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Conserved domains on  [gi|517539698|ref|WP_018709906|]
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recombination mediator RecR [Phocaeicola barnesiae]

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];
5-199 3.17e-119

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


:

Pssm-ID: 440122 [Multi-domain]  Cd Length: 195  Bit Score: 336.23  E-value: 3.17e-119
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517539698   5 YPSVLLEKAVGEFAKLPGIGRKTAMRLVLHLLRQDTQSVEAFGNAMITLKHEVKYCRVCHNISDTDVCRICSDASRDTSV 84
Cdd:COG0353    1 MYPPPLERLIEALSKLPGIGPKSAQRLALHLLKRDEEEAERLAEALLEAKEKVRHCSVCGNLTEEDPCSICADPRRDRSL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517539698  85 VCVVENIRDVMAVENTQQYRGLYHVLGGVISPMDGIGPSDLQIDSLVDRVRAGGVKEVILALSSTMEGDTTNFYIFRKLS 164
Cdd:COG0353   81 ICVVEEPADVLAIERTGEYRGLYHVLGGVLSPLDGIGPEDLNIDELLERLKEGGVKEVILATNPTVEGEATAHYIAELLK 160

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 517539698 165 GFDVKLTVIARGISIGDELEYTDEVTLGRSIVNRI 199
Cdd:COG0353  161 PLGVKVTRLARGLPVGGELEYADEGTLARALEGRR 195
 
Name Accession Description Interval E-value
RecR COG0353
Recombinational DNA repair protein RecR [Replication, recombination and repair];
5-199 3.17e-119

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


Pssm-ID: 440122 [Multi-domain]  Cd Length: 195  Bit Score: 336.23  E-value: 3.17e-119
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517539698   5 YPSVLLEKAVGEFAKLPGIGRKTAMRLVLHLLRQDTQSVEAFGNAMITLKHEVKYCRVCHNISDTDVCRICSDASRDTSV 84
Cdd:COG0353    1 MYPPPLERLIEALSKLPGIGPKSAQRLALHLLKRDEEEAERLAEALLEAKEKVRHCSVCGNLTEEDPCSICADPRRDRSL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517539698  85 VCVVENIRDVMAVENTQQYRGLYHVLGGVISPMDGIGPSDLQIDSLVDRVRAGGVKEVILALSSTMEGDTTNFYIFRKLS 164
Cdd:COG0353   81 ICVVEEPADVLAIERTGEYRGLYHVLGGVLSPLDGIGPEDLNIDELLERLKEGGVKEVILATNPTVEGEATAHYIAELLK 160

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 517539698 165 GFDVKLTVIARGISIGDELEYTDEVTLGRSIVNRI 199
Cdd:COG0353  161 PLGVKVTRLARGLPVGGELEYADEGTLARALEGRR 195
recR TIGR00615
recombination protein RecR; All proteins in this family for which functions are known are ...
 4-199 3.36e-83

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: 244.94  E-value: 3.36e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517539698    4 QYPSvLLEKAVGEFAKLPGIGRKTAMRLVLHLLRQDTQSVEAFGNAMITLKHEVKYCRVCHNISDTDVCRICSDASRDTS 83
Cdd:TIGR00615   1 QYPP-PISKLIESLKKLPGIGPKSAQRLAFHLLKRDPSEVLRLAQALLEAKENLRTCSVCGAISDQEVCNICSDERRDNS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517539698   84 VVCVVENIRDVMAVENTQQYRGLYHVLGGVISPMDGIGPSDLQIDSLVDRVRAGGVKEVILALSSTMEGDTTNFYIFRKL 163
Cdd:TIGR00615  80 VICVVEDPKDVFALEKTKEFRGRYHVLGGHISPLDGIGPEDLTIAALLKRLQEESVKEVILATNPTVEGEATALYIARLL 159

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 517539698  164 SGFDVKLTVIARGISIGDELEYTDEVTLGRSIVNRI 199
Cdd:TIGR00615 160 QPFGVKVTRIASGLPVGGDLEYADEVTLARALEGRR 195
TOPRIM_recR cd01025
TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 83-194 1.37e-59

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: 181.95  E-value: 1.37e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517539698  83 SVVCVVENIRDVMAVENTQQYRGLYHVLGGVISPMDGIGPSDLQIDSLVDRVRAGGVKEVILALSSTMEGDTTNFYIFRK 162
Cdd:cd01025    1 NKLCVVEEPRDVLAIEESGEYRGLYHVLGGLISPLDGIGPDDLNIDKLLERIAKGQVKEVILATNPTVEGEATALYIAKL 80

                         90       100       110
                 ....*....|....*....|....*....|..
gi 517539698 163 LSGFDVKLTVIARGISIGDELEYTDEVTLGRS 194
Cdd:cd01025   81 LKDFGVKVTRLAQGIPVGGELEYADEITLSRA 112
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 83-174 3.13e-26

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: 96.20  E-value: 3.13e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517539698   83 SVVCVVENIRDVMAVENTQqYRGLYHVLGGVISPMDGIGPSDLQIDSLvdrvraGGVKEVILALSSTMEGDTTNFYIFRK 162
Cdd:pfam13662   1 SEIIVVEGYADVIALEKAG-YKGAVAVLGGALSPLDGIGPEDLNIDSL------GGIKEVILALDGDVAGEKTALYLAEA 73

                          90
                  ....*....|..
gi 517539698  163 LSGFDVKLTVIA 174
Cdd:pfam13662  74 LLEEGVKVSRLA 85
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
83-167 8.27e-07

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 44.94  E-value: 8.27e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517539698    83 SVVCVVENIRDVMAVENTQQYRGLYHVLGGVISpmdgigpSDLQIDSLVDRVRAggvKEVILALSSTMEGDTTNFYIFRK 162
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALGGHLL-------SKEQIKLLKKLAKK---AEVILATDPDREGEAIAWELAEL 70


                   ....*
gi 517539698   163 LSGFD 167
Cdd:smart00493  71 LKPAG 75
 
Name Accession Description Interval E-value
RecR COG0353
Recombinational DNA repair protein RecR [Replication, recombination and repair];
5-199 3.17e-119

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


Pssm-ID: 440122 [Multi-domain]  Cd Length: 195  Bit Score: 336.23  E-value: 3.17e-119
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517539698   5 YPSVLLEKAVGEFAKLPGIGRKTAMRLVLHLLRQDTQSVEAFGNAMITLKHEVKYCRVCHNISDTDVCRICSDASRDTSV 84
Cdd:COG0353    1 MYPPPLERLIEALSKLPGIGPKSAQRLALHLLKRDEEEAERLAEALLEAKEKVRHCSVCGNLTEEDPCSICADPRRDRSL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517539698  85 VCVVENIRDVMAVENTQQYRGLYHVLGGVISPMDGIGPSDLQIDSLVDRVRAGGVKEVILALSSTMEGDTTNFYIFRKLS 164
Cdd:COG0353   81 ICVVEEPADVLAIERTGEYRGLYHVLGGVLSPLDGIGPEDLNIDELLERLKEGGVKEVILATNPTVEGEATAHYIAELLK 160

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 517539698 165 GFDVKLTVIARGISIGDELEYTDEVTLGRSIVNRI 199
Cdd:COG0353  161 PLGVKVTRLARGLPVGGELEYADEGTLARALEGRR 195
recR TIGR00615
recombination protein RecR; All proteins in this family for which functions are known are ...
 4-199 3.36e-83

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: 244.94  E-value: 3.36e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517539698    4 QYPSvLLEKAVGEFAKLPGIGRKTAMRLVLHLLRQDTQSVEAFGNAMITLKHEVKYCRVCHNISDTDVCRICSDASRDTS 83
Cdd:TIGR00615   1 QYPP-PISKLIESLKKLPGIGPKSAQRLAFHLLKRDPSEVLRLAQALLEAKENLRTCSVCGAISDQEVCNICSDERRDNS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517539698   84 VVCVVENIRDVMAVENTQQYRGLYHVLGGVISPMDGIGPSDLQIDSLVDRVRAGGVKEVILALSSTMEGDTTNFYIFRKL 163
Cdd:TIGR00615  80 VICVVEDPKDVFALEKTKEFRGRYHVLGGHISPLDGIGPEDLTIAALLKRLQEESVKEVILATNPTVEGEATALYIARLL 159

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 517539698  164 SGFDVKLTVIARGISIGDELEYTDEVTLGRSIVNRI 199
Cdd:TIGR00615 160 QPFGVKVTRIASGLPVGGDLEYADEVTLARALEGRR 195
TOPRIM_recR cd01025
TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 83-194 1.37e-59

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: 181.95  E-value: 1.37e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517539698  83 SVVCVVENIRDVMAVENTQQYRGLYHVLGGVISPMDGIGPSDLQIDSLVDRVRAGGVKEVILALSSTMEGDTTNFYIFRK 162
Cdd:cd01025    1 NKLCVVEEPRDVLAIEESGEYRGLYHVLGGLISPLDGIGPDDLNIDKLLERIAKGQVKEVILATNPTVEGEATALYIAKL 80

                         90       100       110
                 ....*....|....*....|....*....|..
gi 517539698 163 LSGFDVKLTVIARGISIGDELEYTDEVTLGRS 194
Cdd:cd01025   81 LKDFGVKVTRLAQGIPVGGELEYADEITLSRA 112
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 83-174 3.13e-26

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: 96.20  E-value: 3.13e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517539698   83 SVVCVVENIRDVMAVENTQqYRGLYHVLGGVISPMDGIGPSDLQIDSLvdrvraGGVKEVILALSSTMEGDTTNFYIFRK 162
Cdd:pfam13662   1 SEIIVVEGYADVIALEKAG-YKGAVAVLGGALSPLDGIGPEDLNIDSL------GGIKEVILALDGDVAGEKTALYLAEA 73

                          90
                  ....*....|..
gi 517539698  163 LSGFDVKLTVIA 174
Cdd:pfam13662  74 LLEEGVKVSRLA 85
RecR pfam02132
RecR protein;
43-81 1.47e-16

RecR protein;


Pssm-ID: 460456  Cd Length: 40  Bit Score: 70.14  E-value: 1.47e-16
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 517539698   43 VEAFGNAMITLKHEVKYCRVCHNISDTDVCRICSDASRD 81
Cdd:pfam02132   2 AERLAEALLEAKENIRYCSVCGNLTDEDPCPICSDPRRD 40
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 83-174 3.13e-07

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: 46.65  E-value: 3.13e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517539698  83 SVVCVVENIRDVMAVENTQQYRGLYHVLGGVISPmdgigPSDLQIDSLvdrvrAGGVKEVILALSSTMEGDTTNFYIFRK 162
Cdd:cd00188    1 KKLIIVEGPSDALALAQAGGYGGAVVALGGHALN-----KTRELLKRL-----LGEAKEVIIATDADREGEAIALRLLEL 70

                         90
                 ....*....|..
gi 517539698 163 LSGFDVKLTVIA 174
Cdd:cd00188   71 LKSLGKKVRRLL 82
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
83-167 8.27e-07

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 44.94  E-value: 8.27e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517539698    83 SVVCVVENIRDVMAVENTQQYRGLYHVLGGVISpmdgigpSDLQIDSLVDRVRAggvKEVILALSSTMEGDTTNFYIFRK 162
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALGGHLL-------SKEQIKLLKKLAKK---AEVILATDPDREGEAIAWELAEL 70


                   ....*
gi 517539698   163 LSGFD 167
Cdd:smart00493  71 LKPAG 75
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 84-160 3.30e-03

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: 35.41  E-value: 3.30e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 517539698   84 VVCVVENIRDVMAVENT--QQYRGLYHVLGGVISPMDGigPSDLQIDSLvdRVRAGGVKEVILALSSTMEGDTTNFYIF 160
Cdd:pfam01751   1 ELIIVEGPSDAIALEKAlgGGFQAVVAVLGHLLSLEKG--PKKKALKAL--KELALKAKEVILATDPDREGEAIALKLL 75
HHH_5 pfam14520
Helix-hairpin-helix domain;
9-35 4.21e-03

Helix-hairpin-helix domain;


Pssm-ID: 434010 [Multi-domain]  Cd Length: 57  Bit Score: 34.39  E-value: 4.21e-03
                          10        20
                  ....*....|....*....|....*..
gi 517539698    9 LLEKAVGEFAKLPGIGRKTAMRLVLHL 35
Cdd:pfam14520  29 LAEADVDELAEIPGIGEKTAQRIILEL 55
RuvA COG0632
Holliday junction resolvasome RuvABC DNA-binding subunit [Replication, recombination and ...
 14-35 6.14e-03

Holliday junction resolvasome RuvABC DNA-binding subunit [Replication, recombination and repair];


Pssm-ID: 440397 [Multi-domain]  Cd Length: 195  Bit Score: 36.27  E-value: 6.14e-03
                         10        20
                 ....*....|....*....|..
gi 517539698  14 VGEFAKLPGIGRKTAMRLVLHL 35
Cdd:COG0632  107 VKALTKVPGIGKKTAERIILEL 128
 
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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