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Conserved domains on  [gi|1490725961|gb|RLC97023|]
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hypothetical protein DRI40_01525, partial [Chloroflexi bacterium]

Protein Classification

RadC family protein( domain architecture ID 11449512)

RadC family protein is a JAB or Mpr1p, Pad1p N-terminal (MPN) domain-containing protein that contains the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, which is involved in zinc ion coordination; a function as a nuclease has been suggested

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RadC COG2003
DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ...
 2-105 6.39e-44

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: 142.12  E-value: 6.39e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490725961   2 PNEAFLAIYLNTKNEVVDYETIHEGTLDRAIIYPRRVVEAALSRHAAALVLVHNHPSGHADPSTEDVEVTGAIARAAAAL 81
Cdd:COG2003   121 PREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLNAAAIILAHNHPSGDPEPSRADIELTRRLKEAGELL 200

                          90       100
                  ....*....|....*....|....
gi 1490725961  82 DIRVLDHLVVARDGYLSFMEKGLM 105
Cdd:COG2003   201 GIRLLDHIIIGDGGYVSFAEEGLL 224
 
Name Accession Description Interval E-value
RadC COG2003
DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ...
 2-105 6.39e-44

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: 142.12  E-value: 6.39e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490725961   2 PNEAFLAIYLNTKNEVVDYETIHEGTLDRAIIYPRRVVEAALSRHAAALVLVHNHPSGHADPSTEDVEVTGAIARAAAAL 81
Cdd:COG2003   121 PREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLNAAAIILAHNHPSGDPEPSRADIELTRRLKEAGELL 200

                          90       100
                  ....*....|....*....|....
gi 1490725961  82 DIRVLDHLVVARDGYLSFMEKGLM 105
Cdd:COG2003   201 GIRLLDHIIIGDGGYVSFAEEGLL 224
PRK00024 PRK00024
DNA repair protein RadC;
4-105 2.93e-41

DNA repair protein RadC;


Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 135.20  E-value: 2.93e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490725961   4 EAFLAIYLNTKNEVVDYETIHEGTLDRAIIYPRRVVEAALSRHAAALVLVHNHPSGHADPSTEDVEVTGAIARAAAALDI 83
Cdd:PRK00024  123 EHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRALKLNAAALILAHNHPSGDPEPSQADILITKRLKEAGELLGI 202

                          90       100
                  ....*....|....*....|..
gi 1490725961  84 RVLDHLVVARDGYLSFMEKGLM 105
Cdd:PRK00024  203 RLLDHIIIGDGEYVSFAERGLL 224
MPN_DUF2466 cd08071
Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of ...
 1-99 1.98e-38

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: 124.41  E-value: 1.98e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490725961   1 HPNEAFLAIYLNTKNEVVDYETIHEGTLDRAIIYPRRVVEAALSRHAAALVLVHNHPSGHADPSTEDVEVTGAIARAAAA 80
Cdd:cd08071    14 LDQEEFVVLLLDTKNRLIAVETISVGTLNSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSREDIELTKRLKEAGEL 93

                          90
                  ....*....|....*....
gi 1490725961  81 LDIRVLDHLVVARDGYLSF 99
Cdd:cd08071    94 LGIRLLDHIIVGDGGYFSF 112
RadC pfam04002
RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was ...
 2-96 1.40e-36

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: 119.82  E-value: 1.40e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490725961   2 PNEAFLAIYLNTKNEVVDYETIHEGTLDRAIIYPRRVVEAALSRHAAALVLVHNHPSGHADPSTEDVEVTGAIARAAAAL 81
Cdd:pfam04002  19 DQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDPEPSREDIELTRRLKEAGELL 98

                          90
                  ....*....|....*
gi 1490725961  82 DIRVLDHLVVARDGY 96
Cdd:pfam04002  99 GIRLLDHIIIGDGGY 113
radc TIGR00608
DNA repair protein radc; The genes in this family for which the functions are known have an as ...
 2-105 6.74e-32

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: 111.38  E-value: 6.74e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490725961   2 PNEAFLAIYLNTKNEVVDYETIHEGTLDRAIIYPRRVVEAALSRHAAALVLVHNHPSGHADPSTEDVEVTGAIARAAAAL 81
Cdd:TIGR00608 115 TREHFMVLFLDRKNRLIAKEVVFIGTVNHVPVHPREIFKEALKLSASALILAHNHPSGEPSPSQEDILITERLRKAAELL 194

                          90       100
                  ....*....|....*....|....
gi 1490725961  82 DIRVLDHLVVARDGYLSFMEKGLM 105
Cdd:TIGR00608 195 GIELLDHLIIGKGRYVSFREEGLL 218
 
Name Accession Description Interval E-value
RadC COG2003
DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ...
 2-105 6.39e-44

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: 142.12  E-value: 6.39e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490725961   2 PNEAFLAIYLNTKNEVVDYETIHEGTLDRAIIYPRRVVEAALSRHAAALVLVHNHPSGHADPSTEDVEVTGAIARAAAAL 81
Cdd:COG2003   121 PREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLNAAAIILAHNHPSGDPEPSRADIELTRRLKEAGELL 200

                          90       100
                  ....*....|....*....|....
gi 1490725961  82 DIRVLDHLVVARDGYLSFMEKGLM 105
Cdd:COG2003   201 GIRLLDHIIIGDGGYVSFAEEGLL 224
PRK00024 PRK00024
DNA repair protein RadC;
4-105 2.93e-41

DNA repair protein RadC;


Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 135.20  E-value: 2.93e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490725961   4 EAFLAIYLNTKNEVVDYETIHEGTLDRAIIYPRRVVEAALSRHAAALVLVHNHPSGHADPSTEDVEVTGAIARAAAALDI 83
Cdd:PRK00024  123 EHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRALKLNAAALILAHNHPSGDPEPSQADILITKRLKEAGELLGI 202

                          90       100
                  ....*....|....*....|..
gi 1490725961  84 RVLDHLVVARDGYLSFMEKGLM 105
Cdd:PRK00024  203 RLLDHIIIGDGEYVSFAERGLL 224
MPN_DUF2466 cd08071
Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of ...
 1-99 1.98e-38

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: 124.41  E-value: 1.98e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490725961   1 HPNEAFLAIYLNTKNEVVDYETIHEGTLDRAIIYPRRVVEAALSRHAAALVLVHNHPSGHADPSTEDVEVTGAIARAAAA 80
Cdd:cd08071    14 LDQEEFVVLLLDTKNRLIAVETISVGTLNSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSREDIELTKRLKEAGEL 93

                          90
                  ....*....|....*....
gi 1490725961  81 LDIRVLDHLVVARDGYLSF 99
Cdd:cd08071    94 LGIRLLDHIIVGDGGYFSF 112
RadC pfam04002
RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was ...
 2-96 1.40e-36

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: 119.82  E-value: 1.40e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490725961   2 PNEAFLAIYLNTKNEVVDYETIHEGTLDRAIIYPRRVVEAALSRHAAALVLVHNHPSGHADPSTEDVEVTGAIARAAAAL 81
Cdd:pfam04002  19 DQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDPEPSREDIELTRRLKEAGELL 98

                          90
                  ....*....|....*
gi 1490725961  82 DIRVLDHLVVARDGY 96
Cdd:pfam04002  99 GIRLLDHIIIGDGGY 113
radc TIGR00608
DNA repair protein radc; The genes in this family for which the functions are known have an as ...
 2-105 6.74e-32

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: 111.38  E-value: 6.74e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490725961   2 PNEAFLAIYLNTKNEVVDYETIHEGTLDRAIIYPRRVVEAALSRHAAALVLVHNHPSGHADPSTEDVEVTGAIARAAAAL 81
Cdd:TIGR00608 115 TREHFMVLFLDRKNRLIAKEVVFIGTVNHVPVHPREIFKEALKLSASALILAHNHPSGEPSPSQEDILITERLRKAAELL 194

                          90       100
                  ....*....|....*....|....
gi 1490725961  82 DIRVLDHLVVARDGYLSFMEKGLM 105
Cdd:TIGR00608 195 GIELLDHLIIGKGRYVSFREEGLL 218
MPN_prok_mb cd08059
Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); ...
 1-71 8.65e-06

Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); prokaryotic; This family contains bacterial and archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These catalytically active domains contain 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 for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.


Pssm-ID: 163690  Cd Length: 101  Bit Score: 41.01  E-value: 8.65e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1490725961   1 HPNEAFLAIYLNTKNEVVDYETIHEGTLDRAIIYPRrvveAALSRHAAALVLVHNHPSGHADPSTEDVEVT 71
Cdd:cd08059    14 HPDEFCGFLSGSKDNVMDELIFLPFVSGSVSAVIDL----AALEIGMKVVGLVHSHPSGSCRPSEADLSLF 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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