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Conserved domains on  [gi|117956941|gb|ABK58986|]
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topoisomerase I, partial [Vibrio ponticus]

Protein Classification

type I DNA topoisomerase( domain architecture ID 1000362)

DNA topoisomerase I is a type IA DNA topoisomerase that releases the supercoiling and torsional tension of DNA, which is introduced during DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex

EC:  5.6.2.1
Gene Ontology:  GO:0003917|GO:0003677|GO:0006265|GO:0046872
PubMed:  19208647|17293019|9748482|7770916|12042765
SCOP:  4007652|4002819

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK07561 super family cl35595
DNA topoisomerase I subunit omega; Validated
 1-223 1.04e-152

DNA topoisomerase I subunit omega; Validated


The actual alignment was detected with superfamily member PRK07561:

Pssm-ID: 236048 [Multi-domain]  Cd Length: 859  Bit Score: 445.01  E-value: 1.04e-152
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941   1 RVVFNEITKNAIQQAFQSPGELSMDGVNAQQARRFMDRVVGFMVSPLLWKKVARGLSAGRVQSVAVKLLVEREREIKAFI 80
Cdd:PRK07561 120 RVVFNEITKNAIQEAFENPRELDINLVNAQQARRFLDRLVGYMVSPLLWKKIARGLSAGRVQSVAVRLIVEREREIEAFV 199

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941  81 PEEFWDIHANTKTQDKTDFRLQVSQKDGVAFKPV---NEAETKAAMSVLENAAYEVCKREDRPTSSKPSAPFITSTLQQA 157
Cdd:PRK07561 200 PEEYWDIHADLTTPRGDAFEARLTHLDGKKFAPVdllNEAQAEAAVAALEGARYSVASVEDKPTTRKPSAPFTTSTLQQE 279

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 117956941 158 ASTRLGYGVKKTMMLAQRLYEAGYITYMRTDSTNLSAEAVETLRGYISSEFGDAYLPAKANVYGSK 223
Cdd:PRK07561 280 ASRKLGFSVKKTMRIAQRLYEAGYITYMRTDSTNLSQEAINAARGYIGDNYGKKYLPEKPRQYSSK 345
 
Name Accession Description Interval E-value
PRK07561 PRK07561
DNA topoisomerase I subunit omega; Validated
 1-223 1.04e-152

DNA topoisomerase I subunit omega; Validated


Pssm-ID: 236048 [Multi-domain]  Cd Length: 859  Bit Score: 445.01  E-value: 1.04e-152
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941   1 RVVFNEITKNAIQQAFQSPGELSMDGVNAQQARRFMDRVVGFMVSPLLWKKVARGLSAGRVQSVAVKLLVEREREIKAFI 80
Cdd:PRK07561 120 RVVFNEITKNAIQEAFENPRELDINLVNAQQARRFLDRLVGYMVSPLLWKKIARGLSAGRVQSVAVRLIVEREREIEAFV 199

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941  81 PEEFWDIHANTKTQDKTDFRLQVSQKDGVAFKPV---NEAETKAAMSVLENAAYEVCKREDRPTSSKPSAPFITSTLQQA 157
Cdd:PRK07561 200 PEEYWDIHADLTTPRGDAFEARLTHLDGKKFAPVdllNEAQAEAAVAALEGARYSVASVEDKPTTRKPSAPFTTSTLQQE 279

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 117956941 158 ASTRLGYGVKKTMMLAQRLYEAGYITYMRTDSTNLSAEAVETLRGYISSEFGDAYLPAKANVYGSK 223
Cdd:PRK07561 280 ASRKLGFSVKKTMRIAQRLYEAGYITYMRTDSTNLSQEAINAARGYIGDNYGKKYLPEKPRQYSSK 345
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
1-224 8.92e-119

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 440316 [Multi-domain]  Cd Length: 541  Bit Score: 348.24  E-value: 8.92e-119
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941   1 RVVFNEITKNAIQQAFQSPGELSMDGVNAQQARRFMDRVVGFMVSPLLWKKVARGLSAGRVQSVAVKLLVEREREIKAFI 80
Cdd:COG0550  104 RVVFNEITKKAIKEAFKNPRDIDMNLVDAQQARRILDRLVGYNLSPLLWKKVKRGLSAGRVQSPALRLIVEREREIEAFV 183

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941  81 PEEFWDIHANTKTQDKTdFRLQVSQKDGVAFKpvNEAETKAAMSVLENAAYEVCKREDRPTSSKPSAPFITSTLQQAAST 160
Cdd:COG0550  184 PEEYWTIEATFKTGGGE-FTAKLVKIDGKKIL--DEEEAEAILAALKGKTFTVTSVEKKPKKRNPPPPFTTSTLQQEASR 260

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 117956941 161 RLGYGVKKTMMLAQRLYEAGYITYMRTDSTNLSAEAVETLRGYISSEFGDAYLPAKANVYGSKE 224
Cdd:COG0550  261 KLGFSAKKTMSIAQRLYEVGLITYMRTDSVRLSEDAVAAAREYIEALYGKEYLPEKPRVYKTSK 324
topA_bact TIGR01051
DNA topoisomerase I, bacterial; This model describes DNA topoisomerase I among the members of ...
 1-224 3.03e-107

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: 320.87  E-value: 3.03e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941    1 RVVFNEITKNAIQQAFQSPGELSMDGVNAQQARRFMDRVVGFMVSPLLWKKVARGLSAGRVQSVAVKLLVEREREIKAFI 80
Cdd:TIGR01051 103 RIVFNEITKKAIRAALKNPREIDMNLVNAQQARRILDRLVGYTLSPLLWKKVAKGLSAGRVQSVALRLIVDREREIKRFV 182

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941   81 PEEFWDIHANTKTQDKTdFRLQVSQKDG---VAFKPVNEAETKAAMSVLENAAYEVCKREDRPTSSKPSAPFITSTLQQA 157
Cdd:TIGR01051 183 PEEYWTIDATFQKGEET-FEALLTEVNGkklKAGSDLDEAEATALKEQLKGEELVVEEIEKKPKKSRPPPPFTTSTLQQE 261

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 117956941  158 ASTRLGYGVKKTMMLAQRLYEA--------GYITYMRTDSTNLSAEAVETLRGYISSEFGDAYLPAKANVYGSKE 224
Cdd:TIGR01051 262 ASRKLGFSAKKTMMIAQRLYEGvstgdgtiGLITYMRTDSTRLSNQAVNEARNLIDKNYGKEYLGPKPKRYKSKE 336
Topoisom_bac pfam01131
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ...
 21-220 2.15e-67

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: 212.49  E-value: 2.15e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941   21 ELSMDGVNAQQARRFMDRVVGFMVSPLLWKKV--ARGLSAGRVQSVAVKLLVEREREIKAFIPEEFWDIHANTKTQDKTD 98
Cdd:pfam01131   1 EIDENLVDAQLARRELDWLIGFNLSRLLTLKLkgNKLLSAGRVQTPTLALIVEREREIENFVPEPYWTIEATLKDGGGVF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941   99 FRLQVSQKDgvaFKpvNEAETKAAMSVLENAAYEVCKREDRPTSSKPSAPFITSTLQQAASTRLGYGVKKTMMLAQRLYE 178
Cdd:pfam01131  81 ANAKWKRGR---IF--DKEEAEAILEKLKKGTAVVTSVESKEKKKPPPLPFNTTTLQKEASRKLGFSAKKTMSIAQKLYE 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 117956941  179 -AGYITYMRTDSTNLSAEA-VETLRGYISSEFGDaYLPAKANVY 220
Cdd:pfam01131 156 kHGLITYPRTDSTYLSDDAtLKAILEYLTKNYGK-YLPYAPRLL 198
TOP1Ac cd00186
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
 24-223 2.34e-65

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: 206.69  E-value: 2.34e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941  24 MDGVNAQQARRFMDRVVGFMVSPLLWKKVAR--GLSAGRVQSVAVKLLVEREREIKAFIPEEFWDIHAntktqdktdfrl 101
Cdd:cd00186    1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRRkgVLSAGRVQSPTLGLIVEREREIKAFVPEDYWEIKE------------ 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941 102 qvsqkdgvafkpvneaetkaamsvlenaaYEVCKREDRPTSSKPSAPFITSTLQQAASTRLGYGVKKTMMLAQRLYEAGY 181
Cdd:cd00186   69 -----------------------------AVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEAGL 119

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 117956941 182 ITYMRTDSTNLSAEAVETLRGYISSEFGDAYLPAKANVYGSK 223
Cdd:cd00186  120 ITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPLLGRRN 161
TOP1Bc smart00436
Bacterial DNA topoisomeraes I ATP-binding domain; Extension of TOPRIM in Bacterial DNA ...
 1-86 1.89e-42

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: 138.48  E-value: 1.89e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941     1 RVVFNEITKNAIQQAFQSPGELSMDGVNAQQARRFMDRVVGFMVSPLLWKKVAR-GLSAGRVQSVAVKLLVEREREIKAF 79
Cdd:smart00436   3 RIEFSEITKKAIREALKNPREIDENLVNAQLARRILDRLIGFNLSRLLTKKLRNgVLSAGRVQTPTLGLIVEREREIKNF 82


                   ....*..
gi 117956941    80 IPEEFWD 86
Cdd:smart00436  83 VPKPYWE 89
 
Name Accession Description Interval E-value
PRK07561 PRK07561
DNA topoisomerase I subunit omega; Validated
 1-223 1.04e-152

DNA topoisomerase I subunit omega; Validated


Pssm-ID: 236048 [Multi-domain]  Cd Length: 859  Bit Score: 445.01  E-value: 1.04e-152
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941   1 RVVFNEITKNAIQQAFQSPGELSMDGVNAQQARRFMDRVVGFMVSPLLWKKVARGLSAGRVQSVAVKLLVEREREIKAFI 80
Cdd:PRK07561 120 RVVFNEITKNAIQEAFENPRELDINLVNAQQARRFLDRLVGYMVSPLLWKKIARGLSAGRVQSVAVRLIVEREREIEAFV 199

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941  81 PEEFWDIHANTKTQDKTDFRLQVSQKDGVAFKPV---NEAETKAAMSVLENAAYEVCKREDRPTSSKPSAPFITSTLQQA 157
Cdd:PRK07561 200 PEEYWDIHADLTTPRGDAFEARLTHLDGKKFAPVdllNEAQAEAAVAALEGARYSVASVEDKPTTRKPSAPFTTSTLQQE 279

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 117956941 158 ASTRLGYGVKKTMMLAQRLYEAGYITYMRTDSTNLSAEAVETLRGYISSEFGDAYLPAKANVYGSK 223
Cdd:PRK07561 280 ASRKLGFSVKKTMRIAQRLYEAGYITYMRTDSTNLSQEAINAARGYIGDNYGKKYLPEKPRQYSSK 345
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
1-224 8.92e-119

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 440316 [Multi-domain]  Cd Length: 541  Bit Score: 348.24  E-value: 8.92e-119
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941   1 RVVFNEITKNAIQQAFQSPGELSMDGVNAQQARRFMDRVVGFMVSPLLWKKVARGLSAGRVQSVAVKLLVEREREIKAFI 80
Cdd:COG0550  104 RVVFNEITKKAIKEAFKNPRDIDMNLVDAQQARRILDRLVGYNLSPLLWKKVKRGLSAGRVQSPALRLIVEREREIEAFV 183

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941  81 PEEFWDIHANTKTQDKTdFRLQVSQKDGVAFKpvNEAETKAAMSVLENAAYEVCKREDRPTSSKPSAPFITSTLQQAAST 160
Cdd:COG0550  184 PEEYWTIEATFKTGGGE-FTAKLVKIDGKKIL--DEEEAEAILAALKGKTFTVTSVEKKPKKRNPPPPFTTSTLQQEASR 260

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 117956941 161 RLGYGVKKTMMLAQRLYEAGYITYMRTDSTNLSAEAVETLRGYISSEFGDAYLPAKANVYGSKE 224
Cdd:COG0550  261 KLGFSAKKTMSIAQRLYEVGLITYMRTDSVRLSEDAVAAAREYIEALYGKEYLPEKPRVYKTSK 324
PRK06599 PRK06599
DNA topoisomerase I; Validated
 1-223 1.44e-112

DNA topoisomerase I; Validated


Pssm-ID: 235840 [Multi-domain]  Cd Length: 675  Bit Score: 336.44  E-value: 1.44e-112
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941   1 RVVFNEITKNAIQQAFQSPGELSMDGVNAQQARRFMDRVVGFMVSPLLWKKVARGLSAGRVQSVAVKLLVEREREIKAFI 80
Cdd:PRK06599 110 RVVFNEITKKAVQEAIENPRDIDMDLVDAQQARRALDYLVGFKLSPLLWKKVRRGLSAGRVQSVALRLICEREDEIEAFI 189

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941  81 PEEFWDIHANTKTQDKTDFRLQVSQKDG---VAFKPVNEAETKAAMSVLENAAYEVCKREDRPTSSKPSAPFITSTLQQA 157
Cdd:PRK06599 190 PQEYWTIEADLATSNGEPFTAKLVEVNGkklEKFSITNEEQAKALVKALEGQAYTVDKIEKKERKRNPPPPFITSTLQQE 269

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 117956941 158 ASTRLGYGVKKTMMLAQRLYEA--------GYITYMRTDSTNLSAEAVETLRGYISSEFGDAYLPAKANVYGSK 223
Cdd:PRK06599 270 ASRKLGFSAKKTMRIAQKLYEGidlgegtvGLITYMRTDSVRLSNEALDEARKYITKKYGKEYLPAKPRVYKKK 343
topA_bact TIGR01051
DNA topoisomerase I, bacterial; This model describes DNA topoisomerase I among the members of ...
 1-224 3.03e-107

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: 320.87  E-value: 3.03e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941    1 RVVFNEITKNAIQQAFQSPGELSMDGVNAQQARRFMDRVVGFMVSPLLWKKVARGLSAGRVQSVAVKLLVEREREIKAFI 80
Cdd:TIGR01051 103 RIVFNEITKKAIRAALKNPREIDMNLVNAQQARRILDRLVGYTLSPLLWKKVAKGLSAGRVQSVALRLIVDREREIKRFV 182

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941   81 PEEFWDIHANTKTQDKTdFRLQVSQKDG---VAFKPVNEAETKAAMSVLENAAYEVCKREDRPTSSKPSAPFITSTLQQA 157
Cdd:TIGR01051 183 PEEYWTIDATFQKGEET-FEALLTEVNGkklKAGSDLDEAEATALKEQLKGEELVVEEIEKKPKKSRPPPPFTTSTLQQE 261

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 117956941  158 ASTRLGYGVKKTMMLAQRLYEA--------GYITYMRTDSTNLSAEAVETLRGYISSEFGDAYLPAKANVYGSKE 224
Cdd:TIGR01051 262 ASRKLGFSAKKTMMIAQRLYEGvstgdgtiGLITYMRTDSTRLSNQAVNEARNLIDKNYGKEYLGPKPKRYKSKE 336
PRK08780 PRK08780
DNA topoisomerase I; Provisional
 1-223 8.27e-75

DNA topoisomerase I; Provisional


Pssm-ID: 181555 [Multi-domain]  Cd Length: 780  Bit Score: 240.82  E-value: 8.27e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941   1 RVVFNEITKNAIQQAFQSPGELSMDGVNAQQARRFMDRVVGFMVSPLLWKKVARGLSAGRVQSVAVKLLVEREREIKAFI 80
Cdd:PRK08780 111 RVVFTEITPRAIKEAMAKPRDIASDLVDAQQARRALDYLVGFNLSPLLWRKIQRGLSAGRVQSPALRMIVEREEEIEAFI 190

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941  81 PEEFWDIHANTKTQdKTDFRLQVSQKDGVAFKP---VNEAETKAAMSVLENAA---YEVCKREDRPTSSKPSAPFITSTL 154
Cdd:PRK08780 191 AREYWSIEADCAHP-SQPFNAKLIKLDGQKFEQftiTDGDTAEAARLRIQQAAqgtLHVTDVESKERKRNPAPPFTTSTL 269

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 117956941 155 QQAASTRLGYGVKKTMMLAQRLYEA---------GYITYMRTDSTNLSAEAVETLRGYISSEFGDAYLPAKANVYGSK 223
Cdd:PRK08780 270 QQEASRKLGFTTRRTMQVAQKLYEGvdlgdegsvGLITYMRTDSVNLSQDALAEIRDVIARDYGTASLPDQPNTYKTK 347
PRK06319 PRK06319
DNA topoisomerase I/SWI domain fusion protein; Validated
 1-224 8.08e-69

DNA topoisomerase I/SWI domain fusion protein; Validated


Pssm-ID: 235778 [Multi-domain]  Cd Length: 860  Bit Score: 225.86  E-value: 8.08e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941   1 RVVFNEITKNAIQQAFQSPGELSMDGVNAQQARRFMDRVVGFMVSPLLWKKVAR--GLSAGRVQSVAVKLLVEREREIKA 78
Cdd:PRK06319 106 RISFNAITKGAVTEALKHPREIDMALVNAQQARRLLDRIVGYKISPILSRKLQRrsGVSAGRVQSVALKLVVDREKAIEA 185

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941  79 FIPEEFWDIHANTKT-QDKTDFRLQVSQKDGVAFKPV--------------NEAETKAAMSVLENAAYEVCKREDRPTSS 143
Cdd:PRK06319 186 FVPVEYWNIRVHLKDpKTQKTFWAHLYSVDGKKWEKEipegktedevllinSKEKADHIVELLESATYTVTRVESKEKRR 265

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941 144 KPSAPFITSTLQQAASTRLGYGVKKTMMLAQRLYEA---------GYITYMRTDSTNLSAEAVETLRGYISSEFGDAYLP 214
Cdd:PRK06319 266 NAYPPFITSTLQQEASRHFRFSSSRTMNIAQTLYEGvdldsegatGLITYMRTDSVRTDPEALKQVRKYIEGTFGKEFLP 345

                        250
                 ....*....|
gi 117956941 215 AKANVYGSKE 224
Cdd:PRK06319 346 SSPNVYTTKK 355
Topoisom_bac pfam01131
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ...
 21-220 2.15e-67

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: 212.49  E-value: 2.15e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941   21 ELSMDGVNAQQARRFMDRVVGFMVSPLLWKKV--ARGLSAGRVQSVAVKLLVEREREIKAFIPEEFWDIHANTKTQDKTD 98
Cdd:pfam01131   1 EIDENLVDAQLARRELDWLIGFNLSRLLTLKLkgNKLLSAGRVQTPTLALIVEREREIENFVPEPYWTIEATLKDGGGVF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941   99 FRLQVSQKDgvaFKpvNEAETKAAMSVLENAAYEVCKREDRPTSSKPSAPFITSTLQQAASTRLGYGVKKTMMLAQRLYE 178
Cdd:pfam01131  81 ANAKWKRGR---IF--DKEEAEAILEKLKKGTAVVTSVESKEKKKPPPLPFNTTTLQKEASRKLGFSAKKTMSIAQKLYE 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 117956941  179 -AGYITYMRTDSTNLSAEA-VETLRGYISSEFGDaYLPAKANVY 220
Cdd:pfam01131 156 kHGLITYPRTDSTYLSDDAtLKAILEYLTKNYGK-YLPYAPRLL 198
TOP1Ac cd00186
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
 24-223 2.34e-65

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: 206.69  E-value: 2.34e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941  24 MDGVNAQQARRFMDRVVGFMVSPLLWKKVAR--GLSAGRVQSVAVKLLVEREREIKAFIPEEFWDIHAntktqdktdfrl 101
Cdd:cd00186    1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRRkgVLSAGRVQSPTLGLIVEREREIKAFVPEDYWEIKE------------ 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941 102 qvsqkdgvafkpvneaetkaamsvlenaaYEVCKREDRPTSSKPSAPFITSTLQQAASTRLGYGVKKTMMLAQRLYEAGY 181
Cdd:cd00186   69 -----------------------------AVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEAGL 119

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 117956941 182 ITYMRTDSTNLSAEAVETLRGYISSEFGDAYLPAKANVYGSK 223
Cdd:cd00186  120 ITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPLLGRRN 161
TOP1Bc smart00436
Bacterial DNA topoisomeraes I ATP-binding domain; Extension of TOPRIM in Bacterial DNA ...
 1-86 1.89e-42

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: 138.48  E-value: 1.89e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941     1 RVVFNEITKNAIQQAFQSPGELSMDGVNAQQARRFMDRVVGFMVSPLLWKKVAR-GLSAGRVQSVAVKLLVEREREIKAF 79
Cdd:smart00436   3 RIEFSEITKKAIREALKNPREIDENLVNAQLARRILDRLIGFNLSRLLTKKLRNgVLSAGRVQTPTLGLIVEREREIKNF 82


                   ....*..
gi 117956941    80 IPEEFWD 86
Cdd:smart00436  83 VPKPYWE 89
TopG2 COG1110
Reverse gyrase [Replication, recombination and repair];
1-213 2.50e-38

Reverse gyrase [Replication, recombination and repair];


Pssm-ID: 440727 [Multi-domain]  Cd Length: 1219  Bit Score: 140.88  E-value: 2.50e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941    1 RVVFNEITKNAIQQAFQSPGELSMDGVNAQQARRFMDRVVGFMVSPLLWKKVARG-LSAGRVQSVAVKLLVEREREikaF 79
Cdd:COG1110   784 RIEFHEVTRKAILEALKNPREIDENLVEAQIVRRIEDRWIGFTLSQKLWKVFGNRnLSAGRVQTPVLGWIIERYEE---S 860

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941   80 IPEEFWDIHANTKtqdktDFRLQVSQKDGVAFKPVNEAETKAAMSVLEnaayevcKREDRPTSSKPSAPFITSTLQQAAS 159
Cdd:COG1110   861 RKSKKYLIILTLE-----NGRLELSIEDLKEAEEVRKALEKEVKVKVK-------KVEEEEEELNPLPPYTTDTLLRDAS 928

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 117956941  160 TRLGYGVKKTMMLAQRLYEAGYITYMRTDSTNLSAEAVETLRGYISSEFGDAYL 213
Cdd:COG1110   929 RRLGLSAEETMRLAQDLFESGLITYHRTDSTRVSDAGIAVAKEYISERFGEEYF 982
rgy TIGR01054
reverse gyrase; This model describes reverse gyrase, found in both archaeal and bacterial ...
 1-214 1.09e-37

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: 139.20  E-value: 1.09e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941     1 RVVFNEITKNAIQQAFQSPGELSMDGVNAQQARRFMDRVVGFMVSPLLWKKVA-RGLSAGRVQSVAVKLLVEREREIKAF 79
Cdd:TIGR01054  753 RAEFHEVTRRAILEALESPRSVDENLVKAQVVRRIEDRWIGFTLSQKLWEAFNkRWLSAGRVQTPVLGWIIDRYRESREK 832

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941    80 IPEEFwdIHANtktqdKTDFRLQVSQKDGVAFKPVNEAETKAAMSVLENaayevcKREDRPtsskPSAPFITSTLQQAAS 159
Cdd:TIGR01054  833 RGYLL--IFAL-----ESDFRLGLEHDNRLEAKEFEKDLTWLDVEDIAE------REEERN----PLPPYTTDTMLEDAN 895

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 117956941   160 TRLGYGVKKTMMLAQRLYEAGYITYMRTDSTNLSAEAVETLRGYISSEF-GDAYLP 214
Cdd:TIGR01054  896 RKLGLSVKETMQIAQELFENGLITYHRTDSTRVSDVGMRVAKEYLASRLgGEYFYP 951
PRK07219 PRK07219
DNA topoisomerase I; Validated
 1-190 2.11e-37

DNA topoisomerase I; Validated


Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 138.21  E-value: 2.11e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941   1 RVVFNEITKNAIQQAFQSPGELSMDGVNAQQARRFMDRVVG------FMVSPllwKKVARG--LSAGRVQSVAVKLLVER 72
Cdd:PRK07219 132 RARFSSLTKKEIRKAFENPDEIDFNLADAGEARQIIDLYWGaaltrfLSLSV---RQLGRWdfLSVGRVQTPTLAFIVDR 208

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941  73 EREIKAFIPEEFWDIHANTKTQdktdfrlqvSQKDGVAFKPVNEAET----KAAMSVLENAAYE----VCKREDRPTSSK 144
Cdd:PRK07219 209 EREIRAFDPEDYWKIEALLDKE---------AQYFYRDLIGGHEAEKfwdeEEAEEIYEKLKGAkeatVSSVKKRERTIS 279

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 117956941 145 PSAPFITSTLQQAASTRLGYGVKKTMMLAQRLYEAGYITYMRTDST 190
Cdd:PRK07219 280 PPAPFNTTEFLREASKIFGISPKRAMEIAEKLYTAGYISYPRTDNT 325
TOP1Ac smart00437
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ...
 137-219 5.80e-33

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: 119.66  E-value: 5.80e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941   137 EDRPTSSKPSAPFITSTLQQAASTRLGYGVKKTMMLAQRLYEAGYITYMRTDSTNLSAEAVETLRGYISSEFGDAYLPAK 216
Cdd:smart00437   1 EEKEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYIQKLYGKEYLDLA 80


                   ...
gi 117956941   217 ANV 219
Cdd:smart00437  81 VVL 83
PRK07220 PRK07220
DNA topoisomerase I; Validated
 1-190 3.57e-29

DNA topoisomerase I; Validated


Pssm-ID: 180892 [Multi-domain]  Cd Length: 740  Bit Score: 114.47  E-value: 3.57e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941   1 RVVFNEITKNAIQQAFQSPGELSMDGVNAQQARRFMDRVVGFMVSPLLWKKVAR-G---LSAGRVQSVAVKLLVEREREI 76
Cdd:PRK07220 133 RVRYSAITKKEIERAFSNPVEVDFNLADAGHSRQVIDLVWGAALTRYISLAAGRlGkmfLSVGRVQSPTLALIVDREKER 212

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941  77 KAFIPEEFWDIHAnTKTQDKTDFRLQVSQKdgvAFKpvNEAETKAAMSVLENAAyEVCKREDRPTSSKPSAPFITSTLQQ 156
Cdd:PRK07220 213 EAFVPTPYWEIYA-TLENNGETFVAQHSTR---RFW--EKEEADRVFEKLGKTA-EVTEVEKGTKTDKPPTPFNTTEFIS 285

                        170       180       190
                 ....*....|....*....|....*....|....
gi 117956941 157 AASTrLGYGVKKTMMLAQRLYEAGYITYMRTDST 190
Cdd:PRK07220 286 AANS-IGFSAANAMRIAESLYTNGYISYPRTDNT 318
PRK07726 PRK07726
DNA topoisomerase 3;
56-200 9.71e-27

DNA topoisomerase 3;


Pssm-ID: 236078 [Multi-domain]  Cd Length: 658  Bit Score: 107.17  E-value: 9.71e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941  56 LSAGRVQSVAVKLLVEREREIKAFIPEEFWDIHAntKTQDKTDFRLQVSQKDGVAFKP---VNEAETKAAMSVLENAAYE 132
Cdd:PRK07726 187 LSVGRVQTPTLALVVRRDEEIENFVPKPYWEVEA--HLTPGERFTAKWQPSEPYQDEEgrlLDRPLAEQVVARIQGQPAK 264

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 117956941 133 VCKREDRPTSSKPSAPFITSTLQQAASTRLGYGVKKTMMLAQRLYE-AGYITYMRTDSTNLSAEAVETL 200
Cdd:PRK07726 265 VTEVETKRKKEYAPLLYDLSELQIDANKRFGLSAKETLDIAQSLYEtHKLITYPRTDSRYLPEDMVATL 333
PRK14973 PRK14973
DNA topoisomerase I; Provisional
 1-190 2.79e-26

DNA topoisomerase I; Provisional


Pssm-ID: 184936 [Multi-domain]  Cd Length: 936  Bit Score: 106.08  E-value: 2.79e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941   1 RVVFNEITKNAIQQAFQSPGELSMDGVNAQQARRFMDRVVGFMVSPLLWKKVARG----LSAGRVQSVAVKLLVEREREI 76
Cdd:PRK14973 132 RARFSAITKEEIVTAFAEPTDLDFALAAAGEARQIIDLIWGASLTRFISLAAHRGgdniLSVGRVQSPTLAMIVDREKEI 211

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941  77 KAFIPEEFWDIHANTktqdktdfrlqvsQKDGVA---------FKPVNEAE-----TKAAMSVLEnaaYEVCKREDR-PT 141
Cdd:PRK14973 212 EAFVPEKYWMLSLAT-------------EKDGEGiearhthgrFTDSAAAEaaydaTKEPLVVTE---VKEGHKVDRaPT 275

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 117956941 142 sskpsaPFITSTLQQAAStRLGYGVKKTMMLAQRLYEAGYITYMRTDST 190
Cdd:PRK14973 276 ------PFDTTTFIVAAS-RLGFSAANAMRIAEDLYMNGYISYPRTDNT 317
PRK05776 PRK05776
DNA topoisomerase I; Provisional
 1-192 2.23e-24

DNA topoisomerase I; Provisional


Pssm-ID: 235602 [Multi-domain]  Cd Length: 670  Bit Score: 100.45  E-value: 2.23e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941   1 RVVFNEITKNAIQQAFQSPGELSMDGVNAQQARRFMDRVVGFMVSPLLWK--KVARG----LSAGRVQSVAVKLLVERER 74
Cdd:PRK05776 129 RMKFSALTKSDIRRAFRNLETLDYEMINAGIARHELDWLWGINVSRALMSsvRDASGkrviLSAGRVQSPTLKYVVEREI 208

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941  75 EIKAFIPEEFWDIHANTKTQDKTdFRLQVSQKdgvafKPVNEAETKAAMSVLENAAY-EVCKREDRPTSSKPSAPFITST 153
Cdd:PRK05776 209 ERNLFVPLPYFSVSIIIEKNGYE-FTLKYENK-----KFETKEEAKEILEEIKKTGYlKVTKVEVKIEILEPPPPFNLGD 282

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 117956941 154 LQQAASTRLGYGVKKTMMLAQRLYEAGYITYMRTDSTNL 192
Cdd:PRK05776 283 LQVEAARIYGFSPYKTQSIAEDLYLDGLISYPRTNSQKL 321
topB TIGR01056
DNA topoisomerase III, bacteria and conjugative plasmid; This model describes topoisomerase ...
 1-205 5.42e-19

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: 84.90  E-value: 5.42e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941    1 RVVFNEITKNAIQQAFQS--PGELSMDGVNAQQARRFMDRVVGFMVSPLLWKKVARG-----LSAGRVQSVAVKLLVERE 73
Cdd:TIGR01056 130 RLWISSLVDSSIRKAFKNlrPKSETEGLYKSGVARARADWLVGINLTRAFTKLGREAgndgvLSVGRVQTPTLAMVVKRE 209

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941   74 REIKAFIPEEFWDIHAN---------TKTQDKTDFRLQVSQKDgVAFKPVNEAETKAAMsvlenaayeVCKREDRPTSSK 144
Cdd:TIGR01056 210 NEIKNFVGKPFYEVSATinkdeqeftTEWQPYKDEEERELHEF-LAENVVTDLTQKPAL---------VTDIEKERKKTS 279

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 117956941  145 PSAPFITSTLQQAASTRLGYGVKKTMMLAQRLYEAG-YITYMRTDSTNLSAEAVETLRGYIS 205
Cdd:TIGR01056 280 APLFYDLSALQEDANKRFGISAKRTLDIAQKLYETHkLITYPRTDSRYLPEDEKEMLLEVLD 341
PTZ00407 PTZ00407
DNA topoisomerase IA; Provisional
 1-213 2.16e-16

DNA topoisomerase IA; Provisional


Pssm-ID: 173597 [Multi-domain]  Cd Length: 805  Bit Score: 77.29  E-value: 2.16e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941   1 RVVFNEITKNAIQQAFQ--SPGELSMDGVNAQQARRFMDRVVGFMVSPLLWKKVARGLSAGRVQSVAVKLLVEREREIKA 78
Cdd:PTZ00407 162 RAYMHSITEDGIRKAMRerHVEACDYDLANAAETRHAMDRIFGFLGSSVVRAANSQMRSIGRVQTPALILINEREDKIKA 241

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941  79 FIpeefwDIHANTKTQDKTdfrLQVSQKDGVAFKPV-----------NEAETKA-AMSVLENAAYEVCK-----REDRPT 141
Cdd:PTZ00407 242 FL-----ESNKSTFEVQAM---CQFPSPHGTTFSQVvtitpdrkggaSHWATEAeARRCLEQWKLNNCTgfsvpLEPKPQ 313

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 117956941 142 SSK--PSAPFITSTLQQAASTRLGYGVKKTMMLAQRLYEAGYITYMRTDSTNLSAEAVETLRGYISSEFGDAYL 213
Cdd:PTZ00407 314 PSVvpPPQPFTMATAIAKANRQLKYSSEMVSGCLQDLFQLGHITYPRTDSTRIDESALPDIYAAVKKEFGKEFL 387
PRK08173 PRK08173
DNA topoisomerase III; Validated
 59-201 2.94e-15

DNA topoisomerase III; Validated


Pssm-ID: 236172 [Multi-domain]  Cd Length: 862  Bit Score: 73.93  E-value: 2.94e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941  59 GRVQSVAVKLLVEREREIKAFIPEEFWDIHANtktqdktdFRLQVSQKDGVAFKP---VNEAETKAAMSVL--ENAAYE- 132
Cdd:PRK08173 194 GRVQTPTLSIVVEREEKIRRFVPRDYWEVRAE--------FVAAAGFYEGRWFDPkfkKDEFDPEKRASRLwsEAAAEAi 265

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 117956941 133 VCKREDRPTS----SKPS---AP--FITSTLQQAASTRLGYGVKKTMMLAQRLYEA-GYITYMRTDSTNLSAEAVETLR 201
Cdd:PRK08173 266 VAACRGKPGTvteeSKPStqlSPllFDLTSLQREANGRFGFSAKNTLGLAQALYEKhKVLTYPRTDSRALPEDYLGTVK 344
PRK14724 PRK14724
DNA topoisomerase III; Provisional
 1-192 4.04e-15

DNA topoisomerase III; Provisional


Pssm-ID: 237803 [Multi-domain]  Cd Length: 987  Bit Score: 73.84  E-value: 4.04e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941   1 RVVFNEITKNAIQQAFQS-PGELSMDGV-NAQQARRFMDRVVGFMVSPLLWKKVARG-----LSAGRVQSVAVKLLVERE 73
Cdd:PRK14724 137 RLWLQSMTPQAIRDGFDNlRSDAQMQGLaSAARSRSEADWLVGINGTRAMTAFNSRDggfflTTVGRVQTPTLSLVVERE 216

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956941  74 REIKAFIPEEFWDIHANtktqdktdFRLQVSQKDGVAF-----KPVNEAETKAAMSVLENAAYEVCK----------RED 138
Cdd:PRK14724 217 EKIRKFVSRDYWEIHAG--------FHAEAGEYLGKWFdpqwkKASDDPEARADRVWSEREARAIADavrgkaatvtEES 288

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 117956941 139 RPTSSKPSAPFITSTLQQAASTRLGYGVKKTMMLAQRLYEA-GYITYMRTDSTNL 192
Cdd:PRK14724 289 KPTTQASPLLFDLTSLQREANGKFGFSAKTTLALAQSLYERhKALTYPRTDSRAL 343
TOPRIM_TopoIA_TopoI cd03363
TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TOPRIM) domain found in members of the type IA ...
 1-19 2.42e-05

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: 42.55  E-value: 2.42e-05
                         10
                 ....*....|....*....
gi 117956941   1 RVVFNEITKNAIQQAFQSP 19
Cdd:cd03363  105 RVVFNEITKEAIKEALKNP 123
 
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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