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Conserved domains on  [gi|568995040|ref|XP_006522055|]
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DNA topoisomerase 3-beta-1 isoform X1 [Mus musculus]

Protein Classification

DNA topoisomerase III( domain architecture ID 10129755)

topoisomerase III is a type 1a topoisomerase that resolves single strand DNA recombination and replication intermediates

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 ...
 172-593 2.76e-148

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: 2.76e-148
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 172 HNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGdldsslISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQakvhtdk 251
Cdd:cd00186    1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRRKGV------LSAGRVQSPTLGLIVEREREIKAFVPEDYWEIK------- 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 252 eesllldwdrvrvfdweiaqmflnmtklekEAWVEATSRKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAERLYTQ 331
Cdd:cd00186   68 ------------------------------EAVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEA 117

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 332 GYISYPRTETTHYPENFDLKGSLRQQANHPYWADSVKQLLAeGINRPRKGHDAGDHPPITPMK----SATEAELGGDAWR 407
Cdd:cd00186  118 GLITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPLLG-RRNPKRGKKEQGAHEAIRPTKvaptPELEANLSEDEFK 196

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 408 LYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCMGKTVISPGFTEIMPWQSVPLEESLPTCQKGDTFTVGEVKMLEKQ 487
Cdd:cd00186  197 LYELIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEEEPPPLKEGDELKLEEVELEEKE 276

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 488 TSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEsGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVEKQ 567
Cdd:cd00186  277 TQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKE-KKKLIPTELGFAVIELLEKHFPELVDPEFTAKLEEK 355

                        410       420
                 ....*....|....*....|....*.
gi 568995040 568 LNLIAQGKADYHQVLGHTLDIFKRKF 593
Cdd:cd00186  356 LDEIAEGKKDYQEVLEEFYEEFKKIV 381
TOPRIM_TopoIA_TopoIII cd03362
TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type ...
 3-167 1.92e-54

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: 185.13  E-value: 1.92e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040   3 TVLMVAEKPSLAQSIAKILSRGNMSSHKGLNGacsvhkytgTFAGQPVHFKMTSVCGHVMTLDFLGKYNKWDKVDPAE-L 81
Cdd:cd03362    1 MVLIIAEKPSVAKAIAKILGGGSKKKGKGRYY---------EFYGEGGGYVVTWASGHLLELDFPEEYDPWDKVWPLEdP 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  82 FSQAPTEKKEANPKLNMVKFLQVEGRGCDYVVLWLDCDKEGENICFEVLDAVLPVMNnahngeKTVFRARFSSITDTDIC 161
Cdd:cd03362   72 LFPAPFKLKVDKGKKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYAKCVKR------KPVKRAWFSSLTPKAIR 145


                 ....*.
gi 568995040 162 NAMTRL 167
Cdd:cd03362  146 RAFKNL 151
 
Name Accession Description Interval E-value
TOP1Ac cd00186
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
 172-593 2.76e-148

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: 2.76e-148
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 172 HNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGdldsslISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQakvhtdk 251
Cdd:cd00186    1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRRKGV------LSAGRVQSPTLGLIVEREREIKAFVPEDYWEIK------- 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 252 eesllldwdrvrvfdweiaqmflnmtklekEAWVEATSRKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAERLYTQ 331
Cdd:cd00186   68 ------------------------------EAVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEA 117

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 332 GYISYPRTETTHYPENFDLKGSLRQQANHPYWADSVKQLLAeGINRPRKGHDAGDHPPITPMK----SATEAELGGDAWR 407
Cdd:cd00186  118 GLITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPLLG-RRNPKRGKKEQGAHEAIRPTKvaptPELEANLSEDEFK 196

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 408 LYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCMGKTVISPGFTEIMPWQSVPLEESLPTCQKGDTFTVGEVKMLEKQ 487
Cdd:cd00186  197 LYELIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEEEPPPLKEGDELKLEEVELEEKE 276

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 488 TSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEsGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVEKQ 567
Cdd:cd00186  277 TQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKE-KKKLIPTELGFAVIELLEKHFPELVDPEFTAKLEEK 355

                        410       420
                 ....*....|....*....|....*.
gi 568995040 568 LNLIAQGKADYHQVLGHTLDIFKRKF 593
Cdd:cd00186  356 LDEIAEGKKDYQEVLEEFYEEFKKIV 381
PRK07219 PRK07219
DNA topoisomerase I; Validated
 3-691 2.11e-143

DNA topoisomerase I; Validated


Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 444.44  E-value: 2.11e-143
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040   3 TVLMVAEKPSLAQSIAKILSRGNMS--SHKGLNgacsVHKytgtFAGQPVHFKMTSVCGHVMTLDFLGKYNKWDKVDPAE 80
Cdd:PRK07219   1 TELIIAEKNNAARRIADILSGGKAKkkRVNGVP----YYE----FERKGEKWIVIGLSGHIVTVDFPEEYGDWRDVDPAE 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  81 LFSqAPTEKKEANPklNMVKFLQVEGRGCDYVVLWLDCDKEGENICFEVLDAVLPVmnnahnGEKTVFRARFSSITDTDI 160
Cdd:PRK07219  73 LID-ADPVKKITKQ--NYINALKKLAKDADEIIIATDYDREGELIGKEAYHILREV------CQVPVKRARFSSLTKKEI 143

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 161 CNAMTRLSEPDHNEALSVDARQELDLRIGCAFTRFQTKYFqGKYGDLDssLISFGPCQTPTLGFCVERHDKIQSFKPETY 240
Cdd:PRK07219 144 RKAFENPDEIDFNLADAGEARQIIDLYWGAALTRFLSLSV-RQLGRWD--FLSVGRVQTPTLAFIVDREREIRAFDPEDY 220

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 241 WVLQAkVHTDKEESLLLDWDRV----RVFDWEIAQMFLNMTKLEKEAWVEATSRKEKAKQRPLALNTVEMLRVASSALGM 316
Cdd:PRK07219 221 WKIEA-LLDKEAQYFYRDLIGGheaeKFWDEEEAEEIYEKLKGAKEATVSSVKKRERTISPPAPFNTTEFLREASKIFGI 299

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 317 GPQHAMQIAERLYTQGYISYPRTETTHYPENFDLKGSLRQQANHPYWADSVKQLLAEGINRPRKG-HDAGDHPPITPMKS 395
Cdd:PRK07219 300 SPKRAMEIAEKLYTAGYISYPRTDNTVYPDDLDPKELLKKLSKKKEYGPYAESILEQENIKPTEGkKETTDHPPIHPVDV 379

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 396 ATEAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCMGKTVISPGFTEIMPWQSvPLEESLPTCQKGDT 475
Cdd:PRK07219 380 PKREELSDDEWKVYELIVRRFLATLADPAEWEYLKVELDVNGEIFKASGSRLVEEGWHEVYPYEK-FDEKELPDLEEGEK 458

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 476 FTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVtVESGrRLKPTNLGIVLVHGYYKIDAEL 555
Cdd:PRK07219 459 LKVNKIEIEAKETQPPKRYTQSSLIKEMEKRGLGTKATRHDIIEKLYKRGYV-IEGD-PPRPTDLGIAVIEALEKYAPEI 536

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 556 VLPTIRSAVEKQLNLIAQGKADYHQVLGHTLDIFKRKFHYFVDSIAGM-DELMEvSFSPLAATGKPLSRCGKCHRFMKYI 634
Cdd:PRK07219 537 VSEEMTAQLEADMQAIEDGKKKKEDVTEESREMLKEILSELKEKRKEIgDHLAG-SLKAENRSLKTIGKCPECGGDLIII 615

                        650       660       670       680       690       700
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568995040 635 QAKPSR--LHCS---HCDETYTLPQNGTIKLYKELrCPLDDFELVLWssgSRGKSYPL--CPYC 691
Cdd:PRK07219 616 RTDKGSrfVGCSgypDCRNTFPLPSTGRIKVLDEV-CEKCGLPVIKI---LRGKQTFVvgCPDC 675
Topoisom_bac pfam01131
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ...
 169-582 1.57e-138

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: 1.57e-138
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  169 EPDHNEALSVDARQELDLRIGCAFTRFQTKYFQGKygdldsSLISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVH 248
Cdd:pfam01131   1 EIDENLVDAQLARRELDWLIGFNLSRLLTLKLKGN------KLLSAGRVQTPTLALIVEREREIENFVPEPYWTIEATLK 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  249 TDKEESLLLDWDRVRVFDWEIAQMFLNmtKLEK-EAWVEATSRKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAER 327
Cdd:pfam01131  75 DGGGVFANAKWKRGRIFDKEEAEAILE--KLKKgTAVVTSVESKEKKKPPPLPFNTTTLQKEASRKLGFSAKKTMSIAQK 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  328 LYTQ-GYISYPRTETTHYPENFDLKGSLR-QQANHPYWADSVKQLLAEG-INRPRKGHDAGDHPPITPMKSAT-EAELGG 403
Cdd:pfam01131 153 LYEKhGLITYPRTDSTYLSDDATLKAILEyLTKNYGKYLPYAPRLLKKTkGKLTVGNAKVTAHEAIRPTGDIPvLPELSD 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  404 DAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCMGKTVISPGFTEIMPWQSVPLEESLPTCQKGDTFTVGEVKM 483
Cdd:pfam01131 233 DERKLYELIVRRFLASQMPPAVYETTTVVLEVGGEEFRASGKVILEDGWLKVYPYEKKEDEEELPELKEGEELKVTQVEV 312

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  484 LEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEsGRRLKPTNLGIVLVHGYYKIDaELVLPTIRSA 563
Cdd:pfam01131 313 EEKKTKPPPRYTEASLIKAMEKAGIGTPATRATIIETLLERGYVERK-KKSLVPTELGKALVEALEKFP-DLVDPELTAE 390

                         410
                  ....*....|....*....
gi 568995040  564 VEKQLNLIAQGKADYHQVL 582
Cdd:pfam01131 391 LEEKLDEIAEGKLDWKDVL 409
TOP1Ac smart00437
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ...
 290-544 1.02e-106

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: 1.02e-106
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040   290 RKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAERLYTQGYISYPRTETTHYPENFDLKGSLRQQANHP-YWADSVK 368
Cdd:smart00437   2 EKEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYIQKLYGkEYLDLAV 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040   369 QLLAEGInrPRKGHDA-GDHPPITPMKSAT----EAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCM 443
Cdd:smart00437  82 VLLKPRK--PRKGKKAqGAHEAIRPTKPIFtpelEKELSEDEFKLYELIWRRFLASQMPDAKYEETKVTIKIGGEKFKAK 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040   444 GKTVISPGFTEIMPWQSVPLEESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQ 523
Cdd:smart00437 160 GKTLLFDGWLKVYPEEKKEEEIELPTLKKGDELKVEEVEVEEKETKPPARYTEASLIKLMEKRGIGRPSTYASIIETLLD 239

                          250       260
                   ....*....|....*....|.
gi 568995040   524 RNYVTVEsGRRLKPTNLGIVL 544
Cdd:smart00437 240 RGYVTKK-KKKLIPTELGIAV 259
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
5-594 4.39e-93

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 440316 [Multi-domain]  Cd Length: 541  Bit Score: 303.17  E-value: 4.39e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040   5 LMVAEKPSLAQSIAKILSRGnmsshkglngacsvhkytgtfagqpvhFKMTSVCGHVMTLdflgkYNKWDKVDPAELFsq 84
Cdd:COG0550    3 LVIVESPAKAKTIAKYLGKD---------------------------YVVTASVGHLRDL-----PKPELDVDVENDF-- 48

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  85 APT----EKKEanPKLNMVKFLqveGRGCDYVVLWLDCDKEGENICFEVLDAVlpvmnnahNGEKTVFRARFSSITDTDI 160
Cdd:COG0550   49 EPKyeviPGKK--KQVKELKKL---AKKADEVILATDPDREGEAIAWHLLELL--------GDKKPVKRVVFNEITKKAI 115

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 161 CNAMTRLSEPDHNeaLsVDA---RQELDLRIGCAFTRFQTKYFQGKygdldsslISFGPCQTPTLGFCVERHDKIQSFKP 237
Cdd:COG0550  116 KEAFKNPRDIDMN--L-VDAqqaRRILDRLVGYNLSPLLWKKVKRG--------LSAGRVQSPALRLIVEREREIEAFVP 184

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 238 ETYWVLQAKVHTDKE--ESLLLDWDRVRVFDWEIAQMFLNMTKlEKEAWVEATSRKEKAKQRPLALNTVEMLRVASSALG 315
Cdd:COG0550  185 EEYWTIEATFKTGGGefTAKLVKIDGKKILDEEEAEAILAALK-GKTFTVTSVEKKPKKRNPPPPFTTSTLQQEASRKLG 263

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 316 MGPQHAMQIAERLYTQGYISYPRTETTHYPEnfDLKGSLRQQANhpywADSVKQLLAEGINRPRKGHDA-GDHPPITP-M 393
Cdd:COG0550  264 FSAKKTMSIAQRLYEVGLITYMRTDSVRLSE--DAVAAAREYIE----ALYGKEYLPEKPRVYKTSKNAqEAHEAIRPtG 337

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 394 KSATEAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCMGKTVISPGFTEIMPWQSVPLEE----SLPT 469
Cdd:COG0550  338 VTRTPESLSGDEFKLYDLIWKRFLASQMPPAEYETTTVTIEVGGEEFRASGKVIKFPGFLKVYGEGKDDEEEeeekRLPP 417

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 470 CQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIG---TDASIpvhINNICQRNYVTVEsGRRLKPTNLGIV--- 543
Cdd:COG0550  418 LKEGEKLKLKKIEPEQHFTKPPPRYTEASLVKAMEELGIGrpsTYASI---IETLQDRGYVERE-GKRLVPTELGFIvid 493

                        570       580       590       600       610
                 ....*....|....*....|....*....|....*....|....*....|.
gi 568995040 544 LVHGYYKidaELVLPTIRSAVEKQLNLIAQGKADYHQVLGHtldiFKRKFH 594
Cdd:COG0550  494 LLEEHFP---DLVDYEFTAKMEEKLDEIAEGKLDWKDVLEE----FYKPFK 537
TOPRIM_TopoIA_TopoIII cd03362
TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type ...
 3-167 1.92e-54

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: 185.13  E-value: 1.92e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040   3 TVLMVAEKPSLAQSIAKILSRGNMSSHKGLNGacsvhkytgTFAGQPVHFKMTSVCGHVMTLDFLGKYNKWDKVDPAE-L 81
Cdd:cd03362    1 MVLIIAEKPSVAKAIAKILGGGSKKKGKGRYY---------EFYGEGGGYVVTWASGHLLELDFPEEYDPWDKVWPLEdP 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  82 FSQAPTEKKEANPKLNMVKFLQVEGRGCDYVVLWLDCDKEGENICFEVLDAVLPVMNnahngeKTVFRARFSSITDTDIC 161
Cdd:cd03362   72 LFPAPFKLKVDKGKKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYAKCVKR------KPVKRAWFSSLTPKAIR 145


                 ....*.
gi 568995040 162 NAMTRL 167
Cdd:cd03362  146 RAFKNL 151
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 4-155 7.46e-11

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: 59.29  E-value: 7.46e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040    4 VLMVAEKPSLAQSIAKILSRGNmsshkglngacsvhkytgtfagqpvhFKMTSVCGHVMTLDFlgkynkwdkvdpaelfs 83
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGGF--------------------------QAVVAVLGHLLSLEK----------------- 37

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568995040   84 qaptekkeaNPKLNMVKFLQVEGRGCDYVVLWLDCDKEGENICFEVLDAVLPVmnnahngEKTVFRARFSSI 155
Cdd:pfam01751  38 ---------GPKKKALKALKELALKAKEVILATDPDREGEAIALKLLELKELL-------ENAGGRVEFSEL 93
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
4-137 5.30e-06

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 44.94  E-value: 5.30e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040     4 VLMVAEKPSLAQSIAKILSRgnmsshkglngacsvhkytgtfagqpvHFKMTSVCGHVMTLDflgkynkwdkvdpaelfs 83
Cdd:smart00493   2 VLIIVEGPADAIALEKAGGK---------------------------RGNVVALGGHLLSKE------------------ 36

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 568995040    84 qaptekkeanpklnMVKFLQVEGRGCdYVVLWLDCDKEGENICFEVLDAVLPVM 137
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 ...
 172-593 2.76e-148

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: 2.76e-148
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 172 HNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGdldsslISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQakvhtdk 251
Cdd:cd00186    1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRRKGV------LSAGRVQSPTLGLIVEREREIKAFVPEDYWEIK------- 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 252 eesllldwdrvrvfdweiaqmflnmtklekEAWVEATSRKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAERLYTQ 331
Cdd:cd00186   68 ------------------------------EAVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEA 117

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 332 GYISYPRTETTHYPENFDLKGSLRQQANHPYWADSVKQLLAeGINRPRKGHDAGDHPPITPMK----SATEAELGGDAWR 407
Cdd:cd00186  118 GLITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPLLG-RRNPKRGKKEQGAHEAIRPTKvaptPELEANLSEDEFK 196

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 408 LYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCMGKTVISPGFTEIMPWQSVPLEESLPTCQKGDTFTVGEVKMLEKQ 487
Cdd:cd00186  197 LYELIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEEEPPPLKEGDELKLEEVELEEKE 276

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 488 TSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEsGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVEKQ 567
Cdd:cd00186  277 TQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKE-KKKLIPTELGFAVIELLEKHFPELVDPEFTAKLEEK 355

                        410       420
                 ....*....|....*....|....*.
gi 568995040 568 LNLIAQGKADYHQVLGHTLDIFKRKF 593
Cdd:cd00186  356 LDEIAEGKKDYQEVLEEFYEEFKKIV 381
PRK07219 PRK07219
DNA topoisomerase I; Validated
 3-691 2.11e-143

DNA topoisomerase I; Validated


Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 444.44  E-value: 2.11e-143
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040   3 TVLMVAEKPSLAQSIAKILSRGNMS--SHKGLNgacsVHKytgtFAGQPVHFKMTSVCGHVMTLDFLGKYNKWDKVDPAE 80
Cdd:PRK07219   1 TELIIAEKNNAARRIADILSGGKAKkkRVNGVP----YYE----FERKGEKWIVIGLSGHIVTVDFPEEYGDWRDVDPAE 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  81 LFSqAPTEKKEANPklNMVKFLQVEGRGCDYVVLWLDCDKEGENICFEVLDAVLPVmnnahnGEKTVFRARFSSITDTDI 160
Cdd:PRK07219  73 LID-ADPVKKITKQ--NYINALKKLAKDADEIIIATDYDREGELIGKEAYHILREV------CQVPVKRARFSSLTKKEI 143

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 161 CNAMTRLSEPDHNEALSVDARQELDLRIGCAFTRFQTKYFqGKYGDLDssLISFGPCQTPTLGFCVERHDKIQSFKPETY 240
Cdd:PRK07219 144 RKAFENPDEIDFNLADAGEARQIIDLYWGAALTRFLSLSV-RQLGRWD--FLSVGRVQTPTLAFIVDREREIRAFDPEDY 220

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 241 WVLQAkVHTDKEESLLLDWDRV----RVFDWEIAQMFLNMTKLEKEAWVEATSRKEKAKQRPLALNTVEMLRVASSALGM 316
Cdd:PRK07219 221 WKIEA-LLDKEAQYFYRDLIGGheaeKFWDEEEAEEIYEKLKGAKEATVSSVKKRERTISPPAPFNTTEFLREASKIFGI 299

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 317 GPQHAMQIAERLYTQGYISYPRTETTHYPENFDLKGSLRQQANHPYWADSVKQLLAEGINRPRKG-HDAGDHPPITPMKS 395
Cdd:PRK07219 300 SPKRAMEIAEKLYTAGYISYPRTDNTVYPDDLDPKELLKKLSKKKEYGPYAESILEQENIKPTEGkKETTDHPPIHPVDV 379

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 396 ATEAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCMGKTVISPGFTEIMPWQSvPLEESLPTCQKGDT 475
Cdd:PRK07219 380 PKREELSDDEWKVYELIVRRFLATLADPAEWEYLKVELDVNGEIFKASGSRLVEEGWHEVYPYEK-FDEKELPDLEEGEK 458

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 476 FTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVtVESGrRLKPTNLGIVLVHGYYKIDAEL 555
Cdd:PRK07219 459 LKVNKIEIEAKETQPPKRYTQSSLIKEMEKRGLGTKATRHDIIEKLYKRGYV-IEGD-PPRPTDLGIAVIEALEKYAPEI 536

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 556 VLPTIRSAVEKQLNLIAQGKADYHQVLGHTLDIFKRKFHYFVDSIAGM-DELMEvSFSPLAATGKPLSRCGKCHRFMKYI 634
Cdd:PRK07219 537 VSEEMTAQLEADMQAIEDGKKKKEDVTEESREMLKEILSELKEKRKEIgDHLAG-SLKAENRSLKTIGKCPECGGDLIII 615

                        650       660       670       680       690       700
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568995040 635 QAKPSR--LHCS---HCDETYTLPQNGTIKLYKELrCPLDDFELVLWssgSRGKSYPL--CPYC 691
Cdd:PRK07219 616 RTDKGSrfVGCSgypDCRNTFPLPSTGRIKVLDEV-CEKCGLPVIKI---LRGKQTFVvgCPDC 675
Topoisom_bac pfam01131
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ...
 169-582 1.57e-138

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: 1.57e-138
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  169 EPDHNEALSVDARQELDLRIGCAFTRFQTKYFQGKygdldsSLISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVH 248
Cdd:pfam01131   1 EIDENLVDAQLARRELDWLIGFNLSRLLTLKLKGN------KLLSAGRVQTPTLALIVEREREIENFVPEPYWTIEATLK 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  249 TDKEESLLLDWDRVRVFDWEIAQMFLNmtKLEK-EAWVEATSRKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAER 327
Cdd:pfam01131  75 DGGGVFANAKWKRGRIFDKEEAEAILE--KLKKgTAVVTSVESKEKKKPPPLPFNTTTLQKEASRKLGFSAKKTMSIAQK 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  328 LYTQ-GYISYPRTETTHYPENFDLKGSLR-QQANHPYWADSVKQLLAEG-INRPRKGHDAGDHPPITPMKSAT-EAELGG 403
Cdd:pfam01131 153 LYEKhGLITYPRTDSTYLSDDATLKAILEyLTKNYGKYLPYAPRLLKKTkGKLTVGNAKVTAHEAIRPTGDIPvLPELSD 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  404 DAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCMGKTVISPGFTEIMPWQSVPLEESLPTCQKGDTFTVGEVKM 483
Cdd:pfam01131 233 DERKLYELIVRRFLASQMPPAVYETTTVVLEVGGEEFRASGKVILEDGWLKVYPYEKKEDEEELPELKEGEELKVTQVEV 312

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  484 LEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEsGRRLKPTNLGIVLVHGYYKIDaELVLPTIRSA 563
Cdd:pfam01131 313 EEKKTKPPPRYTEASLIKAMEKAGIGTPATRATIIETLLERGYVERK-KKSLVPTELGKALVEALEKFP-DLVDPELTAE 390

                         410
                  ....*....|....*....
gi 568995040  564 VEKQLNLIAQGKADYHQVL 582
Cdd:pfam01131 391 LEEKLDEIAEGKLDWKDVL 409
TOP1Ac smart00437
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ...
 290-544 1.02e-106

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: 1.02e-106
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040   290 RKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAERLYTQGYISYPRTETTHYPENFDLKGSLRQQANHP-YWADSVK 368
Cdd:smart00437   2 EKEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYIQKLYGkEYLDLAV 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040   369 QLLAEGInrPRKGHDA-GDHPPITPMKSAT----EAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCM 443
Cdd:smart00437  82 VLLKPRK--PRKGKKAqGAHEAIRPTKPIFtpelEKELSEDEFKLYELIWRRFLASQMPDAKYEETKVTIKIGGEKFKAK 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040   444 GKTVISPGFTEIMPWQSVPLEESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQ 523
Cdd:smart00437 160 GKTLLFDGWLKVYPEEKKEEEIELPTLKKGDELKVEEVEVEEKETKPPARYTEASLIKLMEKRGIGRPSTYASIIETLLD 239

                          250       260
                   ....*....|....*....|.
gi 568995040   524 RNYVTVEsGRRLKPTNLGIVL 544
Cdd:smart00437 240 RGYVTKK-KKKLIPTELGIAV 259
PRK07220 PRK07220
DNA topoisomerase I; Validated
 5-658 3.85e-101

DNA topoisomerase I; Validated


Pssm-ID: 180892 [Multi-domain]  Cd Length: 740  Bit Score: 330.57  E-value: 3.85e-101
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040   5 LMVAEKPSLAQSIAKILSRGNMSSHKglngACSVHKYTGTFAGQPvhfkmTSVCG---HVMTLDFLGKYNKWDKVDPAEL 81
Cdd:PRK07220   3 LIITEKNIAARRIAQILAPKKPKKTR----VSGVDVYRYEDNGDD-----TVVVGlsgHIVNIDFPKEYNNWQKVDARDL 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  82 FsQAPTEKKEANPKLnmVKFLQVEGRGCDYVVLWLDCDKEGENICFEVLDAVLPVmnnahNGEKTVFRARFSSITDTDIC 161
Cdd:PRK07220  74 I-DAEIITTPTQKKI--VTALKKLGKEADRVTIATDYDREGELIGVEALNIIKKV-----NPDIKFDRVRYSAITKKEIE 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 162 NAMTRLSEPDHNEALSVDARQELDLRIGCAFTRfqtkYFQGKYGDLDSSLISFGPCQTPTLGFCVERHDKIQSFKPETYW 241
Cdd:PRK07220 146 RAFSNPVEVDFNLADAGHSRQVIDLVWGAALTR----YISLAAGRLGKMFLSVGRVQSPTLALIVDREKEREAFVPTPYW 221

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 242 VLQAKVHTDKEEsLLLDWDRVRVfdWEIAQMFLNMTKLEKEAWVEATSRKEKAKQRPLALNTVEMLRVASSaLGMGPQHA 321
Cdd:PRK07220 222 EIYATLENNGET-FVAQHSTRRF--WEKEEADRVFEKLGKTAEVTEVEKGTKTDKPPTPFNTTEFISAANS-IGFSAANA 297

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 322 MQIAERLYTQGYISYPRTETTHYPENFDLKGSLRQQANHPYwADSVKQLLAEGINRPRKG-HDAGDHPPITPMKSATEAE 400
Cdd:PRK07220 298 MRIAESLYTNGYISYPRTDNTVYPESLDLREQIEIFAEGPF-GEYAQKLLEKGELVPTRGkKETTDHPPIYPASLAKKSE 376

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 401 LGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCMGKTVISPGFTEIMPWqSVPLEESLPTCQKGDTFTVGE 480
Cdd:PRK07220 377 LKEDEWKVYELVVRRFFATFAGPAEWETMKLRFDIGGEEFRANGSRLTEPGWRWYYPY-NAPEDRLLPELSEGEELKVKK 455

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 481 VKMLEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVtveSGRRLKPTNLGIVLVHGYYKIDAELVLPTI 560
Cdd:PRK07220 456 KEMLDKETQPPGRYGQGRLIKLMEDLGLGTKATRHEIISKLYSRAYI---HGNPIQPTNTAFAVVDALEKYAPTITKPDM 532

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 561 RSAVEKQLNLIAQGKADYHQVLGHTLDIFKRKFHYFVDSiagMDELMEVSFSPLAATgKPLSRCGKC-HRFMKYIQAKPS 639
Cdd:PRK07220 533 TSRLEEDMDKIAEGKIKEDAVLEESREMLEQVFDELDKN---REKIRESLREGLRED-KIIGKCPLCgSDLMVRRSKRGS 608

                        650       660
                 ....*....|....*....|...
gi 568995040 640 R-LHCS---HCDETYTLPQNGTI 658
Cdd:PRK07220 609 RfIGCEgypECTFSLPLPKSGQI 631
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
5-594 4.39e-93

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 440316 [Multi-domain]  Cd Length: 541  Bit Score: 303.17  E-value: 4.39e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040   5 LMVAEKPSLAQSIAKILSRGnmsshkglngacsvhkytgtfagqpvhFKMTSVCGHVMTLdflgkYNKWDKVDPAELFsq 84
Cdd:COG0550    3 LVIVESPAKAKTIAKYLGKD---------------------------YVVTASVGHLRDL-----PKPELDVDVENDF-- 48

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  85 APT----EKKEanPKLNMVKFLqveGRGCDYVVLWLDCDKEGENICFEVLDAVlpvmnnahNGEKTVFRARFSSITDTDI 160
Cdd:COG0550   49 EPKyeviPGKK--KQVKELKKL---AKKADEVILATDPDREGEAIAWHLLELL--------GDKKPVKRVVFNEITKKAI 115

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 161 CNAMTRLSEPDHNeaLsVDA---RQELDLRIGCAFTRFQTKYFQGKygdldsslISFGPCQTPTLGFCVERHDKIQSFKP 237
Cdd:COG0550  116 KEAFKNPRDIDMN--L-VDAqqaRRILDRLVGYNLSPLLWKKVKRG--------LSAGRVQSPALRLIVEREREIEAFVP 184

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 238 ETYWVLQAKVHTDKE--ESLLLDWDRVRVFDWEIAQMFLNMTKlEKEAWVEATSRKEKAKQRPLALNTVEMLRVASSALG 315
Cdd:COG0550  185 EEYWTIEATFKTGGGefTAKLVKIDGKKILDEEEAEAILAALK-GKTFTVTSVEKKPKKRNPPPPFTTSTLQQEASRKLG 263

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 316 MGPQHAMQIAERLYTQGYISYPRTETTHYPEnfDLKGSLRQQANhpywADSVKQLLAEGINRPRKGHDA-GDHPPITP-M 393
Cdd:COG0550  264 FSAKKTMSIAQRLYEVGLITYMRTDSVRLSE--DAVAAAREYIE----ALYGKEYLPEKPRVYKTSKNAqEAHEAIRPtG 337

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 394 KSATEAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCMGKTVISPGFTEIMPWQSVPLEE----SLPT 469
Cdd:COG0550  338 VTRTPESLSGDEFKLYDLIWKRFLASQMPPAEYETTTVTIEVGGEEFRASGKVIKFPGFLKVYGEGKDDEEEeeekRLPP 417

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 470 CQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIG---TDASIpvhINNICQRNYVTVEsGRRLKPTNLGIV--- 543
Cdd:COG0550  418 LKEGEKLKLKKIEPEQHFTKPPPRYTEASLVKAMEELGIGrpsTYASI---IETLQDRGYVERE-GKRLVPTELGFIvid 493

                        570       580       590       600       610
                 ....*....|....*....|....*....|....*....|....*....|.
gi 568995040 544 LVHGYYKidaELVLPTIRSAVEKQLNLIAQGKADYHQVLGHtldiFKRKFH 594
Cdd:COG0550  494 LLEEHFP---DLVDYEFTAKMEEKLDEIAEGKLDWKDVLEE----FYKPFK 537
PRK14973 PRK14973
DNA topoisomerase I; Provisional
 5-621 6.50e-80

DNA topoisomerase I; Provisional


Pssm-ID: 184936 [Multi-domain]  Cd Length: 936  Bit Score: 277.50  E-value: 6.50e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040   5 LMVAEKPSLAQSIAKILSRGNMSSHKGlNGACSVHKYTGTFAgqpvhfkmTSVCGHVMTLDFLGKYNKWDKVD--PAELF 82
Cdd:PRK14973   3 LIIAEKNIAANRIAQILAGKTKVQVKK-DGGVSTYSFDDTVV--------VGLRGHVVEVDFEPGYTNWRSEEhtPRSLI 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  83 S----QAPTEKKeanpklnMVKFLQVEGRGCDYVVLWLDCDKEGENICFEVLDAVlpvmnNAHNGEKTVFRARFSSITDT 158
Cdd:PRK14973  74 DadtiKKPTEKK-------IVGLIQKLAKKADRVTIATDFDTEGELIGKEAYELV-----RAVNPKVPIDRARFSAITKE 141

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 159 DICNAMTRLSEPDHNEALSVDARQELDLRIGCAFTRFQTkyFQGKYGDldSSLISFGPCQTPTLGFCVERHDKIQSFKPE 238
Cdd:PRK14973 142 EIVTAFAEPTDLDFALAAAGEARQIIDLIWGASLTRFIS--LAAHRGG--DNILSVGRVQSPTLAMIVDREKEIEAFVPE 217

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 239 TYWVLQakVHTDKE-ESLLLDWDRVRVFDWEIAqmflnmtKLEKEAWVE---ATSRKEKAKQ--RPLALNTVEMLrVASS 312
Cdd:PRK14973 218 KYWMLS--LATEKDgEGIEARHTHGRFTDSAAA-------EAAYDATKEplvVTEVKEGHKVdrAPTPFDTTTFI-VAAS 287

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 313 ALGMGPQHAMQIAERLYTQGYISYPRTETTHYPENFDLKGSLRQQANHPYWADsVKQLLAEGINRPRKGH-DAGDHPPIT 391
Cdd:PRK14973 288 RLGFSAANAMRIAEDLYMNGYISYPRTDNTIYPKSLDLNGVLATLAKGAFSKD-VAWVKDNRRPVPTRGKkSSTDHPPIH 366

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 392 PMKSATEAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCMGKTVISPGFTEIMPWqSVPLEESLPTCQ 471
Cdd:PRK14973 367 PTGVATREELGDDRWKLYELVVRRFLATLSPDAEWATMKVNFDAGGEPYTATGGRLLEAGWRTVYPY-SEAKENILPAFA 445

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 472 KGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVtveSGRRLKPTNLGIVLVHGYYKI 551
Cdd:PRK14973 446 LGEKLPILAVNLEEKETQPPARYSQSRLIQRMEELGLGTKSTRHEVIGKLVSRKYI---EGNPLRPTLVGRAVTESLEEH 522

                        570       580       590       600       610       620       630
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568995040 552 DAELVLPTIRSAVEKQLNLIAQGKADYHQVLGHTLDIFKRKFHYFVDSIAGM-DELM-----EVSFSPLAATGKPL 621
Cdd:PRK14973 523 AGTITEPDMTQTLEEHMQQIKERKRTRDDVVTESRKMLHRAFDELEANEAVIgRDIMertaeELTIGPCPVCGKDL 598
PRK05776 PRK05776
DNA topoisomerase I; Provisional
 4-629 3.37e-59

DNA topoisomerase I; Provisional


Pssm-ID: 235602 [Multi-domain]  Cd Length: 670  Bit Score: 214.09  E-value: 3.37e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040   4 VLMVAEKPSLAQSIAKILSRGNMSSHKGlngacSVHKYTGTFAGQpvHFKMTSVCGHVMTLDFLGK-YNKWDkVDPAELF 82
Cdd:PRK05776   3 ILVIAEKPKAARKIAEALSEKPIRCRIY-----GVPYWIVKRDGK--KIVVAPAAGHLFGLHTKSKgFPVFD-YEWKPLY 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  83 sQAPTEKKEANPKLNMVKFLqveGRGCDYVVLWLDCDKEGENICFEVLdavlpvmnNAHNGEKTVFRARFSSITDTDICN 162
Cdd:PRK05776  75 -EIDKGSKYTKKYYELLSSL---SKYADEFINACDYDIEGSVIGYLII--------KYLGDPKKAKRMKFSALTKSDIRR 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 163 AMTRLSEPDHNEALSVDARQELDLRIGCAFTRFQT---KYFQGKygdldSSLISFGPCQTPTLGFCVERHDKIQSFKPET 239
Cdd:PRK05776 143 AFRNLETLDYEMINAGIARHELDWLWGINVSRALMssvRDASGK-----RVILSAGRVQSPTLKYVVEREIERNLFVPLP 217

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 240 YWVLQAKVHTDKEESllldwdRVRVFDWEI-----AQMFLNMTKLEKEAWVEATSRKEKAKQRPLALNTVEMLRVASSAL 314
Cdd:PRK05776 218 YFSVSIIIEKNGYEF------TLKYENKKFetkeeAKEILEEIKKTGYLKVTKVEVKIEILEPPPPFNLGDLQVEAARIY 291

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 315 GMGPQHAMQIAERLYTQGYISYPRTETTHYPENFDLKGSLRQQANHPYWADSVKQLLAE--GINRPRKG-HDAGDHPPIT 391
Cdd:PRK05776 292 GFSPYKTQSIAEDLYLDGLISYPRTNSQKLPPTLNIRNILKGLSRSPQYRPLVNLLLKEtkGVLKPVQGpKDDPAHPAIY 371

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 392 PMKSATEaELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIG--PEHFTCMGKTVISPGFTEIMPWqSVPLEESLPT 469
Cdd:PRK05776 372 PTGEPPK-NLSKDEFKLYDLIVRRFLASFAAPAVLSNTIVTLRVPgfPLVFSASGQRIEERGWLKYYPF-HKFDEEELPL 449

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 470 CQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTvESGRRLKPTNLGIVLVHGYY 549
Cdd:PRK05776 450 LKKGERVKIVDVKVRKSYTKPPSRYSKASLLKWMESVGIGTEATRARIIETLFKRGYLT-SNGKYIEVTPLGFGVAEVLE 528

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 550 KIDAELVLPTIRSAVEKQLNLIAQGKADYHQVLGHT-------LDIFKRKFHYFVDSIAGMDELMevsfsplaatgKPLS 622
Cdd:PRK05776 529 KYFPDIVSVELTRDFEEKLEMIRTGKATREEVIEEAketlnklLEEFKKNKDEIGEELAKALGLI-----------KPVG 597


                 ....*..
gi 568995040 623 RCGKCHR 629
Cdd:PRK05776 598 KCKICGR 604
TOPRIM_TopoIA_TopoIII cd03362
TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type ...
 3-167 1.92e-54

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: 185.13  E-value: 1.92e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040   3 TVLMVAEKPSLAQSIAKILSRGNMSSHKGLNGacsvhkytgTFAGQPVHFKMTSVCGHVMTLDFLGKYNKWDKVDPAE-L 81
Cdd:cd03362    1 MVLIIAEKPSVAKAIAKILGGGSKKKGKGRYY---------EFYGEGGGYVVTWASGHLLELDFPEEYDPWDKVWPLEdP 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  82 FSQAPTEKKEANPKLNMVKFLQVEGRGCDYVVLWLDCDKEGENICFEVLDAVLPVMNnahngeKTVFRARFSSITDTDIC 161
Cdd:cd03362   72 LFPAPFKLKVDKGKKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYAKCVKR------KPVKRAWFSSLTPKAIR 145


                 ....*.
gi 568995040 162 NAMTRL 167
Cdd:cd03362  146 RAFKNL 151
PRK07726 PRK07726
DNA topoisomerase 3;
1-646 3.04e-52

DNA topoisomerase 3;


Pssm-ID: 236078 [Multi-domain]  Cd Length: 658  Bit Score: 193.84  E-value: 3.04e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040   1 MKTVLmvAEKPSLAQSIAKILsrGNMSSHKG-LNGAcsvhKYTGTFAgqpvhfkmtsvCGHVMTL----DFLGKYNKWDK 75
Cdd:PRK07726   1 MRLFI--AEKPSVGRDIADVL--KPHKKGDGyIEGN----GYIVTWA-----------IGHLLELaepeAYDERYKRWRL 61

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  76 VD----PAELFSQApteKKEANPKLNMVKFL--QVegrgcDYVVLWLDCDKEGENICFEVLDAVlpvmnnahNGEKTVFR 149
Cdd:PRK07726  62 EDlpiiPEKWKLVV---KKKTAKQFNVVKKLlkQA-----TEIVIATDADREGELIAREILDYC--------GVRKPIKR 125

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 150 ARFSSITDTDICNAMTRL-----SEPDHNEALsvdARQELDLRIGCAFTR-FQTKYFQGKYGDLdsslISFGPCQTPTLG 223
Cdd:PRK07726 126 LWISSLTDKAIKRAFANLkpgkeTIPLYYSAL---ARSRADWLVGINMTRaYTLLGRKAGYNGV----LSVGRVQTPTLA 198

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 224 FCVERHDKIQSFKPETYWVLQAKVHTDKEESLLldW--------DRVRVFDWEIAQMFLNMTKlEKEAWVEATSRKEKAK 295
Cdd:PRK07726 199 LVVRRDEEIENFVPKPYWEVEAHLTPGERFTAK--WqpsepyqdEEGRLLDRPLAEQVVARIQ-GQPAKVTEVETKRKKE 275

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 296 QRPLALNTVEMLRVASSALGMGPQHAMQIAERLY-TQGYISYPRTETTHYPEnfDLKGSLRQ-----QANHPYwadsvKQ 369
Cdd:PRK07726 276 YAPLLYDLSELQIDANKRFGLSAKETLDIAQSLYeTHKLITYPRTDSRYLPE--DMVATLPEvlnaiSKVDPY-----LL 348

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 370 LLAEGINRPRKGH---DA--GDHPPITP-MKSATEAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCM 443
Cdd:PRK07726 349 LAPPVLDPSIRSRawnDKkvTAHHAIIPtEQPPNLSKLSEDERKVYDLIARRYLAQFLPPAEYDKTTIELEIAGGTFIAK 428

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 444 GKTVISPGFTEIMPWQSVPLEES--LPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLM-----------------E 504
Cdd:PRK07726 429 GKQVVEAGWKALLGKKEEDEEKEqpLPVLAKGDELKVEKGEVKEGQTQPPKRFTEGTLLSAMeniarfvqdkelkktlkE 508

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 505 KHGIGTDA---SIpvhINNICQRNYVTVEsGRRLKPTNLGIVLvhgyykIDA---ELVLPTIRSAVEKQLNLIAQGKADY 578
Cdd:PRK07726 509 TDGLGTEAtraGI---IEKLFKRGYLEKK-GKYIHATDKGKQL------IDAlpeELTSPDMTAKWEQALDQISEGQLSY 578

                        650       660       670       680       690       700       710
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568995040 579 HQvlghtldifkrkfhyFVDSIAG-MDELME---VSFSPLAATGKPLSRCGKCHRFMKyiQAKPSRLHCSHC 646
Cdd:PRK07726 579 QD---------------FMQPLKQwLKQLVEqakQSSEKYKFDNLTGPKCPDCGKPML--KVKGKNGKMLVC 633
TOPRIM_TopoIA cd01028
TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 3-167 3.40e-44

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: 156.23  E-value: 3.40e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040   3 TVLMVAEKPSLAQSIAKILSRGNMSSHkglngacsvhkytgtFAGQPVHFKMTSVCGHVMTLDFLGKYNKWDKVDPAELF 82
Cdd:cd01028    1 KVLIIAEKPSKAKTIAKILGKGSKKKG---------------FYGEGGGYVVTASVGHLLELPFPEEYVDWDKDWPLELF 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  83 sQAPTEKKEANPKLNMVKFLQVEGRGCDYVVLWLDCDKEGENICFEVLDAvlpvmnnAHNGEKTVFRARFSSITDTDICN 162
Cdd:cd01028   66 -PFEPKYVVIPDKKKQLKALKKLAKKADEIVLATDPDREGELIAWEILEV-------LKCDNKPVKRAWFSEITPKAIRE 137


                 ....*
gi 568995040 163 AMTRL 167
Cdd:cd01028  138 AFKNL 142
PRK08173 PRK08173
DNA topoisomerase III; Validated
 1-647 1.55e-37

DNA topoisomerase III; Validated


Pssm-ID: 236172 [Multi-domain]  Cd Length: 862  Bit Score: 151.74  E-value: 1.55e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040   1 MKTVLMVAEKPSLAQSIAKILsrgnmsshkglngacsvhkytGTFAGQPVHFK-----MTSVCGHVMTL----DFLGKYN 71
Cdd:PRK08173   1 MSKALIIAEKPSVANDIARAL---------------------GGFTKHDEYFEsdeyvLSSAVGHLLEIaapeEYEVKRG 59

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  72 KWD----KVDPaELFSQAPTEKKEANPKLnMVKFLQVEgrgcDYVVLWLDCD--KEGENICFEVLDAVlpvmnnahNGEK 145
Cdd:PRK08173  60 KWSfahlPVIP-PHFDLNPIAKTESRLKV-LTKLIKRK----DVTRLINACDagREGELIFRLIAQHA--------KAKK 125

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 146 TVFRARFSSITDTDICNAMTRLSEPDHNEALSvDA---RQELDLRIGCAFTRFQTKyFQGKYGDLdsSLISFGPCQTPTL 222
Cdd:PRK08173 126 PVKRLWLQSMTPQAIRDGFANLRSDEDMQPLA-DAarcRSEADWLVGINGTRAMTA-FNSKGGGF--FLTTVGRVQTPTL 201

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 223 GFCVERHDKIQSFKPETYWVLQA----------------KVHTDKEESllldWDRV-RVFDWEIAQMFLNMTKlEKEAWV 285
Cdd:PRK08173 202 SIVVEREEKIRRFVPRDYWEVRAefvaaagfyegrwfdpKFKKDEFDP----EKRAsRLWSEAAAEAIVAACR-GKPGTV 276

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 286 EATSrKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAERLYTQ-GYISYPRTETTHYPENF--DLKGSLRQQANHPY 362
Cdd:PRK08173 277 TEES-KPSTQLSPLLFDLTSLQREANGRFGFSAKNTLGLAQALYEKhKVLTYPRTDSRALPEDYlgTVKQTLEMLKESNN 355

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 363 WADSVKQLLAEGINRPRK----GHDAGDHPPITPM----KSATEAELggdawRLYEYITRHFIATVSHDCKYLQSTISFR 434
Cdd:PRK08173 356 YLPHAKQILDKGWVKPNKrifdNSKISDHFAIIPTlqapKSLSEPEQ-----KLYDLVVKRFLAVFFPAAEFLVTTRITE 430

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 435 IGPEHFTCMGKTVISPGFTEIMPWQSVPLEESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLME---------- 504
Cdd:PRK08173 431 VAGHHFKTEGKVLVNPGWLAVYGKEAQGADANLVPVQKGEKVKTDKIEAVALTTKPPARYNEATLLSAMEgagklvedde 510

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 505 ------KHGIGTDASIPVHINNICQRNYVtVESGRRLKPT----NLgIVLVHGyYKIDaELVLPTIRSAVEKQLNLIAQG 574
Cdd:PRK08173 511 lreamaEKGLGTPATRAAIIEGLLGEKYL-VREGRELIPTakafQL-MTLLRG-LGVE-ELTSPELTGEWEYKLSQIERG 586

                        650       660       670       680       690       700       710
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568995040 575 K----ADYHQVLGHTLDIFKRKFHYFVDSIAGmdelmevSFSPLAAtgkPLSRCGkchrfmKYIQAKPSRLHCSHCD 647
Cdd:PRK08173 587 KlsrdAFMQEIAQMTQQIVKRAKEYDSDTIPG-------DYATLQT---PCPNCG------GVVKENYRRFACTKCD 647
PRK06599 PRK06599
DNA topoisomerase I; Validated
 1-688 6.91e-35

DNA topoisomerase I; Validated


Pssm-ID: 235840 [Multi-domain]  Cd Length: 675  Bit Score: 142.30  E-value: 6.91e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040   1 MKTVLMVAEKPSLAQSIAKILSRGnmsshkglngacsvhkytgtfagqpvhFKMTSVCGHVMTLDflgkyNKWDKVDPAE 80
Cdd:PRK06599   1 MAKKLVIVESPAKAKTIKKYLGKD---------------------------YKVLASFGHVRDLP-----KKKGGVDPDN 48

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  81 LFsqAPT----EKKEanpklNMVKFLQVEGRGCDYVVLWLDCDKEGENICFEVLDavlpVMNNAHNGEKTVFRARFSSIT 156
Cdd:PRK06599  49 DF--APKyeiiEGKE-----KVVDALKKAAKKADAVYLATDPDREGEAIAWHIAE----VLKEAKLKDKNVKRVVFNEIT 117

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 157 DTDICNAmtrLSEP-DHNEALsVD---ARQELDLRIGcaftrFQ------TKYFQGKygdldssliSFGPCQTPTLGFCV 226
Cdd:PRK06599 118 KKAVQEA---IENPrDIDMDL-VDaqqARRALDYLVG-----FKlspllwKKVRRGL---------SAGRVQSVALRLIC 179

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 227 ERHDKIQSFKPETYWVLQAKVHTDKEESL---LLDWD-----RVRVFDWEIAQMFLNmtKLEKEAW-VEATSRKEKAKQR 297
Cdd:PRK06599 180 EREDEIEAFIPQEYWTIEADLATSNGEPFtakLVEVNgkkleKFSITNEEQAKALVK--ALEGQAYtVDKIEKKERKRNP 257

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 298 PLALNTVEMLRVASSALGMGPQHAMQIAERLY--------TQGYISYPRTetthypenfdlkgslrqqanhpywaDSVkQ 369
Cdd:PRK06599 258 PPPFITSTLQQEASRKLGFSAKKTMRIAQKLYegidlgegTVGLITYMRT-------------------------DSV-R 311

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 370 LLAEGINRPRK------GHD-AGDHPPI--TPMKSATEAE------------------LGGDAWRLYEYITRHFIATVSH 422
Cdd:PRK06599 312 LSNEALDEARKyitkkyGKEyLPAKPRVykKKSKNAQEAHeairptsinrtpeslkpyLTPDQFKLYELIWKRTVASQMA 391

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 423 DCKYLQSTISF--RIGPEHFTCMGKTVISPGFTEIMPwQSVPLEES-----LPTCQKGDTFTVGEVkmLEKQ--TSPPDY 493
Cdd:PRK06599 392 PAILDQTSVDIasENGKYVFRATGSVILFPGFLKVYG-ESKDDEEEddeklLPPLKEGEKLKLDEL--LPEQhfTEPPPR 468

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 494 LTEAELITLMEKHGIG---TDASIpvhINNICQRNYVTVEsGRRLKPTNLG-IV---LVHGY-----YKIDAELvlptir 561
Cdd:PRK06599 469 YSEASLVKKLEEYGIGrpsTYASI---ISTLQDREYVELE-KKRFIPTDLGrIVndfLVEHFpkyvdYDFTAGL------ 538

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 562 savEKQLNLIAQGKADYHQVLGHtldiFKRKFHYFVDSIAGMDELMEVSFSPLAAT-----GKPLS-RCGKCHRFmkyiq 635
Cdd:PRK06599 539 ---EDELDEIAEGKKDWKPVLRE----FWEPFISNLEKVEEDVRTEKVTQEETDETcpkcgGGPLVlKLGKNGKF----- 606

                        730       740       750       760       770       780
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568995040 636 akpsrLHCSH---CDETYTLPQNG-----TIKLYKELRCPLDDFELVLwSSGSRGK-----SYPLC 688
Cdd:PRK06599 607 -----LGCSGypeCKYTKNITRDEdepieEEEIVEEEKCPKCGGPLVL-KKGRYGKflacsGYPEC 666
PRK07561 PRK07561
DNA topoisomerase I subunit omega; Validated
 108-631 7.39e-34

DNA topoisomerase I subunit omega; Validated


Pssm-ID: 236048 [Multi-domain]  Cd Length: 859  Bit Score: 139.93  E-value: 7.39e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 108 GCDYVVLWLDCDKEGENICF---EVLDAvlpvmnnahnGEKTVFRARFSSITDTDICNAMtrlSEP-DHNEALsVDA--- 180
Cdd:PRK07561  86 DADELYLATDPDREGEAIAWhllEVLGG----------DDVPVKRVVFNEITKNAIQEAF---ENPrELDINL-VNAqqa 151

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 181 RQELDlRIgcaftrfqtkyfqgkYGDLDSSLI--------SFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVHTDKE 252
Cdd:PRK07561 152 RRFLD-RL---------------VGYMVSPLLwkkiarglSAGRVQSVAVRLIVEREREIEAFVPEEYWDIHADLTTPRG 215

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 253 ESLLLD--------WDRVRVFDWEIAQMFLnmTKLEKEAWVeATSRKEKAKQR-PLALNTVEMLR-VASSALGMGPQHAM 322
Cdd:PRK07561 216 DAFEARlthldgkkFAPVDLLNEAQAEAAV--AALEGARYS-VASVEDKPTTRkPSAPFTTSTLQqEASRKLGFSVKKTM 292

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 323 QIAERLYTQGYISYPRTetthypenfdlkgslrqqanhpywaDSVkQLLAEGINRPRK--GHDAGDH--PPiTP------ 392
Cdd:PRK07561 293 RIAQRLYEAGYITYMRT-------------------------DST-NLSQEAINAARGyiGDNYGKKylPE-KPrqyssk 345

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 393 MKSATEA-----------------ELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCMGKTVISPGFTEI 455
Cdd:PRK07561 346 AKNAQEAheairpsdvfrtpdqlkGLEGDAQRLYELIWKRFVASQMAPARYDSTTVTIAAGDAELRATGRVLRFDGFLKV 425

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 456 MPWQS--VPLEES--LPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIG---TDASIpvhINNICQRNYVT 528
Cdd:PRK07561 426 YVEGRddALDDEDrrLPALKVGDALTLEKLDPTQHFTKPPARYSEASLVKELEKLGIGrpsTYASI---ISTIQDRGYVR 502

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 529 VEsGRRLKPTNLG-IV--LVHGYYkidAELVLPTIRSAVEKQLNLIAQGKADYHQVlghtLDIFKRKFHYFVDSIA---- 601
Cdd:PRK07561 503 LE-NRRFYPEKMGrIVtdRLEEFF---PRLVDYDFTARMEEELDDIANGEADWKPV----LDDFYKDFSQQLEKAEelre 574

                        570       580       590
                 ....*....|....*....|....*....|...
gi 568995040 602 --GMDELMEVsfsplaatgkPLSR-CGKCHRFM 631
Cdd:PRK07561 575 egGMRPNQMV----------ITDRdCPTCGRGM 597
TOP1Bc smart00436
Bacterial DNA topoisomeraes I ATP-binding domain; Extension of TOPRIM in Bacterial DNA ...
 147-242 1.67e-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: 1.67e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040   147 VFRARFSSITDTDICNAMTRLSEPDHNEALSVDARQELDLRIGCAFTRFQTKYFQGKYgdldsslISFGPCQTPTLGFCV 226
Cdd:smart00436   1 IKRIEFSEITKKAIREALKNPREIDENLVNAQLARRILDRLIGFNLSRLLTKKLRNGV-------LSAGRVQTPTLGLIV 73

                           90
                   ....*....|....*.
gi 568995040   227 ERHDKIQSFKPETYWV 242
Cdd:smart00436  74 EREREIKNFVPKPYWE 89
PRK08780 PRK08780
DNA topoisomerase I; Provisional
 1-635 4.42e-29

DNA topoisomerase I; Provisional


Pssm-ID: 181555 [Multi-domain]  Cd Length: 780  Bit Score: 124.49  E-value: 4.42e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040   1 MKTVLMVAEKPSLAQSIAKILSRGnmsshkglngacsvhkytgtfagqpvhFKMTSVCGHVMTLdflgkYNKWDKVDPAE 80
Cdd:PRK08780   1 MSKHLVIVESPAKAKTINKYLGKD---------------------------FTVLASYGHVRDL-----VPKEGAVDPEN 48

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  81 LFSQ--APTEKKEANpklnmVKFLQVEGRGCDYVVLWLDCDKEGENICFEVLDAVlpvmnnAHNG---EKTVFRARFSSI 155
Cdd:PRK08780  49 GFAMryDLIDKNEKH-----VEAIAKAAKSADDLYLATDPDREGEAISWHLAEIL------KERGllkDKPMQRVVFTEI 117

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 156 TDTDICNAMtrlsepDHNEALSVD------ARQELDLRIGCAFTRFQTKYFQgkygdldsSLISFGPCQTPTLGFCVERH 229
Cdd:PRK08780 118 TPRAIKEAM------AKPRDIASDlvdaqqARRALDYLVGFNLSPLLWRKIQ--------RGLSAGRVQSPALRMIVERE 183

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 230 DKIQSFKPETYWVLQAKVHTDKE----ESLLLDWDRVRVF---DWEIAQMFLNmtKLEKEA----WVEATSRKEKaKQRP 298
Cdd:PRK08780 184 EEIEAFIAREYWSIEADCAHPSQpfnaKLIKLDGQKFEQFtitDGDTAEAARL--RIQQAAqgtlHVTDVESKER-KRNP 260

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 299 LALNTVEMLRV-ASSALGMGPQHAMQIAERLY---------TQGYISYPRTETTHYPEnfDLKGSLRQQANHPYWADSVK 368
Cdd:PRK08780 261 APPFTTSTLQQeASRKLGFTTRRTMQVAQKLYegvdlgdegSVGLITYMRTDSVNLSQ--DALAEIRDVIARDYGTASLP 338

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 369 QLLAEGINRPRKGHDAgdHPPITP---MKSATE--AELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPEH-FTC 442
Cdd:PRK08780 339 DQPNTYKTKSKNAQEA--HEAVRPtsaLRTPAQvaRFLSDDQRRLYELIWKRAVACQMIPATLNTVSVDLAAGSEHvFRA 416

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 443 MGKTVISPGFTEIM-------PWQSVPLEESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIG---TDA 512
Cdd:PRK08780 417 TGSTVVVPGFLAVYeegkddkSAEDEDEGRKLPPMKEGDNVPLERIRAEQHFTEPPPRYTEASLVKALEEYGIGrpsTYA 496

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 513 SIpvhINNICQRNYVTVEsGRRLKPTNLGIVlVHGY----------YKIDAELvlptirsavEKQLNLIAQGKADYHQVL 582
Cdd:PRK08780 497 SI---ISTLQFRKYVEME-GRRFRPTDVGRA-VNKFltghftryvdYDFTARL---------EDDLDAVSRGEKEWIPLM 562

                        650       660       670       680       690
                 ....*....|....*....|....*....|....*....|....*....|....
gi 568995040 583 GHTLDIFKRKFHYFVDSIAGMDELMEVSFSPLAATGKPLS-RCGkchRFMKYIQ 635
Cdd:PRK08780 563 EKFWGPFKELVEEKKDSVDRTEAGQVRELGTDPKSGKPVSvRIG---RFGPMVQ 613
PRK14724 PRK14724
DNA topoisomerase III; Provisional
 1-538 1.57e-24

DNA topoisomerase III; Provisional


Pssm-ID: 237803 [Multi-domain]  Cd Length: 987  Bit Score: 110.43  E-value: 1.57e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040   1 MKTvLMVAEKPSLAQSIAKILSrgnmsshkglngacsvhKYTGTFAGQPVHFK-----MTSVCGHVMTL----DFLGKYN 71
Cdd:PRK14724   1 TKT-LVIAEKPSVAQDIVRALT-----------------PVAGKFEKHDEHFEsdsyvVTSAVGHLVEIqapeEFDVKRG 62

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  72 KWD----KVDPAElFSQAPTEKKEAnpKLNMVkFLQVEGRGCDYVVLWLDCDKEGENIcFEVLDAVlpvMNNAHNG-EKT 146
Cdd:PRK14724  63 KWSfanlPVIPPY-FDLKPVDKTKT--RLNAV-VKLAKRKDVTELVNACDAGREGELI-FRLIEQY---AGGAKGGlGKP 134

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 147 VFRARFSSITDTDICNAMTRLSEPDHNEALSVDAR--QELDLRIGCAFTRFQTKyFQGKYGDLdsSLISFGPCQTPTLGF 224
Cdd:PRK14724 135 VKRLWLQSMTPQAIRDGFDNLRSDAQMQGLASAARsrSEADWLVGINGTRAMTA-FNSRDGGF--FLTTVGRVQTPTLSL 211

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 225 CVERHDKIQSFKPETYWVLQAKVHTDKEESL--LLD--WDRV---------RVFDWEIAQMFLNMTKlEKEAWVEATSrK 291
Cdd:PRK14724 212 VVEREEKIRKFVSRDYWEIHAGFHAEAGEYLgkWFDpqWKKAsddpearadRVWSEREARAIADAVR-GKAATVTEES-K 289

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 292 EKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAERLYTQ-GYISYPRTETTHYPEN--------FDL--KGSLRQQANH 360
Cdd:PRK14724 290 PTTQASPLLFDLTSLQREANGKFGFSAKTTLALAQSLYERhKALTYPRTDSRALPEDylpvakqtFEMlaTSGMRHLAPF 369

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 361 pywadsVKQLLAEGINRPRK----GHDAGDHPPITPMKSA----TEAElggdaWRLYEYITRHFIATVSHDCKYLQST-I 431
Cdd:PRK14724 370 ------AQQALDGNYVRPSKrifdNSKVSDHFAIIPTTQApsglSEAE-----QKLYDLVVRRFMAVFFPSAEYQVTTrI 438

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 432 SFRIGpEHFTCMGKTVISPGFTEIMPWQSVPLEE---------SLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITL 502
Cdd:PRK14724 439 SQVVG-HSFKTEGKVLVKPGWLAIYGKEAANEVEdakdgdkgqPLVPVKPGEMVRTEFAEAKGLKTKPPARYSEATLLGA 517

                        570       580       590       600       610
                 ....*....|....*....|....*....|....*....|....*....|..
gi 568995040 503 ME----------------KHGIGTDASIPVHINNICQRNYVTVEsGRRLKPT 538
Cdd:PRK14724 518 MEsagkqidddelreamqEKGLGTPATRAAIIEGLLTEKYMLRE-GRELIPT 568
PRK06319 PRK06319
DNA topoisomerase I/SWI domain fusion protein; Validated
 1-589 2.88e-22

DNA topoisomerase I/SWI domain fusion protein; Validated


Pssm-ID: 235778 [Multi-domain]  Cd Length: 860  Bit Score: 102.98  E-value: 2.88e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040   1 MKTVLMVAEKPSLAQSIAKILSRGnmsshkglngacsvhkytgtfagqpvhFKMTSVCGHVMTL-----------DFLGK 69
Cdd:PRK06319   1 MKKSLIIVESPAKIKTLQKLLGEG---------------------------FIFASSLGHIVDLpakefgidienDFEPD 53

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040  70 YnkwdkvdpaelfsQAPTEKKEanpklnMVKFLQVEGRGCDYVVLWLDCDKEGENICFEVLDaVLPvmNNAHngektVFR 149
Cdd:PRK06319  54 Y-------------QILPDKEE------VINKICKLAKKCDVVYLSPDPDREGEAIAWHIAN-QLP--KNTK-----IQR 106

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 150 ARFSSITDTDICNAMTRLSEPDHNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGdldsslISFGPCQTPTLGFCVERH 229
Cdd:PRK06319 107 ISFNAITKGAVTEALKHPREIDMALVNAQQARRLLDRIVGYKISPILSRKLQRRSG------VSAGRVQSVALKLVVDRE 180

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 230 DKIQSFKPETYWVLQAKVHTDKEESLLldWDRVRVFD---WE--------IAQMFLNMTK---------LEKEAW-VEAT 288
Cdd:PRK06319 181 KAIEAFVPVEYWNIRVHLKDPKTQKTF--WAHLYSVDgkkWEkeipegktEDEVLLINSKekadhivelLESATYtVTRV 258

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 289 SRKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAERLY---------TQGYISYPRTETTHY-PENFD-LKGSLRQQ 357
Cdd:PRK06319 259 ESKEKRRNAYPPFITSTLQQEASRHFRFSSSRTMNIAQTLYegvdldsegATGLITYMRTDSVRTdPEALKqVRKYIEGT 338

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 358 ANHPYWADSVKQLLAEginrpRKGHDAgdHPPITPMKSATEAE-----LGGDAWRLYEYITRHFIATVSHDCKY--LQST 430
Cdd:PRK06319 339 FGKEFLPSSPNVYTTK-----KMAQDA--HEAIRPTDITLTPEklrskLTEDQYKLYSLIWKRFVASQMIPAIYdtLAIR 411

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 431 ISFRIGPEhFTCMGKTVISPGFT---EIMPWQSVPLEE--SLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEK 505
Cdd:PRK06319 412 ITTNKGID-LRATGSLLKFKGFLavyEEKRDDEGDEEEniHLPKLHEQDVLTKEELSAEQAFTKPLPRFTEASLVKELEK 490

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 506 HGIGTDASIPVHINNICQRNYvTVESGRRLKPTNLGIVLVHGYykidaELVLPTI-----RSAVEKQLNLIAQGKADYHQ 580
Cdd:PRK06319 491 SGIGRPSTYATIMNKIQSREY-TLKENQRLRPTELGKIISQFL-----ETNFPRImdigfTALMEDELELIADNKKPWKL 564


                 ....*....
gi 568995040 581 VLGHTLDIF 589
Cdd:PRK06319 565 LLQEFWELF 573
PTZ00407 PTZ00407
DNA topoisomerase IA; Provisional
 112-573 5.20e-11

DNA topoisomerase IA; Provisional


Pssm-ID: 173597 [Multi-domain]  Cd Length: 805  Bit Score: 66.50  E-value: 5.20e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 112 VVLWLDCDKEGENICFEVLDAV---LPVMNNAHNgektvfRARFSSITDTDICNAMT-RLSEP-DHNEALSVDARQELDl 186
Cdd:PTZ00407 128 IILATDPDREGELIAVHALQTIkrlYPKLKVPFS------RAYMHSITEDGIRKAMReRHVEAcDYDLANAAETRHAMD- 200

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 187 RIgcaftrfqtkyfqgkYGDLDSSLI--------SFGPCQTPTLGFCVERHDKIQSF--KPETYWVLQA----------- 245
Cdd:PTZ00407 201 RI---------------FGFLGSSVVraansqmrSIGRVQTPALILINEREDKIKAFleSNKSTFEVQAmcqfpsphgtt 265

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 246 -----KVHTDKEESLLlDWD-----RVRVFDWEI--AQMFlnmtKLEKEAWVEATsrkEKAKQRPLALNTveMLRVASSA 313
Cdd:PTZ00407 266 fsqvvTITPDRKGGAS-HWAteaeaRRCLEQWKLnnCTGF----SVPLEPKPQPS---VVPPPQPFTMAT--AIAKANRQ 335

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 314 LGMGPQHAMQIAERLYTQGYISYPRTETTHYPENF--DLKGSLRQQANhpywadsvKQLLAEGINRPRKGHDaGDHPPIT 391
Cdd:PTZ00407 336 LKYSSEMVSGCLQDLFQLGHITYPRTDSTRIDESAlpDIYAAVKKEFG--------KEFLYRLEDRTVSAQE-GKGSKKT 406

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 392 PMKSATEAELGGDAWR------------------------------LYEYITRHFIAT--VSHDCKYLQSTISFRIGPE- 438
Cdd:PTZ00407 407 GKKRSTKQKKGADTPVgnvedaheairptnidttgeslslspptraVYDLVRRNTLAVfmIPMKTEKIVATVKFTSGSGe 486

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 439 --HFTCMGKTVISPGFTE----------------------------IMPWQS-------VPLEESLPTCQKGDTFTVGEV 481
Cdd:PTZ00407 487 klEFELQGKRVVEPGWTRafhkgdkgttgpaeetdeditaveegapVVPSLSqeefkaiMNLRSQLGSGVQKGFFELRSP 566

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040 482 KMLEKQTSPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVESGRRLKPTNLGIVLVHgyykiDAELVLPTI- 560
Cdd:PTZ00407 567 QVRENRPVPPLPHSEGTLIEELKNNGVGRPSTYPMIVKTLLARGYIAVNPKGRCETTPVGRMLVE-----TAKSTFPSIv 641

                        570
                 ....*....|....*..
gi 568995040 561 ----RSAVEKQLNLIAQ 573
Cdd:PTZ00407 642 digfTAAFEKKLDRIAK 658
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 4-155 7.46e-11

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: 59.29  E-value: 7.46e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040    4 VLMVAEKPSLAQSIAKILSRGNmsshkglngacsvhkytgtfagqpvhFKMTSVCGHVMTLDFlgkynkwdkvdpaelfs 83
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGGF--------------------------QAVVAVLGHLLSLEK----------------- 37

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568995040   84 qaptekkeaNPKLNMVKFLQVEGRGCDYVVLWLDCDKEGENICFEVLDAVLPVmnnahngEKTVFRARFSSI 155
Cdd:pfam01751  38 ---------GPKKKALKALKELALKAKEVILATDPDREGEAIALKLLELKELL-------ENAGGRVEFSEL 93
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
4-137 5.30e-06

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 44.94  E-value: 5.30e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568995040     4 VLMVAEKPSLAQSIAKILSRgnmsshkglngacsvhkytgtfagqpvHFKMTSVCGHVMTLDflgkynkwdkvdpaelfs 83
Cdd:smart00493   2 VLIIVEGPADAIALEKAGGK---------------------------RGNVVALGGHLLSKE------------------ 36

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 568995040    84 qaptekkeanpklnMVKFLQVEGRGCdYVVLWLDCDKEGENICFEVLDAVLPVM 137
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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