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Conserved domains on  [gi|686341324|ref|WP_031884499|]
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type IA DNA topoisomerase, partial [Staphylococcus aureus]

Protein Classification

type IA DNA topoisomerase( domain architecture ID 13519367)

type IA DNA topoisomerase resolves single strand DNA recombination and replication intermediates

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
topB super family cl36808
DNA topoisomerase III, bacteria and conjugative plasmid; This model describes topoisomerase ...
 1-406 0e+00

DNA topoisomerase III, bacteria and conjugative plasmid; This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent. [DNA metabolism, DNA replication, recombination, and repair]


The actual alignment was detected with superfamily member TIGR01056:

Pssm-ID: 273419 [Multi-domain]  Cd Length: 660  Bit Score: 608.00  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324    1 SEDELHEFLFENDITDLTQKG-LVTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEK-KLITYPRTD 78
Cdd:TIGR01056 245 EERELHEFLAENVVTDLTQKPaLVTDIEKERKKTSAPLFYDLSALQEDANKRFGISAKRTLDIAQKLYEThKLITYPRTD 324

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324   79 SRYITEDEKEMLLENIDYLKEITKINLN----NELTNNSLINPSKIEDHYAILITGNDFNKVDLKEEEINVYKSILQNVA 154
Cdd:TIGR01056 325 SRYLPEDEKEMLLEVLDALKVITPALLPikkrDELTNNRLWNDKKIEDHHAIIPTGNDFNLSDLSEEERNVYKLIAQNYL 404

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  155 MNFMDKEQYETTTIEIAVKKLMFEVKGKIIQDNGFKALLNKQKTSEE----TIPNFEKNEEVDIE-LDLLEKETTPPKRY 229
Cdd:TIGR01056 405 MQFMPKEEYETTTIEIAIGKLMFEAKGKILQDNGWKALLGKQEEDEEtedtTLPAFQKGDELDVEtLELLEKQTKPPARY 484

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  230 TEKTLLKAMANPIETLEDEGLKSTLKEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEgHLLSKPDL 309
Cdd:TIGR01056 485 TEGTLLSAMTNPAAFVQDKGLKKTLKETKGLGTEATRADIIENLFKRGFIQKKKNKIYITKNGKLLCLLLP-ELLTKPDL 563

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  310 TGQWEKYLNGISKGEKDDDSFINTINEMIKKTINEEVKNKESIQKVAKEKVSTNNIAKCPACDNGYLIDRKGFYGCTEYN 389
Cdd:TIGR01056 564 TAQWEQYLNGISAGEKDDDDFINTINEMIKQTINEEKKNPETIQKVAKEPVSCGGIAKCPAKDNGRLIDCKKFPECTEYG 643

                         410
                  ....*....|....*..
gi 686341324  390 NGCEFTIPKKLLEKSIP 406
Cdd:TIGR01056 644 NGCEFTIPKKLREKSIP 660
Toprim_Crpt pfam13342
C-terminal repeat of topoisomerase;
391-428 1.63e-07

C-terminal repeat of topoisomerase;


:

Pssm-ID: 463851 [Multi-domain]  Cd Length: 60  Bit Score: 47.86  E-value: 1.63e-07
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 686341324  391 GCEFTIPKKLLEKSIPPTVVKALCESKTTKKLKGFKSK 428
Cdd:pfam13342   1 GCGFSIGKTIAGKKLSEEQVKELLTKGKTGLIKGFKSK 38
 
Name Accession Description Interval E-value
topB TIGR01056
DNA topoisomerase III, bacteria and conjugative plasmid; This model describes topoisomerase ...
 1-406 0e+00

DNA topoisomerase III, bacteria and conjugative plasmid; This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273419 [Multi-domain]  Cd Length: 660  Bit Score: 608.00  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324    1 SEDELHEFLFENDITDLTQKG-LVTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEK-KLITYPRTD 78
Cdd:TIGR01056 245 EERELHEFLAENVVTDLTQKPaLVTDIEKERKKTSAPLFYDLSALQEDANKRFGISAKRTLDIAQKLYEThKLITYPRTD 324

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324   79 SRYITEDEKEMLLENIDYLKEITKINLN----NELTNNSLINPSKIEDHYAILITGNDFNKVDLKEEEINVYKSILQNVA 154
Cdd:TIGR01056 325 SRYLPEDEKEMLLEVLDALKVITPALLPikkrDELTNNRLWNDKKIEDHHAIIPTGNDFNLSDLSEEERNVYKLIAQNYL 404

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  155 MNFMDKEQYETTTIEIAVKKLMFEVKGKIIQDNGFKALLNKQKTSEE----TIPNFEKNEEVDIE-LDLLEKETTPPKRY 229
Cdd:TIGR01056 405 MQFMPKEEYETTTIEIAIGKLMFEAKGKILQDNGWKALLGKQEEDEEtedtTLPAFQKGDELDVEtLELLEKQTKPPARY 484

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  230 TEKTLLKAMANPIETLEDEGLKSTLKEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEgHLLSKPDL 309
Cdd:TIGR01056 485 TEGTLLSAMTNPAAFVQDKGLKKTLKETKGLGTEATRADIIENLFKRGFIQKKKNKIYITKNGKLLCLLLP-ELLTKPDL 563

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  310 TGQWEKYLNGISKGEKDDDSFINTINEMIKKTINEEVKNKESIQKVAKEKVSTNNIAKCPACDNGYLIDRKGFYGCTEYN 389
Cdd:TIGR01056 564 TAQWEQYLNGISAGEKDDDDFINTINEMIKQTINEEKKNPETIQKVAKEPVSCGGIAKCPAKDNGRLIDCKKFPECTEYG 643

                         410
                  ....*....|....*..
gi 686341324  390 NGCEFTIPKKLLEKSIP 406
Cdd:TIGR01056 644 NGCEFTIPKKLREKSIP 660
PRK07726 PRK07726
DNA topoisomerase 3;
18-399 1.06e-97

DNA topoisomerase 3;


Pssm-ID: 236078 [Multi-domain]  Cd Length: 658  Bit Score: 305.93  E-value: 1.06e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  18 TQKGLVTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEK-KLITYPRTDSRYITEDEKEML------ 90
Cdd:PRK07726 260 GQPAKVTEVETKRKKEYAPLLYDLSELQIDANKRFGLSAKETLDIAQSLYEThKLITYPRTDSRYLPEDMVATLpevlna 339

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  91 LENID-YLKEITKInLNNELtNNSLINPSKIEDHYAILITGNDFNKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIE 169
Cdd:PRK07726 340 ISKVDpYLLLAPPV-LDPSI-RSRAWNDKKVTAHHAIIPTEQPPNLSKLSEDERKVYDLIARRYLAQFLPPAEYDKTTIE 417

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 170 IAVKKLMFEVKGKIIQDNGFKALLNKQKTSEE---TIPNFEKNEEVDIE-LDLLEKETTPPKRYTEKTLLKAMANPIETL 245
Cdd:PRK07726 418 LEIAGGTFIAKGKQVVEAGWKALLGKKEEDEEkeqPLPVLAKGDELKVEkGEVKEGQTQPPKRFTEGTLLSAMENIARFV 497

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 246 EDEGLKSTLKEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGilaCLLLE--GHLLSKPDLTGQWEKYLNGISKG 323
Cdd:PRK07726 498 QDKELKKTLKETDGLGTEATRAGIIEKLFKRGYLEKKGKYIHATDKG---KQLIDalPEELTSPDMTAKWEQALDQISEG 574

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 324 EKDDDSFINTINEMIKKTInEEVKNkesiqkvAKEKVSTNNI--AKCPACdNGYLIDRKG----FYGCTEYNNGCEFTIP 397
Cdd:PRK07726 575 QLSYQDFMQPLKQWLKQLV-EQAKQ-------SSEKYKFDNLtgPKCPDC-GKPMLKVKGkngkMLVCQDRECGKRKNVS 645


                 ..
gi 686341324 398 KK 399
Cdd:PRK07726 646 KK 647
TOP1Ac cd00186
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
 19-342 5.22e-94

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: 287.96  E-value: 5.22e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  19 QKGLVTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEKKLITYPRTDSRYITEDEKEMLLENIDYLK 98
Cdd:cd00186   67 KEAVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEAGLITYPRTDSTRLSEEAILEAREYIQAIY 146

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  99 EITKINLNNELT-NNSLINPSKIEDHYAILITGNDF---NKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIEIAVKK 174
Cdd:cd00186  147 GKEYLYPAPLLGrRNPKRGKKEQGAHEAIRPTKVAPtpeLEANLSEDEFKLYELIWRRFLASQMADAKYEETTVTLEIGG 226

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 175 LMFEVKGKIIQDNGFKALLNKQKTSEETI-PNFEKNEEVDI-ELDLLEKETTPPKRYTEKTLLKAManpietledeglks 252
Cdd:cd00186  227 EKFKASGKVLLEDGWLEVYPEEKDDEEEEpPPLKEGDELKLeEVELEEKETQPPPRYTEASLIKLM-------------- 292

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 253 tlkEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEGH--LLSKPDLTGQWEKYLNGISKGEKDDDSF 330
Cdd:cd00186  293 ---EKRGIGRPSTYASIIETLLDRGYVEKEKKKLIPTELGFAVIELLEKHfpELVDPEFTAKLEEKLDEIAEGKKDYQEV 369

                        330
                 ....*....|..
gi 686341324 331 INTINEMIKKTI 342
Cdd:cd00186  370 LEEFYEEFKKIV 381
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
19-343 8.77e-82

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 440316 [Multi-domain]  Cd Length: 541  Bit Score: 261.18  E-value: 8.77e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  19 QKGLVTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEKKLITYPRTDSRYITEDEKEMLLENI---- 94
Cdd:COG0550  229 KTFTVTSVEKKPKKRNPPPPFTTSTLQQEASRKLGFSAKKTMSIAQRLYEVGLITYMRTDSVRLSEDAVAAAREYIealy 308

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  95 --DYLKEiTKINLNNeltnnsliNPSKIEDHYAILITGNDFNKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIEIAV 172
Cdd:COG0550  309 gkEYLPE-KPRVYKT--------SKNAQEAHEAIRPTGVTRTPESLSGDEFKLYDLIWKRFLASQMPPAEYETTTVTIEV 379

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 173 KKLMFEVKGKIIQDNGFKALLNKQKTSEE-----TIPNFEKNEEVDI-ELDLLEKETTPPKRYTEKTLLKAManpietle 246
Cdd:COG0550  380 GGEEFRASGKVIKFPGFLKVYGEGKDDEEeeeekRLPPLKEGEKLKLkKIEPEQHFTKPPPRYTEASLVKAM-------- 451

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 247 deglkstlkEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEGHL--LSKPDLTGQWEKYLNGISKGE 324
Cdd:COG0550  452 ---------EELGIGRPSTYASIIETLQDRGYVEREGKRLVPTELGFIVIDLLEEHFpdLVDYEFTAKMEEKLDEIAEGK 522

                        330
                 ....*....|....*....
gi 686341324 325 KDDDSFINTINEMIKKTIN 343
Cdd:COG0550  523 LDWKDVLEEFYKPFKELVE 541
TOP1Ac smart00437
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ...
 27-293 1.16e-78

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: 244.08  E-value: 1.16e-78
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324    27 EKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEKKLITYPRTDSRYITEDEKEMLLENIDYLKEITKINLN 106
Cdd:smart00437   1 EEKEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYIQKLYGKEYLDLA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324   107 NELTNNSL--INPSKIEDHYAILITGNDF---NKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIEIAVKKLMFEVKG 181
Cdd:smart00437  81 VVLLKPRKprKGKKAQGAHEAIRPTKPIFtpeLEKELSEDEFKLYELIWRRFLASQMPDAKYEETKVTIKIGGEKFKAKG 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324   182 KIIQDNGFKALLNKQ-KTSEETIPNFEKNEEVDI-ELDLLEKETTPPKRYTEKTLLKAManpietledeglkstlkEVKG 259
Cdd:smart00437 161 KTLLFDGWLKVYPEEkKEEEIELPTLKKGDELKVeEVEVEEKETKPPARYTEASLIKLM-----------------EKRG 223

                          250       260       270
                   ....*....|....*....|....*....|....
gi 686341324   260 LGTPATRADIIENLKKNKYIQVQKNKIYITKNGI 293
Cdd:smart00437 224 IGRPSTYASIIETLLDRGYVTKKKKKLIPTELGI 257
Topoisom_bac pfam01131
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ...
 18-332 2.11e-75

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: 240.99  E-value: 2.11e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324   18 TQKGLVTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEK-KLITYPRTDSRYITEDEK-----EMLL 91
Cdd:pfam01131 105 KGTAVVTSVESKEKKKPPPLPFNTTTLQKEASRKLGFSAKKTMSIAQKLYEKhGLITYPRTDSTYLSDDATlkailEYLT 184

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324   92 ENIDYLKEITKINLnNELTNNSLINPSKIEDHYAILITGNDFNKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIEIA 171
Cdd:pfam01131 185 KNYGKYLPYAPRLL-KKTKGKLTVGNAKVTAHEAIRPTGDIPVLPELSDDERKLYELIVRRFLASQMPPAVYETTTVVLE 263

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  172 VKKLMFEVKGKIIQDNGFKALLNKQKTSEE-TIPNFEKNEEVDIE-LDLLEKETTPPKRYTEKTLLKAManpietledeg 249
Cdd:pfam01131 264 VGGEEFRASGKVILEDGWLKVYPYEKKEDEeELPELKEGEELKVTqVEVEEKKTKPPPRYTEASLIKAM----------- 332

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  250 lkstlkEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEG-HLLSKPDLTGQWEKYLNGISKGEKDDD 328
Cdd:pfam01131 333 ------EKAGIGTPATRATIIETLLERGYVERKKKSLVPTELGKALVEALEKfPDLVDPELTAELEEKLDEIAEGKLDWK 406


                  ....
gi 686341324  329 SFIN 332
Cdd:pfam01131 407 DVLA 410
Toprim_Crpt pfam13342
C-terminal repeat of topoisomerase;
391-428 1.63e-07

C-terminal repeat of topoisomerase;


Pssm-ID: 463851 [Multi-domain]  Cd Length: 60  Bit Score: 47.86  E-value: 1.63e-07
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 686341324  391 GCEFTIPKKLLEKSIPPTVVKALCESKTTKKLKGFKSK 428
Cdd:pfam13342   1 GCGFSIGKTIAGKKLSEEQVKELLTKGKTGLIKGFKSK 38
 
Name Accession Description Interval E-value
topB TIGR01056
DNA topoisomerase III, bacteria and conjugative plasmid; This model describes topoisomerase ...
 1-406 0e+00

DNA topoisomerase III, bacteria and conjugative plasmid; This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273419 [Multi-domain]  Cd Length: 660  Bit Score: 608.00  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324    1 SEDELHEFLFENDITDLTQKG-LVTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEK-KLITYPRTD 78
Cdd:TIGR01056 245 EERELHEFLAENVVTDLTQKPaLVTDIEKERKKTSAPLFYDLSALQEDANKRFGISAKRTLDIAQKLYEThKLITYPRTD 324

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324   79 SRYITEDEKEMLLENIDYLKEITKINLN----NELTNNSLINPSKIEDHYAILITGNDFNKVDLKEEEINVYKSILQNVA 154
Cdd:TIGR01056 325 SRYLPEDEKEMLLEVLDALKVITPALLPikkrDELTNNRLWNDKKIEDHHAIIPTGNDFNLSDLSEEERNVYKLIAQNYL 404

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  155 MNFMDKEQYETTTIEIAVKKLMFEVKGKIIQDNGFKALLNKQKTSEE----TIPNFEKNEEVDIE-LDLLEKETTPPKRY 229
Cdd:TIGR01056 405 MQFMPKEEYETTTIEIAIGKLMFEAKGKILQDNGWKALLGKQEEDEEtedtTLPAFQKGDELDVEtLELLEKQTKPPARY 484

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  230 TEKTLLKAMANPIETLEDEGLKSTLKEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEgHLLSKPDL 309
Cdd:TIGR01056 485 TEGTLLSAMTNPAAFVQDKGLKKTLKETKGLGTEATRADIIENLFKRGFIQKKKNKIYITKNGKLLCLLLP-ELLTKPDL 563

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  310 TGQWEKYLNGISKGEKDDDSFINTINEMIKKTINEEVKNKESIQKVAKEKVSTNNIAKCPACDNGYLIDRKGFYGCTEYN 389
Cdd:TIGR01056 564 TAQWEQYLNGISAGEKDDDDFINTINEMIKQTINEEKKNPETIQKVAKEPVSCGGIAKCPAKDNGRLIDCKKFPECTEYG 643

                         410
                  ....*....|....*..
gi 686341324  390 NGCEFTIPKKLLEKSIP 406
Cdd:TIGR01056 644 NGCEFTIPKKLREKSIP 660
PRK07726 PRK07726
DNA topoisomerase 3;
18-399 1.06e-97

DNA topoisomerase 3;


Pssm-ID: 236078 [Multi-domain]  Cd Length: 658  Bit Score: 305.93  E-value: 1.06e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  18 TQKGLVTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEK-KLITYPRTDSRYITEDEKEML------ 90
Cdd:PRK07726 260 GQPAKVTEVETKRKKEYAPLLYDLSELQIDANKRFGLSAKETLDIAQSLYEThKLITYPRTDSRYLPEDMVATLpevlna 339

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  91 LENID-YLKEITKInLNNELtNNSLINPSKIEDHYAILITGNDFNKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIE 169
Cdd:PRK07726 340 ISKVDpYLLLAPPV-LDPSI-RSRAWNDKKVTAHHAIIPTEQPPNLSKLSEDERKVYDLIARRYLAQFLPPAEYDKTTIE 417

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 170 IAVKKLMFEVKGKIIQDNGFKALLNKQKTSEE---TIPNFEKNEEVDIE-LDLLEKETTPPKRYTEKTLLKAMANPIETL 245
Cdd:PRK07726 418 LEIAGGTFIAKGKQVVEAGWKALLGKKEEDEEkeqPLPVLAKGDELKVEkGEVKEGQTQPPKRFTEGTLLSAMENIARFV 497

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 246 EDEGLKSTLKEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGilaCLLLE--GHLLSKPDLTGQWEKYLNGISKG 323
Cdd:PRK07726 498 QDKELKKTLKETDGLGTEATRAGIIEKLFKRGYLEKKGKYIHATDKG---KQLIDalPEELTSPDMTAKWEQALDQISEG 574

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 324 EKDDDSFINTINEMIKKTInEEVKNkesiqkvAKEKVSTNNI--AKCPACdNGYLIDRKG----FYGCTEYNNGCEFTIP 397
Cdd:PRK07726 575 QLSYQDFMQPLKQWLKQLV-EQAKQ-------SSEKYKFDNLtgPKCPDC-GKPMLKVKGkngkMLVCQDRECGKRKNVS 645


                 ..
gi 686341324 398 KK 399
Cdd:PRK07726 646 KK 647
TOP1Ac cd00186
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
 19-342 5.22e-94

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: 287.96  E-value: 5.22e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  19 QKGLVTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEKKLITYPRTDSRYITEDEKEMLLENIDYLK 98
Cdd:cd00186   67 KEAVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEAGLITYPRTDSTRLSEEAILEAREYIQAIY 146

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  99 EITKINLNNELT-NNSLINPSKIEDHYAILITGNDF---NKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIEIAVKK 174
Cdd:cd00186  147 GKEYLYPAPLLGrRNPKRGKKEQGAHEAIRPTKVAPtpeLEANLSEDEFKLYELIWRRFLASQMADAKYEETTVTLEIGG 226

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 175 LMFEVKGKIIQDNGFKALLNKQKTSEETI-PNFEKNEEVDI-ELDLLEKETTPPKRYTEKTLLKAManpietledeglks 252
Cdd:cd00186  227 EKFKASGKVLLEDGWLEVYPEEKDDEEEEpPPLKEGDELKLeEVELEEKETQPPPRYTEASLIKLM-------------- 292

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 253 tlkEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEGH--LLSKPDLTGQWEKYLNGISKGEKDDDSF 330
Cdd:cd00186  293 ---EKRGIGRPSTYASIIETLLDRGYVEKEKKKLIPTELGFAVIELLEKHfpELVDPEFTAKLEEKLDEIAEGKKDYQEV 369

                        330
                 ....*....|..
gi 686341324 331 INTINEMIKKTI 342
Cdd:cd00186  370 LEEFYEEFKKIV 381
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
19-343 8.77e-82

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 440316 [Multi-domain]  Cd Length: 541  Bit Score: 261.18  E-value: 8.77e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  19 QKGLVTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEKKLITYPRTDSRYITEDEKEMLLENI---- 94
Cdd:COG0550  229 KTFTVTSVEKKPKKRNPPPPFTTSTLQQEASRKLGFSAKKTMSIAQRLYEVGLITYMRTDSVRLSEDAVAAAREYIealy 308

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  95 --DYLKEiTKINLNNeltnnsliNPSKIEDHYAILITGNDFNKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIEIAV 172
Cdd:COG0550  309 gkEYLPE-KPRVYKT--------SKNAQEAHEAIRPTGVTRTPESLSGDEFKLYDLIWKRFLASQMPPAEYETTTVTIEV 379

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 173 KKLMFEVKGKIIQDNGFKALLNKQKTSEE-----TIPNFEKNEEVDI-ELDLLEKETTPPKRYTEKTLLKAManpietle 246
Cdd:COG0550  380 GGEEFRASGKVIKFPGFLKVYGEGKDDEEeeeekRLPPLKEGEKLKLkKIEPEQHFTKPPPRYTEASLVKAM-------- 451

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 247 deglkstlkEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEGHL--LSKPDLTGQWEKYLNGISKGE 324
Cdd:COG0550  452 ---------EELGIGRPSTYASIIETLQDRGYVEREGKRLVPTELGFIVIDLLEEHFpdLVDYEFTAKMEEKLDEIAEGK 522

                        330
                 ....*....|....*....
gi 686341324 325 KDDDSFINTINEMIKKTIN 343
Cdd:COG0550  523 LDWKDVLEEFYKPFKELVE 541
TOP1Ac smart00437
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ...
 27-293 1.16e-78

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: 244.08  E-value: 1.16e-78
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324    27 EKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEKKLITYPRTDSRYITEDEKEMLLENIDYLKEITKINLN 106
Cdd:smart00437   1 EEKEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYIQKLYGKEYLDLA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324   107 NELTNNSL--INPSKIEDHYAILITGNDF---NKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIEIAVKKLMFEVKG 181
Cdd:smart00437  81 VVLLKPRKprKGKKAQGAHEAIRPTKPIFtpeLEKELSEDEFKLYELIWRRFLASQMPDAKYEETKVTIKIGGEKFKAKG 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324   182 KIIQDNGFKALLNKQ-KTSEETIPNFEKNEEVDI-ELDLLEKETTPPKRYTEKTLLKAManpietledeglkstlkEVKG 259
Cdd:smart00437 161 KTLLFDGWLKVYPEEkKEEEIELPTLKKGDELKVeEVEVEEKETKPPARYTEASLIKLM-----------------EKRG 223

                          250       260       270
                   ....*....|....*....|....*....|....
gi 686341324   260 LGTPATRADIIENLKKNKYIQVQKNKIYITKNGI 293
Cdd:smart00437 224 IGRPSTYASIIETLLDRGYVTKKKKKLIPTELGI 257
Topoisom_bac pfam01131
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ...
 18-332 2.11e-75

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: 240.99  E-value: 2.11e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324   18 TQKGLVTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEK-KLITYPRTDSRYITEDEK-----EMLL 91
Cdd:pfam01131 105 KGTAVVTSVESKEKKKPPPLPFNTTTLQKEASRKLGFSAKKTMSIAQKLYEKhGLITYPRTDSTYLSDDATlkailEYLT 184

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324   92 ENIDYLKEITKINLnNELTNNSLINPSKIEDHYAILITGNDFNKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIEIA 171
Cdd:pfam01131 185 KNYGKYLPYAPRLL-KKTKGKLTVGNAKVTAHEAIRPTGDIPVLPELSDDERKLYELIVRRFLASQMPPAVYETTTVVLE 263

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  172 VKKLMFEVKGKIIQDNGFKALLNKQKTSEE-TIPNFEKNEEVDIE-LDLLEKETTPPKRYTEKTLLKAManpietledeg 249
Cdd:pfam01131 264 VGGEEFRASGKVILEDGWLKVYPYEKKEDEeELPELKEGEELKVTqVEVEEKKTKPPPRYTEASLIKAM----------- 332

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  250 lkstlkEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEG-HLLSKPDLTGQWEKYLNGISKGEKDDD 328
Cdd:pfam01131 333 ------EKAGIGTPATRATIIETLLERGYVERKKKSLVPTELGKALVEALEKfPDLVDPELTAELEEKLDEIAEGKLDWK 406


                  ....
gi 686341324  329 SFIN 332
Cdd:pfam01131 407 DVLA 410
PRK08173 PRK08173
DNA topoisomerase III; Validated
 19-428 3.43e-59

DNA topoisomerase III; Validated


Pssm-ID: 236172 [Multi-domain]  Cd Length: 862  Bit Score: 207.21  E-value: 3.43e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  19 QKGLVTDIEKEiGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEK-KLITYPRTDSRYITED-------EKEML 90
Cdd:PRK08173 272 KPGTVTEESKP-STQLSPLLFDLTSLQREANGRFGFSAKNTLGLAQALYEKhKVLTYPRTDSRALPEDylgtvkqTLEML 350

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  91 LENIDYLKEITKINLNNELTNNSLI-NPSKIEDHYAILITGNdfNKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIE 169
Cdd:PRK08173 351 KESNNYLPHAKQILDKGWVKPNKRIfDNSKISDHFAIIPTLQ--APKSLSEPEQKLYDLVVKRFLAVFFPAAEFLVTTRI 428

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 170 IAVKKLMFEVKGKIIQDNGFKALLNKQKTSEE-TIPNFEKNEEV---DIELDLLekETTPPKRYTEKTLLKAMANPIETL 245
Cdd:PRK08173 429 TEVAGHHFKTEGKVLVNPGWLAVYGKEAQGADaNLVPVQKGEKVktdKIEAVAL--TTKPPARYNEATLLSAMEGAGKLV 506

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 246 EDEGLKSTLKEvKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEG---HLLSKPDLTGQWEKYLNGISK 322
Cdd:PRK08173 507 EDDELREAMAE-KGLGTPATRAAIIEGLLGEKYLVREGRELIPTAKAFQLMTLLRGlgvEELTSPELTGEWEYKLSQIER 585

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 323 GEKDDDSFINTINEMiKKTINEEVKNKESiQKVAKEKVSTNniAKCPACdnGYLID---RKgfYGCTeynnGCEFTIPKK 399
Cdd:PRK08173 586 GKLSRDAFMQEIAQM-TQQIVKRAKEYDS-DTIPGDYATLQ--TPCPNC--GGVVKenyRR--FACT----KCDFSISKI 653

                        410       420
                 ....*....|....*....|....*....
gi 686341324 400 LLEKSIPPTVVKALCESKTTKKLKGFKSK 428
Cdd:PRK08173 654 PGGRQFEIAEVEELLRKKEIGPLSGFRSK 682
PRK14724 PRK14724
DNA topoisomerase III; Provisional
 35-428 1.53e-51

DNA topoisomerase III; Provisional


Pssm-ID: 237803 [Multi-domain]  Cd Length: 987  Bit Score: 186.31  E-value: 1.53e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  35 PPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEK-KLITYPRTDSRYITEDEKEMLLENIDYLKE----------ITKI 103
Cdd:PRK14724 295 SPLLFDLTSLQREANGKFGFSAKTTLALAQSLYERhKALTYPRTDSRALPEDYLPVAKQTFEMLATsgmrhlapfaQQAL 374

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 104 NLNNELTNNSLINPSKIEDHYAILITGNdfNKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIEIAVKKLMFEVKGKI 183
Cdd:PRK14724 375 DGNYVRPSKRIFDNSKVSDHFAIIPTTQ--APSGLSEAEQKLYDLVVRRFMAVFFPSAEYQVTTRISQVVGHSFKTEGKV 452

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 184 IQDNGFKALLNKQKTSE----------ETIPNFEKNEEVDIE-LDLLEKETTPPKRYTEKTLLKAMANPIETLEDEGLKS 252
Cdd:PRK14724 453 LVKPGWLAIYGKEAANEvedakdgdkgQPLVPVKPGEMVRTEfAEAKGLKTKPPARYSEATLLGAMESAGKQIDDDELRE 532

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 253 TLKEvKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEG---HLLSKPDLTGQWEKYLNGISKGEKDDDS 329
Cdd:PRK14724 533 AMQE-KGLGTPATRAAIIEGLLTEKYMLREGRELIPTAKAFQLMTLLRGlgvEELSRAELTGEWEYKLAQMEKGQLSREA 611

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 330 FINTINEMIKKTINeevKNKESIQKVAKEKVSTNNiAKCPACdNGYLIDRKGFYGCTEYN---NGCEFTIPKKLLEKSIP 406
Cdd:PRK14724 612 FMQQIAAMTEKLVK---KAKEYDRDTIPGDYATLS-TPCPNC-GGVVKENYRRYACTGANgagEGCGFSFTKSPAGRTFE 686

                        410       420
                 ....*....|....*....|..
gi 686341324 407 PTVVKALCESKTTKKLKGFKSK 428
Cdd:PRK14724 687 TAEAEQLLRDRRIGPLEGFRSK 708
PRK07219 PRK07219
DNA topoisomerase I; Validated
 21-415 2.18e-47

DNA topoisomerase I; Validated


Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 173.65  E-value: 2.18e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  21 GLVTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEKKLITYPRTDS-RYITEDEKEMLLENI----D 95
Cdd:PRK07219 266 ATVSSVKKRERTISPPAPFNTTEFLREASKIFGISPKRAMEIAEKLYTAGYISYPRTDNtVYPDDLDPKELLKKLskkkE 345

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  96 YLKEITKInLNNEltnnsLINPS--KIE--DHYAILITGnDFNKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIEIA 171
Cdd:PRK07219 346 YGPYAESI-LEQE-----NIKPTegKKEttDHPPIHPVD-VPKREELSDDEWKVYELIVRRFLATLADPAEWEYLKVELD 418

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 172 VKKLMFEVKGKIIQDNGFKALLNKQKTSEETIPNFEKNEEVDIE-LDLLEKETTPPKRYTEKTLLKAManpietledegl 250
Cdd:PRK07219 419 VNGEIFKASGSRLVEEGWHEVYPYEKFDEKELPDLEEGEKLKVNkIEIEAKETQPPKRYTQSSLIKEM------------ 486

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 251 kstlkEVKGLGTPATRADIIENLKKNKYIqVQKNKIYITKNGILACLLLEGH--LLSKPDLTGQWEKYLNGISKGEKDDD 328
Cdd:PRK07219 487 -----EKRGLGTKATRHDIIEKLYKRGYV-IEGDPPRPTDLGIAVIEALEKYapEIVSEEMTAQLEADMQAIEDGKKKKE 560

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 329 SFINTINEMIKKTINEEVKNKESI-----QKVAKEKVSTNNIAKCPACDNGYLIDRKG----FYGCTEYNNgCEFTIPkk 399
Cdd:PRK07219 561 DVTEESREMLKEILSELKEKRKEIgdhlaGSLKAENRSLKTIGKCPECGGDLIIIRTDkgsrFVGCSGYPD-CRNTFP-- 637

                        410
                 ....*....|....*.
gi 686341324 400 lLEKSIPPTVVKALCE 415
Cdd:PRK07219 638 -LPSTGRIKVLDEVCE 652
PRK05776 PRK05776
DNA topoisomerase I; Provisional
 23-372 2.07e-39

DNA topoisomerase I; Provisional


Pssm-ID: 235602 [Multi-domain]  Cd Length: 670  Bit Score: 149.76  E-value: 2.07e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  23 VTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEKKLITYPRTDSRYI--TEDEKEML--LENIDYLK 98
Cdd:PRK05776 262 VTKVEVKIEILEPPPPFNLGDLQVEAARIYGFSPYKTQSIAEDLYLDGLISYPRTNSQKLppTLNIRNILkgLSRSPQYR 341

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  99 EITKINLNneLTNNSLI-NPSKIED--HYAILITGNdfNKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIEIAVKK- 174
Cdd:PRK05776 342 PLVNLLLK--ETKGVLKpVQGPKDDpaHPAIYPTGE--PPKNLSKDEFKLYDLIVRRFLASFAAPAVLSNTIVTLRVPGf 417

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 175 -LMFEVKGKIIQDNGFKALLNKQKTSEETIPNFEKNEEVDI-ELDLLEKETTPPKRYTEKTLLKAManpietledeglks 252
Cdd:PRK05776 418 pLVFSASGQRIEERGWLKYYPFHKFDEEELPLLKKGERVKIvDVKVRKSYTKPPSRYSKASLLKWM-------------- 483

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 253 tlkEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEGHL--LSKPDLTGQWEKYLNGISKGEKDDDSF 330
Cdd:PRK05776 484 ---ESVGIGTEATRARIIETLFKRGYLTSNGKYIEVTPLGFGVAEVLEKYFpdIVSVELTRDFEEKLEMIRTGKATREEV 560

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|...
gi 686341324 331 INTINEMIKKTINEEVKNKESI-QKVAKEKVSTNNIAKCPACD 372
Cdd:PRK05776 561 IEEAKETLNKLLEEFKKNKDEIgEELAKALGLIKPVGKCKICG 603
PRK07220 PRK07220
DNA topoisomerase I; Validated
 17-415 4.42e-33

DNA topoisomerase I; Validated


Pssm-ID: 180892 [Multi-domain]  Cd Length: 740  Bit Score: 131.80  E-value: 4.42e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  17 LTQKGLVTDIEKEIGYTMPPKFYDLSALQEDMNDkYKISAKRTLEIAQTLYEKKLITYPRTDSRYITEDEKemLLENIDY 96
Cdd:PRK07220 256 LGKTAEVTEVEKGTKTDKPPTPFNTTEFISAANS-IGFSAANAMRIAESLYTNGYISYPRTDNTVYPESLD--LREQIEI 332

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  97 LKEITKINLNNELTNNSLINPSK----IEDHYAILITGNDfNKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIEIAV 172
Cdd:PRK07220 333 FAEGPFGEYAQKLLEKGELVPTRgkkeTTDHPPIYPASLA-KKSELKEDEWKVYELVVRRFFATFAGPAEWETMKLRFDI 411

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 173 KKLMFEVKGKIIQDNGFKALLNKQKTSEETIPNFEKNEEVD-IELDLLEKETTPPKRYTEKTLLKAManpietledeglk 251
Cdd:PRK07220 412 GGEEFRANGSRLTEPGWRWYYPYNAPEDRLLPELSEGEELKvKKKEMLDKETQPPGRYGQGRLIKLM------------- 478

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 252 stlkEVKGLGTPATRADIIENLKKNKYIqvQKNKIYITKNGILACLLLEGH--LLSKPDLTGQWEKYLNGISKGEKDDDS 329
Cdd:PRK07220 479 ----EDLGLGTKATRHEIISKLYSRAYI--HGNPIQPTNTAFAVVDALEKYapTITKPDMTSRLEEDMDKIAEGKIKEDA 552

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 330 FINTINEMIKKTINEEVKNKESIQKVAKEKVSTNN-IAKCPACDNGYLIDR----KGFYGCTEYNNgCEFTIPkklLEKS 404
Cdd:PRK07220 553 VLEESREMLEQVFDELDKNREKIRESLREGLREDKiIGKCPLCGSDLMVRRskrgSRFIGCEGYPE-CTFSLP---LPKS 628

                        410
                 ....*....|.
gi 686341324 405 IPPTVVKALCE 415
Cdd:PRK07220 629 GQIIVTDKVCE 639
topA_bact TIGR01051
DNA topoisomerase I, bacterial; This model describes DNA topoisomerase I among the members of ...
 23-397 3.04e-30

DNA topoisomerase I, bacterial; This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273416 [Multi-domain]  Cd Length: 610  Bit Score: 122.88  E-value: 3.04e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324   23 VTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEKK--------LITYPRTDSRYITEDEKEMLLENI 94
Cdd:TIGR01051 237 VEEIEKKPKKSRPPPPFTTSTLQQEASRKLGFSAKKTMMIAQRLYEGVstgdgtigLITYMRTDSTRLSNQAVNEARNLI 316

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324   95 D------YLKEITKINLNNEltNNSLinpskiEDHYAI-----LITGNDFnKVDLKEEEINVYKSILQNVAMNFMDKEQY 163
Cdd:TIGR01051 317 DknygkeYLGPKPKRYKSKE--KNAQ------EAHEAIrptsvFRTPEEL-KDYLKRDEFRLYELIWKRFVASQMADARY 387

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  164 ETTTIEIAVKK--LMFEVKGKIIQDNGF----KALLNKQKTSEETI-PNFEKNEEVDI-ELDLLEKETTPPKRYTEKTLL 235
Cdd:TIGR01051 388 DSTSVRLTNEDgeYVFKATGRKLIFDGYykvyVEGSDDPLEEKDRIlPPLKEGDAVKLvEVKPNQHFTQPPARYTEASLV 467

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  236 KAManpietledeglkstlkEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEGHL--LSKPDLTGQW 313
Cdd:TIGR01051 468 KEL-----------------EELGIGRPSTYASIISTIQDRGYVKKENKRLYPTELGFAVTDLLEKHFgdVVDYDFTAKM 530

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  314 EKYLNGISKGEKDDDSFINTI----NEMIKKTINEEVKNKESIQKVakekvstnniakCPACDN--GYLIDRKGFY-GCT 386
Cdd:TIGR01051 531 EKDLDEIAEGKAEWKPVLKNFytgfSSKVKKLRNMRIIVDFKTSQD------------CPLCGRpmVVKLGKYGPFlACS 598

                         410
                  ....*....|.
gi 686341324  387 EYNNgCEFTIP 397
Cdd:TIGR01051 599 NFPE-CKYTKS 608
PRK06599 PRK06599
DNA topoisomerase I; Validated
 42-397 5.82e-28

DNA topoisomerase I; Validated


Pssm-ID: 235840 [Multi-domain]  Cd Length: 675  Bit Score: 116.50  E-value: 5.82e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  42 SALQEDMNDKYKISAKRTLEIAQTLYE--------KKLITYPRTDSRYITEDEKEMLLENI------DYLKEITKInlnn 107
Cdd:PRK06599 264 STLQQEASRKLGFSAKKTMRIAQKLYEgidlgegtVGLITYMRTDSVRLSNEALDEARKYItkkygkEYLPAKPRV---- 339

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 108 eltnnsLINPSK--IEDHYAILITGNDFNKVDLKE----EEINVYKSILQNVAMNFMDKEQYETTTIEIAV--KKLMFEV 179
Cdd:PRK06599 340 ------YKKKSKnaQEAHEAIRPTSINRTPESLKPyltpDQFKLYELIWKRTVASQMAPAILDQTSVDIASenGKYVFRA 413

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 180 KGKIIQDNGFKALLNKQKTSEE-----TIPNFEKNEEVDieLDLLEKE---TTPPKRYTEKTLLKAManpietledeglk 251
Cdd:PRK06599 414 TGSVILFPGFLKVYGESKDDEEeddekLLPPLKEGEKLK--LDELLPEqhfTEPPPRYSEASLVKKL------------- 478

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 252 stlkEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEGHLlskPDL-----TGQWEKYLNGISKGEKD 326
Cdd:PRK06599 479 ----EEYGIGRPSTYASIISTLQDREYVELEKKRFIPTDLGRIVNDFLVEHF---PKYvdydfTAGLEDELDEIAEGKKD 551

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 327 --------DDSFINTInemikktinEEVKNKESIQKVAKEKVStnniAKCPACDNGYLIDRKG----FYGCTEYNNgCEF 394
Cdd:PRK06599 552 wkpvlrefWEPFISNL---------EKVEEDVRTEKVTQEETD----ETCPKCGGGPLVLKLGkngkFLGCSGYPE-CKY 617


                 ...
gi 686341324 395 TIP 397
Cdd:PRK06599 618 TKN 620
PRK07561 PRK07561
DNA topoisomerase I subunit omega; Validated
 42-397 5.32e-25

DNA topoisomerase I subunit omega; Validated


Pssm-ID: 236048 [Multi-domain]  Cd Length: 859  Bit Score: 107.96  E-value: 5.32e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  42 SALQEDMNDKYKISAKRTLEIAQTLYEKKLITYPRTDSRYITEDEKEMLLENI------DYLKEitkinlnneltnnsli 115
Cdd:PRK07561 274 STLQQEASRKLGFSVKKTMRIAQRLYEAGYITYMRTDSTNLSQEAINAARGYIgdnygkKYLPE---------------- 337

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 116 NP----SKIED----HYAILITgnDFNKV-----DLKEEEINVYKSI-LQNVAMNFMDkEQYETTTIEIAVKKLMFEVKG 181
Cdd:PRK07561 338 KPrqysSKAKNaqeaHEAIRPS--DVFRTpdqlkGLEGDAQRLYELIwKRFVASQMAP-ARYDSTTVTIAAGDAELRATG 414

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 182 KIIQDNGFKALLNKQKTSEE-----TIPNFEKNEEVDIE-LDLLEKETTPPKRYTEKTLLKAManpietledeglkstlk 255
Cdd:PRK07561 415 RVLRFDGFLKVYVEGRDDALddedrRLPALKVGDALTLEkLDPTQHFTKPPARYSEASLVKEL----------------- 477

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 256 EVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEGHL--LSKPDLTGQWEKYLNGISKGEKD----DDS 329
Cdd:PRK07561 478 EKLGIGRPSTYASIISTIQDRGYVRLENRRFYPEKMGRIVTDRLEEFFprLVDYDFTARMEEELDDIANGEADwkpvLDD 557

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 686341324 330 FINTINEMIKKTinEEVKNKESIQkvAKEKVSTNNIakCPACDNGYLIdRKG----FYGCTEYNNG--CEFTIP 397
Cdd:PRK07561 558 FYKDFSQQLEKA--EELREEGGMR--PNQMVITDRD--CPTCGRGMGI-RTGktgvFLGCSGYALKerCKTTRN 624
PRK14973 PRK14973
DNA topoisomerase I; Provisional
 54-408 1.37e-23

DNA topoisomerase I; Provisional


Pssm-ID: 184936 [Multi-domain]  Cd Length: 936  Bit Score: 103.77  E-value: 1.37e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  54 ISAKRTLEIAQTLYEKKLITYPRTDS----RYITEDEKEMLLENIDYLKEI--TKINLNNELTNNSlinpSKIEDHYAIL 127
Cdd:PRK14973 291 FSAANAMRIAEDLYMNGYISYPRTDNtiypKSLDLNGVLATLAKGAFSKDVawVKDNRRPVPTRGK----KSSTDHPPIH 366

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 128 ITGNDfNKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIEIAVKKLMFEVKGKIIQDNGFKALLNKQKTSEETIPNFE 207
Cdd:PRK14973 367 PTGVA-TREELGDDRWKLYELVVRRFLATLSPDAEWATMKVNFDAGGEPYTATGGRLLEAGWRTVYPYSEAKENILPAFA 445

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 208 KNEEVDIE-LDLLEKETTPPKRYTEKTLLKAManpietledeglkstlkEVKGLGTPATRADIIENLKKNKYIqvQKNKI 286
Cdd:PRK14973 446 LGEKLPILaVNLEEKETQPPARYSQSRLIQRM-----------------EELGLGTKSTRHEVIGKLVSRKYI--EGNPL 506

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 287 YITKNGILACLLLEGH--LLSKPDLTGQWEKYLNGISKGEKDDDSFINTINEMIKKTINEEVKNKESI-QKVAKEKVSTN 363
Cdd:PRK14973 507 RPTLVGRAVTESLEEHagTITEPDMTQTLEEHMQQIKERKRTRDDVVTESRKMLHRAFDELEANEAVIgRDIMERTAEEL 586

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*...
gi 686341324 364 NIAKCPACDNGYLIDRKG---FYGCTEYNNgCEFTIpkkllekSIPPT 408
Cdd:PRK14973 587 TIGPCPVCGKDLRIKHIGssqFIGCSGYPD-CTFNI-------GLPGT 626
PRK08780 PRK08780
DNA topoisomerase I; Provisional
 23-326 4.83e-18

DNA topoisomerase I; Provisional


Pssm-ID: 181555 [Multi-domain]  Cd Length: 780  Bit Score: 86.74  E-value: 4.83e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  23 VTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEK---------KLITYPRTDSRYITEDEkemllen 93
Cdd:PRK08780 248 VTDVESKERKRNPAPPFTTSTLQQEASRKLGFTTRRTMQVAQKLYEGvdlgdegsvGLITYMRTDSVNLSQDA------- 320

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  94 idyLKEITKInLNNELTNNSLINPSKI---------EDHYAILITGN----DFNKVDLKEEEINVYKSILQNVAMNFMDK 160
Cdd:PRK08780 321 ---LAEIRDV-IARDYGTASLPDQPNTyktksknaqEAHEAVRPTSAlrtpAQVARFLSDDQRRLYELIWKRAVACQMIP 396

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 161 EQYETTTIEIAV-KKLMFEVKGKIIQDNGFKALL-----NKQKTSEET---IPNFEKNEEVDIELDLLEKE-TTPPKRYT 230
Cdd:PRK08780 397 ATLNTVSVDLAAgSEHVFRATGSTVVVPGFLAVYeegkdDKSAEDEDEgrkLPPMKEGDNVPLERIRAEQHfTEPPPRYT 476

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 231 EKTLLKAManpietledeglkstlkEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEGHL--LSKPD 308
Cdd:PRK08780 477 EASLVKAL-----------------EEYGIGRPSTYASIISTLQFRKYVEMEGRRFRPTDVGRAVNKFLTGHFtrYVDYD 539

                        330
                 ....*....|....*...
gi 686341324 309 LTGQWEKYLNGISKGEKD 326
Cdd:PRK08780 540 FTARLEDDLDAVSRGEKE 557
PRK06319 PRK06319
DNA topoisomerase I/SWI domain fusion protein; Validated
 23-401 1.50e-17

DNA topoisomerase I/SWI domain fusion protein; Validated


Pssm-ID: 235778 [Multi-domain]  Cd Length: 860  Bit Score: 85.26  E-value: 1.50e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  23 VTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYE---------KKLITYPRTDSRYItedEKEMLLEN 93
Cdd:PRK06319 255 VTRVESKEKRRNAYPPFITSTLQQEASRHFRFSSSRTMNIAQTLYEgvdldsegaTGLITYMRTDSVRT---DPEALKQV 331

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  94 IDYLKEITKINLNNELTNNSLINPSKIEDHYAILIT----GNDFNKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIE 169
Cdd:PRK06319 332 RKYIEGTFGKEFLPSSPNVYTTKKMAQDAHEAIRPTditlTPEKLRSKLTEDQYKLYSLIWKRFVASQMIPAIYDTLAIR 411

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 170 IAV-KKLMFEVKGKIIQDNGFKALLNKQKTSEET------IPNFEKNEEVDI-ELDLLEKETTPPKRYTEKTLLKAManp 241
Cdd:PRK06319 412 ITTnKGIDLRATGSLLKFKGFLAVYEEKRDDEGDeeenihLPKLHEQDVLTKeELSAEQAFTKPLPRFTEASLVKEL--- 488

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 242 ietledeglkstlkEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEGHLLSKPDL--TGQWEKYLNG 319
Cdd:PRK06319 489 --------------EKSGIGRPSTYATIMNKIQSREYTLKENQRLRPTELGKIISQFLETNFPRIMDIgfTALMEDELEL 554

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 320 ISKGEKDDDSFINTINEMIKKTINEEVKNKeSIQKVAKEkvstnniAKCPACDNGYLID----RKGFYGCTEYNNgCEFT 395
Cdd:PRK06319 555 IADNKKPWKLLLQEFWELFLPVVVTAEKEA-FIPRIVTE-------IDCPKCHKGKLVKiwakNRYFYGCSEYPE-CDYK 625


                 ....*.
gi 686341324 396 IPKKLL 401
Cdd:PRK06319 626 TSEEEL 631
rgy TIGR01054
reverse gyrase; This model describes reverse gyrase, found in both archaeal and bacterial ...
 4-339 8.01e-14

reverse gyrase; This model describes reverse gyrase, found in both archaeal and bacterial thermophiles. This enzyme, a fusion of a type I topoisomerase domain and a helicase domain, introduces positive supercoiling to increase the melting temperature of DNA double strands. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273418 [Multi-domain]  Cd Length: 1171  Bit Score: 73.71  E-value: 8.01e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324     4 ELHEFLFENDIT-DLTQKGLVTDIEKEIGYTMPPKfYDLSALQEDMNDKYKISAKRTLEIAQTLYEKKLITYPRTDSRYI 82
Cdd:TIGR01054  850 EHDNRLEAKEFEkDLTWLDVEDIAEREEERNPLPP-YTTDTMLEDANRKLGLSVKETMQIAQELFENGLITYHRTDSTRV 928

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324    83 TEDEKEMLLEnidYLKEitkiNLNNELTNN---------SLINPSK-IE-DHYAILITGNDFNKVDLKEEEINVYKSILQ 151
Cdd:TIGR01054  929 SDVGMRVAKE---YLAS----RLGGEYFYPrewgeggahECIRPTRpLDvDDLQRLILEGVIELEGLTREHLRLYDLIFR 1001

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324   152 nvamNFMDKEQYETT--TIEIAVKKLMFEVKGKIIQD---NGFkALLNKQKTSEEtIPNFEKNEEVDIELDLLEKetTPP 226
Cdd:TIGR01054 1002 ----RFMASQMRPAKvdTKEITLKADGKEAEEEGIVEiveRGF-ELVYPLWRKNE-LEKGSTFIVKDKELRSVPK--VYP 1073

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324   227 krYTEKTLLKAManpietledeglkstlKEvKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEGHL--L 304
Cdd:TIGR01054 1074 --YTQGEIVQEM----------------KE-RGIGRPSTYATIVEKLLRRGYVVESKGFLIPTKLGIEVYNYLTNRYpkL 1134

                          330       340       350
                   ....*....|....*....|....*....|....*
gi 686341324   305 SKPDLTGQWEKYLNGISKGEKDDDSFINTINEMIK 339
Cdd:TIGR01054 1135 VSEDRTRELEEAMDKIERGELDYLEVLESVYREIK 1169
TopG2 COG1110
Reverse gyrase [Replication, recombination and repair];
23-346 2.53e-08

Reverse gyrase [Replication, recombination and repair];


Pssm-ID: 440727 [Multi-domain]  Cd Length: 1219  Bit Score: 56.52  E-value: 2.53e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324   23 VTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEKKLITYPRTDSRYITED----EKEMLLENI--DY 96
Cdd:COG1110   902 VKKVEEEEEELNPLPPYTTDTLLRDASRRLGLSAEETMRLAQDLFESGLITYHRTDSTRVSDAgiavAKEYISERFgeEY 981

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324   97 LK-----------------EITKINLNNELTNNSLINPSKI-EDHYAI--LItgndFNK--------VDLKEEEINVykS 148
Cdd:COG1110   982 FKprrwgeggaheairptrPLDAEDLRRLIEEGVIELPIPLtRRHLRLydLI----FRRfmasqmrpAKVEKVKLRV--S 1055

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  149 ILQNvamnfmdkeqYETTTIEIAVKklmfevkgkiIQDNGFKALLnkqktseetiPNFEKNEEV-DIELDLLEKE----- 222
Cdd:COG1110  1056 LELP----------GGEIEEERIVE----------IIEDGFLLIY----------PPIKVEPELkEGEYKVTEVKirkvp 1105

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  223 TTPPkrYTEKTLLKAManpietledeglkstlKEvKGLGTPATRADIIENLKKNKYIQVQK--NKIYITKNGILA--CLL 298
Cdd:COG1110  1106 KVPL--YTQGDLVREM----------------KE-RGIGRPSTYAKIVETLLRRGYVVESKkgKKLVPTKLGIEVynYLS 1166

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|
gi 686341324  299 LE-GHLLSKpDLTGQWEKYLNGISKGEKDDDSFINTI-NEMIKKTINEEV 346
Cdd:COG1110  1167 ENfPDLVSE-ERTRELEEKMDEIEEGEADYQDVLEELyNELRELVLSPES 1215
Toprim_Crpt pfam13342
C-terminal repeat of topoisomerase;
391-428 1.63e-07

C-terminal repeat of topoisomerase;


Pssm-ID: 463851 [Multi-domain]  Cd Length: 60  Bit Score: 47.86  E-value: 1.63e-07
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 686341324  391 GCEFTIPKKLLEKSIPPTVVKALCESKTTKKLKGFKSK 428
Cdd:pfam13342   1 GCGFSIGKTIAGKKLSEEQVKELLTKGKTGLIKGFKSK 38
YrdD COG0551
DNA topoisomerase I, ssDNA-binding Zn-finger and Zn-ribbon domains [Replication, recombination ...
 33-404 1.20e-06

DNA topoisomerase I, ssDNA-binding Zn-finger and Zn-ribbon domains [Replication, recombination and repair];


Pssm-ID: 440317 [Multi-domain]  Cd Length: 695  Bit Score: 50.63  E-value: 1.20e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324  33 TMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEKKLITYPRTDSRYITEDEKEMLLENIDYLKEITKINLNNELTNN 112
Cdd:COG0551  271 ALPEALATTSLTAAAAASALAAALLEEEGELLYTGGYIRYTRTPKSSEADALAALEALKKIAEEPPDERAKKKKKKAKKK 350

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 113 SLINPSKIEDHYAILITGNDFNKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIEIAVKKLMFEVKGKIIQDNGFKAL 192
Cdd:COG0551  351 KASEAKETTDHPPIPPTTAAALLELLEDRKLLLELLVRRRFAAAADLAKVEELTKVEEADEEELVEAEGGLLEVLGEEEE 430

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 193 LNKQKTSEETIPNFEKNEEVDIELDLLEKETTPPKRYTEKTLLKAManpietledeglkstlKEVKGLGTPATRADIIEN 272
Cdd:COG0551  431 DDEDEEEELLLPPLEEGEPLLLEELLLEKQTTTPPPRYTTELLLKK----------------LEEEGGGGRGTTATIIIL 494

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 686341324 273 LKKNKYIQVQKNKIYITKNGILACLLLEGHLLSKPDLTGQWEKYLNGISKGEKDDDSfINTINEMIKKTINEEVKNKESI 352
Cdd:COG0551  495 ILKRRYVVLEEKKTTPTELLVEVVLLLLLPFPKLEDTTETAEEEEALLDKEEGKEDK-VVEIREEEYPFFKKLLEIAEEE 573

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 686341324 353 QKVAKEKVSTNNIAKCPACdNGYLIDRKG----FYGCTEYNNgCEFTIPKKLLEKS 404
Cdd:COG0551  574 GEEELSEEDEVLGEKCPKC-GKPLVIKKGrygkFLGCSNYPE-CKYTKPLPKPEVT 627
 
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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