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Conserved domains on  [gi|1786678|gb|AAC73574|]
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recombination mediator protein RecR [Escherichia coli str. K-12 substr. MG1655]

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];
4-196 9.71e-124

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


:

Pssm-ID: 440122 [Multi-domain]  Cd Length: 195  Bit Score: 347.40  E-value: 9.71e-124
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786678    4 SPLLTQLMEALRCLPGVGPKSAQRMAFTLLQRDRSGGMRLAQALTRAMSEIGHCADCRTFTEQEVCNICSNPRRqENGQI 83
Cdd:COG0353   3 PPPLERLIEALSKLPGIGPKSAQRLALHLLKRDEEEAERLAEALLEAKEKVRHCSVCGNLTEEDPCSICADPRR-DRSLI 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786678   84 CVVESPADIYAIEQTGQFSGRYFVLMGHLSPLDGIGPDDIGLDRLEQRLAEEKITEVILATNPTVEGEATANYIAELCAQ 163
Cdd:COG0353  82 CVVEEPADVLAIERTGEYRGLYHVLGGVLSPLDGIGPEDLNIDELLERLKEGGVKEVILATNPTVEGEATAHYIAELLKP 161

                       170       180       190
                ....*....|....*....|....*....|...
gi 1786678  164 YDVEASRIAHGVPVGGELEMVDGTTLSHSLAGR 196
Cdd:COG0353 162 LGVKVTRLARGLPVGGELEYADEGTLARALEGR 194
 
Name Accession Description Interval E-value
RecR COG0353
Recombinational DNA repair protein RecR [Replication, recombination and repair];
4-196 9.71e-124

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


Pssm-ID: 440122 [Multi-domain]  Cd Length: 195  Bit Score: 347.40  E-value: 9.71e-124
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786678    4 SPLLTQLMEALRCLPGVGPKSAQRMAFTLLQRDRSGGMRLAQALTRAMSEIGHCADCRTFTEQEVCNICSNPRRqENGQI 83
Cdd:COG0353   3 PPPLERLIEALSKLPGIGPKSAQRLALHLLKRDEEEAERLAEALLEAKEKVRHCSVCGNLTEEDPCSICADPRR-DRSLI 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786678   84 CVVESPADIYAIEQTGQFSGRYFVLMGHLSPLDGIGPDDIGLDRLEQRLAEEKITEVILATNPTVEGEATANYIAELCAQ 163
Cdd:COG0353  82 CVVEEPADVLAIERTGEYRGLYHVLGGVLSPLDGIGPEDLNIDELLERLKEGGVKEVILATNPTVEGEATAHYIAELLKP 161

                       170       180       190
                ....*....|....*....|....*....|...
gi 1786678  164 YDVEASRIAHGVPVGGELEMVDGTTLSHSLAGR 196
Cdd:COG0353 162 LGVKVTRLARGLPVGGELEYADEGTLARALEGR 194
recR TIGR00615
recombination protein RecR; All proteins in this family for which functions are known are ...
 2-197 3.73e-116

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: 328.14  E-value: 3.73e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786678      2 QTSPLLTQLMEALRCLPGVGPKSAQRMAFTLLQRDRSGGMRLAQALTRAMSEIGHCADCRTFTEQEVCNICSNPRRQeNG 81
Cdd:TIGR00615   1 QYPPPISKLIESLKKLPGIGPKSAQRLAFHLLKRDPSEVLRLAQALLEAKENLRTCSVCGAISDQEVCNICSDERRD-NS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786678     82 QICVVESPADIYAIEQTGQFSGRYFVLMGHLSPLDGIGPDDIGLDRLEQRLAEEKITEVILATNPTVEGEATANYIAELC 161
Cdd:TIGR00615  80 VICVVEDPKDVFALEKTKEFRGRYHVLGGHISPLDGIGPEDLTIAALLKRLQEESVKEVILATNPTVEGEATALYIARLL 159

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1786678    162 AQYDVEASRIAHGVPVGGELEMVDGTTLSHSLAGRH 197
Cdd:TIGR00615 160 QPFGVKVTRIASGLPVGGDLEYADEVTLARALEGRR 195
TOPRIM_recR cd01025
TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 81-192 1.19e-65

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: 197.36  E-value: 1.19e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786678   81 GQICVVESPADIYAIEQTGQFSGRYFVLMGHLSPLDGIGPDDIGLDRLEQRLAEEKITEVILATNPTVEGEATANYIAEL 160
Cdd:cd01025   1 NKLCVVEEPRDVLAIEESGEYRGLYHVLGGLISPLDGIGPDDLNIDKLLERIAKGQVKEVILATNPTVEGEATALYIAKL 80

                        90       100       110
                ....*....|....*....|....*....|..
gi 1786678  161 CAQYDVEASRIAHGVPVGGELEMVDGTTLSHS 192
Cdd:cd01025  81 LKDFGVKVTRLAQGIPVGGELEYADEITLSRA 112
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 81-172 6.75e-31

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: 108.14  E-value: 6.75e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786678     81 GQICVVESPADIYAIEQTGqFSGRYFVLMGHLSPLDGIGPDDIGLDRLEqrlaeeKITEVILATNPTVEGEATANYIAEL 160
Cdd:pfam13662   1 SEIIVVEGYADVIALEKAG-YKGAVAVLGGALSPLDGIGPEDLNIDSLG------GIKEVILALDGDVAGEKTALYLAEA 73

                          90
                  ....*....|..
gi 1786678    161 CAQYDVEASRIA 172
Cdd:pfam13662  74 LLEEGVKVSRLA 85
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
82-165 1.57e-17

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 73.45  E-value: 1.57e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786678      82 QICVVESPADIYAIEQTGQFSGRYFVLMGHLSPLDGIgpddigldRLEQRLAEEKitEVILATNPTVEGEATANYIAELC 161
Cdd:smart00493   2 VLIIVEGPADAIALEKAGGKRGNVVALGGHLLSKEQI--------KLLKKLAKKA--EVILATDPDREGEAIAWELAELL 71


                   ....
gi 1786678     162 AQYD 165
Cdd:smart00493  72 KPAG 75
 
Name Accession Description Interval E-value
RecR COG0353
Recombinational DNA repair protein RecR [Replication, recombination and repair];
4-196 9.71e-124

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


Pssm-ID: 440122 [Multi-domain]  Cd Length: 195  Bit Score: 347.40  E-value: 9.71e-124
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786678    4 SPLLTQLMEALRCLPGVGPKSAQRMAFTLLQRDRSGGMRLAQALTRAMSEIGHCADCRTFTEQEVCNICSNPRRqENGQI 83
Cdd:COG0353   3 PPPLERLIEALSKLPGIGPKSAQRLALHLLKRDEEEAERLAEALLEAKEKVRHCSVCGNLTEEDPCSICADPRR-DRSLI 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786678   84 CVVESPADIYAIEQTGQFSGRYFVLMGHLSPLDGIGPDDIGLDRLEQRLAEEKITEVILATNPTVEGEATANYIAELCAQ 163
Cdd:COG0353  82 CVVEEPADVLAIERTGEYRGLYHVLGGVLSPLDGIGPEDLNIDELLERLKEGGVKEVILATNPTVEGEATAHYIAELLKP 161

                       170       180       190
                ....*....|....*....|....*....|...
gi 1786678  164 YDVEASRIAHGVPVGGELEMVDGTTLSHSLAGR 196
Cdd:COG0353 162 LGVKVTRLARGLPVGGELEYADEGTLARALEGR 194
recR TIGR00615
recombination protein RecR; All proteins in this family for which functions are known are ...
 2-197 3.73e-116

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: 328.14  E-value: 3.73e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786678      2 QTSPLLTQLMEALRCLPGVGPKSAQRMAFTLLQRDRSGGMRLAQALTRAMSEIGHCADCRTFTEQEVCNICSNPRRQeNG 81
Cdd:TIGR00615   1 QYPPPISKLIESLKKLPGIGPKSAQRLAFHLLKRDPSEVLRLAQALLEAKENLRTCSVCGAISDQEVCNICSDERRD-NS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786678     82 QICVVESPADIYAIEQTGQFSGRYFVLMGHLSPLDGIGPDDIGLDRLEQRLAEEKITEVILATNPTVEGEATANYIAELC 161
Cdd:TIGR00615  80 VICVVEDPKDVFALEKTKEFRGRYHVLGGHISPLDGIGPEDLTIAALLKRLQEESVKEVILATNPTVEGEATALYIARLL 159

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1786678    162 AQYDVEASRIAHGVPVGGELEMVDGTTLSHSLAGRH 197
Cdd:TIGR00615 160 QPFGVKVTRIASGLPVGGDLEYADEVTLARALEGRR 195
TOPRIM_recR cd01025
TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 81-192 1.19e-65

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: 197.36  E-value: 1.19e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786678   81 GQICVVESPADIYAIEQTGQFSGRYFVLMGHLSPLDGIGPDDIGLDRLEQRLAEEKITEVILATNPTVEGEATANYIAEL 160
Cdd:cd01025   1 NKLCVVEEPRDVLAIEESGEYRGLYHVLGGLISPLDGIGPDDLNIDKLLERIAKGQVKEVILATNPTVEGEATALYIAKL 80

                        90       100       110
                ....*....|....*....|....*....|..
gi 1786678  161 CAQYDVEASRIAHGVPVGGELEMVDGTTLSHS 192
Cdd:cd01025  81 LKDFGVKVTRLAQGIPVGGELEYADEITLSRA 112
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 81-172 6.75e-31

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: 108.14  E-value: 6.75e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786678     81 GQICVVESPADIYAIEQTGqFSGRYFVLMGHLSPLDGIGPDDIGLDRLEqrlaeeKITEVILATNPTVEGEATANYIAEL 160
Cdd:pfam13662   1 SEIIVVEGYADVIALEKAG-YKGAVAVLGGALSPLDGIGPEDLNIDSLG------GIKEVILALDGDVAGEKTALYLAEA 73

                          90
                  ....*....|..
gi 1786678    161 CAQYDVEASRIA 172
Cdd:pfam13662  74 LLEEGVKVSRLA 85
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
82-165 1.57e-17

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 73.45  E-value: 1.57e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786678      82 QICVVESPADIYAIEQTGQFSGRYFVLMGHLSPLDGIgpddigldRLEQRLAEEKitEVILATNPTVEGEATANYIAELC 161
Cdd:smart00493   2 VLIIVEGPADAIALEKAGGKRGNVVALGGHLLSKEQI--------KLLKKLAKKA--EVILATDPDREGEAIAWELAELL 71


                   ....
gi 1786678     162 AQYD 165
Cdd:smart00493  72 KPAG 75
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 82-171 1.21e-15

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: 68.92  E-value: 1.21e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786678     82 QICVVESPADIYAIEQ-TGQFSGRYFVLMGHLSPLDGiGPDDIGLDRLEQRLaeEKITEVILATNPTVEGEATANYIAEL 160
Cdd:pfam01751   1 ELIIVEGPSDAIALEKaLGGGFQAVVAVLGHLLSLEK-GPKKKALKALKELA--LKAKEVILATDPDREGEAIALKLLEL 77

                          90
                  ....*....|....*.
gi 1786678    161 C-----AQYDVEASRI 171
Cdd:pfam01751  78 KellenAGGRVEFSEL 93
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 82-172 6.55e-14

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: 64.37  E-value: 6.55e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786678   82 QICVVESPADIYAIEQTGQFSGRYFVLMGHLSPLdgigpddigLDRLEQRLAEEKItEVILATNPTVEGEATANYIAELC 161
Cdd:cd00188   2 KLIIVEGPSDALALAQAGGYGGAVVALGGHALNK---------TRELLKRLLGEAK-EVIIATDADREGEAIALRLLELL 71

                        90
                ....*....|.
gi 1786678  162 AQYDVEASRIA 172
Cdd:cd00188  72 KSLGKKVRRLL 82
RecR pfam02132
RecR protein;
39-77 2.05e-13

RecR protein;


Pssm-ID: 460456  Cd Length: 40  Bit Score: 61.67  E-value: 2.05e-13
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1786678     39 GGMRLAQALTRAMSEIGHCADCRTFTEQEVCNICSNPRR 77
Cdd:pfam02132   1 EAERLAEALLEAKENIRYCSVCGNLTDEDPCPICSDPRR 39
TOPRIM_TopoIA_TopoI cd03363
TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TOPRIM) domain found in members of the type IA ...
 85-160 1.60e-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: 37.16  E-value: 1.60e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1786678   85 VVESPADIYAIEQtgqFSGR-YFVL--MGHLS--PLDGIG--PDDIG-------LDRLEQRLAE-----EKITEVILATN 145
Cdd:cd03363   5 IVESPAKAKTIKK---YLGKeYEVLasVGHIRdlPKKGLGvdGEDDGfepkyvvIPGKKKVVKElkklaKKADEIYLATD 81

                        90
                ....*....|....*
gi 1786678  146 PTVEGEATANYIAEL 160
Cdd:cd03363  82 PDREGEAIAWHLAEV 96
 
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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