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Conserved domains on  [gi|6323263|ref|NP_013335|]
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DNA topoisomerase 3 [Saccharomyces cerevisiae S288C]

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 ...
 173-635 1.05e-137

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: 407.76  E-value: 1.05e-137
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263  173 MKSVHAVGTRIEIDLRAGVTFTRLLTETLRNKlrnqatmtkdgakhrggnkndsQVVSYGTCQFPTLGFVVDRFERIRNF 252
Cdd:cd00186   1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRRK----------------------GVLSAGRVQSPTLGLIVEREREIKAF 58

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263  253 VPEEFWYIQlvvenkdnggtttfqwdrghlfdrlsvltfyetcietagnVAQVVDLKSKPTTKYRPLPLTTVELQKNCAR 332
Cdd:cd00186  59 VPEDYWEIK----------------------------------------EAVVVSVEKKEKKKNPPPPFTTSTLQQEASS 98

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263  333 YLRLNAKQSLDAAEKLYQKGFISYPRTETDTFPHAMDLKSLVEKQAQLDQlaaggrtaWASYAASLLQPentsnnnkfKF 412
Cdd:cd00186  99 KLGFSAKKTMQIAQKLYEAGLITYPRTDSTRLSEEAILEAREYIQAIYGK--------EYLYPAPLLGR---------RN 161

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263  413 PRSGSHDDKAHPPIHP---IVSLGPEANVSPVERRVYEYVARHFLACCSEDAKGQSMTLVLDWAVERFSASGLVVLERNF 489
Cdd:cd00186 162 PKRGKKEQGAHEAIRPtkvAPTPELEANLSEDEFKLYELIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGW 241

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263  490 LDVYPWARWETTKQLPRLEMNALVDIAKAEMKAGTTAPPKPMTESELILLMDTNGIGTDATIAEHIDKIQVRNYVRSEKv 569
Cdd:cd00186 242 LEVYPEEKDDEEEEPPPLKEGDELKLEEVELEEKETQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKEK- 320

                       410       420       430       440       450       460
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6323263  570 gkeTYLQPTTLGVSLVHGFEAIGLEdsFAKPFQRREMEQDLKKICEGHASKTDVVKDIVEKYRKYW 635
Cdd:cd00186 321 ---KKLIPTELGFAVIELLEKHFPE--LVDPEFTAKLEEKLDEIAEGKKDYQEVLEEFYEEFKKIV 381
TOPRIM_TopoIA_TopoIII cd03362
TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type ...
 2-168 4.65e-49

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: 168.18  E-value: 4.65e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    2 KVLCVAEKNSIAKAVSQILGGGRSTSRdsgymyvknydfmfSGFPFARNGANCEVTMTSVAGHLTGIDFSHDSHGWGKCA 81
Cdd:cd03362   1 MVLIIAEKPSVAKAIAKILGGGSKKKG--------------KGRYYEFYGEGGGYVVTWASGHLLELDFPEEYDPWDKVW 66

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   82 IQE--LFDAPLNEIMNNNQKKIASNIKREARNADYLMIWTDCDREGEYIGWEIWQEAKRGnrliQNDQVYRAVFSHLERQ 159
Cdd:cd03362  67 PLEdpLFPAPFKLKVDKGKKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYAKCV----KRKPVKRAWFSSLTPK 142


                ....*....
gi 6323263  160 HILNAARNP 168
Cdd:cd03362 143 AIRRAFKNL 151
 
Name Accession Description Interval E-value
TOP1Ac cd00186
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
 173-635 1.05e-137

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: 407.76  E-value: 1.05e-137
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263  173 MKSVHAVGTRIEIDLRAGVTFTRLLTETLRNKlrnqatmtkdgakhrggnkndsQVVSYGTCQFPTLGFVVDRFERIRNF 252
Cdd:cd00186   1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRRK----------------------GVLSAGRVQSPTLGLIVEREREIKAF 58

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263  253 VPEEFWYIQlvvenkdnggtttfqwdrghlfdrlsvltfyetcietagnVAQVVDLKSKPTTKYRPLPLTTVELQKNCAR 332
Cdd:cd00186  59 VPEDYWEIK----------------------------------------EAVVVSVEKKEKKKNPPPPFTTSTLQQEASS 98

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263  333 YLRLNAKQSLDAAEKLYQKGFISYPRTETDTFPHAMDLKSLVEKQAQLDQlaaggrtaWASYAASLLQPentsnnnkfKF 412
Cdd:cd00186  99 KLGFSAKKTMQIAQKLYEAGLITYPRTDSTRLSEEAILEAREYIQAIYGK--------EYLYPAPLLGR---------RN 161

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263  413 PRSGSHDDKAHPPIHP---IVSLGPEANVSPVERRVYEYVARHFLACCSEDAKGQSMTLVLDWAVERFSASGLVVLERNF 489
Cdd:cd00186 162 PKRGKKEQGAHEAIRPtkvAPTPELEANLSEDEFKLYELIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGW 241

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263  490 LDVYPWARWETTKQLPRLEMNALVDIAKAEMKAGTTAPPKPMTESELILLMDTNGIGTDATIAEHIDKIQVRNYVRSEKv 569
Cdd:cd00186 242 LEVYPEEKDDEEEEPPPLKEGDELKLEEVELEEKETQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKEK- 320

                       410       420       430       440       450       460
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6323263  570 gkeTYLQPTTLGVSLVHGFEAIGLEdsFAKPFQRREMEQDLKKICEGHASKTDVVKDIVEKYRKYW 635
Cdd:cd00186 321 ---KKLIPTELGFAVIELLEKHFPE--LVDPEFTAKLEEKLDEIAEGKKDYQEVLEEFYEEFKKIV 381
Topoisom_bac pfam01131
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ...
 170-625 2.21e-123

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: 371.96  E-value: 2.21e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    170 RLDMKSVHAVGTRIEIDLRAGVTFTRLLTETLRNKlrnqatmtkdgakhrggnkndsQVVSYGTCQFPTLGFVVDRFERI 249
Cdd:pfam01131   1 EIDENLVDAQLARRELDWLIGFNLSRLLTLKLKGN----------------------KLLSAGRVQTPTLALIVEREREI 58

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    250 RNFVPEEFWYIQLVVEnKDNGGTTTFQWDRGHLFDRLSVLTFYETCIETagnVAQVVDLKSKPTTKYRPLPLTTVELQKN 329
Cdd:pfam01131  59 ENFVPEPYWTIEATLK-DGGGVFANAKWKRGRIFDKEEAEAILEKLKKG---TAVVTSVESKEKKKPPPLPFNTTTLQKE 134

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    330 CARYLRLNAKQSLDAAEKLYQK-GFISYPRTETDTFPHAMDLKSLVEKQAQLDQlaaggrtAWASYAASLLQPentsnnN 408
Cdd:pfam01131 135 ASRKLGFSAKKTMSIAQKLYEKhGLITYPRTDSTYLSDDATLKAILEYLTKNYG-------KYLPYAPRLLKK------T 201

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    409 KFKFPRSGShDDKAHPPIHPIVSLGPEANVSPVERRVYEYVARHFLACCSEDAKGQSMTLVLDWAVERFSASGLVVLERN 488
Cdd:pfam01131 202 KGKLTVGNA-KVTAHEAIRPTGDIPVLPELSDDERKLYELIVRRFLASQMPPAVYETTTVVLEVGGEEFRASGKVILEDG 280

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    489 FLDVYPWARWETTKQLPRLEMNALVDIAKAEMKAGTTAPPKPMTESELILLMDTNGIGTDATIAEHIDKIQVRNYVRSEK 568
Cdd:pfam01131 281 WLKVYPYEKKEDEEELPELKEGEELKVTQVEVEEKKTKPPPRYTEASLIKAMEKAGIGTPATRATIIETLLERGYVERKK 360

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 6323263    569 vgkeTYLQPTTLGVSLVHGFEAIgleDSFAKPFQRREMEQDLKKICEGHASKTDVVK 625
Cdd:pfam01131 361 ----KSLVPTELGKALVEALEKF---PDLVDPELTAELEEKLDEIAEGKLDWKDVLA 410
PRK07219 PRK07219
DNA topoisomerase I; Validated
 3-633 3.20e-111

DNA topoisomerase I; Validated


Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 353.54  E-value: 3.20e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263     3 VLCVAEKNSIAKAVSQILGGGRSTS-RDSGYMYVKnydfmfsgfpFARNGANCEVTmtSVAGHLTGIDFSHDSHGWGKCA 81
Cdd:PRK07219   2 ELIIAEKNNAARRIADILSGGKAKKkRVNGVPYYE----------FERKGEKWIVI--GLSGHIVTVDFPEEYGDWRDVD 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    82 IQELFDAPLNEimNNNQKKIASNIKREARNADYLMIWTDCDREGEYIGweiwQEAKRGNRLIQNDQVYRAVFSHLERQHI 161
Cdd:PRK07219  70 PAELIDADPVK--KITKQNYINALKKLAKDADEIIIATDYDREGELIG----KEAYHILREVCQVPVKRARFSSLTKKEI 143

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   162 LNAARNPSRLDMKSVHAVGTRIEIDLRAGVTFTRLLTETLRNKlrnqatmtkdgakhrggnkNDSQVVSYGTCQFPTLGF 241
Cdd:PRK07219 144 RKAFENPDEIDFNLADAGEARQIIDLYWGAALTRFLSLSVRQL-------------------GRWDFLSVGRVQTPTLAF 204

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   242 VVDRFERIRNFVPEEFWYIQLVVENKDNGGTTTFQWDR--GHLFDRLSVLTFYETcIETAGNvAQVVDLKSKPTTKYRPL 319
Cdd:PRK07219 205 IVDREREIRAFDPEDYWKIEALLDKEAQYFYRDLIGGHeaEKFWDEEEAEEIYEK-LKGAKE-ATVSSVKKRERTISPPA 282

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   320 PLTTVELQKNCARYLRLNAKQSLDAAEKLYQKGFISYPRTETDTFPHAMDLKSLVEKQAqldqlaagGRTAWASYAASLL 399
Cdd:PRK07219 283 PFNTTEFLREASKIFGISPKRAMEIAEKLYTAGYISYPRTDNTVYPDDLDPKELLKKLS--------KKKEYGPYAESIL 354

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   400 QPENTSnnnkfkfPRSGSHDDKAHPPIHPIVSLgPEANVSPVERRVYEYVARHFLACCSEDAKGQSMTLVLDWAVERFSA 479
Cdd:PRK07219 355 EQENIK-------PTEGKKETTDHPPIHPVDVP-KREELSDDEWKVYELIVRRFLATLADPAEWEYLKVELDVNGEIFKA 426

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   480 SGLVVLERNFLDVYPWARWEtTKQLPRLEMNALVDIAKAEMKAGTTAPPKPMTESELILLMDTNGIGTDATIAEHIDKIQ 559
Cdd:PRK07219 427 SGSRLVEEGWHEVYPYEKFD-EKELPDLEEGEKLKVNKIEIEAKETQPPKRYTQSSLIKEMEKRGLGTKATRHDIIEKLY 505

                        570       580       590       600       610       620       630
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 6323263   560 VRNYVRSEKVgketyLQPTTLGVSLVHGFEaiGLEDSFAKPFQRREMEQDLKKICEGHASKTDVVKDIVEKYRK 633
Cdd:PRK07219 506 KRGYVIEGDP-----PRPTDLGIAVIEALE--KYAPEIVSEEMTAQLEADMQAIEDGKKKKEDVTEESREMLKE 572
TOP1Ac smart00437
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ...
 309-584 2.21e-95

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: 294.15  E-value: 2.21e-95
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263     309 KSKPTTKYRPLPLTTVELQKNCARYLRLNAKQSLDAAEKLYQKGFISYPRTETDTFPHAMDLKSLVEKQAQLDQLaaggr 388
Cdd:smart00437   1 EEKEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYIQKLYGKE----- 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263     389 taWASYAASLLQPentsnnnkfKFPRSGSHDDKAHPPIHP---IVSLGPEANVSPVERRVYEYVARHFLACCSEDAKGQS 465
Cdd:smart00437  76 --YLDLAVVLLKP---------RKPRKGKKAQGAHEAIRPtkpIFTPELEKELSEDEFKLYELIWRRFLASQMPDAKYEE 144

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263     466 MTLVLDWAVERFSASGLVVLERNFLDVYPWARWETTKQLPRLEMNALVDIAKAEMKAGTTAPPKPMTESELILLMDTNGI 545
Cdd:smart00437 145 TKVTIKIGGEKFKAKGKTLLFDGWLKVYPEEKKEEEIELPTLKKGDELKVEEVEVEEKETKPPARYTEASLIKLMEKRGI 224

                          250       260       270
                   ....*....|....*....|....*....|....*....
gi 6323263     546 GTDATIAEHIDKIQVRNYVRSEKVgketYLQPTTLGVSL 584
Cdd:smart00437 225 GRPSTYASIIETLLDRGYVTKKKK----KLIPTELGIAV 259
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
99-633 2.93e-87

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 440316 [Multi-domain]  Cd Length: 541  Bit Score: 282.75  E-value: 2.93e-87
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   99 KKIASNIKREARNADYLMIWTDCDREGEYIGWEIWQEAKRgnrliqNDQVYRAVFSHLERQHILNAARNPSRLDMKSVHA 178
Cdd:COG0550  59 KKQVKELKKLAKKADEVILATDPDREGEAIAWHLLELLGD------KKPVKRVVFNEITKKAIKEAFKNPRDIDMNLVDA 132

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263  179 VGTRIEIDLRAGVTFTRLLTETLRNKLrnqatmtkdgakhrggnkndsqvvSYGTCQFPTLGFVVDRFERIRNFVPEEFW 258
Cdd:COG0550 133 QQARRILDRLVGYNLSPLLWKKVKRGL------------------------SAGRVQSPALRLIVEREREIEAFVPEEYW 188

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263  259 YIQLVVENKDNGGTTTFQWDRGH-LFDRLSVLTFYETCietAGNVAQVVDLKSKPTTKYRPLPLTTVELQKNCARYLRLN 337
Cdd:COG0550 189 TIEATFKTGGGEFTAKLVKIDGKkILDEEEAEAILAAL---KGKTFTVTSVEKKPKKRNPPPPFTTSTLQQEASRKLGFS 265

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263  338 AKQSLDAAEKLYQKGFISYPRTE----TDTFphAMDLKSLVEKQAQLDQLAAGGRTawasYaasllqpeNTSNNnkfkfp 413
Cdd:COG0550 266 AKKTMSIAQRLYEVGLITYMRTDsvrlSEDA--VAAAREYIEALYGKEYLPEKPRV----Y--------KTSKN------ 325

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263  414 rsgshDDKAHPPIHPI-VSLGPEaNVSPVERRVYEYVARHFLACCSEDAKGQSMTLVLDWAVERFSASGLVVLERNFLDV 492
Cdd:COG0550 326 -----AQEAHEAIRPTgVTRTPE-SLSGDEFKLYDLIWKRFLASQMPPAEYETTTVTIEVGGEEFRASGKVIKFPGFLKV 399

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263  493 YPWAR----WETTKQLPRLEMNALVDIAKAEMKAGTTAPPKPMTESELILLMDTNGIGTDATIAEHIDKIQVRNYVrsEK 568
Cdd:COG0550 400 YGEGKddeeEEEEKRLPPLKEGEKLKLKKIEPEQHFTKPPPRYTEASLVKAMEELGIGRPSTYASIIETLQDRGYV--ER 477

                       490       500       510       520       530       540
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6323263  569 VGKEtyLQPTTLGVS----LVHGFEAIgLEDSFakpfqRREMEQDLKKICEGHASKTDVVKDIVEKYRK 633
Cdd:COG0550 478 EGKR--LVPTELGFIvidlLEEHFPDL-VDYEF-----TAKMEEKLDEIAEGKLDWKDVLEEFYKPFKE 538
topA_arch TIGR01057
DNA topoisomerase I, archaeal; This model describes topoisomerase I from archaea. These ...
 6-633 3.59e-68

DNA topoisomerase I, archaeal; This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273420 [Multi-domain]  Cd Length: 618  Bit Score: 233.95  E-value: 3.59e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263      6 VAEKNSIAKAVSQILGGGRStsrdsgymyVKNYDFMFSGFPFARNGAncEVTMTSVAGHLTGIDFSHDSHgwgkcaiQEL 85
Cdd:TIGR01057   1 IAEKPKVAAKIAGALSDGRV---------LKKSEYGVPYWEVRRDGK--KIIVASAVGHLFGLHPKSRGG-------YPV 62

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263     86 FD---APLNEIMNNNQ--KKIASNIKREARNADYLMIWTDCDREGEYIGWEIWQEAkrGNRliqnDQVYRAVFSHLERQH 160
Cdd:TIGR01057  63 FDiewVPIFEFDKGKGyvSKYIKALSKLAKGADEYINACDYDIEGEVIGFKALKYF--CGV----ERAKRMKFSTLTKQD 136

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    161 ILNAARNPSRLDMKSVHAVGTRIEIDLRAGVTFTRLLTETLRnklrnQATmtkdgakhrggnkNDSQVVSYGTCQFPTLG 240
Cdd:TIGR01057 137 IRRAYANPEEIDYGMVDAGMARHILDWYWGINLSRALMEAIR-----AAA-------------GRWVILSAGRVQGPTLA 198

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    241 FVVDRFERIRNFVPEEFWYIQLVVEnkDNGGTTTFQWDRGHLFDRLSVLTFYETCIETAgnVAQVVDLKSKPTTKYRPLP 320
Cdd:TIGR01057 199 FLVEREREINLFVPKPYWVIKATLE--KGGGVFDARPEKWKIWSEEEAKSIKEELKKSP--WAAVEEVRSERSILKPPPP 274

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    321 LTTVELQKNCARYLRLNAKQSLDAAEKLYQKGFISYPRTETDTFPHAMDLKSLvekqaqLDQLAAGGRtaWASYAASLLQ 400
Cdd:TIGR01057 275 FDLGTLQREAYRIFGFSPKKTQSIAQELYEEALISYPRTSSQKLPPSINYRAI------LDNLAKGPL--YREAAERLLE 346

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    401 PENTSnnnkfkfPRSGSHDDKAHPPIHPiVSLGPEANVSPVERRVYEYVARHFLACCSEDAKGQSMTLVLDWAVERFSAS 480
Cdd:TIGR01057 347 TGVLK-------PVEGKKEDPAHPAIHP-TGEIPSQELSKDEKKVYDLIVRRFLAAFSEEAIREKSKVLLRIGQEKFRLS 418

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    481 GLVVLERNFLDVYPWARWEtTKQLPRLEMNALVDIAKAEMKAGTTAPPKPMTESELILLMDTNGIGTDATIAEHIDKIQV 560
Cdd:TIGR01057 419 GLRVVKLGWLEYYHYSKFE-EKELPPLDRGDKIKVVRVDVRVKETQPPARYDKASLIREMESRGLGTKATRARIIETLYK 497

                         570       580       590       600       610       620       630
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6323263    561 RNYVRSEKvgketYLQPTTLGVSLVHGFEAIGLEdsFAKPFQRREMEQDLKKICEGHASKTDVVKDIVEKYRK 633
Cdd:TIGR01057 498 RGYIEGKK-----SIKVTPLGEAVIETLQRYCPE--IISEELTRRFESKLEDIMSGRITKDEVIDEAKKRLRK 563
TOPRIM_TopoIA_TopoIII cd03362
TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type ...
 2-168 4.65e-49

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: 168.18  E-value: 4.65e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    2 KVLCVAEKNSIAKAVSQILGGGRSTSRdsgymyvknydfmfSGFPFARNGANCEVTMTSVAGHLTGIDFSHDSHGWGKCA 81
Cdd:cd03362   1 MVLIIAEKPSVAKAIAKILGGGSKKKG--------------KGRYYEFYGEGGGYVVTWASGHLLELDFPEEYDPWDKVW 66

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   82 IQE--LFDAPLNEIMNNNQKKIASNIKREARNADYLMIWTDCDREGEYIGWEIWQEAKRGnrliQNDQVYRAVFSHLERQ 159
Cdd:cd03362  67 PLEdpLFPAPFKLKVDKGKKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYAKCV----KRKPVKRAWFSSLTPK 142


                ....*....
gi 6323263  160 HILNAARNP 168
Cdd:cd03362 143 AIRRAFKNL 151
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 3-156 2.46e-09

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: 54.67  E-value: 2.46e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263      3 VLCVAEKNSIAKAVSQILGGGrstsrdsgymyvknydfmfsgfpfarngancEVTMTSVAGHLTgidfshdshgwgkcai 82
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGG-------------------------------FQAVVAVLGHLL---------------- 33

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 6323263     83 qelfdaplnEIMNNNQKKIASNIKREARNADYLMIWTDCDREGEYIGWEIWQeakrgNRLIQNDQVYRAVFSHL 156
Cdd:pfam01751  34 ---------SLEKGPKKKALKALKELALKAKEVILATDPDREGEAIALKLLE-----LKELLENAGGRVEFSEL 93
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
2-140 1.79e-07

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 48.80  E-value: 1.79e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263       2 KVLCVAEKNSIAKAVSQILGggrstsrdsgymyvknydfmfsgfpfarnganCEVTMTSVAGHLTgidfshdshgwgkca 81
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGG--------------------------------KRGNVVALGGHLL--------------- 33

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 6323263      82 iqelfdaplneimnnnQKKIASNIKREARNAdYLMIWTDCDREGEYIGWEIWQEAKRGN 140
Cdd:smart00493  34 ----------------SKEQIKLLKKLAKKA-EVILATDPDREGEAIAWELAELLKPAG 75
 
Name Accession Description Interval E-value
TOP1Ac cd00186
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
 173-635 1.05e-137

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: 407.76  E-value: 1.05e-137
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263  173 MKSVHAVGTRIEIDLRAGVTFTRLLTETLRNKlrnqatmtkdgakhrggnkndsQVVSYGTCQFPTLGFVVDRFERIRNF 252
Cdd:cd00186   1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRRK----------------------GVLSAGRVQSPTLGLIVEREREIKAF 58

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263  253 VPEEFWYIQlvvenkdnggtttfqwdrghlfdrlsvltfyetcietagnVAQVVDLKSKPTTKYRPLPLTTVELQKNCAR 332
Cdd:cd00186  59 VPEDYWEIK----------------------------------------EAVVVSVEKKEKKKNPPPPFTTSTLQQEASS 98

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263  333 YLRLNAKQSLDAAEKLYQKGFISYPRTETDTFPHAMDLKSLVEKQAQLDQlaaggrtaWASYAASLLQPentsnnnkfKF 412
Cdd:cd00186  99 KLGFSAKKTMQIAQKLYEAGLITYPRTDSTRLSEEAILEAREYIQAIYGK--------EYLYPAPLLGR---------RN 161

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263  413 PRSGSHDDKAHPPIHP---IVSLGPEANVSPVERRVYEYVARHFLACCSEDAKGQSMTLVLDWAVERFSASGLVVLERNF 489
Cdd:cd00186 162 PKRGKKEQGAHEAIRPtkvAPTPELEANLSEDEFKLYELIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGW 241

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263  490 LDVYPWARWETTKQLPRLEMNALVDIAKAEMKAGTTAPPKPMTESELILLMDTNGIGTDATIAEHIDKIQVRNYVRSEKv 569
Cdd:cd00186 242 LEVYPEEKDDEEEEPPPLKEGDELKLEEVELEEKETQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKEK- 320

                       410       420       430       440       450       460
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6323263  570 gkeTYLQPTTLGVSLVHGFEAIGLEdsFAKPFQRREMEQDLKKICEGHASKTDVVKDIVEKYRKYW 635
Cdd:cd00186 321 ---KKLIPTELGFAVIELLEKHFPE--LVDPEFTAKLEEKLDEIAEGKKDYQEVLEEFYEEFKKIV 381
Topoisom_bac pfam01131
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ...
 170-625 2.21e-123

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: 371.96  E-value: 2.21e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    170 RLDMKSVHAVGTRIEIDLRAGVTFTRLLTETLRNKlrnqatmtkdgakhrggnkndsQVVSYGTCQFPTLGFVVDRFERI 249
Cdd:pfam01131   1 EIDENLVDAQLARRELDWLIGFNLSRLLTLKLKGN----------------------KLLSAGRVQTPTLALIVEREREI 58

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    250 RNFVPEEFWYIQLVVEnKDNGGTTTFQWDRGHLFDRLSVLTFYETCIETagnVAQVVDLKSKPTTKYRPLPLTTVELQKN 329
Cdd:pfam01131  59 ENFVPEPYWTIEATLK-DGGGVFANAKWKRGRIFDKEEAEAILEKLKKG---TAVVTSVESKEKKKPPPLPFNTTTLQKE 134

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    330 CARYLRLNAKQSLDAAEKLYQK-GFISYPRTETDTFPHAMDLKSLVEKQAQLDQlaaggrtAWASYAASLLQPentsnnN 408
Cdd:pfam01131 135 ASRKLGFSAKKTMSIAQKLYEKhGLITYPRTDSTYLSDDATLKAILEYLTKNYG-------KYLPYAPRLLKK------T 201

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    409 KFKFPRSGShDDKAHPPIHPIVSLGPEANVSPVERRVYEYVARHFLACCSEDAKGQSMTLVLDWAVERFSASGLVVLERN 488
Cdd:pfam01131 202 KGKLTVGNA-KVTAHEAIRPTGDIPVLPELSDDERKLYELIVRRFLASQMPPAVYETTTVVLEVGGEEFRASGKVILEDG 280

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    489 FLDVYPWARWETTKQLPRLEMNALVDIAKAEMKAGTTAPPKPMTESELILLMDTNGIGTDATIAEHIDKIQVRNYVRSEK 568
Cdd:pfam01131 281 WLKVYPYEKKEDEEELPELKEGEELKVTQVEVEEKKTKPPPRYTEASLIKAMEKAGIGTPATRATIIETLLERGYVERKK 360

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 6323263    569 vgkeTYLQPTTLGVSLVHGFEAIgleDSFAKPFQRREMEQDLKKICEGHASKTDVVK 625
Cdd:pfam01131 361 ----KSLVPTELGKALVEALEKF---PDLVDPELTAELEEKLDEIAEGKLDWKDVLA 410
PRK07219 PRK07219
DNA topoisomerase I; Validated
 3-633 3.20e-111

DNA topoisomerase I; Validated


Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 353.54  E-value: 3.20e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263     3 VLCVAEKNSIAKAVSQILGGGRSTS-RDSGYMYVKnydfmfsgfpFARNGANCEVTmtSVAGHLTGIDFSHDSHGWGKCA 81
Cdd:PRK07219   2 ELIIAEKNNAARRIADILSGGKAKKkRVNGVPYYE----------FERKGEKWIVI--GLSGHIVTVDFPEEYGDWRDVD 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    82 IQELFDAPLNEimNNNQKKIASNIKREARNADYLMIWTDCDREGEYIGweiwQEAKRGNRLIQNDQVYRAVFSHLERQHI 161
Cdd:PRK07219  70 PAELIDADPVK--KITKQNYINALKKLAKDADEIIIATDYDREGELIG----KEAYHILREVCQVPVKRARFSSLTKKEI 143

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   162 LNAARNPSRLDMKSVHAVGTRIEIDLRAGVTFTRLLTETLRNKlrnqatmtkdgakhrggnkNDSQVVSYGTCQFPTLGF 241
Cdd:PRK07219 144 RKAFENPDEIDFNLADAGEARQIIDLYWGAALTRFLSLSVRQL-------------------GRWDFLSVGRVQTPTLAF 204

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   242 VVDRFERIRNFVPEEFWYIQLVVENKDNGGTTTFQWDR--GHLFDRLSVLTFYETcIETAGNvAQVVDLKSKPTTKYRPL 319
Cdd:PRK07219 205 IVDREREIRAFDPEDYWKIEALLDKEAQYFYRDLIGGHeaEKFWDEEEAEEIYEK-LKGAKE-ATVSSVKKRERTISPPA 282

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   320 PLTTVELQKNCARYLRLNAKQSLDAAEKLYQKGFISYPRTETDTFPHAMDLKSLVEKQAqldqlaagGRTAWASYAASLL 399
Cdd:PRK07219 283 PFNTTEFLREASKIFGISPKRAMEIAEKLYTAGYISYPRTDNTVYPDDLDPKELLKKLS--------KKKEYGPYAESIL 354

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   400 QPENTSnnnkfkfPRSGSHDDKAHPPIHPIVSLgPEANVSPVERRVYEYVARHFLACCSEDAKGQSMTLVLDWAVERFSA 479
Cdd:PRK07219 355 EQENIK-------PTEGKKETTDHPPIHPVDVP-KREELSDDEWKVYELIVRRFLATLADPAEWEYLKVELDVNGEIFKA 426

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   480 SGLVVLERNFLDVYPWARWEtTKQLPRLEMNALVDIAKAEMKAGTTAPPKPMTESELILLMDTNGIGTDATIAEHIDKIQ 559
Cdd:PRK07219 427 SGSRLVEEGWHEVYPYEKFD-EKELPDLEEGEKLKVNKIEIEAKETQPPKRYTQSSLIKEMEKRGLGTKATRHDIIEKLY 505

                        570       580       590       600       610       620       630
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 6323263   560 VRNYVRSEKVgketyLQPTTLGVSLVHGFEaiGLEDSFAKPFQRREMEQDLKKICEGHASKTDVVKDIVEKYRK 633
Cdd:PRK07219 506 KRGYVIEGDP-----PRPTDLGIAVIEALE--KYAPEIVSEEMTAQLEADMQAIEDGKKKKEDVTEESREMLKE 572
TOP1Ac smart00437
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ...
 309-584 2.21e-95

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: 294.15  E-value: 2.21e-95
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263     309 KSKPTTKYRPLPLTTVELQKNCARYLRLNAKQSLDAAEKLYQKGFISYPRTETDTFPHAMDLKSLVEKQAQLDQLaaggr 388
Cdd:smart00437   1 EEKEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYIQKLYGKE----- 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263     389 taWASYAASLLQPentsnnnkfKFPRSGSHDDKAHPPIHP---IVSLGPEANVSPVERRVYEYVARHFLACCSEDAKGQS 465
Cdd:smart00437  76 --YLDLAVVLLKP---------RKPRKGKKAQGAHEAIRPtkpIFTPELEKELSEDEFKLYELIWRRFLASQMPDAKYEE 144

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263     466 MTLVLDWAVERFSASGLVVLERNFLDVYPWARWETTKQLPRLEMNALVDIAKAEMKAGTTAPPKPMTESELILLMDTNGI 545
Cdd:smart00437 145 TKVTIKIGGEKFKAKGKTLLFDGWLKVYPEEKKEEEIELPTLKKGDELKVEEVEVEEKETKPPARYTEASLIKLMEKRGI 224

                          250       260       270
                   ....*....|....*....|....*....|....*....
gi 6323263     546 GTDATIAEHIDKIQVRNYVRSEKVgketYLQPTTLGVSL 584
Cdd:smart00437 225 GRPSTYASIIETLLDRGYVTKKKK----KLIPTELGIAV 259
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
99-633 2.93e-87

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 440316 [Multi-domain]  Cd Length: 541  Bit Score: 282.75  E-value: 2.93e-87
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   99 KKIASNIKREARNADYLMIWTDCDREGEYIGWEIWQEAKRgnrliqNDQVYRAVFSHLERQHILNAARNPSRLDMKSVHA 178
Cdd:COG0550  59 KKQVKELKKLAKKADEVILATDPDREGEAIAWHLLELLGD------KKPVKRVVFNEITKKAIKEAFKNPRDIDMNLVDA 132

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263  179 VGTRIEIDLRAGVTFTRLLTETLRNKLrnqatmtkdgakhrggnkndsqvvSYGTCQFPTLGFVVDRFERIRNFVPEEFW 258
Cdd:COG0550 133 QQARRILDRLVGYNLSPLLWKKVKRGL------------------------SAGRVQSPALRLIVEREREIEAFVPEEYW 188

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263  259 YIQLVVENKDNGGTTTFQWDRGH-LFDRLSVLTFYETCietAGNVAQVVDLKSKPTTKYRPLPLTTVELQKNCARYLRLN 337
Cdd:COG0550 189 TIEATFKTGGGEFTAKLVKIDGKkILDEEEAEAILAAL---KGKTFTVTSVEKKPKKRNPPPPFTTSTLQQEASRKLGFS 265

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263  338 AKQSLDAAEKLYQKGFISYPRTE----TDTFphAMDLKSLVEKQAQLDQLAAGGRTawasYaasllqpeNTSNNnkfkfp 413
Cdd:COG0550 266 AKKTMSIAQRLYEVGLITYMRTDsvrlSEDA--VAAAREYIEALYGKEYLPEKPRV----Y--------KTSKN------ 325

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263  414 rsgshDDKAHPPIHPI-VSLGPEaNVSPVERRVYEYVARHFLACCSEDAKGQSMTLVLDWAVERFSASGLVVLERNFLDV 492
Cdd:COG0550 326 -----AQEAHEAIRPTgVTRTPE-SLSGDEFKLYDLIWKRFLASQMPPAEYETTTVTIEVGGEEFRASGKVIKFPGFLKV 399

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263  493 YPWAR----WETTKQLPRLEMNALVDIAKAEMKAGTTAPPKPMTESELILLMDTNGIGTDATIAEHIDKIQVRNYVrsEK 568
Cdd:COG0550 400 YGEGKddeeEEEEKRLPPLKEGEKLKLKKIEPEQHFTKPPPRYTEASLVKAMEELGIGRPSTYASIIETLQDRGYV--ER 477

                       490       500       510       520       530       540
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6323263  569 VGKEtyLQPTTLGVS----LVHGFEAIgLEDSFakpfqRREMEQDLKKICEGHASKTDVVKDIVEKYRK 633
Cdd:COG0550 478 EGKR--LVPTELGFIvidlLEEHFPDL-VDYEF-----TAKMEEKLDEIAEGKLDWKDVLEEFYKPFKE 538
PRK07220 PRK07220
DNA topoisomerase I; Validated
 4-626 6.50e-86

DNA topoisomerase I; Validated


Pssm-ID: 180892 [Multi-domain]  Cd Length: 740  Bit Score: 284.73  E-value: 6.50e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263     4 LCVAEKNSIAKAVSQILGGGRST-SRDSGYMYvknydfmfsgFPFARNGANCEVTMTSvaGHLTGIDFSHDSHGWGKCAI 82
Cdd:PRK07220   3 LIITEKNIAARRIAQILAPKKPKkTRVSGVDV----------YRYEDNGDDTVVVGLS--GHIVNIDFPKEYNNWQKVDA 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    83 QELFDAPLneIMNNNQKKIASNIKREARNADYLMIWTDCDREGEYIGWEIWQEAKRGNRLIQNDqvyRAVFSHLERQHIL 162
Cdd:PRK07220  71 RDLIDAEI--ITTPTQKKIVTALKKLGKEADRVTIATDYDREGELIGVEALNIIKKVNPDIKFD---RVRYSAITKKEIE 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   163 NAARNPSRLDMKSVHAVGTRIEIDLRAGVTFTRLLTETLRnklrnqatmtkdgakhRGGNkndsQVVSYGTCQFPTLGFV 242
Cdd:PRK07220 146 RAFSNPVEVDFNLADAGHSRQVIDLVWGAALTRYISLAAG----------------RLGK----MFLSVGRVQSPTLALI 205

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   243 VDRFERIRNFVPEEFWYIQlvVENKDNGGTTTFQWDRGHLFDRLSVltfyETCIETAGNVAQVVDLKSKPTTKYRPLPLT 322
Cdd:PRK07220 206 VDREKEREAFVPTPYWEIY--ATLENNGETFVAQHSTRRFWEKEEA----DRVFEKLGKTAEVTEVEKGTKTDKPPTPFN 279

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   323 TVELQKnCARYLRLNAKQSLDAAEKLYQKGFISYPRTETDTFPHAMDLKslvekqAQLDQLAAGGrtaWASYAASLLQPE 402
Cdd:PRK07220 280 TTEFIS-AANSIGFSAANAMRIAESLYTNGYISYPRTDNTVYPESLDLR------EQIEIFAEGP---FGEYAQKLLEKG 349

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   403 NTSnnnkfkfPRSGSHDDKAHPPIHPiVSLGPEANVSPVERRVYEYVARHFLACCSEDAKGQSMTLVLDWAVERFSASGL 482
Cdd:PRK07220 350 ELV-------PTRGKKETTDHPPIYP-ASLAKKSELKEDEWKVYELVVRRFFATFAGPAEWETMKLRFDIGGEEFRANGS 421

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   483 VVLERNFLDVYPWARWETtKQLPRLEMNALVDIAKAEMKAGTTAPPKPMTESELILLMDTNGIGTDATIAEHIDKIQVRN 562
Cdd:PRK07220 422 RLTEPGWRWYYPYNAPED-RLLPELSEGEELKVKKKEMLDKETQPPGRYGQGRLIKLMEDLGLGTKATRHEIISKLYSRA 500

                        570       580       590       600       610       620
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 6323263   563 YVRSEKVgketylQPTTLGVSLVHGFEAIGleDSFAKPFQRREMEQDLKKICEGHASKTDVVKD 626
Cdd:PRK07220 501 YIHGNPI------QPTNTAFAVVDALEKYA--PTITKPDMTSRLEEDMDKIAEGKIKEDAVLEE 556
topA_arch TIGR01057
DNA topoisomerase I, archaeal; This model describes topoisomerase I from archaea. These ...
 6-633 3.59e-68

DNA topoisomerase I, archaeal; This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273420 [Multi-domain]  Cd Length: 618  Bit Score: 233.95  E-value: 3.59e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263      6 VAEKNSIAKAVSQILGGGRStsrdsgymyVKNYDFMFSGFPFARNGAncEVTMTSVAGHLTGIDFSHDSHgwgkcaiQEL 85
Cdd:TIGR01057   1 IAEKPKVAAKIAGALSDGRV---------LKKSEYGVPYWEVRRDGK--KIIVASAVGHLFGLHPKSRGG-------YPV 62

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263     86 FD---APLNEIMNNNQ--KKIASNIKREARNADYLMIWTDCDREGEYIGWEIWQEAkrGNRliqnDQVYRAVFSHLERQH 160
Cdd:TIGR01057  63 FDiewVPIFEFDKGKGyvSKYIKALSKLAKGADEYINACDYDIEGEVIGFKALKYF--CGV----ERAKRMKFSTLTKQD 136

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    161 ILNAARNPSRLDMKSVHAVGTRIEIDLRAGVTFTRLLTETLRnklrnQATmtkdgakhrggnkNDSQVVSYGTCQFPTLG 240
Cdd:TIGR01057 137 IRRAYANPEEIDYGMVDAGMARHILDWYWGINLSRALMEAIR-----AAA-------------GRWVILSAGRVQGPTLA 198

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    241 FVVDRFERIRNFVPEEFWYIQLVVEnkDNGGTTTFQWDRGHLFDRLSVLTFYETCIETAgnVAQVVDLKSKPTTKYRPLP 320
Cdd:TIGR01057 199 FLVEREREINLFVPKPYWVIKATLE--KGGGVFDARPEKWKIWSEEEAKSIKEELKKSP--WAAVEEVRSERSILKPPPP 274

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    321 LTTVELQKNCARYLRLNAKQSLDAAEKLYQKGFISYPRTETDTFPHAMDLKSLvekqaqLDQLAAGGRtaWASYAASLLQ 400
Cdd:TIGR01057 275 FDLGTLQREAYRIFGFSPKKTQSIAQELYEEALISYPRTSSQKLPPSINYRAI------LDNLAKGPL--YREAAERLLE 346

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    401 PENTSnnnkfkfPRSGSHDDKAHPPIHPiVSLGPEANVSPVERRVYEYVARHFLACCSEDAKGQSMTLVLDWAVERFSAS 480
Cdd:TIGR01057 347 TGVLK-------PVEGKKEDPAHPAIHP-TGEIPSQELSKDEKKVYDLIVRRFLAAFSEEAIREKSKVLLRIGQEKFRLS 418

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    481 GLVVLERNFLDVYPWARWEtTKQLPRLEMNALVDIAKAEMKAGTTAPPKPMTESELILLMDTNGIGTDATIAEHIDKIQV 560
Cdd:TIGR01057 419 GLRVVKLGWLEYYHYSKFE-EKELPPLDRGDKIKVVRVDVRVKETQPPARYDKASLIREMESRGLGTKATRARIIETLYK 497

                         570       580       590       600       610       620       630
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6323263    561 RNYVRSEKvgketYLQPTTLGVSLVHGFEAIGLEdsFAKPFQRREMEQDLKKICEGHASKTDVVKDIVEKYRK 633
Cdd:TIGR01057 498 RGYIEGKK-----SIKVTPLGEAVIETLQRYCPE--IISEELTRRFESKLEDIMSGRITKDEVIDEAKKRLRK 563
PRK05776 PRK05776
DNA topoisomerase I; Provisional
 1-645 1.12e-67

DNA topoisomerase I; Provisional


Pssm-ID: 235602 [Multi-domain]  Cd Length: 670  Bit Score: 233.73  E-value: 1.12e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263     1 MKVLCVAEKNSIAKAVSQILGGGRSTSRDSGYMYvknYDFMfsgfpfaRNGANceVTMTSVAGHLTGIdfSHDSHGWgkc 80
Cdd:PRK05776   1 GYILVIAEKPKAARKIAEALSEKPIRCRIYGVPY---WIVK-------RDGKK--IVVAPAAGHLFGL--HTKSKGF--- 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    81 aiqELFDA---PLNEIMNNNQ--KKIASNIKREARNADYLMIWTDCDREGEYIGWEIWQEAKRGNRliqndqVYRAVFSH 155
Cdd:PRK05776  64 ---PVFDYewkPLYEIDKGSKytKKYYELLSSLSKYADEFINACDYDIEGSVIGYLIIKYLGDPKK------AKRMKFSA 134

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   156 LERQHILNAARNPSRLDMKSVHAVGTRIEIDLRAGVTFTRLLTETLRnklrnqatmtkDGAKHRggnkndsQVVSYGTCQ 235
Cdd:PRK05776 135 LTKSDIRRAFRNLETLDYEMINAGIARHELDWLWGINVSRALMSSVR-----------DASGKR-------VILSAGRVQ 196

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   236 FPTLGFVVDRFERIRNFVPEEFWYIQLVVENkdNGGTTTFQWDRGHLFDRLSVLTFYETCIETAgnVAQVVDLKSKPTTK 315
Cdd:PRK05776 197 SPTLKYVVEREIERNLFVPLPYFSVSIIIEK--NGYEFTLKYENKKFETKEEAKEILEEIKKTG--YLKVTKVEVKIEIL 272

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   316 YRPLPLTTVELQKNCARYLRLNAKQSLDAAEKLYQKGFISYPRTETDTFPHAMDLKSLVEKQAQLDQlaaggrtaWASYA 395
Cdd:PRK05776 273 EPPPPFNLGDLQVEAARIYGFSPYKTQSIAEDLYLDGLISYPRTNSQKLPPTLNIRNILKGLSRSPQ--------YRPLV 344

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   396 ASLLQpentSNNNKFKfPRSGSHDDKAHPPIHPIvslG-PEANVSPVERRVYEYVARHFLACCSEDAKGQSMTLVLDW-- 472
Cdd:PRK05776 345 NLLLK----ETKGVLK-PVQGPKDDPAHPAIYPT---GePPKNLSKDEFKLYDLIVRRFLASFAAPAVLSNTIVTLRVpg 416

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   473 AVERFSASGLVVLERNFLDVYPWARWEtTKQLPRLEMNALVDIAKAEMKAGTTAPPKPMTESELILLMDTNGIGTDATIA 552
Cdd:PRK05776 417 FPLVFSASGQRIEERGWLKYYPFHKFD-EEELPLLKKGERVKIVDVKVRKSYTKPPSRYSKASLLKWMESVGIGTEATRA 495

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   553 EHIDKIQVRNYVRSEKvgkeTYLQPTTLGVSLVhgfEAigLEDSF---AKPFQRREMEQDLKKICEGHASKTDVVKDIVE 629
Cdd:PRK05776 496 RIIETLFKRGYLTSNG----KYIEVTPLGFGVA---EV--LEKYFpdiVSVELTRDFEEKLEMIRTGKATREEVIEEAKE 566

                        650
                 ....*....|....*.
gi 6323263   630 KYRKYWHKTNACKNTL 645
Cdd:PRK05776 567 TLNKLLEEFKKNKDEI 582
PRK14973 PRK14973
DNA topoisomerase I; Provisional
 4-637 6.79e-62

DNA topoisomerase I; Provisional


Pssm-ID: 184936 [Multi-domain]  Cd Length: 936  Bit Score: 222.03  E-value: 6.79e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263     4 LCVAEKNSIAKAVSQILGGGR--STSRDSGymyVKNYDFmfsgfpfarngaNCEVTMtSVAGHLTGIDFSHDSHGW--GK 79
Cdd:PRK14973   3 LIIAEKNIAANRIAQILAGKTkvQVKKDGG---VSTYSF------------DDTVVV-GLRGHVVEVDFEPGYTNWrsEE 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    80 CAIQELFDAPLneIMNNNQKKIASNIKREARNADYLMIWTDCDREGEYIGWEIWQEAKRGNRLIQNDqvyRAVFSHLERQ 159
Cdd:PRK14973  67 HTPRSLIDADT--IKKPTEKKIVGLIQKLAKKADRVTIATDFDTEGELIGKEAYELVRAVNPKVPID---RARFSAITKE 141

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   160 HILNAARNPSRLDMKSVHAVGTRIEIDLRAGVTFTRLLTEtlrnklrnqatmtkdgAKHRGGNkndsQVVSYGTCQFPTL 239
Cdd:PRK14973 142 EIVTAFAEPTDLDFALAAAGEARQIIDLIWGASLTRFISL----------------AAHRGGD----NILSVGRVQSPTL 201

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   240 GFVVDRFERIRNFVPEEFWYIQLVVEnKDnGGTTTFQWDRGHLFDRLSVLTFYETCIETAgnvaQVVDLKSKPTTKYRPL 319
Cdd:PRK14973 202 AMIVDREKEIEAFVPEKYWMLSLATE-KD-GEGIEARHTHGRFTDSAAAEAAYDATKEPL----VVTEVKEGHKVDRAPT 275

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   320 PLTTVELQKNCARyLRLNAKQSLDAAEKLYQKGFISYPRTETDTFPHAMDLkslvekQAQLDQLAAGGRTAWASYAASLL 399
Cdd:PRK14973 276 PFDTTTFIVAASR-LGFSAANAMRIAEDLYMNGYISYPRTDNTIYPKSLDL------NGVLATLAKGAFSKDVAWVKDNR 348

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   400 QPEntsnnnkfkfPRSGSHDDKAHPPIHPiVSLGPEANVSPVERRVYEYVARHFLACCSEDAKGQSMTLVLDWAVERFSA 479
Cdd:PRK14973 349 RPV----------PTRGKKSSTDHPPIHP-TGVATREELGDDRWKLYELVVRRFLATLSPDAEWATMKVNFDAGGEPYTA 417

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   480 SGLVVLERNFLDVYPWARWETTKqLPRLEMNALVDIAKAEMKAGTTAPPKPMTESELILLMDTNGIGTDATIAEHIDKIQ 559
Cdd:PRK14973 418 TGGRLLEAGWRTVYPYSEAKENI-LPAFALGEKLPILAVNLEEKETQPPARYSQSRLIQRMEELGLGTKSTRHEVIGKLV 496

                        570       580       590       600       610       620       630
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6323263   560 VRNYVRSEKvgketyLQPTTLGVSLVHGFEAIGleDSFAKPFQRREMEQDLKKICEGHASKTDVVKDivekYRKYWHK 637
Cdd:PRK14973 497 SRKYIEGNP------LRPTLVGRAVTESLEEHA--GTITEPDMTQTLEEHMQQIKERKRTRDDVVTE----SRKMLHR 562
TOPRIM_TopoIA_TopoIII cd03362
TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type ...
 2-168 4.65e-49

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: 168.18  E-value: 4.65e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    2 KVLCVAEKNSIAKAVSQILGGGRSTSRdsgymyvknydfmfSGFPFARNGANCEVTMTSVAGHLTGIDFSHDSHGWGKCA 81
Cdd:cd03362   1 MVLIIAEKPSVAKAIAKILGGGSKKKG--------------KGRYYEFYGEGGGYVVTWASGHLLELDFPEEYDPWDKVW 66

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   82 IQE--LFDAPLNEIMNNNQKKIASNIKREARNADYLMIWTDCDREGEYIGWEIWQEAKRGnrliQNDQVYRAVFSHLERQ 159
Cdd:cd03362  67 PLEdpLFPAPFKLKVDKGKKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYAKCV----KRKPVKRAWFSSLTPK 142


                ....*....
gi 6323263  160 HILNAARNP 168
Cdd:cd03362 143 AIRRAFKNL 151
PRK07726 PRK07726
DNA topoisomerase 3;
105-629 2.36e-45

DNA topoisomerase 3;


Pssm-ID: 236078 [Multi-domain]  Cd Length: 658  Bit Score: 171.50  E-value: 2.36e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   105 IKREARNADYLMIWTDCDREGEYIGWEIWQEAK-RGN--RL-I--QNDQVYRAVFSHLerqhilnaaRNPSRLDMKSVHA 178
Cdd:PRK07726  86 VKKLLKQATEIVIATDADREGELIAREILDYCGvRKPikRLwIssLTDKAIKRAFANL---------KPGKETIPLYYSA 156

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   179 VGtRIEIDLRAGVTFTRLLTetlrnklrnqatmTKdgakhrGGNKNDSQVVSYGTCQFPTLGFVVDRFERIRNFVPEEFW 258
Cdd:PRK07726 157 LA-RSRADWLVGINMTRAYT-------------LL------GRKAGYNGVLSVGRVQTPTLALVVRRDEEIENFVPKPYW 216

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   259 YIQLVVenkDNGGTTTFQW--------DRGHLFDRlsvltfyetciETAGNV--------AQVVDLKSKPTTKYRPLP-- 320
Cdd:PRK07726 217 EVEAHL---TPGERFTAKWqpsepyqdEEGRLLDR-----------PLAEQVvariqgqpAKVTEVETKRKKEYAPLLyd 282

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   321 LTTveLQKNCARYLRLNAKQSLDAAEKLYQK-GFISYPRTE-----TDTFPHAMDLkslvekqaqLDQLAAGGrtawaSY 394
Cdd:PRK07726 283 LSE--LQIDANKRFGLSAKETLDIAQSLYEThKLITYPRTDsrylpEDMVATLPEV---------LNAISKVD-----PY 346

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   395 AASLLQPENTSNNNKFkfprsgsHDDK---AHppiHPI------VSLgpeANVSPVERRVYEYVARHFLACCSEDAKGQS 465
Cdd:PRK07726 347 LLLAPPVLDPSIRSRA-------WNDKkvtAH---HAIipteqpPNL---SKLSEDERKVYDLIARRYLAQFLPPAEYDK 413

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   466 MTLVLDWAVERFSASGLVVLERNFLDVYPW--ARWETTKQLPRLEMNALVDIAKAEMKAGTTAPPKPMTESELILLM--- 540
Cdd:PRK07726 414 TTIELEIAGGTFIAKGKQVVEAGWKALLGKkeEDEEKEQPLPVLAKGDELKVEKGEVKEGQTQPPKRFTEGTLLSAMeni 493

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   541 --------------DTNGIGTDATIAEHIDKIQVRNYVrsEKVGKetYLQPTTLGVSLVHgfeaiGLEDSFAKPfqrrEM 606
Cdd:PRK07726 494 arfvqdkelkktlkETDGLGTEATRAGIIEKLFKRGYL--EKKGK--YIHATDKGKQLID-----ALPEELTSP----DM 560

                        570       580
                 ....*....|....*....|....*..
gi 6323263   607 ----EQDLKKICEGHASKTDVVKDIVE 629
Cdd:PRK07726 561 takwEQALDQISEGQLSYQDFMQPLKQ 587
TOPRIM_TopoIA cd01028
TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 2-168 1.77e-42

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: 150.07  E-value: 1.77e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    2 KVLCVAEKNSIAKAVSQILGGGRSTSRDsgymyvknydfmfsgfpfarNGANCEVTMTSVAGHLTGIDFSHDSHGWGKCA 81
Cdd:cd01028   1 KVLIIAEKPSKAKTIAKILGKGSKKKGF--------------------YGEGGGYVVTASVGHLLELPFPEEYVDWDKDW 60

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   82 IQELFDAPLNEIMNNNQKKIASNIKREARNADYLMIWTDCDREGEYIGWEIWQEAKRgnrliQNDQVYRAVFSHLERQHI 161
Cdd:cd01028  61 PLELFPFEPKYVVIPDKKKQLKALKKLAKKADEIVLATDPDREGELIAWEILEVLKC-----DNKPVKRAWFSEITPKAI 135


                ....*..
gi 6323263  162 LNAARNP 168
Cdd:cd01028 136 REAFKNL 142
PRK06599 PRK06599
DNA topoisomerase I; Validated
 67-626 2.74e-35

DNA topoisomerase I; Validated


Pssm-ID: 235840 [Multi-domain]  Cd Length: 675  Bit Score: 141.92  E-value: 2.74e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    67 GIDFSHDshgwgkcaiqelFdAPLNEIMNNNQKKIaSNIKREARNADYLMIWTDCDREGEYIGWEIWQEAKrgNRLIQND 146
Cdd:PRK06599  43 GVDPDND------------F-APKYEIIEGKEKVV-DALKKAAKKADAVYLATDPDREGEAIAWHIAEVLK--EAKLKDK 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   147 QVYRAVFSHLERQHILNAARNPSRLDMKSVHAVGTRIEIDLRAGVTFTRLLTETLRNKLrnqatmtkdgakhrggnknds 226
Cdd:PRK06599 107 NVKRVVFNEITKKAVQEAIENPRDIDMDLVDAQQARRALDYLVGFKLSPLLWKKVRRGL--------------------- 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   227 qvvSYGTCQFPTLGFVVDRFERIRNFVPEEFWYIQLVVENKDNGGTTTFQW-------DRGHLFDRlsvltfyetciETA 299
Cdd:PRK06599 166 ---SAGRVQSVALRLICEREDEIEAFIPQEYWTIEADLATSNGEPFTAKLVevngkklEKFSITNE-----------EQA 231

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   300 GNVAQ--------VVDLKSKPTTKYRPLPLTTVELQKNCARYLRLNAKQSLDAAEKLYQ--------KGFISYPRteTDT 363
Cdd:PRK06599 232 KALVKalegqaytVDKIEKKERKRNPPPPFITSTLQQEASRKLGFSAKKTMRIAQKLYEgidlgegtVGLITYMR--TDS 309

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   364 FphamdlkslvekqaqldQLAAGGRTAWASYAASLLQPENTSNN-NKFKFPRSGSHDdkAHPPIHPI-VSLGPEA---NV 438
Cdd:PRK06599 310 V-----------------RLSNEALDEARKYITKKYGKEYLPAKpRVYKKKSKNAQE--AHEAIRPTsINRTPESlkpYL 370

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   439 SPVERRVYEYVARHFLACCSEDAKGQSMTLVL--DWAVERFSASGLVVLERNFLDVYP----WARWETTKQLPRLEMNAL 512
Cdd:PRK06599 371 TPDQFKLYELIWKRTVASQMAPAILDQTSVDIasENGKYVFRATGSVILFPGFLKVYGeskdDEEEDDEKLLPPLKEGEK 450

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   513 VDIAKAEMKAGTTAPPKPMTESELILLMDTNGIG---TDATIaehIDKIQVRNYVRSEKvgKEtyLQPTTLGVsLVHGFe 589
Cdd:PRK06599 451 LKLDELLPEQHFTEPPPRYSEASLVKKLEEYGIGrpsTYASI---ISTLQDREYVELEK--KR--FIPTDLGR-IVNDF- 521

                        570       580       590       600
                 ....*....|....*....|....*....|....*....|
gi 6323263   590 aigLEDSFAKPFQRR---EMEQDLKKICEGHASKTDVVKD 626
Cdd:PRK06599 522 ---LVEHFPKYVDYDftaGLEDELDEIAEGKKDWKPVLRE 558
PRK07561 PRK07561
DNA topoisomerase I subunit omega; Validated
 99-626 3.27e-34

DNA topoisomerase I subunit omega; Validated


Pssm-ID: 236048 [Multi-domain]  Cd Length: 859  Bit Score: 139.54  E-value: 3.27e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    99 KKIASNIKREARNADYLMIWTDCDREGEYIGWEIwQEAKRGNrliqNDQVYRAVFSHLERQHILNAARNPSRLDMKSVHA 178
Cdd:PRK07561  74 EKVVSELKKAAKDADELYLATDPDREGEAIAWHL-LEVLGGD----DVPVKRVVFNEITKNAIQEAFENPRELDINLVNA 148

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   179 VGTRieidlRA-----GVTFTRLLTETLRNKLrnqatmtkdgakhrggnkndsqvvSYGTCQFPTLGFVVDRfER-IRNF 252
Cdd:PRK07561 149 QQAR-----RFldrlvGYMVSPLLWKKIARGL------------------------SAGRVQSVAVRLIVER-EReIEAF 198

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   253 VPEEFWYIQLVVENKDNggtTTFQWDRGHL----FDRLSVLTfyetciETAGNVA---------QVVDLKSKPTTKYRPL 319
Cdd:PRK07561 199 VPEEYWDIHADLTTPRG---DAFEARLTHLdgkkFAPVDLLN------EAQAEAAvaalegarySVASVEDKPTTRKPSA 269

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   320 PLTTVELQKNCARYLRLNAKQSLDAAEKLYQKGFISYPRTE-TDTFPHAMD-LKSLVEKQaqldqlaaggrtawasYAAS 397
Cdd:PRK07561 270 PFTTSTLQQEASRKLGFSVKKTMRIAQRLYEAGYITYMRTDsTNLSQEAINaARGYIGDN----------------YGKK 333

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   398 LLQPENTSNNNKFKfprsGSHDdkAHPPIHPI-VSLGPE--ANVSPVERRVYEYVARHFLACCSEDAKGQSMTLVLDWAV 474
Cdd:PRK07561 334 YLPEKPRQYSSKAK----NAQE--AHEAIRPSdVFRTPDqlKGLEGDAQRLYELIWKRFVASQMAPARYDSTTVTIAAGD 407

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   475 ERFSASGLVVLERNFLDVYPWAR----WETTKQLPRLEMNALVDIAKAEMKAGTTAPPKPMTESELILLMDTNGIG---T 547
Cdd:PRK07561 408 AELRATGRVLRFDGFLKVYVEGRddalDDEDRRLPALKVGDALTLEKLDPTQHFTKPPARYSEASLVKELEKLGIGrpsT 487

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   548 DATIaehIDKIQVRNYVRSEKvgkeTYLQPTTLGvSLVHGFeaigLEDSFAK----PFQRReMEQDLKKICEGHASKTDV 623
Cdd:PRK07561 488 YASI---ISTIQDRGYVRLEN----RRFYPEKMG-RIVTDR----LEEFFPRlvdyDFTAR-MEEELDDIANGEADWKPV 554


                 ...
gi 6323263   624 VKD 626
Cdd:PRK07561 555 LDD 557
TOP1Bc smart00436
Bacterial DNA topoisomeraes I ATP-binding domain; Extension of TOPRIM in Bacterial DNA ...
 148-259 1.29e-31

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: 117.68  E-value: 1.29e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263     148 VYRAVFSHLERQHILNAARNPSRLDMKSVHAVGTRIEIDLRAGVTFTRLLTETLRNklrnqatmtkdgakhrggnkndsQ 227
Cdd:smart00436   1 IKRIEFSEITKKAIREALKNPREIDENLVNAQLARRILDRLIGFNLSRLLTKKLRN-----------------------G 57

                           90       100       110
                   ....*....|....*....|....*....|..
gi 6323263     228 VVSYGTCQFPTLGFVVDRFERIRNFVPEEFWY 259
Cdd:smart00436  58 VLSAGRVQTPTLGLIVEREREIKNFVPKPYWE 89
PRK06319 PRK06319
DNA topoisomerase I/SWI domain fusion protein; Validated
 67-631 4.80e-29

DNA topoisomerase I/SWI domain fusion protein; Validated


Pssm-ID: 235778 [Multi-domain]  Cd Length: 860  Bit Score: 123.39  E-value: 4.80e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    67 GIDFSHDshgwgkcaiqelFDaPLNEIMNNNQKKIaSNIKREARNADYLMIWTDCDREGEYIGWEIwqeakrGNRLIQND 146
Cdd:PRK06319  43 GIDIEND------------FE-PDYQILPDKEEVI-NKICKLAKKCDVVYLSPDPDREGEAIAWHI------ANQLPKNT 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   147 QVYRAVFSHLERQHILNAARNPSRLDMKSVHAVGTRIEIDLRAGVTFTRLLTETLrnklrnqatmtkdgaKHRGGnknds 226
Cdd:PRK06319 103 KIQRISFNAITKGAVTEALKHPREIDMALVNAQQARRLLDRIVGYKISPILSRKL---------------QRRSG----- 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   227 qvVSYGTCQFPTLGFVVDRFERIRNFVPEEFWYIQLVVenKDNGGTTTF----------QWDR----GHLFDRLSVLTFY 292
Cdd:PRK06319 163 --VSAGRVQSVALKLVVDREKAIEAFVPVEYWNIRVHL--KDPKTQKTFwahlysvdgkKWEKeipeGKTEDEVLLINSK 238

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   293 ETC------IETAGNVAQVVDLKSKptTKYRPLPLTTVELQKNCARYLRLNAKQSLDAAEKLYQ---------KGFISYP 357
Cdd:PRK06319 239 EKAdhivelLESATYTVTRVESKEK--RRNAYPPFITSTLQQEASRHFRFSSSRTMNIAQTLYEgvdldsegaTGLITYM 316

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   358 RTET-DTFPHAMD-LKSLVEKQAQLDQLaaggrtawasyaasllqPENTSNNNKFKFPRSgshddkAHPPIHPI-VSLGP 434
Cdd:PRK06319 317 RTDSvRTDPEALKqVRKYIEGTFGKEFL-----------------PSSPNVYTTKKMAQD------AHEAIRPTdITLTP 373

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   435 E---ANVSPVERRVYEYVARHFLAccSEDAKGQSMTLVLDWAVER---FSASGLVVLERNFLDVYPWAR-----WETTKQ 503
Cdd:PRK06319 374 EklrSKLTEDQYKLYSLIWKRFVA--SQMIPAIYDTLAIRITTNKgidLRATGSLLKFKGFLAVYEEKRddegdEEENIH 451

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   504 LPRLEMNALVDIAKAEMKAGTTAPPKPMTESELILLMDTNGIGTDATIAEHIDKIQVRNYVRSEKvgkeTYLQPTTLGvS 583
Cdd:PRK06319 452 LPKLHEQDVLTKEELSAEQAFTKPLPRFTEASLVKELEKSGIGRPSTYATIMNKIQSREYTLKEN----QRLRPTELG-K 526

                        570       580       590       600       610
                 ....*....|....*....|....*....|....*....|....*....|.
gi 6323263   584 LVHGFeaigLEDSFAKPFQ---RREMEQDLKKICEGHASKTDVVKDIVEKY 631
Cdd:PRK06319 527 IISQF----LETNFPRIMDigfTALMEDELELIADNKKPWKLLLQEFWELF 573
PRK08780 PRK08780
DNA topoisomerase I; Provisional
 92-635 2.43e-27

DNA topoisomerase I; Provisional


Pssm-ID: 181555 [Multi-domain]  Cd Length: 780  Bit Score: 117.94  E-value: 2.43e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    92 EIMNNNQKKIASnIKREARNADYLMIWTDCDREGEYIGWEIWQEAK-RGnrLIQNDQVYRAVFSHLERQHILNAARNPSR 170
Cdd:PRK08780  55 DLIDKNEKHVEA-IAKAAKSADDLYLATDPDREGEAISWHLAEILKeRG--LLKDKPMQRVVFTEITPRAIKEAMAKPRD 131

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   171 LDMKSVHAVGTRIEIDLRAGVTFTRLLTETLRnklrnqatmtkdgakhRGgnkndsqvVSYGTCQFPTLGFVVDRFERIR 250
Cdd:PRK08780 132 IASDLVDAQQARRALDYLVGFNLSPLLWRKIQ----------------RG--------LSAGRVQSPALRMIVEREEEIE 187

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   251 NFVPEEFWYIQLVVENKDNGGTTTFQWDRGHLFDRLSV------LTFYETCIETAGNVAQVVDLKSKPTTKYRPLPLTTV 324
Cdd:PRK08780 188 AFIAREYWSIEADCAHPSQPFNAKLIKLDGQKFEQFTItdgdtaEAARLRIQQAAQGTLHVTDVESKERKRNPAPPFTTS 267

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   325 ELQKNCARYLRLNAKQSLDAAEKLYQK---------GFISYPRTETDTFPHamdlkslvEKQAQLDQLAAgGRTAWASYA 395
Cdd:PRK08780 268 TLQQEASRKLGFTTRRTMQVAQKLYEGvdlgdegsvGLITYMRTDSVNLSQ--------DALAEIRDVIA-RDYGTASLP 338

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   396 ASLLQPENTSNNNKfkfprsgshddKAHPPIHPI-VSLGPE---ANVSPVERRVYEYVARHFLACCSEDAKGQSMTLVLD 471
Cdd:PRK08780 339 DQPNTYKTKSKNAQ-----------EAHEAVRPTsALRTPAqvaRFLSDDQRRLYELIWKRAVACQMIPATLNTVSVDLA 407

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   472 WAVER-FSASGLVVLERNFLDVYPWAR-------WETTKQLPRLEMNALVDIAKAEMKAGTTAPPKPMTESELILLMDTN 543
Cdd:PRK08780 408 AGSEHvFRATGSTVVVPGFLAVYEEGKddksaedEDEGRKLPPMKEGDNVPLERIRAEQHFTEPPPRYTEASLVKALEEY 487

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   544 GIGTDATIAEHIDKIQVRNYVRSEkvGKEtyLQPTTLGvSLVHGFeaigLEDSFAK----PFQRReMEQDLKKICEGHas 619
Cdd:PRK08780 488 GIGRPSTYASIISTLQFRKYVEME--GRR--FRPTDVG-RAVNKF----LTGHFTRyvdyDFTAR-LEDDLDAVSRGE-- 555

                        570
                 ....*....|....*.
gi 6323263   620 ktdvvKDIVEKYRKYW 635
Cdd:PRK08780 556 -----KEWIPLMEKFW 566
PRK08173 PRK08173
DNA topoisomerase III; Validated
 2-629 1.00e-25

DNA topoisomerase III; Validated


Pssm-ID: 236172 [Multi-domain]  Cd Length: 862  Bit Score: 112.84  E-value: 1.00e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263     2 KVLCVAEKNSIAKAVSQILGGgrstsrdsgymYVKNYDFMFSGfpfarngancEVTMTSVAGHLTGI------------- 68
Cdd:PRK08173   3 KALIIAEKPSVANDIARALGG-----------FTKHDEYFESD----------EYVLSSAVGHLLEIaapeeyevkrgkw 61

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    69 DFSHDShgwgkcAIQELFDapLNEImnnnqKKIASNIK---REARNADYLMIWTDCD--REGEYIGWEIWQEAKRG---N 140
Cdd:PRK08173  62 SFAHLP------VIPPHFD--LNPI-----AKTESRLKvltKLIKRKDVTRLINACDagREGELIFRLIAQHAKAKkpvK 128

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   141 RL-IQN--DQVYRAVFSHL----ERQHILNAARnpsrldmksvhavgTRIEIDLRAGVTFTRLLTetlrnklrnqATMTK 213
Cdd:PRK08173 129 RLwLQSmtPQAIRDGFANLrsdeDMQPLADAAR--------------CRSEADWLVGINGTRAMT----------AFNSK 184

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   214 DGAKHrggnkndsqVVSYGTCQFPTLGFVVDRFERIRNFVPEEFWYIQLVVENKdnGGTTTFQW---------------- 277
Cdd:PRK08173 185 GGGFF---------LTTVGRVQTPTLSIVVEREEKIRRFVPRDYWEVRAEFVAA--AGFYEGRWfdpkfkkdefdpekra 253

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   278 DRghLFDRLSVLTFYETCIETAGNVAQvvdlKSKPTTKYRPL--PLTTVELQKNcARYlRLNAKQSLDAAEKLYQK-GFI 354
Cdd:PRK08173 254 SR--LWSEAAAEAIVAACRGKPGTVTE----ESKPSTQLSPLlfDLTSLQREAN-GRF-GFSAKNTLGLAQALYEKhKVL 325

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   355 SYPRTETDTFPHamDLKSLVeKQAqLDQLAagGRTAWASYAASLLQpENTSNNNKFKFPRSGSHDdkaHPPIHPIVSLgP 434
Cdd:PRK08173 326 TYPRTDSRALPE--DYLGTV-KQT-LEMLK--ESNNYLPHAKQILD-KGWVKPNKRIFDNSKISD---HFAIIPTLQA-P 394

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   435 EaNVSPVERRVYEYVARHFLACCSEDAKGQSMTLVLDWAVERFSASGLVVLERNFLDVYPWARWETTKQLPRLEMNALVD 514
Cdd:PRK08173 395 K-SLSEPEQKLYDLVVKRFLAVFFPAAEFLVTTRITEVAGHHFKTEGKVLVNPGWLAVYGKEAQGADANLVPVQKGEKVK 473

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   515 IAKAEMKAGTTAPPKPMTES----------------ELILLMDTNGIGTDATIAEHIDKIQVRNYVRSEkvGKEtyLQPT 578
Cdd:PRK08173 474 TDKIEAVALTTKPPARYNEAtllsamegagklveddELREAMAEKGLGTPATRAAIIEGLLGEKYLVRE--GRE--LIPT 549

                        650       660       670       680       690
                 ....*....|....*....|....*....|....*....|....*....|.
gi 6323263   579 TLGVSLVHGFEAIGLEDsFAKPFQRREMEQDLKKICEGHASKTDVVKDIVE 629
Cdd:PRK08173 550 AKAFQLMTLLRGLGVEE-LTSPELTGEWEYKLSQIERGKLSRDAFMQEIAQ 599
PRK14724 PRK14724
DNA topoisomerase III; Provisional
 1-634 9.05e-22

DNA topoisomerase III; Provisional


Pssm-ID: 237803 [Multi-domain]  Cd Length: 987  Bit Score: 100.41  E-value: 9.05e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263     1 MKVLCVAEKNSIAKAVSQILG--GGRSTSRDSgymYVKNYDFMfsgfpfarngancevtMTSVAGHLTGI----DFSHDS 74
Cdd:PRK14724   1 TKTLVIAEKPSVAQDIVRALTpvAGKFEKHDE---HFESDSYV----------------VTSAVGHLVEIqapeEFDVKR 61

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    75 HGWGKC---AIQELFD-APLNEimnnnQKKIASNIKREARNADYLMIWTDCD--REGEYIGWEIWQEAKrGNRLIQNDQV 148
Cdd:PRK14724  62 GKWSFAnlpVIPPYFDlKPVDK-----TKTRLNAVVKLAKRKDVTELVNACDagREGELIFRLIEQYAG-GAKGGLGKPV 135

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   149 YRAVFSHLERQHI---LNAARNPSRLdMKSVHAVGTRIEIDLRAGVTFTRLLTetlrnklrnqATMTKDGAKHrggnknd 225
Cdd:PRK14724 136 KRLWLQSMTPQAIrdgFDNLRSDAQM-QGLASAARSRSEADWLVGINGTRAMT----------AFNSRDGGFF------- 197

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   226 sqVVSYGTCQFPTLGFVVDRFERIRNFVPEEFWYIQLVVENKdnGGTTTFQW----------DRGHLFDRlsVLTFYET- 294
Cdd:PRK14724 198 --LTTVGRVQTPTLSLVVEREEKIRKFVSRDYWEIHAGFHAE--AGEYLGKWfdpqwkkasdDPEARADR--VWSEREAr 271

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   295 CIETA--GNVAQVVDlKSKPTTKYRPLPLTTVELQKNCARYLRLNAKQSLDAAEKLYQK-GFISYPRTETDTFPHamDLK 371
Cdd:PRK14724 272 AIADAvrGKAATVTE-ESKPTTQASPLLFDLTSLQREANGKFGFSAKTTLALAQSLYERhKALTYPRTDSRALPE--DYL 348

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   372 SLVEKqaQLDQLAAGGRTAWASYAASLLQpENTSNNNKFKFPRSGSHDdkaHPPIHPivSLGPEANVSPVERRVYEYVAR 451
Cdd:PRK14724 349 PVAKQ--TFEMLATSGMRHLAPFAQQALD-GNYVRPSKRIFDNSKVSD---HFAIIP--TTQAPSGLSEAEQKLYDLVVR 420

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   452 HFLACCSEDAKGQSMTLVLDWAVERFSASGLVVLERNFLDVY-PWARWETT--------KQLPRLEMNALVDIAKAEMKA 522
Cdd:PRK14724 421 RFMAVFFPSAEYQVTTRISQVVGHSFKTEGKVLVKPGWLAIYgKEAANEVEdakdgdkgQPLVPVKPGEMVRTEFAEAKG 500

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   523 GTTAPP----------------KPMTESELILLMDTNGIGTDATIAEHIDKIQVRNYVRSEkvGKEtyLQPTTLGVSLVH 586
Cdd:PRK14724 501 LKTKPParyseatllgamesagKQIDDDELREAMQEKGLGTPATRAAIIEGLLTEKYMLRE--GRE--LIPTAKAFQLMT 576

                        650       660       670       680       690
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 6323263   587 GFEAIGLEDsFAKPFQRREMEQDLKKICEGHASKTDVVKDI-------VEKYRKY 634
Cdd:PRK14724 577 LLRGLGVEE-LSRAELTGEWEYKLAQMEKGQLSREAFMQQIaamteklVKKAKEY 630
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 3-156 2.46e-09

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: 54.67  E-value: 2.46e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263      3 VLCVAEKNSIAKAVSQILGGGrstsrdsgymyvknydfmfsgfpfarngancEVTMTSVAGHLTgidfshdshgwgkcai 82
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGG-------------------------------FQAVVAVLGHLL---------------- 33

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 6323263     83 qelfdaplnEIMNNNQKKIASNIKREARNADYLMIWTDCDREGEYIGWEIWQeakrgNRLIQNDQVYRAVFSHL 156
Cdd:pfam01751  34 ---------SLEKGPKKKALKALKELALKAKEVILATDPDREGEAIALKLLE-----LKELLENAGGRVEFSEL 93
TOPRIM_TopoIA_TopoI cd03363
TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TOPRIM) domain found in members of the type IA ...
 99-168 2.62e-08

TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TOPRIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. 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: 173783 [Multi-domain]  Cd Length: 123  Bit Score: 52.56  E-value: 2.62e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   99 KKIASNIKREARNADYLMIWTDCDREGEYIGWEIWQEAKrgnrliQNDQVYRAVFSHLERQHILNAARNP 168
Cdd:cd03363  60 KKVVKELKKLAKKADEIYLATDPDREGEAIAWHLAEVLK------LKKNVKRVVFNEITKEAIKEALKNP 123
PTZ00407 PTZ00407
DNA topoisomerase IA; Provisional
 98-603 7.02e-08

DNA topoisomerase IA; Provisional


Pssm-ID: 173597 [Multi-domain]  Cd Length: 805  Bit Score: 55.72  E-value: 7.02e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263    98 QKKIASNIKREARNADYLMIWTDCDREGEYIGweiwqeakrgnrlIQNDQVYRAVFSHLERQHilnaarnpSRLDMKSVH 177
Cdd:PTZ00407 111 QETLERYIEEKADNVTEIILATDPDREGELIA-------------VHALQTIKRLYPKLKVPF--------SRAYMHSIT 169

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   178 AVGTRIEIDLRAGVTFTRllteTLRNKLRNQATMTK-----DGAKHRGGNkndSQVVSYGTCQFPTLGFVVDRFERIRNF 252
Cdd:PTZ00407 170 EDGIRKAMRERHVEACDY----DLANAAETRHAMDRifgflGSSVVRAAN---SQMRSIGRVQTPALILINEREDKIKAF 242

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   253 -----------------VPEEFWYIQLVVENKDNGGTTTfQW-DRGHLFDRLSvltfyETCIETAGNVAQVVDLKSKPTT 314
Cdd:PTZ00407 243 lesnkstfevqamcqfpSPHGTTFSQVVTITPDRKGGAS-HWaTEAEARRCLE-----QWKLNNCTGFSVPLEPKPQPSV 316

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   315 KYRPLPLTTVELQKNCARYLRLNAKQSLDAAEKLYQKGFISYPRTETDTFPHAM--DLKSLVEKQ-------AQLDQLAA 385
Cdd:PTZ00407 317 VPPPQPFTMATAIAKANRQLKYSSEMVSGCLQDLFQLGHITYPRTDSTRIDESAlpDIYAAVKKEfgkeflyRLEDRTVS 396

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   386 GGRTAWASYAASllqpENTSNNNKFKFPRSGSHDDkAHPPIHP--IVSLGPEANVSPVERRVYEYVARHFLA-------- 455
Cdd:PTZ00407 397 AQEGKGSKKTGK----KRSTKQKKGADTPVGNVED-AHEAIRPtnIDTTGESLSLSPPTRAVYDLVRRNTLAvfmipmkt 471

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   456 --------CCSedAKGQSMTLVLD--------W--AVERFSASGLVVLERNFLDVYpwARWETTKQLPRL---EMNALVD 514
Cdd:PTZ00407 472 ekivatvkFTS--GSGEKLEFELQgkrvvepgWtrAFHKGDKGTTGPAEETDEDIT--AVEEGAPVVPSLsqeEFKAIMN 547

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263   515 IAKA----------EMKAGTTA-----PPKPMTESELILLMDTNGIGTDATIAEHIDKIQVRNYVRSEKVGK-ETylqpT 578
Cdd:PTZ00407 548 LRSQlgsgvqkgffELRSPQVRenrpvPPLPHSEGTLIEELKNNGVGRPSTYPMIVKTLLARGYIAVNPKGRcET----T 623

                        570       580       590
                 ....*....|....*....|....*....|..
gi 6323263   579 TLGVSLVHGFEA-------IGLEDSFAKPFQR 603
Cdd:PTZ00407 624 PVGRMLVETAKStfpsivdIGFTAAFEKKLDR 655
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
2-140 1.79e-07

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 48.80  E-value: 1.79e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323263       2 KVLCVAEKNSIAKAVSQILGggrstsrdsgymyvknydfmfsgfpfarnganCEVTMTSVAGHLTgidfshdshgwgkca 81
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGG--------------------------------KRGNVVALGGHLL--------------- 33

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 6323263      82 iqelfdaplneimnnnQKKIASNIKREARNAdYLMIWTDCDREGEYIGWEIWQEAKRGN 140
Cdd:smart00493  34 ----------------SKEQIKLLKKLAKKA-EVILATDPDREGEAIAWELAELLKPAG 75
TOPRIM_TopoIA_RevGyr cd03361
TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA ...
 104-168 1.01e-06

TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. 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. 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: 173781 [Multi-domain]  Cd Length: 170  Bit Score: 49.23  E-value: 1.01e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6323263  104 NIKRE-ARNADYLMIWTDCDREGEYIGWEIWQEAKRGNRliqndQVYRAVFSHLERQHILNAARNP 168
Cdd:cd03361 110 EALRElALEVDEVLIATDPDTEGEKIAWDVYLALRPYNK-----NIKRAEFHEVTRRAILEALRNP 170
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 100-153 2.49e-05

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.


Pssm-ID: 173773 [Multi-domain]  Cd Length: 83  Bit Score: 42.80  E-value: 2.49e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 6323263  100 KIASNIKREARNADYLMIWTDCDREGEYIGWEIWQEAKRgnrliQNDQVYRAVF 153
Cdd:cd00188  35 KTRELLKRLLGEAKEVIIATDADREGEAIALRLLELLKS-----LGKKVRRLLL 83
 
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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