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Conserved domains on  [gi|1702392886|gb|TQT91461|]
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type I DNA topoisomerase, partial [Xanthomonas perforans]

Protein Classification

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List of domain hits

 Name Accession Description Interval E-value
TOPRIM_TopoIA_TopoI cd03363
TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TOPRIM) domain found in members of the type IA ...
 1-129 2.39e-53

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: 163.89  E-value: 2.39e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1702392886   1 MKLMVVESPNKVASIQGYLGDDWKVVASVGHIRDLPQREFGISKPDFSLQYEYIPPqkvgdrtfPGAAERVARIKREVAK 80
Cdd:cd03363     1 KKLVIVESPAKAKTIKKYLGKEYEVLASVGHIRDLPKKGLGVDGEDDGFEPKYVVI--------PGKKKVVKELKKLAKK 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1702392886  81 AEVVYLATDPDREGEAISWHLKEALQLGEgDYERVTFTEITPKAIQASL 129
Cdd:cd03363    73 ADEIYLATDPDREGEAIAWHLAEVLKLKK-NVKRVVFNEITKEAIKEAL 120
 
Name Accession Description Interval E-value
TOPRIM_TopoIA_TopoI cd03363
TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TOPRIM) domain found in members of the type IA ...
 1-129 2.39e-53

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: 163.89  E-value: 2.39e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1702392886   1 MKLMVVESPNKVASIQGYLGDDWKVVASVGHIRDLPQREFGISKPDFSLQYEYIPPqkvgdrtfPGAAERVARIKREVAK 80
Cdd:cd03363     1 KKLVIVESPAKAKTIKKYLGKEYEVLASVGHIRDLPKKGLGVDGEDDGFEPKYVVI--------PGKKKVVKELKKLAKK 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1702392886  81 AEVVYLATDPDREGEAISWHLKEALQLGEgDYERVTFTEITPKAIQASL 129
Cdd:cd03363    73 ADEIYLATDPDREGEAIAWHLAEVLKLKK-NVKRVVFNEITKEAIKEAL 120
PRK06599 PRK06599
DNA topoisomerase I; Validated
 1-135 2.21e-46

DNA topoisomerase I; Validated


Pssm-ID: 235840 [Multi-domain]  Cd Length: 675  Bit Score: 158.87  E-value: 2.21e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1702392886   1 MKLMVVESPNKVASIQGYLGDDWKVVASVGHIRDLPQREFGIS-KPDFSLQYEYIPpqkvgdrtfpGAAERVARIKREVA 79
Cdd:PRK06599    3 KKLVIVESPAKAKTIKKYLGKDYKVLASFGHVRDLPKKKGGVDpDNDFAPKYEIIE----------GKEKVVDALKKAAK 72

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1702392886  80 KAEVVYLATDPDREGEAISWHLKEALQLGEGD---YERVTFTEITPKAIQASLRAARRI 135
Cdd:PRK06599   73 KADAVYLATDPDREGEAIAWHIAEVLKEAKLKdknVKRVVFNEITKKAVQEAIENPRDI 131
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
1-135 1.75e-43

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 440316 [Multi-domain]  Cd Length: 541  Bit Score: 149.48  E-value: 1.75e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1702392886   1 MKLMVVESPNKVASIQGYLGDDWKVVASVGHIRDLPQREFGI-SKPDFSLQYEYIPpqkvgdrtfpGAAERVARIKREVA 79
Cdd:COG0550     1 KKLVIVESPAKAKTIAKYLGKDYVVTASVGHLRDLPKPELDVdVENDFEPKYEVIP----------GKKKQVKELKKLAK 70

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1702392886  80 KAEVVYLATDPDREGEAISWHLKEALQLGEgDYERVTFTEITPKAIQASLRAARRI 135
Cdd:COG0550    71 KADEVILATDPDREGEAIAWHLLELLGDKK-PVKRVVFNEITKKAIKEAFKNPRDI 125
topA_bact TIGR01051
DNA topoisomerase I, bacterial; This model describes DNA topoisomerase I among the members of ...
 3-135 3.03e-41

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: 144.06  E-value: 3.03e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1702392886   3 LMVVESPNKVASIQGYLGDDWKVVASVGHIRDLPQREFGIsKPDFSLQYEYIppqkvgdrTFPGAAERVARIKREVAKAE 82
Cdd:TIGR01051   1 LVIVESPAKAKTIKKYLGDEYEVEASMGHIRDLPKSRLGV-DIEKDFEPEYV--------VSKGKKKVVKELKTLAKKAD 71

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1702392886  83 VVYLATDPDREGEAISWHLKEALQLGEGDYERVTFTEITPKAIQASLRAARRI 135
Cdd:TIGR01051  72 EVYLATDPDREGEAIAWHLAEVLKPKDPVYKRIVFNEITKKAIRAALKNPREI 124
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 2-120 5.92e-20

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


Pssm-ID: 396354 [Multi-domain]  Cd Length: 93  Bit Score: 78.17  E-value: 5.92e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1702392886   2 KLMVVESPNKVASIQGYLGDDWK-VVASVGHIRDLPQRefgiskpdfslqyeyippqkvgdrtfpGAAERVARIKREVAK 80
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGGFQaVVAVLGHLLSLEKG---------------------------PKKKALKALKELALK 53

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1702392886  81 AEVVYLATDPDREGEAISWHLKEALQLGEGDYERVTFTEI 120
Cdd:pfam01751  54 AKEVILATDPDREGEAIALKLLELKELLENAGGRVEFSEL 93
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
1-106 2.79e-17

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 70.75  E-value: 2.79e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1702392886    1 MKLMVVESPNKVASIQGYLGDDWKVVASVGHIRDLPQrefgiskpdfslqyeyippqkvgdrtfpgaaerVARIKREVAK 80
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALGGHLLSKEQ---------------------------------IKLLKKLAKK 47

                           90       100
                   ....*....|....*....|....*.
gi 1702392886   81 AEVvYLATDPDREGEAISWHLKEALQ 106
Cdd:smart00493  48 AEV-ILATDPDREGEAIAWELAELLK 72
 
Name Accession Description Interval E-value
TOPRIM_TopoIA_TopoI cd03363
TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TOPRIM) domain found in members of the type IA ...
 1-129 2.39e-53

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: 163.89  E-value: 2.39e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1702392886   1 MKLMVVESPNKVASIQGYLGDDWKVVASVGHIRDLPQREFGISKPDFSLQYEYIPPqkvgdrtfPGAAERVARIKREVAK 80
Cdd:cd03363     1 KKLVIVESPAKAKTIKKYLGKEYEVLASVGHIRDLPKKGLGVDGEDDGFEPKYVVI--------PGKKKVVKELKKLAKK 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1702392886  81 AEVVYLATDPDREGEAISWHLKEALQLGEgDYERVTFTEITPKAIQASL 129
Cdd:cd03363    73 ADEIYLATDPDREGEAIAWHLAEVLKLKK-NVKRVVFNEITKEAIKEAL 120
PRK06599 PRK06599
DNA topoisomerase I; Validated
 1-135 2.21e-46

DNA topoisomerase I; Validated


Pssm-ID: 235840 [Multi-domain]  Cd Length: 675  Bit Score: 158.87  E-value: 2.21e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1702392886   1 MKLMVVESPNKVASIQGYLGDDWKVVASVGHIRDLPQREFGIS-KPDFSLQYEYIPpqkvgdrtfpGAAERVARIKREVA 79
Cdd:PRK06599    3 KKLVIVESPAKAKTIKKYLGKDYKVLASFGHVRDLPKKKGGVDpDNDFAPKYEIIE----------GKEKVVDALKKAAK 72

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1702392886  80 KAEVVYLATDPDREGEAISWHLKEALQLGEGD---YERVTFTEITPKAIQASLRAARRI 135
Cdd:PRK06599   73 KADAVYLATDPDREGEAIAWHIAEVLKEAKLKdknVKRVVFNEITKKAVQEAIENPRDI 131
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
1-135 1.75e-43

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 440316 [Multi-domain]  Cd Length: 541  Bit Score: 149.48  E-value: 1.75e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1702392886   1 MKLMVVESPNKVASIQGYLGDDWKVVASVGHIRDLPQREFGI-SKPDFSLQYEYIPpqkvgdrtfpGAAERVARIKREVA 79
Cdd:COG0550     1 KKLVIVESPAKAKTIAKYLGKDYVVTASVGHLRDLPKPELDVdVENDFEPKYEVIP----------GKKKQVKELKKLAK 70

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1702392886  80 KAEVVYLATDPDREGEAISWHLKEALQLGEgDYERVTFTEITPKAIQASLRAARRI 135
Cdd:COG0550    71 KADEVILATDPDREGEAIAWHLLELLGDKK-PVKRVVFNEITKKAIKEAFKNPRDI 125
PRK07561 PRK07561
DNA topoisomerase I subunit omega; Validated
 1-135 6.00e-42

DNA topoisomerase I subunit omega; Validated


Pssm-ID: 236048 [Multi-domain]  Cd Length: 859  Bit Score: 147.25  E-value: 6.00e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1702392886   1 MKLMVVESPNKVASIQGYLGDDWKVVASVGHIRDLPQREFGISKP---------------DFSLQYEyIPPqkvgdrtfp 65
Cdd:PRK07561    2 KSLVIVESPAKAKTINKYLGSDYVVKASVGHIRDLPTSASSVPAKekgalwarmgvdpdhDFEALYE-VLP--------- 71

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1702392886  66 GAAERVARIKREVAKAEVVYLATDPDREGEAISWHLKEALQLGEGDYERVTFTEITPKAIQASLRAARRI 135
Cdd:PRK07561   72 GKEKVVSELKKAAKDADELYLATDPDREGEAIAWHLLEVLGGDDVPVKRVVFNEITKNAIQEAFENPREL 141
topA_bact TIGR01051
DNA topoisomerase I, bacterial; This model describes DNA topoisomerase I among the members of ...
 3-135 3.03e-41

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: 144.06  E-value: 3.03e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1702392886   3 LMVVESPNKVASIQGYLGDDWKVVASVGHIRDLPQREFGIsKPDFSLQYEYIppqkvgdrTFPGAAERVARIKREVAKAE 82
Cdd:TIGR01051   1 LVIVESPAKAKTIKKYLGDEYEVEASMGHIRDLPKSRLGV-DIEKDFEPEYV--------VSKGKKKVVKELKTLAKKAD 71

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1702392886  83 VVYLATDPDREGEAISWHLKEALQLGEGDYERVTFTEITPKAIQASLRAARRI 135
Cdd:TIGR01051  72 EVYLATDPDREGEAIAWHLAEVLKPKDPVYKRIVFNEITKKAIRAALKNPREI 124
TOPRIM_TopoIA cd01028
TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 1-130 1.01e-39

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


Pssm-ID: 173778 [Multi-domain]  Cd Length: 142  Bit Score: 130.04  E-value: 1.01e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1702392886   1 MKLMVVESPNKVASIQGYLG------------DDWKVVASVGHIRDLPQREFGIskPDFSLQYEYIPPQKVGDRTFPGAA 68
Cdd:cd01028     1 KVLIIAEKPSKAKTIAKILGkgskkkgfygegGGYVVTASVGHLLELPFPEEYV--DWDKDWPLELFPFEPKYVVIPDKK 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1702392886  69 ERVARIKREVAKAEVVYLATDPDREGEAISWHLKEALQLGEGDYERVTFTEITPKAIQASLR 130
Cdd:cd01028    79 KQLKALKKLAKKADEIVLATDPDREGELIAWEILEVLKCDNKPVKRAWFSEITPKAIREAFK 140
PRK08780 PRK08780
DNA topoisomerase I; Provisional
 3-135 5.00e-30

DNA topoisomerase I; Provisional


Pssm-ID: 181555 [Multi-domain]  Cd Length: 780  Bit Score: 113.32  E-value: 5.00e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1702392886   3 LMVVESPNKVASIQGYLGDDWKVVASVGHIRDLPQREfGISKPD--FSLQYEYIppqkvgDRTfpgaAERVARIKREVAK 80
Cdd:PRK08780    5 LVIVESPAKAKTINKYLGKDFTVLASYGHVRDLVPKE-GAVDPEngFAMRYDLI------DKN----EKHVEAIAKAAKS 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1702392886  81 AEVVYLATDPDREGEAISWHLKEALQ----LGEGDYERVTFTEITPKAIQASLRAARRI 135
Cdd:PRK08780   74 ADDLYLATDPDREGEAISWHLAEILKerglLKDKPMQRVVFTEITPRAIKEAMAKPRDI 132
PRK06319 PRK06319
DNA topoisomerase I/SWI domain fusion protein; Validated
 1-135 1.53e-29

DNA topoisomerase I/SWI domain fusion protein; Validated


Pssm-ID: 235778 [Multi-domain]  Cd Length: 860  Bit Score: 111.84  E-value: 1.53e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1702392886   1 MK--LMVVESPNKVASIQGYLGDDWKVVASVGHIRDLPQREFGIS-KPDFSLQYEyippqkvgdrTFPGAAERVARIKRE 77
Cdd:PRK06319    1 MKksLIIVESPAKIKTLQKLLGEGFIFASSLGHIVDLPAKEFGIDiENDFEPDYQ----------ILPDKEEVINKICKL 70

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1702392886  78 VAKAEVVYLATDPDREGEAISWHLkeALQLGEG-DYERVTFTEITPKAIQASLRAARRI 135
Cdd:PRK06319   71 AKKCDVVYLSPDPDREGEAIAWHI--ANQLPKNtKIQRISFNAITKGAVTEALKHPREI 127
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 2-120 5.92e-20

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


Pssm-ID: 396354 [Multi-domain]  Cd Length: 93  Bit Score: 78.17  E-value: 5.92e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1702392886   2 KLMVVESPNKVASIQGYLGDDWK-VVASVGHIRDLPQRefgiskpdfslqyeyippqkvgdrtfpGAAERVARIKREVAK 80
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGGFQaVVAVLGHLLSLEKG---------------------------PKKKALKALKELALK 53

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1702392886  81 AEVVYLATDPDREGEAISWHLKEALQLGEGDYERVTFTEI 120
Cdd:pfam01751  54 AKEVILATDPDREGEAIALKLLELKELLENAGGRVEFSEL 93
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
1-106 2.79e-17

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 70.75  E-value: 2.79e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1702392886    1 MKLMVVESPNKVASIQGYLGDDWKVVASVGHIRDLPQrefgiskpdfslqyeyippqkvgdrtfpgaaerVARIKREVAK 80
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALGGHLLSKEQ---------------------------------IKLLKKLAKK 47

                           90       100
                   ....*....|....*....|....*.
gi 1702392886   81 AEVvYLATDPDREGEAISWHLKEALQ 106
Cdd:smart00493  48 AEV-ILATDPDREGEAIAWELAELLK 72
TOPRIM_TopoIA_RevGyr cd03361
TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA ...
 3-130 1.21e-16

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


Pssm-ID: 173781 [Multi-domain]  Cd Length: 170  Bit Score: 71.58  E-value: 1.21e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1702392886   3 LMVVESPNKVASIQGYLGDDWK-------------------VVASVGHIRDLPQREFGISKPDfsLQYEYIP-------- 55
Cdd:cd03361     3 LMIVESPNKARTIANFFGRPSVrrlgglvvyevstgdgvlmITASGGHVYDLVTKEGGHGVVE--DDGRYVPvydsikrc 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1702392886  56 -------------PQKVGDRTFPGAAERVaRIKREVA-KAEVVYLATDPDREGEAISWHLKEALQLGEGDYERVTFTEIT 121
Cdd:cd03361    81 rdcgyqftedsdkCPRCGSENIDDKLETL-EALRELAlEVDEVLIATDPDTEGEKIAWDVYLALRPYNKNIKRAEFHEVT 159


                  ....*....
gi 1702392886 122 PKAIQASLR 130
Cdd:cd03361   160 RRAILEALR 168
TOPRIM_TopoIA_TopoIII cd03362
TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type ...
 1-130 4.61e-16

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


Pssm-ID: 173782 [Multi-domain]  Cd Length: 151  Bit Score: 69.57  E-value: 4.61e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1702392886   1 MKLMVVESPN---KVASIQG---------------YLGDDWKVVASVGHIRDL--PQREFGISKPDFslQYEYIPPQKVG 60
Cdd:cd03362     1 MVLIIAEKPSvakAIAKILGggskkkgkgryyefyGEGGGYVVTWASGHLLELdfPEEYDPWDKVWP--LEDPLFPAPFK 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1702392886  61 DRTFPGAAERVARIKREVAKAEVVYLATDPDREGEAISWHLKEALQLGEG-DYERVTFTEITPKAIQASLR 130
Cdd:cd03362    79 LKVDKGKKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYAKCVKRkPVKRAWFSSLTPKAIRRAFK 149
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 1-117 1.32e-10

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


Pssm-ID: 173773 [Multi-domain]  Cd Length: 83  Bit Score: 53.97  E-value: 1.32e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1702392886   1 MKLMVVESPNKVASIQGYLGDDWKVVASVGHIRDlpqrefgiskpdfslqyeyippqkvgdrtfpgaaERVARIKREVAK 80
Cdd:cd00188     1 KKLIIVEGPSDALALAQAGGYGGAVVALGGHALN----------------------------------KTRELLKRLLGE 46

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1702392886  81 AEVVYLATDPDREGEAISWHLKEALQLGEGDYERVTF 117
Cdd:cd00188    47 AKEVIIATDADREGEAIALRLLELLKSLGKKVRRLLL 83
PTZ00407 PTZ00407
DNA topoisomerase IA; Provisional
 2-107 9.85e-09

DNA topoisomerase IA; Provisional


Pssm-ID: 173597 [Multi-domain]  Cd Length: 805  Bit Score: 52.25  E-value: 9.85e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1702392886   2 KLMVVESPNKVASIQGYLGD-----DWK-----------------VVASVGHIRDLPQREF---------GISKPD---- 46
Cdd:PTZ00407   11 KLVIVESPNKVIKVEGLLSDpkvipDWSfkqshlrrigtgaekavAMATTGHFMALKEITWspqasspasVVGAGDepfp 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1702392886  47 -------FSLQYEYIPPQKVGD---RTFPGAAERVARIkrevakaevvYLATDPDREGEAISWHlkeALQL 107
Cdd:PTZ00407   91 sngtlaeYTLEWELLPGRRIQEtleRYIEEKADNVTEI----------ILATDPDREGELIAVH---ALQT 148
PRK07219 PRK07219
DNA topoisomerase I; Validated
 20-126 1.29e-07

DNA topoisomerase I; Validated


Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 48.84  E-value: 1.29e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1702392886  20 GDDWKVVASVGHIRDLpqrEFgisKPDFSlQYEYIPPQKVGDRT---FPGAAERVARIKREVAKAEVVYLATDPDREGEA 96
Cdd:PRK07219   41 GEKWIVIGLSGHIVTV---DF---PEEYG-DWRDVDPAELIDADpvkKITKQNYINALKKLAKDADEIIIATDYDREGEL 113

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1702392886  97 ISWHLKEAL-QLGEGDYERVTFTEITPKAIQ 126
Cdd:PRK07219  114 IGKEAYHILrEVCQVPVKRARFSSLTKKEIR 144
topB TIGR01056
DNA topoisomerase III, bacteria and conjugative plasmid; This model describes topoisomerase ...
 1-133 5.40e-07

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: 47.15  E-value: 5.40e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1702392886   1 MKLMVVESPNKVASI----------QGYL--GDDWKVVASVGHIRDLPQ-REFGISKPDFSLQYEYIPPQKVGDRTFPGA 67
Cdd:TIGR01056   1 MTLVLCEKPSQARDLatvlakkkkgNGYLeiGVGGFVTWAVGHLVELAEpEEYDEKYKNWRTYDLPLEPEDWQLVVSDKT 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1702392886  68 AERVARIKREVAKAEV--VYLATDPDREGEAISWHLKEALQL-GEGDYERVTFTEITPKAIQASLRAAR 133
Cdd:TIGR01056  81 KKQFNVIKRILKENKVdeVVIATDPDREGELIAREILDYLKVtDKVTIKRLWISSLVDSSIRKAFKNLR 149
PRK07220 PRK07220
DNA topoisomerase I; Validated
 20-128 9.82e-06

DNA topoisomerase I; Validated


Pssm-ID: 180892 [Multi-domain]  Cd Length: 740  Bit Score: 43.59  E-value: 9.82e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1702392886  20 GDDWKVVASVGHIrdlpqreFGISKPDfslqyEYIPPQKVGDR--------TFPGAAERVARIKREVAKAEVVYLATDPD 91
Cdd:PRK07220   41 GDDTVVVGLSGHI-------VNIDFPK-----EYNNWQKVDARdlidaeiiTTPTQKKIVTALKKLGKEADRVTIATDYD 108

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1702392886  92 REGEAISwhlKEALQLGEG-----DYERVTFTEITPKAIQAS 128
Cdd:PRK07220  109 REGELIG---VEALNIIKKvnpdiKFDRVRYSAITKKEIERA 147
PRK07726 PRK07726
DNA topoisomerase 3;
74-97 6.39e-03

DNA topoisomerase 3;


Pssm-ID: 236078 [Multi-domain]  Cd Length: 658  Bit Score: 35.52  E-value: 6.39e-03
                          10        20
                  ....*....|....*....|....
gi 1702392886  74 IKREVAKAEVVYLATDPDREGEAI 97
Cdd:PRK07726   86 VKKLLKQATEIVIATDADREGELI 109
 
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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