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Conserved domains on  [gi|2560883443|ref|WP_305264174|]
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DNA repair protein RadC [Nitrosomonas sp.]

Protein Classification

Mov34/MPN/PAD-1 family protein( domain architecture ID 1001617)

Mov34/MPN/PAD-1 family protein contains a protein domain of unknown function with the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity

Gene Ontology:  GO:0046872|GO:0008237|GO:0006508
PubMed:  18556794|10369758

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK00024 super family cl31993
DNA repair protein RadC;
7-188 1.58e-69

DNA repair protein RadC;


The actual alignment was detected with superfamily member PRK00024:

Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 210.70  E-value: 1.58e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2560883443   7 SNAELLAML--VGKRK------ANKLYRN--TLASLF------FARE---GNDNYTkELAAAKELVTRSLNEELQQQDAF 67
Cdd:PRK00024   25 SDAELLAILlrTGTKGksvldlARELLQRfgSLRGLLdasleeLQSIkgiGPAKAA-QLKAALELARRILAERLREREVL 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2560883443  68 TAPAKVAEYLKLMLVGYEHEVFVTLFLDAQNRLIVAEELFRGTLTNTAVYPREVVKRALSLNAGNVIFAHNHPSGLATPS 147
Cdd:PRK00024  104 LSPEDVADYLMAELRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRALKLNAAALILAHNHPSGDPEPS 183

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2560883443 148 HADKALTETLKQALALVDVKVLDHLVIGDAAAVSFAESGWL 188
Cdd:PRK00024  184 QADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGLL 224
 
Name Accession Description Interval E-value
PRK00024 PRK00024
DNA repair protein RadC;
7-188 1.58e-69

DNA repair protein RadC;


Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 210.70  E-value: 1.58e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2560883443   7 SNAELLAML--VGKRK------ANKLYRN--TLASLF------FARE---GNDNYTkELAAAKELVTRSLNEELQQQDAF 67
Cdd:PRK00024   25 SDAELLAILlrTGTKGksvldlARELLQRfgSLRGLLdasleeLQSIkgiGPAKAA-QLKAALELARRILAERLREREVL 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2560883443  68 TAPAKVAEYLKLMLVGYEHEVFVTLFLDAQNRLIVAEELFRGTLTNTAVYPREVVKRALSLNAGNVIFAHNHPSGLATPS 147
Cdd:PRK00024  104 LSPEDVADYLMAELRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRALKLNAAALILAHNHPSGDPEPS 183

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2560883443 148 HADKALTETLKQALALVDVKVLDHLVIGDAAAVSFAESGWL 188
Cdd:PRK00024  184 QADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGLL 224
RadC COG2003
DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ...
 7-188 2.55e-68

DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, recombination and repair];


Pssm-ID: 441606 [Multi-domain]  Cd Length: 224  Bit Score: 207.60  E-value: 2.55e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2560883443   7 SNAELLAMLVG---KRK-----ANKLYR--NTLASLFFARE---------GNDNYTkELAAAKELVTRSLNEELQQQDAF 67
Cdd:COG2003    25 SDAELLAILLRtgtPGKdavelAKELLArfGSLRGLLRASVeelrkikgiGEAKAA-QLKAALELGRRLLREELEERPVI 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2560883443  68 TAPAKVAEYLKLMLVGYEHEVFVTLFLDAQNRLIVAEELFRGTLTNTAVYPREVVKRALSLNAGNVIFAHNHPSGLATPS 147
Cdd:COG2003   104 SSPEDVADYLRARLAHLPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLNAAAIILAHNHPSGDPEPS 183

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2560883443 148 HADKALTETLKQALALVDVKVLDHLVIGDAAAVSFAESGWL 188
Cdd:COG2003   184 RADIELTRRLKEAGELLGIRLLDHIIIGDGGYVSFAEEGLL 224
RadC pfam04002
RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was ...
 67-176 2.98e-54

RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was named initially with reference to the E. coli radC102 mutation which suggested that RadC was involved in repair of DNA lesions. However the relevant mutation has subsequently been shown to be in recG, where radC is in fact an allele of recG. In addition, a personal communication from Claverys, J-P, et al, indicates a total failure of all attempts to characterize a radiation-related function for RadC in Streptococcus pneumoniae, suggesting that it is not involved in repair of DNA lesions, in recombination during transformation, in gene conversion, nor in mismatch repair. Computational analysis, however, provides a possible function. The RadC-like family belong to the JAB superfamily of metalloproteins. The domain shows fusions to an N-terminal Helix-hairpin-Helix (HhH) domain in most instances. Other domain combinations include fusions to the anti-restriction module ArdC, the DinG/RAD3-like superfamily II helicases and the DNAG-like primase. In some bacteria, closely related DinG/Rad3- like superfamily II helicases are fused to a 3'-5' exonuclease in the same position as the RadC-like JAB domain. These conserved domain associations lead to the hypothesis that the RadC-like JAB domains might function as a nuclease.


Pssm-ID: 461124  Cd Length: 113  Bit Score: 167.97  E-value: 2.98e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2560883443  67 FTAPAKVAEYLKLMLVGYEHEVFVTLFLDAQNRLIVAEELFRGTLTNTAVYPREVVKRALSLNAGNVIFAHNHPSGLATP 146
Cdd:pfam04002   1 ITSPEDVAEYLMEELRDLDQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDPEP 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 2560883443 147 SHADKALTETLKQALALVDVKVLDHLVIGD 176
Cdd:pfam04002  81 SREDIELTRRLKEAGELLGIRLLDHIIIGD 110
MPN_DUF2466 cd08071
Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of ...
 72-183 5.48e-54

Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of unknown function contains the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. However, to date, the name RadC has been misleading and no function has been determined.


Pssm-ID: 163702  Cd Length: 113  Bit Score: 167.17  E-value: 5.48e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2560883443  72 KVAEYLKLMLVGYEHEVFVTLFLDAQNRLIVAEELFRGTLTNTAVYPREVVKRALSLNAGNVIFAHNHPSGLATPSHADK 151
Cdd:cd08071     2 DVAEYLREELGDLDQEEFVVLLLDTKNRLIAVETISVGTLNSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSREDI 81

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2560883443 152 ALTETLKQALALVDVKVLDHLVIGDAAAVSFA 183
Cdd:cd08071    82 ELTKRLKEAGELLGIRLLDHIIVGDGGYFSFR 113
radc TIGR00608
DNA repair protein radc; The genes in this family for which the functions are known have an as ...
 45-188 2.27e-46

DNA repair protein radc; The genes in this family for which the functions are known have an as yet porrly defined role in determining sensitivity to DNA damaging agents such as UV irradiation. 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: 273171 [Multi-domain]  Cd Length: 218  Bit Score: 151.44  E-value: 2.27e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2560883443  45 ELAAAKELVTRSLNEELQQQDAFTAPAKVAEYLKLMLVGYEHEVFVTLFLDAQNRLIVAEELFRGTLTNTAVYPREVVKR 124
Cdd:TIGR00608  75 QLKAAVELAKRYAKSRMLERPVIRSPEAAAEFLHTDLAHETREHFMVLFLDRKNRLIAKEVVFIGTVNHVPVHPREIFKE 154

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2560883443 125 ALSLNAGNVIFAHNHPSGLATPSHADKALTETLKQALALVDVKVLDHLVIGDAAAVSFAESGWL 188
Cdd:TIGR00608 155 ALKLSASALILAHNHPSGEPSPSQEDILITERLRKAAELLGIELLDHLIIGKGRYVSFREEGLL 218
 
Name Accession Description Interval E-value
PRK00024 PRK00024
DNA repair protein RadC;
7-188 1.58e-69

DNA repair protein RadC;


Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 210.70  E-value: 1.58e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2560883443   7 SNAELLAML--VGKRK------ANKLYRN--TLASLF------FARE---GNDNYTkELAAAKELVTRSLNEELQQQDAF 67
Cdd:PRK00024   25 SDAELLAILlrTGTKGksvldlARELLQRfgSLRGLLdasleeLQSIkgiGPAKAA-QLKAALELARRILAERLREREVL 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2560883443  68 TAPAKVAEYLKLMLVGYEHEVFVTLFLDAQNRLIVAEELFRGTLTNTAVYPREVVKRALSLNAGNVIFAHNHPSGLATPS 147
Cdd:PRK00024  104 LSPEDVADYLMAELRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRALKLNAAALILAHNHPSGDPEPS 183

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2560883443 148 HADKALTETLKQALALVDVKVLDHLVIGDAAAVSFAESGWL 188
Cdd:PRK00024  184 QADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGLL 224
RadC COG2003
DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ...
 7-188 2.55e-68

DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, recombination and repair];


Pssm-ID: 441606 [Multi-domain]  Cd Length: 224  Bit Score: 207.60  E-value: 2.55e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2560883443   7 SNAELLAMLVG---KRK-----ANKLYR--NTLASLFFARE---------GNDNYTkELAAAKELVTRSLNEELQQQDAF 67
Cdd:COG2003    25 SDAELLAILLRtgtPGKdavelAKELLArfGSLRGLLRASVeelrkikgiGEAKAA-QLKAALELGRRLLREELEERPVI 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2560883443  68 TAPAKVAEYLKLMLVGYEHEVFVTLFLDAQNRLIVAEELFRGTLTNTAVYPREVVKRALSLNAGNVIFAHNHPSGLATPS 147
Cdd:COG2003   104 SSPEDVADYLRARLAHLPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLNAAAIILAHNHPSGDPEPS 183

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2560883443 148 HADKALTETLKQALALVDVKVLDHLVIGDAAAVSFAESGWL 188
Cdd:COG2003   184 RADIELTRRLKEAGELLGIRLLDHIIIGDGGYVSFAEEGLL 224
RadC pfam04002
RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was ...
 67-176 2.98e-54

RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was named initially with reference to the E. coli radC102 mutation which suggested that RadC was involved in repair of DNA lesions. However the relevant mutation has subsequently been shown to be in recG, where radC is in fact an allele of recG. In addition, a personal communication from Claverys, J-P, et al, indicates a total failure of all attempts to characterize a radiation-related function for RadC in Streptococcus pneumoniae, suggesting that it is not involved in repair of DNA lesions, in recombination during transformation, in gene conversion, nor in mismatch repair. Computational analysis, however, provides a possible function. The RadC-like family belong to the JAB superfamily of metalloproteins. The domain shows fusions to an N-terminal Helix-hairpin-Helix (HhH) domain in most instances. Other domain combinations include fusions to the anti-restriction module ArdC, the DinG/RAD3-like superfamily II helicases and the DNAG-like primase. In some bacteria, closely related DinG/Rad3- like superfamily II helicases are fused to a 3'-5' exonuclease in the same position as the RadC-like JAB domain. These conserved domain associations lead to the hypothesis that the RadC-like JAB domains might function as a nuclease.


Pssm-ID: 461124  Cd Length: 113  Bit Score: 167.97  E-value: 2.98e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2560883443  67 FTAPAKVAEYLKLMLVGYEHEVFVTLFLDAQNRLIVAEELFRGTLTNTAVYPREVVKRALSLNAGNVIFAHNHPSGLATP 146
Cdd:pfam04002   1 ITSPEDVAEYLMEELRDLDQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDPEP 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 2560883443 147 SHADKALTETLKQALALVDVKVLDHLVIGD 176
Cdd:pfam04002  81 SREDIELTRRLKEAGELLGIRLLDHIIIGD 110
MPN_DUF2466 cd08071
Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of ...
 72-183 5.48e-54

Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of unknown function contains the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. However, to date, the name RadC has been misleading and no function has been determined.


Pssm-ID: 163702  Cd Length: 113  Bit Score: 167.17  E-value: 5.48e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2560883443  72 KVAEYLKLMLVGYEHEVFVTLFLDAQNRLIVAEELFRGTLTNTAVYPREVVKRALSLNAGNVIFAHNHPSGLATPSHADK 151
Cdd:cd08071     2 DVAEYLREELGDLDQEEFVVLLLDTKNRLIAVETISVGTLNSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSREDI 81

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2560883443 152 ALTETLKQALALVDVKVLDHLVIGDAAAVSFA 183
Cdd:cd08071    82 ELTKRLKEAGELLGIRLLDHIIVGDGGYFSFR 113
radc TIGR00608
DNA repair protein radc; The genes in this family for which the functions are known have an as ...
 45-188 2.27e-46

DNA repair protein radc; The genes in this family for which the functions are known have an as yet porrly defined role in determining sensitivity to DNA damaging agents such as UV irradiation. 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: 273171 [Multi-domain]  Cd Length: 218  Bit Score: 151.44  E-value: 2.27e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2560883443  45 ELAAAKELVTRSLNEELQQQDAFTAPAKVAEYLKLMLVGYEHEVFVTLFLDAQNRLIVAEELFRGTLTNTAVYPREVVKR 124
Cdd:TIGR00608  75 QLKAAVELAKRYAKSRMLERPVIRSPEAAAEFLHTDLAHETREHFMVLFLDRKNRLIAKEVVFIGTVNHVPVHPREIFKE 154

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2560883443 125 ALSLNAGNVIFAHNHPSGLATPSHADKALTETLKQALALVDVKVLDHLVIGDAAAVSFAESGWL 188
Cdd:TIGR00608 155 ALKLSASALILAHNHPSGEPSPSQEDILITERLRKAAELLGIELLDHLIIGKGRYVSFREEGLL 218
 
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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