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MULTISPECIES: recombination mediator RecR [Mycobacteriaceae]

Protein Classification

recombination mediator RecR( domain architecture ID 11417471)

recombination protein RecR is a recombination mediator protein in the RecFOR pathway of homologous recombinational repair

Gene Ontology:  GO:0006281|GO:0006310|GO:0003677|GO:0046872
PubMed:  15116069|9722641|17581636|23019218|9363943
SCOP:  4007649|4007650|3000737|4002927

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RecR COG0353
Recombinational DNA repair protein RecR [Replication, recombination and repair];
1-200 5.95e-114

Recombinational DNA repair protein RecR [Replication, recombination and repair];


:

Pssm-ID: 440122 [Multi-domain]  Cd Length: 195  Bit Score: 322.75  E-value: 5.95e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499881545   1 MFEGPVQDLIDELGKLPGIGPKSAQRIAFHLLSVEPPDIDRLTAVLNRIRDGVKFCEVCGNVSDADRCRICSDPRRDASL 80
Cdd:COG0353    1 MYPPPLERLIEALSKLPGIGPKSAQRLALHLLKRDEEEAERLAEALLEAKEKVRHCSVCGNLTEEDPCSICADPRRDRSL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499881545  81 VCVVEEPKDVQAVERTREFRGRYHVLGGALDPLSGVGPDQLRIRELLNRIGERvdgvDVAEVIIATDPNTEGEATATYLV 160
Cdd:COG0353   81 ICVVEEPADVLAIERTGEYRGLYHVLGGVLSPLDGIGPEDLNIDELLERLKEG----GVKEVILATNPTVEGEATAHYIA 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 499881545 161 RMLRDIpGLTVTRIASGLPMGGDLEFADELTLGRALAGRR 200
Cdd:COG0353  157 ELLKPL-GVKVTRLARGLPVGGELEYADEGTLARALEGRR 195
 
Name Accession Description Interval E-value
RecR COG0353
Recombinational DNA repair protein RecR [Replication, recombination and repair];
1-200 5.95e-114

Recombinational DNA repair protein RecR [Replication, recombination and repair];


Pssm-ID: 440122 [Multi-domain]  Cd Length: 195  Bit Score: 322.75  E-value: 5.95e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499881545   1 MFEGPVQDLIDELGKLPGIGPKSAQRIAFHLLSVEPPDIDRLTAVLNRIRDGVKFCEVCGNVSDADRCRICSDPRRDASL 80
Cdd:COG0353    1 MYPPPLERLIEALSKLPGIGPKSAQRLALHLLKRDEEEAERLAEALLEAKEKVRHCSVCGNLTEEDPCSICADPRRDRSL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499881545  81 VCVVEEPKDVQAVERTREFRGRYHVLGGALDPLSGVGPDQLRIRELLNRIGERvdgvDVAEVIIATDPNTEGEATATYLV 160
Cdd:COG0353   81 ICVVEEPADVLAIERTGEYRGLYHVLGGVLSPLDGIGPEDLNIDELLERLKEG----GVKEVILATNPTVEGEATAHYIA 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 499881545 161 RMLRDIpGLTVTRIASGLPMGGDLEFADELTLGRALAGRR 200
Cdd:COG0353  157 ELLKPL-GVKVTRLARGLPVGGELEYADEGTLARALEGRR 195
recR TIGR00615
recombination protein RecR; All proteins in this family for which functions are known are ...
 1-200 1.99e-105

recombination protein RecR; All proteins in this family for which functions are known are involved in the initiation of recombination and recombinational repair. RecF is also required. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273176 [Multi-domain]  Cd Length: 195  Bit Score: 301.18  E-value: 1.99e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499881545    1 MFEGPVQDLIDELGKLPGIGPKSAQRIAFHLLSVEPPDIDRLTAVLNRIRDGVKFCEVCGNVSDADRCRICSDPRRDASL 80
Cdd:TIGR00615   1 QYPPPISKLIESLKKLPGIGPKSAQRLAFHLLKRDPSEVLRLAQALLEAKENLRTCSVCGAISDQEVCNICSDERRDNSV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499881545   81 VCVVEEPKDVQAVERTREFRGRYHVLGGALDPLSGVGPDQLRIRELLNRIGErvdgVDVAEVIIATDPNTEGEATATYLV 160
Cdd:TIGR00615  81 ICVVEDPKDVFALEKTKEFRGRYHVLGGHISPLDGIGPEDLTIAALLKRLQE----ESVKEVILATNPTVEGEATALYIA 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 499881545  161 RMLRDIPgLTVTRIASGLPMGGDLEFADELTLGRALAGRR 200
Cdd:TIGR00615 157 RLLQPFG-VKVTRIASGLPVGGDLEYADEVTLARALEGRR 195
TOPRIM_recR cd01025
TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 79-195 6.65e-56

TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR. RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a single-stranded DNA molecule coated with RecA to allow invasion of a homologous molecule. The RecFOR system directs the loading of RecA onto gapped DNA coated with SSB protein. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). In RecR sequences this glutamate in the first turn of the TOPRIM domain is semiconserved, the DXD motif is not conserved.


Pssm-ID: 173775  Cd Length: 112  Bit Score: 172.70  E-value: 6.65e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499881545  79 SLVCVVEEPKDVQAVERTREFRGRYHVLGGALDPLSGVGPDQLRIRELLNRIGERvdgvDVAEVIIATDPNTEGEATATY 158
Cdd:cd01025    1 NKLCVVEEPRDVLAIEESGEYRGLYHVLGGLISPLDGIGPDDLNIDKLLERIAKG----QVKEVILATNPTVEGEATALY 76

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 499881545 159 LVRMLRDiPGLTVTRIASGLPMGGDLEFADELTLGRA 195
Cdd:cd01025   77 IAKLLKD-FGVKVTRLAQGIPVGGELEYADEITLSRA 112
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 79-175 2.28e-24

Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic acid manipulation.


Pssm-ID: 433387 [Multi-domain]  Cd Length: 85  Bit Score: 91.58  E-value: 2.28e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499881545   79 SLVCVVEEPKDVQAVERTrEFRGRYHVLGGALDPLSGVGPDQLRIRELLNrigervdgvdVAEVIIATDPNTEGEATATY 158
Cdd:pfam13662   1 SEIIVVEGYADVIALEKA-GYKGAVAVLGGALSPLDGIGPEDLNIDSLGG----------IKEVILALDGDVAGEKTALY 69

                          90
                  ....*....|....*..
gi 499881545  159 LVRMLRDiPGLTVTRIA 175
Cdd:pfam13662  70 LAEALLE-EGVKVSRLA 85
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
81-164 4.69e-15

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 66.90  E-value: 4.69e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499881545    81 VCVVEEPKDVQAVERTREFRGRYHVLGGALDplsgvgpdqlrIRELLNRIGERVDGvdvAEVIIATDPNTEGEATATYLV 160
Cdd:smart00493   3 LIIVEGPADAIALEKAGGKRGNVVALGGHLL-----------SKEQIKLLKKLAKK---AEVILATDPDREGEAIAWELA 68


                   ....
gi 499881545   161 RMLR 164
Cdd:smart00493  69 ELLK 72
PTZ00407 PTZ00407
DNA topoisomerase IA; Provisional
 122-171 2.10e-03

DNA topoisomerase IA; Provisional


Pssm-ID: 173597 [Multi-domain]  Cd Length: 805  Bit Score: 38.38  E-value: 2.10e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 499881545 122 RIRELLNR-IGERVDgvDVAEVIIATDPNTEGEATATYLVRMLRDI-PGLTV 171
Cdd:PTZ00407 109 RIQETLERyIEEKAD--NVTEIILATDPDREGELIAVHALQTIKRLyPKLKV 158
 
Name Accession Description Interval E-value
RecR COG0353
Recombinational DNA repair protein RecR [Replication, recombination and repair];
1-200 5.95e-114

Recombinational DNA repair protein RecR [Replication, recombination and repair];


Pssm-ID: 440122 [Multi-domain]  Cd Length: 195  Bit Score: 322.75  E-value: 5.95e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499881545   1 MFEGPVQDLIDELGKLPGIGPKSAQRIAFHLLSVEPPDIDRLTAVLNRIRDGVKFCEVCGNVSDADRCRICSDPRRDASL 80
Cdd:COG0353    1 MYPPPLERLIEALSKLPGIGPKSAQRLALHLLKRDEEEAERLAEALLEAKEKVRHCSVCGNLTEEDPCSICADPRRDRSL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499881545  81 VCVVEEPKDVQAVERTREFRGRYHVLGGALDPLSGVGPDQLRIRELLNRIGERvdgvDVAEVIIATDPNTEGEATATYLV 160
Cdd:COG0353   81 ICVVEEPADVLAIERTGEYRGLYHVLGGVLSPLDGIGPEDLNIDELLERLKEG----GVKEVILATNPTVEGEATAHYIA 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 499881545 161 RMLRDIpGLTVTRIASGLPMGGDLEFADELTLGRALAGRR 200
Cdd:COG0353  157 ELLKPL-GVKVTRLARGLPVGGELEYADEGTLARALEGRR 195
recR TIGR00615
recombination protein RecR; All proteins in this family for which functions are known are ...
 1-200 1.99e-105

recombination protein RecR; All proteins in this family for which functions are known are involved in the initiation of recombination and recombinational repair. RecF is also required. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273176 [Multi-domain]  Cd Length: 195  Bit Score: 301.18  E-value: 1.99e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499881545    1 MFEGPVQDLIDELGKLPGIGPKSAQRIAFHLLSVEPPDIDRLTAVLNRIRDGVKFCEVCGNVSDADRCRICSDPRRDASL 80
Cdd:TIGR00615   1 QYPPPISKLIESLKKLPGIGPKSAQRLAFHLLKRDPSEVLRLAQALLEAKENLRTCSVCGAISDQEVCNICSDERRDNSV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499881545   81 VCVVEEPKDVQAVERTREFRGRYHVLGGALDPLSGVGPDQLRIRELLNRIGErvdgVDVAEVIIATDPNTEGEATATYLV 160
Cdd:TIGR00615  81 ICVVEDPKDVFALEKTKEFRGRYHVLGGHISPLDGIGPEDLTIAALLKRLQE----ESVKEVILATNPTVEGEATALYIA 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 499881545  161 RMLRDIPgLTVTRIASGLPMGGDLEFADELTLGRALAGRR 200
Cdd:TIGR00615 157 RLLQPFG-VKVTRIASGLPVGGDLEYADEVTLARALEGRR 195
TOPRIM_recR cd01025
TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 79-195 6.65e-56

TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR. RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a single-stranded DNA molecule coated with RecA to allow invasion of a homologous molecule. The RecFOR system directs the loading of RecA onto gapped DNA coated with SSB protein. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). In RecR sequences this glutamate in the first turn of the TOPRIM domain is semiconserved, the DXD motif is not conserved.


Pssm-ID: 173775  Cd Length: 112  Bit Score: 172.70  E-value: 6.65e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499881545  79 SLVCVVEEPKDVQAVERTREFRGRYHVLGGALDPLSGVGPDQLRIRELLNRIGERvdgvDVAEVIIATDPNTEGEATATY 158
Cdd:cd01025    1 NKLCVVEEPRDVLAIEESGEYRGLYHVLGGLISPLDGIGPDDLNIDKLLERIAKG----QVKEVILATNPTVEGEATALY 76

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 499881545 159 LVRMLRDiPGLTVTRIASGLPMGGDLEFADELTLGRA 195
Cdd:cd01025   77 IAKLLKD-FGVKVTRLAQGIPVGGELEYADEITLSRA 112
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 79-175 2.28e-24

Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic acid manipulation.


Pssm-ID: 433387 [Multi-domain]  Cd Length: 85  Bit Score: 91.58  E-value: 2.28e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499881545   79 SLVCVVEEPKDVQAVERTrEFRGRYHVLGGALDPLSGVGPDQLRIRELLNrigervdgvdVAEVIIATDPNTEGEATATY 158
Cdd:pfam13662   1 SEIIVVEGYADVIALEKA-GYKGAVAVLGGALSPLDGIGPEDLNIDSLGG----------IKEVILALDGDVAGEKTALY 69

                          90
                  ....*....|....*..
gi 499881545  159 LVRMLRDiPGLTVTRIA 175
Cdd:pfam13662  70 LAEALLE-EGVKVSRLA 85
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
81-164 4.69e-15

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 66.90  E-value: 4.69e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499881545    81 VCVVEEPKDVQAVERTREFRGRYHVLGGALDplsgvgpdqlrIRELLNRIGERVDGvdvAEVIIATDPNTEGEATATYLV 160
Cdd:smart00493   3 LIIVEGPADAIALEKAGGKRGNVVALGGHLL-----------SKEQIKLLKKLAKK---AEVILATDPDREGEAIAWELA 68


                   ....
gi 499881545   161 RMLR 164
Cdd:smart00493  69 ELLK 72
RecR pfam02132
RecR protein;
38-77 1.43e-13

RecR protein;


Pssm-ID: 460456  Cd Length: 40  Bit Score: 62.05  E-value: 1.43e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 499881545   38 DIDRLTAVLNRIRDGVKFCEVCGNVSDADRCRICSDPRRD 77
Cdd:pfam02132   1 EAERLAEALLEAKENIRYCSVCGNLTDEDPCPICSDPRRD 40
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 81-174 4.62e-11

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


Pssm-ID: 396354 [Multi-domain]  Cd Length: 93  Bit Score: 56.98  E-value: 4.62e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499881545   81 VCVVEEPKDVQAVERTR--EFRGRYHVLGGALDPlsgvgpDQLRIRELLNRIGERVDGVDvaEVIIATDPNTEGEATATY 158
Cdd:pfam01751   2 LIIVEGPSDAIALEKALggGFQAVVAVLGHLLSL------EKGPKKKALKALKELALKAK--EVILATDPDREGEAIALK 73

                          90       100
                  ....*....|....*....|
gi 499881545  159 LVRML----RDIPGLTVTRI 174
Cdd:pfam01751  74 LLELKelleNAGGRVEFSEL 93
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 81-175 4.95e-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: 4.95e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499881545  81 VCVVEEPKDVQAVERTREFRGRYHVLGGALDplsgvgpdqLRIRELLNRIGERVDgvdvaEVIIATDPNTEGEATATYLV 160
Cdd:cd00188    3 LIIVEGPSDALALAQAGGYGGAVVALGGHAL---------NKTRELLKRLLGEAK-----EVIIATDADREGEAIALRLL 68

                         90
                 ....*....|....*
gi 499881545 161 RMLRDIpGLTVTRIA 175
Cdd:cd00188   69 ELLKSL-GKKVRRLL 82
HHH pfam00633
Helix-hairpin-helix motif; The helix-hairpin-helix DNA-binding motif is found to be duplicated ...
 2-27 1.63e-03

Helix-hairpin-helix motif; The helix-hairpin-helix DNA-binding motif is found to be duplicated in the central domain of RuvA. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain.


Pssm-ID: 425789 [Multi-domain]  Cd Length: 30  Bit Score: 34.70  E-value: 1.63e-03
                          10        20
                  ....*....|....*....|....*.
gi 499881545    2 FEGPVQDLIDELGKLPGIGPKSAQRI 27
Cdd:pfam00633   2 LEGLIPASVEELLALPGVGPKTAEAI 27
PTZ00407 PTZ00407
DNA topoisomerase IA; Provisional
 122-171 2.10e-03

DNA topoisomerase IA; Provisional


Pssm-ID: 173597 [Multi-domain]  Cd Length: 805  Bit Score: 38.38  E-value: 2.10e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 499881545 122 RIRELLNR-IGERVDgvDVAEVIIATDPNTEGEATATYLVRMLRDI-PGLTV 171
Cdd:PTZ00407 109 RIQETLERyIEEKAD--NVTEIILATDPDREGELIAVHALQTIKRLyPKLKV 158
TOPRIM_TopoIA_TopoI cd03363
TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TOPRIM) domain found in members of the type IA ...
 124-165 2.60e-03

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: 36.39  E-value: 2.60e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 499881545 124 RELLNRIGERVDGVDvaEVIIATDPNTEGEATATYLVRMLRD 165
Cdd:cd03363   60 KKVVKELKKLAKKAD--EIYLATDPDREGEAIAWHLAEVLKL 99
TOPRIM_TopoIA cd01028
TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 111-164 5.05e-03

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: 36.05  E-value: 5.05e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 499881545 111 DPLSGVGPDQLRIRELLNRIGERVDgvdvaEVIIATDPNTEGEATATYLVRMLR 164
Cdd:cd01028   68 EPKYVVIPDKKKQLKALKKLAKKAD-----EIVLATDPDREGELIAWEILEVLK 116
 
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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