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Conserved domains on  [gi|1124707388|ref|WP_074985372|]
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MULTISPECIES: recombination mediator RecR [Pseudomonas]

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];
2-195 5.10e-115

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


:

Pssm-ID: 440122 [Multi-domain]  Cd Length: 195  Bit Score: 325.06  E-value: 5.10e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124707388   2 SFSPLIRQLIDALRILPGVGQKSAQRMALQLLERDRTGGLRLAQALTQAMEGVGHCKQCRTLSEEELCPQCADPRRDDSL 81
Cdd:COG0353     1 MYPPPLERLIEALSKLPGIGPKSAQRLALHLLKRDEEEAERLAEALLEAKEKVRHCSVCGNLTEEDPCSICADPRRDRSL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124707388  82 LCVVEGPLDVFAVEQTG-YRGRFFVLKGHLSPLDGLGPEAIGIPELEARIKAGSFAEIILATNPTVEGEATAHYIAQLLA 160
Cdd:COG0353    81 ICVVEEPADVLAIERTGeYRGLYHVLGGVLSPLDGIGPEDLNIDELLERLKEGGVKEVILATNPTVEGEATAHYIAELLK 160

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1124707388 161 GSGLVLSRIAHGVPLGGELELVDGGTLAHALAGRR 195
Cdd:COG0353   161 PLGVKVTRLARGLPVGGELEYADEGTLARALEGRR 195
 
Name Accession Description Interval E-value
RecR COG0353
Recombinational DNA repair protein RecR [Replication, recombination and repair];
2-195 5.10e-115

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


Pssm-ID: 440122 [Multi-domain]  Cd Length: 195  Bit Score: 325.06  E-value: 5.10e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124707388   2 SFSPLIRQLIDALRILPGVGQKSAQRMALQLLERDRTGGLRLAQALTQAMEGVGHCKQCRTLSEEELCPQCADPRRDDSL 81
Cdd:COG0353     1 MYPPPLERLIEALSKLPGIGPKSAQRLALHLLKRDEEEAERLAEALLEAKEKVRHCSVCGNLTEEDPCSICADPRRDRSL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124707388  82 LCVVEGPLDVFAVEQTG-YRGRFFVLKGHLSPLDGLGPEAIGIPELEARIKAGSFAEIILATNPTVEGEATAHYIAQLLA 160
Cdd:COG0353    81 ICVVEEPADVLAIERTGeYRGLYHVLGGVLSPLDGIGPEDLNIDELLERLKEGGVKEVILATNPTVEGEATAHYIAELLK 160

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1124707388 161 GSGLVLSRIAHGVPLGGELELVDGGTLAHALAGRR 195
Cdd:COG0353   161 PLGVKVTRLARGLPVGGELEYADEGTLARALEGRR 195
recR TIGR00615
recombination protein RecR; All proteins in this family for which functions are known are ...
 3-195 2.15e-91

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: 265.36  E-value: 2.15e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124707388   3 FSPLIRQLIDALRILPGVGQKSAQRMALQLLERDRTGGLRLAQALTQAMEGVGHCKQCRTLSEEELCPQCADPRRDDSLL 82
Cdd:TIGR00615   2 YPPPISKLIESLKKLPGIGPKSAQRLAFHLLKRDPSEVLRLAQALLEAKENLRTCSVCGAISDQEVCNICSDERRDNSVI 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124707388  83 CVVEGPLDVFAVEQTG-YRGRFFVLKGHLSPLDGLGPEAIGIPELEARIKAGSFAEIILATNPTVEGEATAHYIAQLLAG 161
Cdd:TIGR00615  82 CVVEDPKDVFALEKTKeFRGRYHVLGGHISPLDGIGPEDLTIAALLKRLQEESVKEVILATNPTVEGEATALYIARLLQP 161

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1124707388 162 SGLVLSRIAHGVPLGGELELVDGGTLAHALAGRR 195
Cdd:TIGR00615 162 FGVKVTRIASGLPVGGDLEYADEVTLARALEGRR 195
TOPRIM_recR cd01025
TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 80-190 1.73e-55

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: 171.55  E-value: 1.73e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124707388  80 SLLCVVEGPLDVFAVEQTG-YRGRFFVLKGHLSPLDGLGPEAIGIPELEARIKAGSFAEIILATNPTVEGEATAHYIAQL 158
Cdd:cd01025     1 NKLCVVEEPRDVLAIEESGeYRGLYHVLGGLISPLDGIGPDDLNIDKLLERIAKGQVKEVILATNPTVEGEATALYIAKL 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1124707388 159 LAGSGLVLSRIAHGVPLGGELELVDGGTLAHA 190
Cdd:cd01025    81 LKDFGVKVTRLAQGIPVGGELEYADEITLSRA 112
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 80-170 5.14e-28

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: 100.82  E-value: 5.14e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124707388  80 SLLCVVEGPLDVFAVEQTGYRGRFFVLKGHLSPLDGLGPEAIGIPELearikaGSFAEIILATNPTVEGEATAHYIAQLL 159
Cdd:pfam13662   1 SEIIVVEGYADVIALEKAGYKGAVAVLGGALSPLDGIGPEDLNIDSL------GGIKEVILALDGDVAGEKTALYLAEAL 74

                          90
                  ....*....|.
gi 1124707388 160 AGSGLVLSRIA 170
Cdd:pfam13662  75 LEEGVKVSRLA 85
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
82-163 6.07e-13

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 61.51  E-value: 6.07e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124707388   82 LCVVEGPLDVFAVEQTG-YRGRFFVLKGHLSPLDGlgpeaigIPELEARIKAgsfAEIILATNPTVEGEATAHYIAQLLA 160
Cdd:smart00493   3 LIIVEGPADAIALEKAGgKRGNVVALGGHLLSKEQ-------IKLLKKLAKK---AEVILATDPDREGEAIAWELAELLK 72


                   ...
gi 1124707388  161 GSG 163
Cdd:smart00493  73 PAG 75
 
Name Accession Description Interval E-value
RecR COG0353
Recombinational DNA repair protein RecR [Replication, recombination and repair];
2-195 5.10e-115

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


Pssm-ID: 440122 [Multi-domain]  Cd Length: 195  Bit Score: 325.06  E-value: 5.10e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124707388   2 SFSPLIRQLIDALRILPGVGQKSAQRMALQLLERDRTGGLRLAQALTQAMEGVGHCKQCRTLSEEELCPQCADPRRDDSL 81
Cdd:COG0353     1 MYPPPLERLIEALSKLPGIGPKSAQRLALHLLKRDEEEAERLAEALLEAKEKVRHCSVCGNLTEEDPCSICADPRRDRSL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124707388  82 LCVVEGPLDVFAVEQTG-YRGRFFVLKGHLSPLDGLGPEAIGIPELEARIKAGSFAEIILATNPTVEGEATAHYIAQLLA 160
Cdd:COG0353    81 ICVVEEPADVLAIERTGeYRGLYHVLGGVLSPLDGIGPEDLNIDELLERLKEGGVKEVILATNPTVEGEATAHYIAELLK 160

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1124707388 161 GSGLVLSRIAHGVPLGGELELVDGGTLAHALAGRR 195
Cdd:COG0353   161 PLGVKVTRLARGLPVGGELEYADEGTLARALEGRR 195
recR TIGR00615
recombination protein RecR; All proteins in this family for which functions are known are ...
 3-195 2.15e-91

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: 265.36  E-value: 2.15e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124707388   3 FSPLIRQLIDALRILPGVGQKSAQRMALQLLERDRTGGLRLAQALTQAMEGVGHCKQCRTLSEEELCPQCADPRRDDSLL 82
Cdd:TIGR00615   2 YPPPISKLIESLKKLPGIGPKSAQRLAFHLLKRDPSEVLRLAQALLEAKENLRTCSVCGAISDQEVCNICSDERRDNSVI 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124707388  83 CVVEGPLDVFAVEQTG-YRGRFFVLKGHLSPLDGLGPEAIGIPELEARIKAGSFAEIILATNPTVEGEATAHYIAQLLAG 161
Cdd:TIGR00615  82 CVVEDPKDVFALEKTKeFRGRYHVLGGHISPLDGIGPEDLTIAALLKRLQEESVKEVILATNPTVEGEATALYIARLLQP 161

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1124707388 162 SGLVLSRIAHGVPLGGELELVDGGTLAHALAGRR 195
Cdd:TIGR00615 162 FGVKVTRIASGLPVGGDLEYADEVTLARALEGRR 195
TOPRIM_recR cd01025
TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 80-190 1.73e-55

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: 171.55  E-value: 1.73e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124707388  80 SLLCVVEGPLDVFAVEQTG-YRGRFFVLKGHLSPLDGLGPEAIGIPELEARIKAGSFAEIILATNPTVEGEATAHYIAQL 158
Cdd:cd01025     1 NKLCVVEEPRDVLAIEESGeYRGLYHVLGGLISPLDGIGPDDLNIDKLLERIAKGQVKEVILATNPTVEGEATALYIAKL 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1124707388 159 LAGSGLVLSRIAHGVPLGGELELVDGGTLAHA 190
Cdd:cd01025    81 LKDFGVKVTRLAQGIPVGGELEYADEITLSRA 112
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 80-170 5.14e-28

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: 100.82  E-value: 5.14e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124707388  80 SLLCVVEGPLDVFAVEQTGYRGRFFVLKGHLSPLDGLGPEAIGIPELearikaGSFAEIILATNPTVEGEATAHYIAQLL 159
Cdd:pfam13662   1 SEIIVVEGYADVIALEKAGYKGAVAVLGGALSPLDGIGPEDLNIDSL------GGIKEVILALDGDVAGEKTALYLAEAL 74

                          90
                  ....*....|.
gi 1124707388 160 AGSGLVLSRIA 170
Cdd:pfam13662  75 LEEGVKVSRLA 85
RecR pfam02132
RecR protein;
39-78 4.43e-16

RecR protein;


Pssm-ID: 460456  Cd Length: 40  Bit Score: 68.60  E-value: 4.43e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1124707388  39 GGLRLAQALTQAMEGVGHCKQCRTLSEEELCPQCADPRRD 78
Cdd:pfam02132   1 EAERLAEALLEAKENIRYCSVCGNLTDEDPCPICSDPRRD 40
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
82-163 6.07e-13

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 61.51  E-value: 6.07e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124707388   82 LCVVEGPLDVFAVEQTG-YRGRFFVLKGHLSPLDGlgpeaigIPELEARIKAgsfAEIILATNPTVEGEATAHYIAQLLA 160
Cdd:smart00493   3 LIIVEGPADAIALEKAGgKRGNVVALGGHLLSKEQ-------IKLLKKLAKK---AEVILATDPDREGEAIAWELAELLK 72


                   ...
gi 1124707388  161 GSG 163
Cdd:smart00493  73 PAG 75
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 82-159 3.77e-10

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: 54.28  E-value: 3.77e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124707388  82 LCVVEGPLDVFAVEQTGYRGRFFV--LKGHLSPLDGlGPEAIGIPELEARIKAGSfaEIILATNPTVEGEATAHYIAQLL 159
Cdd:pfam01751   2 LIIVEGPSDAIALEKALGGGFQAVvaVLGHLLSLEK-GPKKKALKALKELALKAK--EVILATDPDREGEAIALKLLELK 78
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 82-170 2.17e-09

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: 52.04  E-value: 2.17e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124707388  82 LCVVEGPLDVFAVEQTG-YRGRFFVLKGHLSPLdglgpeaigiPELEARIKAGSFAEIILATNPTVEGEATAHYIAQLLA 160
Cdd:cd00188     3 LIIVEGPSDALALAQAGgYGGAVVALGGHALNK----------TRELLKRLLGEAKEVIIATDADREGEAIALRLLELLK 72

                          90
                  ....*....|
gi 1124707388 161 GSGLVLSRIA 170
Cdd:cd00188    73 SLGKKVRRLL 82
RING-HC_RNF220 cd16563
RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins; ...
 56-77 4.61e-03

RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins; RNF220 is an E3 ubiquitin-protein ligase that promotes the ubiquitination and proteasomal degradation of Sin3B, a scaffold protein of the Sin3/HDAC (histone deacetylase) corepressor complex. It can also bind E2 and mediate auto-ubiquitination of itself. Moreover, RNF220 specifically interacts with beta-catenin, and enhances canonical Wnt signaling through ubiquitin-specific protease 7 (USP7)-mediated deubiquitination and stabilization of beta-catenin, which is independent of its E3 ligase activity. RNF220 contains a characteristic C3HC4-type RING-HC finger at its C-terminus.


Pssm-ID: 438225 [Multi-domain]  Cd Length: 52  Bit Score: 33.97  E-value: 4.61e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 1124707388  56 HCKQC--RTLSEEELCPQC------ADPRR 77
Cdd:cd16563    23 HCEECwlRTLGAKKLCPQCntitspADLRR 52
 
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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