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Conserved domains on  [gi|1402841277|ref|WP_110711279|]
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MULTISPECIES: recombination mediator RecR [Stenotrophomonas]

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];
1-194 4.26e-114

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


:

Pssm-ID: 440122 [Multi-domain]  Cd Length: 195  Bit Score: 322.75  E-value: 4.26e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402841277   1 MSAPLLEQLIDALRVLPGVGQKTAQRMAYHLLEREREGGQRLAETLALAVERIGHCAQCRDFSETELCPTCANSSRERSQ 80
Cdd:COG0353     1 MYPPPLERLIEALSKLPGIGPKSAQRLALHLLKRDEEEAERLAEALLEAKEKVRHCSVCGNLTEEDPCSICADPRRDRSL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402841277  81 LCVVESPADRLAIENATGFRGVYFVLQGRLSPLDGIGPRELGLEQLEQRLAEGEVQELIIATSATVEGEATAHYLAQLAR 160
Cdd:COG0353    81 ICVVEEPADVLAIERTGEYRGLYHVLGGVLSPLDGIGPEDLNIDELLERLKEGGVKEVILATNPTVEGEATAHYIAELLK 160

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1402841277 161 ARRVQPSRLAQGLPLGGELEYVDRGTLSHAFGTR 194
Cdd:COG0353   161 PLGVKVTRLARGLPVGGELEYADEGTLARALEGR 194
 
Name Accession Description Interval E-value
RecR COG0353
Recombinational DNA repair protein RecR [Replication, recombination and repair];
1-194 4.26e-114

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


Pssm-ID: 440122 [Multi-domain]  Cd Length: 195  Bit Score: 322.75  E-value: 4.26e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402841277   1 MSAPLLEQLIDALRVLPGVGQKTAQRMAYHLLEREREGGQRLAETLALAVERIGHCAQCRDFSETELCPTCANSSRERSQ 80
Cdd:COG0353     1 MYPPPLERLIEALSKLPGIGPKSAQRLALHLLKRDEEEAERLAEALLEAKEKVRHCSVCGNLTEEDPCSICADPRRDRSL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402841277  81 LCVVESPADRLAIENATGFRGVYFVLQGRLSPLDGIGPRELGLEQLEQRLAEGEVQELIIATSATVEGEATAHYLAQLAR 160
Cdd:COG0353    81 ICVVEEPADVLAIERTGEYRGLYHVLGGVLSPLDGIGPEDLNIDELLERLKEGGVKEVILATNPTVEGEATAHYIAELLK 160

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1402841277 161 ARRVQPSRLAQGLPLGGELEYVDRGTLSHAFGTR 194
Cdd:COG0353   161 PLGVKVTRLARGLPVGGELEYADEGTLARALEGR 194
recR TIGR00615
recombination protein RecR; All proteins in this family for which functions are known are ...
 1-194 1.08e-84

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: 248.41  E-value: 1.08e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402841277   1 MSAPLLEQLIDALRVLPGVGQKTAQRMAYHLLEREREGGQRLAETLALAVERIGHCAQCRDFSETELCPTCANSSRERSQ 80
Cdd:TIGR00615   1 QYPPPISKLIESLKKLPGIGPKSAQRLAFHLLKRDPSEVLRLAQALLEAKENLRTCSVCGAISDQEVCNICSDERRDNSV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402841277  81 LCVVESPADRLAIENATGFRGVYFVLQGRLSPLDGIGPRELGLEQLEQRLAEGEVQELIIATSATVEGEATAHYLAQLAR 160
Cdd:TIGR00615  81 ICVVEDPKDVFALEKTKEFRGRYHVLGGHISPLDGIGPEDLTIAALLKRLQEESVKEVILATNPTVEGEATALYIARLLQ 160

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1402841277 161 ARRVQPSRLAQGLPLGGELEYVDRGTLSHAFGTR 194
Cdd:TIGR00615 161 PFGVKVTRIASGLPVGGDLEYADEVTLARALEGR 194
TOPRIM_recR cd01025
TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 79-190 1.28e-58

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: 179.25  E-value: 1.28e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402841277  79 SQLCVVESPADRLAIENATGFRGVYFVLQGRLSPLDGIGPRELGLEQLEQRLAEGEVQELIIATSATVEGEATAHYLAQL 158
Cdd:cd01025     1 NKLCVVEEPRDVLAIEESGEYRGLYHVLGGLISPLDGIGPDDLNIDKLLERIAKGQVKEVILATNPTVEGEATALYIAKL 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1402841277 159 ARARRVQPSRLAQGLPLGGELEYVDRGTLSHA 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 ...
 79-170 5.35e-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: 98.13  E-value: 5.35e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402841277  79 SQLCVVESPADRLAIENAtGFRGVYFVLQGRLSPLDGIGPRELGLEQLEQrlaegeVQELIIATSATVEGEATAHYLAQL 158
Cdd:pfam13662   1 SEIIVVEGYADVIALEKA-GYKGAVAVLGGALSPLDGIGPEDLNIDSLGG------IKEVILALDGDVAGEKTALYLAEA 73

                          90
                  ....*....|..
gi 1402841277 159 ARARRVQPSRLA 170
Cdd:pfam13662  74 LLEEGVKVSRLA 85
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
79-162 6.65e-12

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 58.81  E-value: 6.65e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402841277   79 SQLCVVESPADRLAIENATGFRGVYFVLQGRLSPLDGIgprelglEQLEQRLAEGEVqelIIATSATVEGEATAHYLAQL 158
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALGGHLLSKEQI-------KLLKKLAKKAEV---ILATDPDREGEAIAWELAEL 70


                   ....
gi 1402841277  159 ARAR 162
Cdd:smart00493  71 LKPA 74
 
Name Accession Description Interval E-value
RecR COG0353
Recombinational DNA repair protein RecR [Replication, recombination and repair];
1-194 4.26e-114

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


Pssm-ID: 440122 [Multi-domain]  Cd Length: 195  Bit Score: 322.75  E-value: 4.26e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402841277   1 MSAPLLEQLIDALRVLPGVGQKTAQRMAYHLLEREREGGQRLAETLALAVERIGHCAQCRDFSETELCPTCANSSRERSQ 80
Cdd:COG0353     1 MYPPPLERLIEALSKLPGIGPKSAQRLALHLLKRDEEEAERLAEALLEAKEKVRHCSVCGNLTEEDPCSICADPRRDRSL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402841277  81 LCVVESPADRLAIENATGFRGVYFVLQGRLSPLDGIGPRELGLEQLEQRLAEGEVQELIIATSATVEGEATAHYLAQLAR 160
Cdd:COG0353    81 ICVVEEPADVLAIERTGEYRGLYHVLGGVLSPLDGIGPEDLNIDELLERLKEGGVKEVILATNPTVEGEATAHYIAELLK 160

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1402841277 161 ARRVQPSRLAQGLPLGGELEYVDRGTLSHAFGTR 194
Cdd:COG0353   161 PLGVKVTRLARGLPVGGELEYADEGTLARALEGR 194
recR TIGR00615
recombination protein RecR; All proteins in this family for which functions are known are ...
 1-194 1.08e-84

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: 248.41  E-value: 1.08e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402841277   1 MSAPLLEQLIDALRVLPGVGQKTAQRMAYHLLEREREGGQRLAETLALAVERIGHCAQCRDFSETELCPTCANSSRERSQ 80
Cdd:TIGR00615   1 QYPPPISKLIESLKKLPGIGPKSAQRLAFHLLKRDPSEVLRLAQALLEAKENLRTCSVCGAISDQEVCNICSDERRDNSV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402841277  81 LCVVESPADRLAIENATGFRGVYFVLQGRLSPLDGIGPRELGLEQLEQRLAEGEVQELIIATSATVEGEATAHYLAQLAR 160
Cdd:TIGR00615  81 ICVVEDPKDVFALEKTKEFRGRYHVLGGHISPLDGIGPEDLTIAALLKRLQEESVKEVILATNPTVEGEATALYIARLLQ 160

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1402841277 161 ARRVQPSRLAQGLPLGGELEYVDRGTLSHAFGTR 194
Cdd:TIGR00615 161 PFGVKVTRIASGLPVGGDLEYADEVTLARALEGR 194
TOPRIM_recR cd01025
TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 79-190 1.28e-58

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: 179.25  E-value: 1.28e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402841277  79 SQLCVVESPADRLAIENATGFRGVYFVLQGRLSPLDGIGPRELGLEQLEQRLAEGEVQELIIATSATVEGEATAHYLAQL 158
Cdd:cd01025     1 NKLCVVEEPRDVLAIEESGEYRGLYHVLGGLISPLDGIGPDDLNIDKLLERIAKGQVKEVILATNPTVEGEATALYIAKL 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1402841277 159 ARARRVQPSRLAQGLPLGGELEYVDRGTLSHA 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 ...
 79-170 5.35e-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: 98.13  E-value: 5.35e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402841277  79 SQLCVVESPADRLAIENAtGFRGVYFVLQGRLSPLDGIGPRELGLEQLEQrlaegeVQELIIATSATVEGEATAHYLAQL 158
Cdd:pfam13662   1 SEIIVVEGYADVIALEKA-GYKGAVAVLGGALSPLDGIGPEDLNIDSLGG------IKEVILALDGDVAGEKTALYLAEA 73

                          90
                  ....*....|..
gi 1402841277 159 ARARRVQPSRLA 170
Cdd:pfam13662  74 LLEEGVKVSRLA 85
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
79-162 6.65e-12

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 58.81  E-value: 6.65e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402841277   79 SQLCVVESPADRLAIENATGFRGVYFVLQGRLSPLDGIgprelglEQLEQRLAEGEVqelIIATSATVEGEATAHYLAQL 158
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALGGHLLSKEQI-------KLLKKLAKKAEV---ILATDPDREGEAIAWELAEL 70


                   ....
gi 1402841277  159 ARAR 162
Cdd:smart00493  71 LKPA 74
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 79-170 8.08e-11

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: 55.90  E-value: 8.08e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402841277  79 SQLCVVESPADRLAIENATGFRGVYFVLQGRLSPLdgigprelgLEQLEQRLAeGEVQELIIATSATVEGEATAHYLAQL 158
Cdd:cd00188     1 KKLIIVEGPSDALALAQAGGYGGAVVALGGHALNK---------TRELLKRLL-GEAKEVIIATDADREGEAIALRLLEL 70

                          90
                  ....*....|..
gi 1402841277 159 ARARRVQPSRLA 170
Cdd:cd00188    71 LKSLGKKVRRLL 82
RecR pfam02132
RecR protein;
38-76 2.81e-10

RecR protein;


Pssm-ID: 460456  Cd Length: 40  Bit Score: 53.19  E-value: 2.81e-10
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1402841277  38 GGQRLAETLALAVERIGHCAQCRDFSETELCPTCANSSR 76
Cdd:pfam02132   1 EAERLAEALLEAKENIRYCSVCGNLTDEDPCPICSDPRR 39
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 80-161 8.35e-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: 53.51  E-value: 8.35e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402841277  80 QLCVVESPADRLAIENATG--FRGVYFVLqGRLSPLDGiGPRELGLEQLEQRLAEgeVQELIIATSATVEGEATAHYLAQ 157
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGggFQAVVAVL-GHLLSLEK-GPKKKALKALKELALK--AKEVILATDPDREGEAIALKLLE 76


                  ....
gi 1402841277 158 LARA 161
Cdd:pfam01751  77 LKEL 80
 
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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