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Conserved domains on  [gi|1176773596|gb|OQY91472|]
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MAG: recombination protein RecR [Anaerolineae bacterium UTCFX1]

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:  9722641
SCOP:  4007649|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];
2-126 1.19e-80

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


:

Pssm-ID: 440122 [Multi-domain]  Cd Length: 195  Bit Score: 235.31  E-value: 1.19e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176773596   2 CESARRDGSIICVVEEALDVLALERTAGFNGKYHVLQGVLSPIEGIGPDDLKIKQLLARVAGGGVKEVILATNPSMEGDA 81
Cdd:COG0353    71 CADPRRDRSLICVVEEPADVLAIERTGEYRGLYHVLGGVLSPLDGIGPEDLNIDELLERLKEGGVKEVILATNPTVEGEA 150

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1176773596  82 TALYLQNQLRQFGVHVTRLARGLPMGGDLEYADQNTLLRALSGRR 126
Cdd:COG0353   151 TAHYIAELLKPLGVKVTRLARGLPVGGELEYADEGTLARALEGRR 195
 
Name Accession Description Interval E-value
RecR COG0353
Recombinational DNA repair protein RecR [Replication, recombination and repair];
2-126 1.19e-80

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


Pssm-ID: 440122 [Multi-domain]  Cd Length: 195  Bit Score: 235.31  E-value: 1.19e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176773596   2 CESARRDGSIICVVEEALDVLALERTAGFNGKYHVLQGVLSPIEGIGPDDLKIKQLLARVAGGGVKEVILATNPSMEGDA 81
Cdd:COG0353    71 CADPRRDRSLICVVEEPADVLAIERTGEYRGLYHVLGGVLSPLDGIGPEDLNIDELLERLKEGGVKEVILATNPTVEGEA 150

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1176773596  82 TALYLQNQLRQFGVHVTRLARGLPMGGDLEYADQNTLLRALSGRR 126
Cdd:COG0353   151 TAHYIAELLKPLGVKVTRLARGLPVGGELEYADEGTLARALEGRR 195
recR TIGR00615
recombination protein RecR; All proteins in this family for which functions are known are ...
 2-126 5.11e-65

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: 195.63  E-value: 5.11e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176773596   2 CESARRDGSIICVVEEALDVLALERTAGFNGKYHVLQGVLSPIEGIGPDDLKIKQLLARVAGGGVKEVILATNPSMEGDA 81
Cdd:TIGR00615  71 CSDERRDNSVICVVEDPKDVFALEKTKEFRGRYHVLGGHISPLDGIGPEDLTIAALLKRLQEESVKEVILATNPTVEGEA 150

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1176773596  82 TALYLQNQLRQFGVHVTRLARGLPMGGDLEYADQNTLLRALSGRR 126
Cdd:TIGR00615 151 TALYIARLLQPFGVKVTRIASGLPVGGDLEYADEVTLARALEGRR 195
TOPRIM_recR cd01025
TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 10-121 2.78e-63

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: 188.50  E-value: 2.78e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176773596  10 SIICVVEEALDVLALERTAGFNGKYHVLQGVLSPIEGIGPDDLKIKQLLARVAGGGVKEVILATNPSMEGDATALYLQNQ 89
Cdd:cd01025     1 NKLCVVEEPRDVLAIEESGEYRGLYHVLGGLISPLDGIGPDDLNIDKLLERIAKGQVKEVILATNPTVEGEATALYIAKL 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1176773596  90 LRQFGVHVTRLARGLPMGGDLEYADQNTLLRA 121
Cdd:cd01025    81 LKDFGVKVTRLAQGIPVGGELEYADEITLSRA 112
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 10-101 3.59e-27

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: 3.59e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176773596  10 SIICVVEEALDVLALERtAGFNGKYHVLQGVLSPIEGIGPDDLKIKQLlarvagGGVKEVILATNPSMEGDATALYLQNQ 89
Cdd:pfam13662   1 SEIIVVEGYADVIALEK-AGYKGAVAVLGGALSPLDGIGPEDLNIDSL------GGIKEVILALDGDVAGEKTALYLAEA 73

                          90
                  ....*....|..
gi 1176773596  90 LRQFGVHVTRLA 101
Cdd:pfam13662  74 LLEEGVKVSRLA 85
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
10-94 5.12e-12

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 57.27  E-value: 5.12e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176773596   10 SIICVVEEALDVLALERTAGFNGKYHVLQGVLspiegigpDDLKIKQLLARVAGGgvKEVILATNPSMEGDATALYLQNQ 89
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALGGHL--------LSKEQIKLLKKLAKK--AEVILATDPDREGEAIAWELAEL 70


                   ....*
gi 1176773596   90 LRQFG 94
Cdd:smart00493  71 LKPAG 75
 
Name Accession Description Interval E-value
RecR COG0353
Recombinational DNA repair protein RecR [Replication, recombination and repair];
2-126 1.19e-80

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


Pssm-ID: 440122 [Multi-domain]  Cd Length: 195  Bit Score: 235.31  E-value: 1.19e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176773596   2 CESARRDGSIICVVEEALDVLALERTAGFNGKYHVLQGVLSPIEGIGPDDLKIKQLLARVAGGGVKEVILATNPSMEGDA 81
Cdd:COG0353    71 CADPRRDRSLICVVEEPADVLAIERTGEYRGLYHVLGGVLSPLDGIGPEDLNIDELLERLKEGGVKEVILATNPTVEGEA 150

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1176773596  82 TALYLQNQLRQFGVHVTRLARGLPMGGDLEYADQNTLLRALSGRR 126
Cdd:COG0353   151 TAHYIAELLKPLGVKVTRLARGLPVGGELEYADEGTLARALEGRR 195
recR TIGR00615
recombination protein RecR; All proteins in this family for which functions are known are ...
 2-126 5.11e-65

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: 195.63  E-value: 5.11e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176773596   2 CESARRDGSIICVVEEALDVLALERTAGFNGKYHVLQGVLSPIEGIGPDDLKIKQLLARVAGGGVKEVILATNPSMEGDA 81
Cdd:TIGR00615  71 CSDERRDNSVICVVEDPKDVFALEKTKEFRGRYHVLGGHISPLDGIGPEDLTIAALLKRLQEESVKEVILATNPTVEGEA 150

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1176773596  82 TALYLQNQLRQFGVHVTRLARGLPMGGDLEYADQNTLLRALSGRR 126
Cdd:TIGR00615 151 TALYIARLLQPFGVKVTRIASGLPVGGDLEYADEVTLARALEGRR 195
TOPRIM_recR cd01025
TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 10-121 2.78e-63

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: 188.50  E-value: 2.78e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176773596  10 SIICVVEEALDVLALERTAGFNGKYHVLQGVLSPIEGIGPDDLKIKQLLARVAGGGVKEVILATNPSMEGDATALYLQNQ 89
Cdd:cd01025     1 NKLCVVEEPRDVLAIEESGEYRGLYHVLGGLISPLDGIGPDDLNIDKLLERIAKGQVKEVILATNPTVEGEATALYIAKL 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1176773596  90 LRQFGVHVTRLARGLPMGGDLEYADQNTLLRA 121
Cdd:cd01025    81 LKDFGVKVTRLAQGIPVGGELEYADEITLSRA 112
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 10-101 3.59e-27

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: 3.59e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176773596  10 SIICVVEEALDVLALERtAGFNGKYHVLQGVLSPIEGIGPDDLKIKQLlarvagGGVKEVILATNPSMEGDATALYLQNQ 89
Cdd:pfam13662   1 SEIIVVEGYADVIALEK-AGYKGAVAVLGGALSPLDGIGPEDLNIDSL------GGIKEVILALDGDVAGEKTALYLAEA 73

                          90
                  ....*....|..
gi 1176773596  90 LRQFGVHVTRLA 101
Cdd:pfam13662  74 LLEEGVKVSRLA 85
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
10-94 5.12e-12

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 57.27  E-value: 5.12e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176773596   10 SIICVVEEALDVLALERTAGFNGKYHVLQGVLspiegigpDDLKIKQLLARVAGGgvKEVILATNPSMEGDATALYLQNQ 89
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALGGHL--------LSKEQIKLLKKLAKK--AEVILATDPDREGEAIAWELAEL 70


                   ....*
gi 1176773596   90 LRQFG 94
Cdd:smart00493  71 LKPAG 75
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 10-101 1.62e-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: 53.58  E-value: 1.62e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176773596  10 SIICVVEEALDVLALERTAGFNGKYHVLQGVLSpiegigpddLKIKQLLARVAGGgVKEVILATNPSMEGDATALYLQNQ 89
Cdd:cd00188     1 KKLIIVEGPSDALALAQAGGYGGAVVALGGHAL---------NKTRELLKRLLGE-AKEVIIATDADREGEAIALRLLEL 70

                          90
                  ....*....|..
gi 1176773596  90 LRQFGVHVTRLA 101
Cdd:cd00188    71 LKSLGKKVRRLL 82
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 12-100 1.12e-06

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: 43.88  E-value: 1.12e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176773596  12 ICVVEEALDVLALERTAGFNGK--YHVLQGVLSPIEGIGPDDLKIKQLLARvaggGVKEVILATNPSMEGDATALYLQNQ 89
Cdd:pfam01751   2 LIIVEGPSDAIALEKALGGGFQavVAVLGHLLSLEKGPKKKALKALKELAL----KAKEVILATDPDREGEAIALKLLEL 77

                          90
                  ....*....|....*.
gi 1176773596  90 L-----RQFGVHVTRL 100
Cdd:pfam01751  78 KellenAGGRVEFSEL 93
COG4026 COG4026
Uncharacterized conserved protein, contains TOPRIM domain, potential nuclease [General ...
 14-121 6.24e-04

Uncharacterized conserved protein, contains TOPRIM domain, potential nuclease [General function prediction only];


Pssm-ID: 443204 [Multi-domain]  Cd Length: 287  Bit Score: 38.17  E-value: 6.24e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176773596  14 VVEEALDV----LALERTAgFNGKYHVlqgVLSPIegIGPDDLKIkqllARVAGGGVKEVILATNPSMEGDATALYLQNQ 89
Cdd:COG4026    12 IVEGASDVevvsKALQNLA-LGSEYNI---TISSI--IPTTNVEI----AKSAVAGADLVLIATDADRVGRELAEKFFEE 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1176773596  90 LRQFGVHVTRLArgLPMGGDLEYAD--------QNTLLRA 121
Cdd:COG4026    82 LKGMVGHVERMK--LPLGHDVEYVDvelvrkeiKNAIIRA 119
TOPRIM_TopoIA_TopoI cd03363
TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TOPRIM) domain found in members of the type IA ...
 54-92 7.87e-04

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: 36.77  E-value: 7.87e-04
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1176773596  54 IKQLlaRVAGGGVKEVILATNPSMEGDATALYLQNQLRQ 92
Cdd:cd03363    63 VKEL--KKLAKKADEIYLATDPDREGEAIAWHLAEVLKL 99
 
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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