRG--------LSAGRVQSPALRLIVEREREIEAFVPEEYWTIEATFKTGGGefTAKLVKIDG 210

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 165 VRVFDWEIAQMFLNMTKlEKEAWVEATSRKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAERLYTQGYISYPRTET 244
Cdd:COG0550   211 KKILDEEEAEAILAALK-GKTFTVTSVEKKPKKRNPPPPFTTSTLQQEASRKLGFSAKKTMSIAQRLYEVGLITYMRTDS 289

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 245 THYPEnfDLKGSLRQQANhpywADSVKQLLAEGINRPRKGHDA-GDHPPITP-MKSATEAELGGDAWRLYEYITRHFIAT 322
Cdd:COG0550   290 VRLSE--DAVAAAREYIE----ALYGKEYLPEKPRVYKTSKNAqEAHEAIRPtGVTRTPESLSGDEFKLYDLIWKRFLAS 363

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 323 VSHDCKYLQSTISFRIGPEHFTCMGKTVISPGFTEIMPWQSVPLEE----SLPTCQKGDTFTVGEVKMLEKQTSPPDYLT 398
Cdd:COG0550   364 QMPPAEYETTTVTIEVGGEEFRASGKVIKFPGFLKVYGEGKDDEEEeeekRLPPLKEGEKLKLKKIEPEQHFTKPPPRYT 443

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 399 EAELITLMEKHGIG---TDASIpvhINNICQRNYVTVEsGRRLKPTNLGIV---LVHGYYKidaELVLPTIRSAVEKQLN 472
Cdd:COG0550   444 EASLVKAMEELGIGrpsTYASI---IETLQDRGYVERE-GKRLVPTELGFIvidLLEEHFP---DLVDYEFTAKMEEKLD 516

                         490       500
                  ....*....|....*....|....*
gi 1720386791 473 LIAQGKADYHQVLGHtldiFKRKFH 497
Cdd:COG0550   517 EIAEGKLDWKDVLEE----FYKPFK 537
TOPRIM_TopoIA_TopoIII cd03362
TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type ...
 1-70 9.12e-22

TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173782 [Multi-domain]  Cd Length: 151  Bit Score: 92.30  E-value: 9.12e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791   1 MVKFLQVEGRGCDYVVLWLDCDKEGENICFEVLDAVLPVMNnahngeKTVFRARFSSITDTDICNAMTRL 70
Cdd:cd03362    88 QFKVLKKLAKRADEIVIATDADREGELIGREILEYAKCVKR------KPVKRAWFSSLTPKAIRRAFKNL 151
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 1-58 5.79e-05

Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.


Pssm-ID: 396354 [Multi-domain]  Cd Length: 93  Bit Score: 42.34  E-value: 5.79e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1720386791   1 MVKFLQVEGRGCDYVVLWLDCDKEGENICFEVLDAVLPVmnnahngEKTVFRARFSSI 58
Cdd:pfam01751  43 ALKALKELALKAKEVILATDPDREGEAIALKLLELKELL-------ENAGGRVEFSEL 93
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
1-40 9.82e-04

topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 38.40  E-value: 9.82e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1720386791    1 MVKFLQVEGRGCdYVVLWLDCDKEGENICFEVLDAVLPVM 40
Cdd:smart00493  37 QIKLLKKLAKKA-EVILATDPDREGEAIAWELAELLKPAG 75
 
Name Accession Description Interval E-value
TOP1Ac cd00186
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
 75-496 1.74e-149

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: 441.66  E-value: 1.74e-149
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  75 HNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGdldsslISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQakvhtdk 154
Cdd:cd00186     1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRRKGV------LSAGRVQSPTLGLIVEREREIKAFVPEDYWEIK------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 155 eesllldwdrvrvfdweiaqmflnmtklekEAWVEATSRKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAERLYTQ 234
Cdd:cd00186    68 ------------------------------EAVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEA 117

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 235 GYISYPRTETTHYPENFDLKGSLRQQANHPYWADSVKQLLAeGINRPRKGHDAGDHPPITPMK----SATEAELGGDAWR 310
Cdd:cd00186   118 GLITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPLLG-RRNPKRGKKEQGAHEAIRPTKvaptPELEANLSEDEFK 196

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 311 LYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCMGKTVISPGFTEIMPWQSVPLEESLPTCQKGDTFTVGEVKMLEKQ 390
Cdd:cd00186   197 LYELIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEEEPPPLKEGDELKLEEVELEEKE 276

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 391 TSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEsGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVEKQ 470
Cdd:cd00186   277 TQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKE-KKKLIPTELGFAVIELLEKHFPELVDPEFTAKLEEK 355

                         410       420
                  ....*....|....*....|....*.
gi 1720386791 471 LNLIAQGKADYHQVLGHTLDIFKRKF 496
Cdd:cd00186   356 LDEIAEGKKDYQEVLEEFYEEFKKIV 381
Topoisom_bac pfam01131
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ...
 72-485 1.08e-139

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: 417.41  E-value: 1.08e-139
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  72 EPDHNEALSVDARQELDLRIGCAFTRFQTKYFQGKygdldsSLISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVH 151
Cdd:pfam01131   1 EIDENLVDAQLARRELDWLIGFNLSRLLTLKLKGN------KLLSAGRVQTPTLALIVEREREIENFVPEPYWTIEATLK 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 152 TDKEESLLLDWDRVRVFDWEIAQMFLNmtKLEK-EAWVEATSRKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAER 230
Cdd:pfam01131  75 DGGGVFANAKWKRGRIFDKEEAEAILE--KLKKgTAVVTSVESKEKKKPPPLPFNTTTLQKEASRKLGFSAKKTMSIAQK 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 231 LYTQ-GYISYPRTETTHYPENFDLKGSLR-QQANHPYWADSVKQLLAEG-INRPRKGHDAGDHPPITPMKSAT-EAELGG 306
Cdd:pfam01131 153 LYEKhGLITYPRTDSTYLSDDATLKAILEyLTKNYGKYLPYAPRLLKKTkGKLTVGNAKVTAHEAIRPTGDIPvLPELSD 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 307 DAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCMGKTVISPGFTEIMPWQSVPLEESLPTCQKGDTFTVGEVKM 386
Cdd:pfam01131 233 DERKLYELIVRRFLASQMPPAVYETTTVVLEVGGEEFRASGKVILEDGWLKVYPYEKKEDEEELPELKEGEELKVTQVEV 312

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 387 LEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEsGRRLKPTNLGIVLVHGYYKIDaELVLPTIRSA 466
Cdd:pfam01131 313 EEKKTKPPPRYTEASLIKAMEKAGIGTPATRATIIETLLERGYVERK-KKSLVPTELGKALVEALEKFP-DLVDPELTAE 390

                         410
                  ....*....|....*....
gi 1720386791 467 VEKQLNLIAQGKADYHQVL 485
Cdd:pfam01131 391 LEEKLDEIAEGKLDWKDVL 409
PRK07219 PRK07219
DNA topoisomerase I; Validated
 10-594 1.02e-123

DNA topoisomerase I; Validated


Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 389.75  E-value: 1.02e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  10 RGCDYVVLWLDCDKEGENICFEVLDAVLPVmnnahnGEKTVFRARFSSITDTDICNAMTRLSEPDHNEALSVDARQELDL 89
Cdd:PRK07219   96 KDADEIIIATDYDREGELIGKEAYHILREV------CQVPVKRARFSSLTKKEIRKAFENPDEIDFNLADAGEARQIIDL 169

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  90 RIGCAFTRFQTKYFqGKYGDLDssLISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAkVHTDKEESLLLDWDRV---- 165
Cdd:PRK07219  170 YWGAALTRFLSLSV-RQLGRWD--FLSVGRVQTPTLAFIVDREREIRAFDPEDYWKIEA-LLDKEAQYFYRDLIGGheae 245

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 166 RVFDWEIAQMFLNMTKLEKEAWVEATSRKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAERLYTQGYISYPRTETT 245
Cdd:PRK07219  246 KFWDEEEAEEIYEKLKGAKEATVSSVKKRERTISPPAPFNTTEFLREASKIFGISPKRAMEIAEKLYTAGYISYPRTDNT 325

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 246 HYPENFDLKGSLRQQANHPYWADSVKQLLAEGINRPRKG-HDAGDHPPITPMKSATEAELGGDAWRLYEYITRHFIATVS 324
Cdd:PRK07219  326 VYPDDLDPKELLKKLSKKKEYGPYAESILEQENIKPTEGkKETTDHPPIHPVDVPKREELSDDEWKVYELIVRRFLATLA 405

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 325 HDCKYLQSTISFRIGPEHFTCMGKTVISPGFTEIMPWQSvPLEESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELIT 404
Cdd:PRK07219  406 DPAEWEYLKVELDVNGEIFKASGSRLVEEGWHEVYPYEK-FDEKELPDLEEGEKLKVNKIEIEAKETQPPKRYTQSSLIK 484

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 405 LMEKHGIGTDASIPVHINNICQRNYVtVESGrRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVEKQLNLIAQGKADYHQV 484
Cdd:PRK07219  485 EMEKRGLGTKATRHDIIEKLYKRGYV-IEGD-PPRPTDLGIAVIEALEKYAPEIVSEEMTAQLEADMQAIEDGKKKKEDV 562

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 485 LGHTLDIFKRKFHYFVDSIAGM-DELMEvSFSPLAATGKPLSRCGKCHRFMKYIQAKPSR--LHCS---HCDETYTLPQN 558
Cdd:PRK07219  563 TEESREMLKEILSELKEKRKEIgDHLAG-SLKAENRSLKTIGKCPECGGDLIIIRTDKGSrfVGCSgypDCRNTFPLPST 641

                         570       580       590
                  ....*....|....*....|....*....|....*...
gi 1720386791 559 GTIKLYKELrCPLDDFELVLWssgSRGKSYPL--CPYC 594
Cdd:PRK07219  642 GRIKVLDEV-CEKCGLPVIKI---LRGKQTFVvgCPDC 675
TOP1Ac smart00437
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ...
 193-447 1.10e-107

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: 329.21  E-value: 1.10e-107
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  193 RKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAERLYTQGYISYPRTETTHYPENFDLKGSLRQQANHP-YWADSVK 271
Cdd:smart00437   2 EKEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYIQKLYGkEYLDLAV 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  272 QLLAEGInrPRKGHDA-GDHPPITPMKSAT----EAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCM 346
Cdd:smart00437  82 VLLKPRK--PRKGKKAqGAHEAIRPTKPIFtpelEKELSEDEFKLYELIWRRFLASQMPDAKYEETKVTIKIGGEKFKAK 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  347 GKTVISPGFTEIMPWQSVPLEESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQ 426
Cdd:smart00437 160 GKTLLFDGWLKVYPEEKKEEEIELPTLKKGDELKVEEVEVEEKETKPPARYTEASLIKLMEKRGIGRPSTYASIIETLLD 239

                          250       260
                   ....*....|....*....|.
gi 1720386791  427 RNYVTVEsGRRLKPTNLGIVL 447
Cdd:smart00437 240 RGYVTKK-KKKLIPTELGIAV 259
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
10-497 9.25e-89

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 440316 [Multi-domain]  Cd Length: 541  Bit Score: 289.69  E-value: 9.25e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  10 RGCDYVVLWLDCDKEGENICFEVLDAVlpvmnnahNGEKTVFRARFSSITDTDICNAMTRLSEPDHNeaLsVDA---RQE 86
Cdd:COG0550    70 KKADEVILATDPDREGEAIAWHLLELL--------GDKKPVKRVVFNEITKKAIKEAFKNPRDIDMN--L-VDAqqaRRI 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  87 LDLRIGCAFTRFQTKYFQGKygdldsslISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVHTDKE--ESLLLDWDR 164
Cdd:COG0550   139 LDRLVGYNLSPLLWKKVKRG--------LSAGRVQSPALRLIVEREREIEAFVPEEYWTIEATFKTGGGefTAKLVKIDG 210

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 165 VRVFDWEIAQMFLNMTKlEKEAWVEATSRKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAERLYTQGYISYPRTET 244
Cdd:COG0550   211 KKILDEEEAEAILAALK-GKTFTVTSVEKKPKKRNPPPPFTTSTLQQEASRKLGFSAKKTMSIAQRLYEVGLITYMRTDS 289

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 245 THYPEnfDLKGSLRQQANhpywADSVKQLLAEGINRPRKGHDA-GDHPPITP-MKSATEAELGGDAWRLYEYITRHFIAT 322
Cdd:COG0550   290 VRLSE--DAVAAAREYIE----ALYGKEYLPEKPRVYKTSKNAqEAHEAIRPtGVTRTPESLSGDEFKLYDLIWKRFLAS 363

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 323 VSHDCKYLQSTISFRIGPEHFTCMGKTVISPGFTEIMPWQSVPLEE----SLPTCQKGDTFTVGEVKMLEKQTSPPDYLT 398
Cdd:COG0550   364 QMPPAEYETTTVTIEVGGEEFRASGKVIKFPGFLKVYGEGKDDEEEeeekRLPPLKEGEKLKLKKIEPEQHFTKPPPRYT 443

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 399 EAELITLMEKHGIG---TDASIpvhINNICQRNYVTVEsGRRLKPTNLGIV---LVHGYYKidaELVLPTIRSAVEKQLN 472
Cdd:COG0550   444 EASLVKAMEELGIGrpsTYASI---IETLQDRGYVERE-GKRLVPTELGFIvidLLEEHFP---DLVDYEFTAKMEEKLD 516

                         490       500
                  ....*....|....*....|....*
gi 1720386791 473 LIAQGKADYHQVLGHtldiFKRKFH 497
Cdd:COG0550   517 EIAEGKLDWKDVLEE----FYKPFK 537
PRK07220 PRK07220
DNA topoisomerase I; Validated
 9-561 1.26e-88

DNA topoisomerase I; Validated


Pssm-ID: 180892 [Multi-domain]  Cd Length: 740  Bit Score: 294.74  E-value: 1.26e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791   9 GRGCDYVVLWLDCDKEGENICFEVLDAVLPVmnnahNGEKTVFRARFSSITDTDICNAMTRLSEPDHNEALSVDARQELD 88
Cdd:PRK07220   95 GKEADRVTIATDYDREGELIGVEALNIIKKV-----NPDIKFDRVRYSAITKKEIERAFSNPVEVDFNLADAGHSRQVID 169

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  89 LRIGCAFTRfqtkYFQGKYGDLDSSLISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVHTDKEEsLLLDWDRVRVf 168
Cdd:PRK07220  170 LVWGAALTR----YISLAAGRLGKMFLSVGRVQSPTLALIVDREKEREAFVPTPYWEIYATLENNGET-FVAQHSTRRF- 243

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 169 dWEIAQMFLNMTKLEKEAWVEATSRKEKAKQRPLALNTVEMLRVASSaLGMGPQHAMQIAERLYTQGYISYPRTETTHYP 248
Cdd:PRK07220  244 -WEKEEADRVFEKLGKTAEVTEVEKGTKTDKPPTPFNTTEFISAANS-IGFSAANAMRIAESLYTNGYISYPRTDNTVYP 321

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 249 ENFDLKGSLRQQANHPYwADSVKQLLAEGINRPRKG-HDAGDHPPITPMKSATEAELGGDAWRLYEYITRHFIATVSHDC 327
Cdd:PRK07220  322 ESLDLREQIEIFAEGPF-GEYAQKLLEKGELVPTRGkKETTDHPPIYPASLAKKSELKEDEWKVYELVVRRFFATFAGPA 400

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 328 KYLQSTISFRIGPEHFTCMGKTVISPGFTEIMPWqSVPLEESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLME 407
Cdd:PRK07220  401 EWETMKLRFDIGGEEFRANGSRLTEPGWRWYYPY-NAPEDRLLPELSEGEELKVKKKEMLDKETQPPGRYGQGRLIKLME 479

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 408 KHGIGTDASIPVHINNICQRNYVtveSGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVEKQLNLIAQGKADYHQVLGH 487
Cdd:PRK07220  480 DLGLGTKATRHEIISKLYSRAYI---HGNPIQPTNTAFAVVDALEKYAPTITKPDMTSRLEEDMDKIAEGKIKEDAVLEE 556

                         490       500       510       520       530       540       550
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1720386791 488 TLDIFKRKFHYFVDSiagMDELMEVSFSPLAATgKPLSRCGKC-HRFMKYIQAKPSR-LHCS---HCDETYTLPQNGTI 561
Cdd:PRK07220  557 SREMLEQVFDELDKN---REKIRESLREGLRED-KIIGKCPLCgSDLMVRRSKRGSRfIGCEgypECTFSLPLPKSGQI 631
PRK14973 PRK14973
DNA topoisomerase I; Provisional
 1-524 2.82e-71

DNA topoisomerase I; Provisional


Pssm-ID: 184936 [Multi-domain]  Cd Length: 936  Bit Score: 251.31  E-value: 2.82e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791   1 MVKFLQVEGRGCDYVVLWLDCDKEGENICFEVLDAVlpvmnNAHNGEKTVFRARFSSITDTDICNAMTRLSEPDHNEALS 80
Cdd:PRK14973   86 IVGLIQKLAKKADRVTIATDFDTEGELIGKEAYELV-----RAVNPKVPIDRARFSAITKEEIVTAFAEPTDLDFALAAA 160

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  81 VDARQELDLRIGCAFTRFQTkyFQGKYGDldSSLISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQakVHTDKE-ESLL 159
Cdd:PRK14973  161 GEARQIIDLIWGASLTRFIS--LAAHRGG--DNILSVGRVQSPTLAMIVDREKEIEAFVPEKYWMLS--LATEKDgEGIE 234

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 160 LDWDRVRVFDWEIAqmflnmtKLEKEAWVE---ATSRKEKAKQ--RPLALNTVEMLrVASSALGMGPQHAMQIAERLYTQ 234
Cdd:PRK14973  235 ARHTHGRFTDSAAA-------EAAYDATKEplvVTEVKEGHKVdrAPTPFDTTTFI-VAASRLGFSAANAMRIAEDLYMN 306

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 235 GYISYPRTETTHYPENFDLKGSLRQQANHPYWADsVKQLLAEGINRPRKGH-DAGDHPPITPMKSATEAELGGDAWRLYE 313
Cdd:PRK14973  307 GYISYPRTDNTIYPKSLDLNGVLATLAKGAFSKD-VAWVKDNRRPVPTRGKkSSTDHPPIHPTGVATREELGDDRWKLYE 385

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 314 YITRHFIATVSHDCKYLQSTISFRIGPEHFTCMGKTVISPGFTEIMPWqSVPLEESLPTCQKGDTFTVGEVKMLEKQTSP 393
Cdd:PRK14973  386 LVVRRFLATLSPDAEWATMKVNFDAGGEPYTATGGRLLEAGWRTVYPY-SEAKENILPAFALGEKLPILAVNLEEKETQP 464

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 394 PDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVtveSGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVEKQLNL 473
Cdd:PRK14973  465 PARYSQSRLIQRMEELGLGTKSTRHEVIGKLVSRKYI---EGNPLRPTLVGRAVTESLEEHAGTITEPDMTQTLEEHMQQ 541

                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1720386791 474 IAQGKADYHQVLGHTLDIFKRKFHYFVDSIAGM-DELM-----EVSFSPLAATGKPL 524
Cdd:PRK14973  542 IKERKRTRDDVVTESRKMLHRAFDELEANEAVIgRDIMertaeELTIGPCPVCGKDL 598
PRK05776 PRK05776
DNA topoisomerase I; Provisional
 12-532 1.16e-59

DNA topoisomerase I; Provisional


Pssm-ID: 235602 [Multi-domain]  Cd Length: 670  Bit Score: 214.09  E-value: 1.16e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  12 CDYvvlwldcDKEGENICFEVLdavlpvmnNAHNGEKTVFRARFSSITDTDICNAMTRLSEPDHNEALSVDARQELDLRI 91
Cdd:PRK05776  104 CDY-------DIEGSVIGYLII--------KYLGDPKKAKRMKFSALTKSDIRRAFRNLETLDYEMINAGIARHELDWLW 168

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  92 GCAFTRFQT---KYFQGKygdldSSLISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVHTDKEESllldwdRVRVF 168
Cdd:PRK05776  169 GINVSRALMssvRDASGK-----RVILSAGRVQSPTLKYVVEREIERNLFVPLPYFSVSIIIEKNGYEF------TLKYE 237

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 169 DWEI-----AQMFLNMTKLEKEAWVEATSRKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAERLYTQGYISYPRTE 243
Cdd:PRK05776  238 NKKFetkeeAKEILEEIKKTGYLKVTKVEVKIEILEPPPPFNLGDLQVEAARIYGFSPYKTQSIAEDLYLDGLISYPRTN 317

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 244 TTHYPENFDLKGSLRQQANHPYWADSVKQLLAE--GINRPRKG-HDAGDHPPITPMKSATEaELGGDAWRLYEYITRHFI 320
Cdd:PRK05776  318 SQKLPPTLNIRNILKGLSRSPQYRPLVNLLLKEtkGVLKPVQGpKDDPAHPAIYPTGEPPK-NLSKDEFKLYDLIVRRFL 396

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 321 ATVSHDCKYLQSTISFRIG--PEHFTCMGKTVISPGFTEIMPWqSVPLEESLPTCQKGDTFTVGEVKMLEKQTSPPDYLT 398
Cdd:PRK05776  397 ASFAAPAVLSNTIVTLRVPgfPLVFSASGQRIEERGWLKYYPF-HKFDEEELPLLKKGERVKIVDVKVRKSYTKPPSRYS 475

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 399 EAELITLMEKHGIGTDASIPVHINNICQRNYVTvESGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVEKQLNLIAQGK 478
Cdd:PRK05776  476 KASLLKWMESVGIGTEATRARIIETLFKRGYLT-SNGKYIEVTPLGFGVAEVLEKYFPDIVSVELTRDFEEKLEMIRTGK 554

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1720386791 479 ADYHQVLGHT-------LDIFKRKFHYFVDSIAGMDELMevsfsplaatgKPLSRCGKCHR 532
Cdd:PRK05776  555 ATREEVIEEAketlnklLEEFKKNKDEIGEELAKALGLI-----------KPVGKCKICGR 604
PRK07726 PRK07726
DNA topoisomerase 3;
20-549 2.92e-50

DNA topoisomerase 3;


Pssm-ID: 236078 [Multi-domain]  Cd Length: 658  Bit Score: 187.29  E-value: 2.92e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  20 DCDKEGENICFEVLDAVlpvmnnahNGEKTVFRARFSSITDTDICNAMTRL-----SEPDHNEALsvdARQELDLRIGCA 94
Cdd:PRK07726  101 DADREGELIAREILDYC--------GVRKPIKRLWISSLTDKAIKRAFANLkpgkeTIPLYYSAL---ARSRADWLVGIN 169

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  95 FTR-FQTKYFQGKYGDLdsslISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVHTDKEESLLldW--------DRV 165
Cdd:PRK07726  170 MTRaYTLLGRKAGYNGV----LSVGRVQTPTLALVVRRDEEIENFVPKPYWEVEAHLTPGERFTAK--WqpsepyqdEEG 243

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 166 RVFDWEIAQMFLNMTKlEKEAWVEATSRKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAERLY-TQGYISYPRTET 244
Cdd:PRK07726  244 RLLDRPLAEQVVARIQ-GQPAKVTEVETKRKKEYAPLLYDLSELQIDANKRFGLSAKETLDIAQSLYeTHKLITYPRTDS 322

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 245 THYPEnfDLKGSLRQ-----QANHPYwadsvKQLLAEGINRPRKGH---DA--GDHPPITP-MKSATEAELGGDAWRLYE 313
Cdd:PRK07726  323 RYLPE--DMVATLPEvlnaiSKVDPY-----LLLAPPVLDPSIRSRawnDKkvTAHHAIIPtEQPPNLSKLSEDERKVYD 395

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 314 YITRHFIATVSHDCKYLQSTISFRIGPEHFTCMGKTVISPGFTEIMPWQSVPLEES--LPTCQKGDTFTVGEVKMLEKQT 391
Cdd:PRK07726  396 LIARRYLAQFLPPAEYDKTTIELEIAGGTFIAKGKQVVEAGWKALLGKKEEDEEKEqpLPVLAKGDELKVEKGEVKEGQT 475

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 392 SPPDYLTEAELITLM-----------------EKHGIGTDA---SIpvhINNICQRNYVTVEsGRRLKPTNLGIVLvhgy 451
Cdd:PRK07726  476 QPPKRFTEGTLLSAMeniarfvqdkelkktlkETDGLGTEAtraGI---IEKLFKRGYLEKK-GKYIHATDKGKQL---- 547

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 452 ykIDA---ELVLPTIRSAVEKQLNLIAQGKADYHQvlghtldifkrkfhyFVDSIAG-MDELME---VSFSPLAATGKPL 524
Cdd:PRK07726  548 --IDAlpeELTSPDMTAKWEQALDQISEGQLSYQD---------------FMQPLKQwLKQLVEqakQSSEKYKFDNLTG 610

                         570       580
                  ....*....|....*....|....*
gi 1720386791 525 SRCGKCHRFMKyiQAKPSRLHCSHC 549
Cdd:PRK07726  611 PKCPDCGKPML--KVKGKNGKMLVC 633
PRK06599 PRK06599
DNA topoisomerase I; Validated
 10-591 4.49e-34

DNA topoisomerase I; Validated


Pssm-ID: 235840 [Multi-domain]  Cd Length: 675  Bit Score: 139.22  E-value: 4.49e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  10 RGCDYVVLWLDCDKEGENICFEVLDavlpVMNNAHNGEKTVFRARFSSITDTDICNAmtrLSEP-DHNEALsVD---ARQ 85
Cdd:PRK06599   72 KKADAVYLATDPDREGEAIAWHIAE----VLKEAKLKDKNVKRVVFNEITKKAVQEA---IENPrDIDMDL-VDaqqARR 143

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  86 ELDLRIGcaftrFQ------TKYFQGKygdldssliSFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVHTDKEESL- 158
Cdd:PRK06599  144 ALDYLVG-----FKlspllwKKVRRGL---------SAGRVQSVALRLICEREDEIEAFIPQEYWTIEADLATSNGEPFt 209

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 159 --LLDWD-----RVRVFDWEIAQMFLNmtKLEKEAW-VEATSRKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAER 230
Cdd:PRK06599  210 akLVEVNgkkleKFSITNEEQAKALVK--ALEGQAYtVDKIEKKERKRNPPPPFITSTLQQEASRKLGFSAKKTMRIAQK 287

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 231 LY--------TQGYISYPRTetthypenfdlkgslrqqanhpywaDSVkQLLAEGINRPRK------GHD-AGDHPPI-- 293
Cdd:PRK06599  288 LYegidlgegTVGLITYMRT-------------------------DSV-RLSNEALDEARKyitkkyGKEyLPAKPRVyk 341

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 294 TPMKSATEAE------------------LGGDAWRLYEYITRHFIATVSHDCKYLQSTISF--RIGPEHFTCMGKTVISP 353
Cdd:PRK06599  342 KKSKNAQEAHeairptsinrtpeslkpyLTPDQFKLYELIWKRTVASQMAPAILDQTSVDIasENGKYVFRATGSVILFP 421

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 354 GFTEIMPwQSVPLEES-----LPTCQKGDTFTVGEVkmLEKQ--TSPPDYLTEAELITLMEKHGIG---TDASIpvhINN 423
Cdd:PRK06599  422 GFLKVYG-ESKDDEEEddeklLPPLKEGEKLKLDEL--LPEQhfTEPPPRYSEASLVKKLEEYGIGrpsTYASI---IST 495

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 424 ICQRNYVTVEsGRRLKPTNLG-IV---LVHGY-----YKIDAELvlptirsavEKQLNLIAQGKADYHQVLGHtldiFKR 494
Cdd:PRK06599  496 LQDREYVELE-KKRFIPTDLGrIVndfLVEHFpkyvdYDFTAGL---------EDELDEIAEGKKDWKPVLRE----FWE 561

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 495 KFHYFVDSIAGMDELMEVSFSPLAAT-----GKPLS-RCGKCHRFmkyiqakpsrLHCSH---CDETYTLPQNG-----T 560
Cdd:PRK06599  562 PFISNLEKVEEDVRTEKVTQEETDETcpkcgGGPLVlKLGKNGKF----------LGCSGypeCKYTKNITRDEdepieE 631

                         650       660       670
                  ....*....|....*....|....*....|....*.
gi 1720386791 561 IKLYKELRCPLDDFELVLwSSGSRGK-----SYPLC 591
Cdd:PRK06599  632 EEIVEEEKCPKCGGPLVL-KKGRYGKflacsGYPEC 666
PRK07561 PRK07561
DNA topoisomerase I subunit omega; Validated
 11-534 4.84e-34

DNA topoisomerase I subunit omega; Validated


Pssm-ID: 236048 [Multi-domain]  Cd Length: 859  Bit Score: 139.93  E-value: 4.84e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  11 GCDYVVLWLDCDKEGENICF---EVLDAvlpvmnnahnGEKTVFRARFSSITDTDICNAMtrlSEP-DHNEALsVDA--- 83
Cdd:PRK07561   86 DADELYLATDPDREGEAIAWhllEVLGG----------DDVPVKRVVFNEITKNAIQEAF---ENPrELDINL-VNAqqa 151

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  84 RQELDlRIgcaftrfqtkyfqgkYGDLDSSLI--------SFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVHTDKE 155
Cdd:PRK07561  152 RRFLD-RL---------------VGYMVSPLLwkkiarglSAGRVQSVAVRLIVEREREIEAFVPEEYWDIHADLTTPRG 215

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 156 ESLLLD--------WDRVRVFDWEIAQMFLnmTKLEKEAWVeATSRKEKAKQR-PLALNTVEMLR-VASSALGMGPQHAM 225
Cdd:PRK07561  216 DAFEARlthldgkkFAPVDLLNEAQAEAAV--AALEGARYS-VASVEDKPTTRkPSAPFTTSTLQqEASRKLGFSVKKTM 292

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 226 QIAERLYTQGYISYPRTetthypenfdlkgslrqqanhpywaDSVkQLLAEGINRPRK--GHDAGDH--PPiTP------ 295
Cdd:PRK07561  293 RIAQRLYEAGYITYMRT-------------------------DST-NLSQEAINAARGyiGDNYGKKylPE-KPrqyssk 345

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 296 MKSATEA-----------------ELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCMGKTVISPGFTEI 358
Cdd:PRK07561  346 AKNAQEAheairpsdvfrtpdqlkGLEGDAQRLYELIWKRFVASQMAPARYDSTTVTIAAGDAELRATGRVLRFDGFLKV 425

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 359 MPWQS--VPLEES--LPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIG---TDASIpvhINNICQRNYVT 431
Cdd:PRK07561  426 YVEGRddALDDEDrrLPALKVGDALTLEKLDPTQHFTKPPARYSEASLVKELEKLGIGrpsTYASI---ISTIQDRGYVR 502

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 432 VEsGRRLKPTNLG-IV--LVHGYYkidAELVLPTIRSAVEKQLNLIAQGKADYHQVlghtLDIFKRKFHYFVDSIA---- 504
Cdd:PRK07561  503 LE-NRRFYPEKMGrIVtdRLEEFF---PRLVDYDFTARMEEELDDIANGEADWKPV----LDDFYKDFSQQLEKAEelre 574

                         570       580       590
                  ....*....|....*....|....*....|...
gi 1720386791 505 --GMDELMEVsfsplaatgkPLSR-CGKCHRFM 534
Cdd:PRK07561  575 egGMRPNQMV----------ITDRdCPTCGRGM 597
TOP1Bc smart00436
Bacterial DNA topoisomeraes I ATP-binding domain; Extension of TOPRIM in Bacterial DNA ...
 50-145 1.45e-32

Bacterial DNA topoisomeraes I ATP-binding domain; Extension of TOPRIM in Bacterial DNA topoisomeraes I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase beta subunit


Pssm-ID: 214662 [Multi-domain]  Cd Length: 89  Bit Score: 120.77  E-value: 1.45e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791   50 VFRARFSSITDTDICNAMTRLSEPDHNEALSVDARQELDLRIGCAFTRFQTKYFQGKYgdldsslISFGPCQTPTLGFCV 129
Cdd:smart00436   1 IKRIEFSEITKKAIREALKNPREIDENLVNAQLARRILDRLIGFNLSRLLTKKLRNGV-------LSAGRVQTPTLGLIV 73

                           90
                   ....*....|....*.
gi 1720386791  130 ERHDKIQSFKPETYWV 145
Cdd:smart00436  74 EREREIKNFVPKPYWE 89
PRK08173 PRK08173
DNA topoisomerase III; Validated
 21-550 2.21e-30

DNA topoisomerase III; Validated


Pssm-ID: 236172 [Multi-domain]  Cd Length: 862  Bit Score: 128.25  E-value: 2.21e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  21 CD--KEGENICFEVLDAVlpvmnnahNGEKTVFRARFSSITDTDICNAMTRLSEPDHNEALSvDA---RQELDLRIGCAF 95
Cdd:PRK08173  104 CDagREGELIFRLIAQHA--------KAKKPVKRLWLQSMTPQAIRDGFANLRSDEDMQPLA-DAarcRSEADWLVGING 174

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  96 TRFQTKyFQGKYGDLdsSLISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQA----------------KVHTDKEESll 159
Cdd:PRK08173  175 TRAMTA-FNSKGGGF--FLTTVGRVQTPTLSIVVEREEKIRRFVPRDYWEVRAefvaaagfyegrwfdpKFKKDEFDP-- 249

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 160 ldWDRV-RVFDWEIAQMFLNMTKlEKEAWVEATSrKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAERLYTQ-GYI 237
Cdd:PRK08173  250 --EKRAsRLWSEAAAEAIVAACR-GKPGTVTEES-KPSTQLSPLLFDLTSLQREANGRFGFSAKNTLGLAQALYEKhKVL 325

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 238 SYPRTETTHYPENF--DLKGSLRQQANHPYWADSVKQLLAEGINRPRK----GHDAGDHPPITPM----KSATEAELggd 307
Cdd:PRK08173  326 TYPRTDSRALPEDYlgTVKQTLEMLKESNNYLPHAKQILDKGWVKPNKrifdNSKISDHFAIIPTlqapKSLSEPEQ--- 402

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 308 awRLYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCMGKTVISPGFTEIMPWQSVPLEESLPTCQKGDTFTVGEVKML 387
Cdd:PRK08173  403 --KLYDLVVKRFLAVFFPAAEFLVTTRITEVAGHHFKTEGKVLVNPGWLAVYGKEAQGADANLVPVQKGEKVKTDKIEAV 480

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 388 EKQTSPPDYLTEAELITLME----------------KHGIGTDASIPVHINNICQRNYVtVESGRRLKPT----NLgIVL 447
Cdd:PRK08173  481 ALTTKPPARYNEATLLSAMEgagklveddelreamaEKGLGTPATRAAIIEGLLGEKYL-VREGRELIPTakafQL-MTL 558

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 448 VHGyYKIDaELVLPTIRSAVEKQLNLIAQGK----ADYHQVLGHTLDIFKRKFHYFVDSIAGmdelmevSFSPLAAtgkP 523
Cdd:PRK08173  559 LRG-LGVE-ELTSPELTGEWEYKLSQIERGKlsrdAFMQEIAQMTQQIVKRAKEYDSDTIPG-------DYATLQT---P 626

                         570       580
                  ....*....|....*....|....*..
gi 1720386791 524 LSRCGkchrfmKYIQAKPSRLHCSHCD 550
Cdd:PRK08173  627 CPNCG------GVVKENYRRFACTKCD 647
PRK08780 PRK08780
DNA topoisomerase I; Provisional
 10-538 1.25e-28

DNA topoisomerase I; Provisional


Pssm-ID: 181555 [Multi-domain]  Cd Length: 780  Bit Score: 122.56  E-value: 1.25e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  10 RGCDYVVLWLDCDKEGENICFEVLDAVlpvmnnAHNG---EKTVFRARFSSITDTDICNAMtrlsepDHNEALSVD---- 82
Cdd:PRK08780   72 KSADDLYLATDPDREGEAISWHLAEIL------KERGllkDKPMQRVVFTEITPRAIKEAM------AKPRDIASDlvda 139

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  83 --ARQELDLRIGCAFTRFQTKYFQgkygdldsSLISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVHTDKE----E 156
Cdd:PRK08780  140 qqARRALDYLVGFNLSPLLWRKIQ--------RGLSAGRVQSPALRMIVEREEEIEAFIAREYWSIEADCAHPSQpfnaK 211

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 157 SLLLDWDRVRVF---DWEIAQMFLNmtKLEKEA----WVEATSRKEKaKQRPLALNTVEMLRV-ASSALGMGPQHAMQIA 228
Cdd:PRK08780  212 LIKLDGQKFEQFtitDGDTAEAARL--RIQQAAqgtlHVTDVESKER-KRNPAPPFTTSTLQQeASRKLGFTTRRTMQVA 288

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 229 ERLY---------TQGYISYPRTETTHYPEnfDLKGSLRQQANHPYWADSVKQLLAEGINRPRKGHDAgdHPPITP---M 296
Cdd:PRK08780  289 QKLYegvdlgdegSVGLITYMRTDSVNLSQ--DALAEIRDVIARDYGTASLPDQPNTYKTKSKNAQEA--HEAVRPtsaL 364

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 297 KSATE--AELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPEH-FTCMGKTVISPGFTEIM-------PWQSVPL 366
Cdd:PRK08780  365 RTPAQvaRFLSDDQRRLYELIWKRAVACQMIPATLNTVSVDLAAGSEHvFRATGSTVVVPGFLAVYeegkddkSAEDEDE 444

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 367 EESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIG---TDASIpvhINNICQRNYVTVEsGRRLKPTNL 443
Cdd:PRK08780  445 GRKLPPMKEGDNVPLERIRAEQHFTEPPPRYTEASLVKALEEYGIGrpsTYASI---ISTLQFRKYVEME-GRRFRPTDV 520

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 444 GIVlVHGY----------YKIDAELvlptirsavEKQLNLIAQGKADYHQVLGHTLDIFKRKFHYFVDSIAGMDELMEVS 513
Cdd:PRK08780  521 GRA-VNKFltghftryvdYDFTARL---------EDDLDAVSRGEKEWIPLMEKFWGPFKELVEEKKDSVDRTEAGQVRE 590

                         570       580
                  ....*....|....*....|....*.
gi 1720386791 514 FSPLAATGKPLS-RCGkchRFMKYIQ 538
Cdd:PRK08780  591 LGTDPKSGKPVSvRIG---RFGPMVQ 613
PRK06319 PRK06319
DNA topoisomerase I/SWI domain fusion protein; Validated
 8-492 8.37e-22

DNA topoisomerase I/SWI domain fusion protein; Validated


Pssm-ID: 235778 [Multi-domain]  Cd Length: 860  Bit Score: 101.05  E-value: 8.37e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791   8 EGRGCDYVVLWLDCDKEGENICFEVLDaVLPvmNNAHngektVFRARFSSITDTDICNAMTRLSEPDHNEALSVDARQEL 87
Cdd:PRK06319   70 LAKKCDVVYLSPDPDREGEAIAWHIAN-QLP--KNTK-----IQRISFNAITKGAVTEALKHPREIDMALVNAQQARRLL 141

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  88 DLRIGCAFTRFQTKYFQGKYGdldsslISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVHTDKEESLLldWDRVRV 167
Cdd:PRK06319  142 DRIVGYKISPILSRKLQRRSG------VSAGRVQSVALKLVVDREKAIEAFVPVEYWNIRVHLKDPKTQKTF--WAHLYS 213

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 168 FD---WE--------IAQMFLNMTK---------LEKEAW-VEATSRKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQ 226
Cdd:PRK06319  214 VDgkkWEkeipegktEDEVLLINSKekadhivelLESATYtVTRVESKEKRRNAYPPFITSTLQQEASRHFRFSSSRTMN 293

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 227 IAERLY---------TQGYISYPRTETTHY-PENFD-LKGSLRQQANHPYWADSVKQLLAEginrpRKGHDAgdHPPITP 295
Cdd:PRK06319  294 IAQTLYegvdldsegATGLITYMRTDSVRTdPEALKqVRKYIEGTFGKEFLPSSPNVYTTK-----KMAQDA--HEAIRP 366

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 296 MKSATEAE-----LGGDAWRLYEYITRHFIATVSHDCKY--LQSTISFRIGPEhFTCMGKTVISPGFT---EIMPWQSVP 365
Cdd:PRK06319  367 TDITLTPEklrskLTEDQYKLYSLIWKRFVASQMIPAIYdtLAIRITTNKGID-LRATGSLLKFKGFLavyEEKRDDEGD 445

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 366 LEE--SLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYvTVESGRRLKPTNL 443
Cdd:PRK06319  446 EEEniHLPKLHEQDVLTKEELSAEQAFTKPLPRFTEASLVKELEKSGIGRPSTYATIMNKIQSREY-TLKENQRLRPTEL 524

                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1720386791 444 GIVLVHGYykidaELVLPTI-----RSAVEKQLNLIAQGKADYHQVLGHTLDIF 492
Cdd:PRK06319  525 GKIISQFL-----ETNFPRImdigfTALMEDELELIADNKKPWKLLLQEFWELF 573
TOPRIM_TopoIA_TopoIII cd03362
TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type ...
 1-70 9.12e-22

TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173782 [Multi-domain]  Cd Length: 151  Bit Score: 92.30  E-value: 9.12e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791   1 MVKFLQVEGRGCDYVVLWLDCDKEGENICFEVLDAVLPVMNnahngeKTVFRARFSSITDTDICNAMTRL 70
Cdd:cd03362    88 QFKVLKKLAKRADEIVIATDADREGELIGREILEYAKCVKR------KPVKRAWFSSLTPKAIRRAFKNL 151
PRK14724 PRK14724
DNA topoisomerase III; Provisional
 20-441 5.64e-19

DNA topoisomerase III; Provisional


Pssm-ID: 237803 [Multi-domain]  Cd Length: 987  Bit Score: 92.33  E-value: 5.64e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  20 DCDKEGENIcFEVLDAVlpvMNNAHNG-EKTVFRARFSSITDTDICNAMTRLSEPDHNEALSVDAR--QELDLRIGCAFT 96
Cdd:PRK14724  108 DAGREGELI-FRLIEQY---AGGAKGGlGKPVKRLWLQSMTPQAIRDGFDNLRSDAQMQGLASAARsrSEADWLVGINGT 183

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  97 RFQTKyFQGKYGDLdsSLISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVHTDKEESL--LLD--WDRV------- 165
Cdd:PRK14724  184 RAMTA-FNSRDGGF--FLTTVGRVQTPTLSLVVEREEKIRKFVSRDYWEIHAGFHAEAGEYLgkWFDpqWKKAsddpear 260

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 166 --RVFDWEIAQMFLNMTKlEKEAWVEATSrKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAERLYTQ-GYISYPRT 242
Cdd:PRK14724  261 adRVWSEREARAIADAVR-GKAATVTEES-KPTTQASPLLFDLTSLQREANGKFGFSAKTTLALAQSLYERhKALTYPRT 338

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 243 ETTHYPEN--------FDL--KGSLRQQANHpywadsVKQLLAEGINRPRK----GHDAGDHPPITPMKSA----TEAEl 304
Cdd:PRK14724  339 DSRALPEDylpvakqtFEMlaTSGMRHLAPF------AQQALDGNYVRPSKrifdNSKVSDHFAIIPTTQApsglSEAE- 411

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 305 ggdaWRLYEYITRHFIATVSHDCKYLQST-ISFRIGpEHFTCMGKTVISPGFTEIMPWQSVPLEE---------SLPTCQ 374
Cdd:PRK14724  412 ----QKLYDLVVRRFMAVFFPSAEYQVTTrISQVVG-HSFKTEGKVLVKPGWLAIYGKEAANEVEdakdgdkgqPLVPVK 486

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 375 KGDTFTVGEVKMLEKQTSPPDYLTEAELITLME----------------KHGIGTDASIPVHINNICQRNYVTVEsGRRL 438
Cdd:PRK14724  487 PGEMVRTEFAEAKGLKTKPPARYSEATLLGAMEsagkqidddelreamqEKGLGTPATRAAIIEGLLTEKYMLRE-GREL 565


                  ...
gi 1720386791 439 KPT 441
Cdd:PRK14724  566 IPT 568
TOPRIM_TopoIA cd01028
TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 1-70 6.48e-18

TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA). This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173778 [Multi-domain]  Cd Length: 142  Bit Score: 80.73  E-value: 6.48e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791   1 MVKFLQVEGRGCDYVVLWLDCDKEGENICFEVLDAvlpvmnnAHNGEKTVFRARFSSITDTDICNAMTRL 70
Cdd:cd01028    80 QLKALKKLAKKADEIVLATDPDREGELIAWEILEV-------LKCDNKPVKRAWFSEITPKAIREAFKNL 142
PTZ00407 PTZ00407
DNA topoisomerase IA; Provisional
 15-476 4.35e-11

DNA topoisomerase IA; Provisional


Pssm-ID: 173597 [Multi-domain]  Cd Length: 805  Bit Score: 66.50  E-value: 4.35e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  15 VVLWLDCDKEGENICFEVLDAV---LPVMNNAHNgektvfRARFSSITDTDICNAMT-RLSEP-DHNEALSVDARQELDl 89
Cdd:PTZ00407  128 IILATDPDREGELIAVHALQTIkrlYPKLKVPFS------RAYMHSITEDGIRKAMReRHVEAcDYDLANAAETRHAMD- 200

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791  90 RIgcaftrfqtkyfqgkYGDLDSSLI--------SFGPCQTPTLGFCVERHDKIQSF--KPETYWVLQA----------- 148
Cdd:PTZ00407  201 RI---------------FGFLGSSVVraansqmrSIGRVQTPALILINEREDKIKAFleSNKSTFEVQAmcqfpsphgtt 265

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 149 -----KVHTDKEESLLlDWD-----RVRVFDWEI--AQMFlnmtKLEKEAWVEATsrkEKAKQRPLALNTveMLRVASSA 216
Cdd:PTZ00407  266 fsqvvTITPDRKGGAS-HWAteaeaRRCLEQWKLnnCTGF----SVPLEPKPQPS---VVPPPQPFTMAT--AIAKANRQ 335

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 217 LGMGPQHAMQIAERLYTQGYISYPRTETTHYPENF--DLKGSLRQQANhpywadsvKQLLAEGINRPRKGHDaGDHPPIT 294
Cdd:PTZ00407  336 LKYSSEMVSGCLQDLFQLGHITYPRTDSTRIDESAlpDIYAAVKKEFG--------KEFLYRLEDRTVSAQE-GKGSKKT 406

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 295 PMKSATEAELGGDAWR------------------------------LYEYITRHFIAT--VSHDCKYLQSTISFRIGPE- 341
Cdd:PTZ00407  407 GKKRSTKQKKGADTPVgnvedaheairptnidttgeslslspptraVYDLVRRNTLAVfmIPMKTEKIVATVKFTSGSGe 486

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 342 --HFTCMGKTVISPGFTE----------------------------IMPWQS-------VPLEESLPTCQKGDTFTVGEV 384
Cdd:PTZ00407  487 klEFELQGKRVVEPGWTRafhkgdkgttgpaeetdeditaveegapVVPSLSqeefkaiMNLRSQLGSGVQKGFFELRSP 566

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720386791 385 KMLEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVESGRRLKPTNLGIVLVHgyykiDAELVLPTI- 463
Cdd:PTZ00407  567 QVRENRPVPPLPHSEGTLIEELKNNGVGRPSTYPMIVKTLLARGYIAVNPKGRCETTPVGRMLVE-----TAKSTFPSIv 641

                         570
                  ....*....|....*..
gi 1720386791 464 ----RSAVEKQLNLIAQ 476
Cdd:PTZ00407  642 digfTAAFEKKLDRIAK 658
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 1-58 5.79e-05

Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.


Pssm-ID: 396354 [Multi-domain]  Cd Length: 93  Bit Score: 42.34  E-value: 5.79e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1720386791   1 MVKFLQVEGRGCDYVVLWLDCDKEGENICFEVLDAVLPVmnnahngEKTVFRARFSSI 58
Cdd:pfam01751  43 ALKALKELALKAKEVILATDPDREGEAIALKLLELKELL-------ENAGGRVEFSEL 93
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
1-40 9.82e-04

topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 38.40  E-value: 9.82e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1720386791    1 MVKFLQVEGRGCdYVVLWLDCDKEGENICFEVLDAVLPVM 40
Cdd:smart00493  37 QIKLLKKLAKKA-EVILATDPDREGEAIAWELAELLKPAG 75
 
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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