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Conserved domains on  [gi|1011019383|ref|WP_061975957|]
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DNA repair protein RadC [Aureimonas sp. AU20]

Protein Classification

JAB domain-containing protein( domain architecture ID 11449512)

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

Gene Ontology:  GO:0046872|GO:0008237|GO:0006508
PubMed:  18556794|14737182

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, ...
 45-261 2.32e-110

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: 317.00  E-value: 2.32e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011019383  45 HRDRLRDRFAEAGAVALADYELLELVLFRSIPRRDVKPIAKALLQRFGSLEDVLNAPTHLLQEVDGMGRSSALDLRIVAA 124
Cdd:COG2003     8 HRERPRERLLAKGAAALSDAELLAILLRTGTPGKDAVELAKELLARFGSLRGLLRASVEELRKIKGIGEAKAAQLKAALE 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011019383 125 LLQRAMRSGIRSREVLSSWSAVIDYCHAAMAHETREQFRVLFLDKKNTLIADEVQQTGTVDHTPVYPREVIRRALELSAS 204
Cdd:COG2003    88 LGRRLLREELEERPVISSPEDVADYLRARLAHLPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLNAA 167

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1011019383 205 ALVLVHNHPSGDPAPSNADIEMTKIIVDTCRPLGIVVHDHLIIGRNGHTSFKSLRLM 261
Cdd:COG2003   168 AIILAHNHPSGDPEPSRADIELTRRLKEAGELLGIRLLDHIIIGDGGYVSFAEEGLL 224
 
Name Accession Description Interval E-value
RadC COG2003
DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ...
 45-261 2.32e-110

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: 317.00  E-value: 2.32e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011019383  45 HRDRLRDRFAEAGAVALADYELLELVLFRSIPRRDVKPIAKALLQRFGSLEDVLNAPTHLLQEVDGMGRSSALDLRIVAA 124
Cdd:COG2003     8 HRERPRERLLAKGAAALSDAELLAILLRTGTPGKDAVELAKELLARFGSLRGLLRASVEELRKIKGIGEAKAAQLKAALE 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011019383 125 LLQRAMRSGIRSREVLSSWSAVIDYCHAAMAHETREQFRVLFLDKKNTLIADEVQQTGTVDHTPVYPREVIRRALELSAS 204
Cdd:COG2003    88 LGRRLLREELEERPVISSPEDVADYLRARLAHLPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLNAA 167

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1011019383 205 ALVLVHNHPSGDPAPSNADIEMTKIIVDTCRPLGIVVHDHLIIGRNGHTSFKSLRLM 261
Cdd:COG2003   168 AIILAHNHPSGDPEPSRADIELTRRLKEAGELLGIRLLDHIIIGDGGYVSFAEEGLL 224
PRK00024 PRK00024
DNA repair protein RadC;
41-261 6.53e-105

DNA repair protein RadC;


Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 303.53  E-value: 6.53e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011019383  41 HHDGHRDRLRDRFAEAGAVALADYELLELVLFRSIPRRDVKPIAKALLQRFGSLEDVLNAPTHLLQEVDGMGRSSALDLR 120
Cdd:PRK00024    4 KDWPEEERPRERLLKYGAAALSDAELLAILLRTGTKGKSVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLK 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011019383 121 IVAALLQRAMRSGIRSREVLSSWSAVIDYCHAAMAHETREQFRVLFLDKKNTLIADEVQQTGTVDHTPVYPREVIRRALE 200
Cdd:PRK00024   84 AALELARRILAERLREREVLLSPEDVADYLMAELRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRALK 163

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1011019383 201 LSASALVLVHNHPSGDPAPSNADIEMTKIIVDTCRPLGIVVHDHLIIGRNGHTSFKSLRLM 261
Cdd:PRK00024  164 LNAAALILAHNHPSGDPEPSQADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGLL 224
radc TIGR00608
DNA repair protein radc; The genes in this family for which the functions are known have an as ...
 48-256 6.27e-79

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: 237.34  E-value: 6.27e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011019383  48 RLRDRFAEAGAVALADYELLELVLFRSIPR-RDVKPIAKALLQRFGSLED---VLNAPTHLLQEVDGMGRSSALDLRIVA 123
Cdd:TIGR00608   1 MPREKLLKFGAEALSDYELLAIILRTGTPKgLDVLSLSKRLLDVFGRQDSlghLLSAPPEELSSVPGIGEAKAIQLKAAV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011019383 124 ALLQRAMRSGIRSREVLSSWSAVIDYCHAAMAHETREQFRVLFLDKKNTLIADEVQQTGTVDHTPVYPREVIRRALELSA 203
Cdd:TIGR00608  81 ELAKRYAKSRMLERPVIRSPEAAAEFLHTDLAHETREHFMVLFLDRKNRLIAKEVVFIGTVNHVPVHPREIFKEALKLSA 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1011019383 204 SALVLVHNHPSGDPAPSNADIEMTKIIVDTCRPLGIVVHDHLIIGRNGHTSFK 256
Cdd:TIGR00608 161 SALILAHNHPSGEPSPSQEDILITERLRKAAELLGIELLDHLIIGKGRYVSFR 213
RadC pfam04002
RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was ...
 140-252 2.24e-56

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: 176.06  E-value: 2.24e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011019383 140 LSSWSAVIDYCHAAMAHETREQFRVLFLDKKNTLIADEVQQTGTVDHTPVYPREVIRRALELSASALVLVHNHPSGDPAP 219
Cdd:pfam04002   1 ITSPEDVAEYLMEELRDLDQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDPEP 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1011019383 220 SNADIEMTKIIVDTCRPLGIVVHDHLIIGRNGH 252
Cdd:pfam04002  81 SREDIELTRRLKEAGELLGIRLLDHIIIGDGGY 113
MPN_DUF2466 cd08071
Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of ...
 144-256 1.42e-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: 171.41  E-value: 1.42e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011019383 144 SAVIDYCHAAMAHETREQFRVLFLDKKNTLIADEVQQTGTVDHTPVYPREVIRRALELSASALVLVHNHPSGDPAPSNAD 223
Cdd:cd08071     1 EDVAEYLREELGDLDQEEFVVLLLDTKNRLIAVETISVGTLNSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSRED 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1011019383 224 IEMTKIIVDTCRPLGIVVHDHLIIGRNGHTSFK 256
Cdd:cd08071    81 IELTKRLKEAGELLGIRLLDHIIVGDGGYFSFR 113
 
Name Accession Description Interval E-value
RadC COG2003
DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ...
 45-261 2.32e-110

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: 317.00  E-value: 2.32e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011019383  45 HRDRLRDRFAEAGAVALADYELLELVLFRSIPRRDVKPIAKALLQRFGSLEDVLNAPTHLLQEVDGMGRSSALDLRIVAA 124
Cdd:COG2003     8 HRERPRERLLAKGAAALSDAELLAILLRTGTPGKDAVELAKELLARFGSLRGLLRASVEELRKIKGIGEAKAAQLKAALE 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011019383 125 LLQRAMRSGIRSREVLSSWSAVIDYCHAAMAHETREQFRVLFLDKKNTLIADEVQQTGTVDHTPVYPREVIRRALELSAS 204
Cdd:COG2003    88 LGRRLLREELEERPVISSPEDVADYLRARLAHLPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLNAA 167

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1011019383 205 ALVLVHNHPSGDPAPSNADIEMTKIIVDTCRPLGIVVHDHLIIGRNGHTSFKSLRLM 261
Cdd:COG2003   168 AIILAHNHPSGDPEPSRADIELTRRLKEAGELLGIRLLDHIIIGDGGYVSFAEEGLL 224
PRK00024 PRK00024
DNA repair protein RadC;
41-261 6.53e-105

DNA repair protein RadC;


Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 303.53  E-value: 6.53e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011019383  41 HHDGHRDRLRDRFAEAGAVALADYELLELVLFRSIPRRDVKPIAKALLQRFGSLEDVLNAPTHLLQEVDGMGRSSALDLR 120
Cdd:PRK00024    4 KDWPEEERPRERLLKYGAAALSDAELLAILLRTGTKGKSVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLK 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011019383 121 IVAALLQRAMRSGIRSREVLSSWSAVIDYCHAAMAHETREQFRVLFLDKKNTLIADEVQQTGTVDHTPVYPREVIRRALE 200
Cdd:PRK00024   84 AALELARRILAERLREREVLLSPEDVADYLMAELRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRALK 163

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1011019383 201 LSASALVLVHNHPSGDPAPSNADIEMTKIIVDTCRPLGIVVHDHLIIGRNGHTSFKSLRLM 261
Cdd:PRK00024  164 LNAAALILAHNHPSGDPEPSQADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGLL 224
radc TIGR00608
DNA repair protein radc; The genes in this family for which the functions are known have an as ...
 48-256 6.27e-79

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: 237.34  E-value: 6.27e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011019383  48 RLRDRFAEAGAVALADYELLELVLFRSIPR-RDVKPIAKALLQRFGSLED---VLNAPTHLLQEVDGMGRSSALDLRIVA 123
Cdd:TIGR00608   1 MPREKLLKFGAEALSDYELLAIILRTGTPKgLDVLSLSKRLLDVFGRQDSlghLLSAPPEELSSVPGIGEAKAIQLKAAV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011019383 124 ALLQRAMRSGIRSREVLSSWSAVIDYCHAAMAHETREQFRVLFLDKKNTLIADEVQQTGTVDHTPVYPREVIRRALELSA 203
Cdd:TIGR00608  81 ELAKRYAKSRMLERPVIRSPEAAAEFLHTDLAHETREHFMVLFLDRKNRLIAKEVVFIGTVNHVPVHPREIFKEALKLSA 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1011019383 204 SALVLVHNHPSGDPAPSNADIEMTKIIVDTCRPLGIVVHDHLIIGRNGHTSFK 256
Cdd:TIGR00608 161 SALILAHNHPSGEPSPSQEDILITERLRKAAELLGIELLDHLIIGKGRYVSFR 213
RadC pfam04002
RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was ...
 140-252 2.24e-56

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: 176.06  E-value: 2.24e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011019383 140 LSSWSAVIDYCHAAMAHETREQFRVLFLDKKNTLIADEVQQTGTVDHTPVYPREVIRRALELSASALVLVHNHPSGDPAP 219
Cdd:pfam04002   1 ITSPEDVAEYLMEELRDLDQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDPEP 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1011019383 220 SNADIEMTKIIVDTCRPLGIVVHDHLIIGRNGH 252
Cdd:pfam04002  81 SREDIELTRRLKEAGELLGIRLLDHIIIGDGGY 113
MPN_DUF2466 cd08071
Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of ...
 144-256 1.42e-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: 171.41  E-value: 1.42e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011019383 144 SAVIDYCHAAMAHETREQFRVLFLDKKNTLIADEVQQTGTVDHTPVYPREVIRRALELSASALVLVHNHPSGDPAPSNAD 223
Cdd:cd08071     1 EDVAEYLREELGDLDQEEFVVLLLDTKNRLIAVETISVGTLNSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSRED 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1011019383 224 IEMTKIIVDTCRPLGIVVHDHLIIGRNGHTSFK 256
Cdd:cd08071    81 IELTKRLKEAGELLGIRLLDHIIVGDGGYFSFR 113
MPN_prok_mb cd08059
Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); ...
 151-257 1.28e-07

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: 48.71  E-value: 1.28e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011019383 151 HAAMAHeTREQFRVLFLDKKNTLIADEVQQTGTVDHTPVYPREvirrALELSASALVLVHNHPSGDPAPSNADIEMTKIi 230
Cdd:cd08059     9 HAKDAH-PDEFCGFLSGSKDNVMDELIFLPFVSGSVSAVIDLA----ALEIGMKVVGLVHSHPSGSCRPSEADLSLFTR- 82

                          90       100
                  ....*....|....*....|....*..
gi 1011019383 231 vdtcrpLGIvvhDHLIIGRNGHTSFKS 257
Cdd:cd08059    83 ------FGL---YHVIVCYPYENSWKC 100
MUS81 COG1948
ERCC4-type crossover junction endonuclease [Replication, recombination and repair];
74-120 4.66e-06

ERCC4-type crossover junction endonuclease [Replication, recombination and repair];


Pssm-ID: 441551 [Multi-domain]  Cd Length: 214  Bit Score: 46.32  E-value: 4.66e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1011019383  74 SIPrrDVKP-IAKALLQRFGSLEDVLNAPTHLLQEVDGMGRSSALDLR 120
Cdd:COG1948   159 SLP--GIGPkLARRLLEHFGSVEAVFNASEEELMKVEGIGEKTAERIR 204
PRK13766 PRK13766
Hef nuclease; Provisional
 74-116 2.45e-04

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 42.17  E-value: 2.45e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1011019383  74 SIPrrDVKP-IAKALLQRFGSLEDVLNAPTHLLQEVDGMGRSSA 116
Cdd:PRK13766  719 SLP--DVGPvLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTA 760
UvrC COG0322
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];
48-125 2.31e-03

Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];


Pssm-ID: 440091 [Multi-domain]  Cd Length: 603  Bit Score: 38.95  E-value: 2.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011019383  48 RLRD---RFAEAGAVALADYELLELVLFrSIP-----RRdvkpiaKALLQRFGSLEDVLNAPTHLLQEVDGMGRSSAldL 119
Cdd:COG0322   524 RIRDeahRFAITFHRKLRSKARLKSVLD-EIPgigpkRR------KALLKHFGSLKAIKEASVEELAAVPGISKKLA--E 594


                  ....*.
gi 1011019383 120 RIVAAL 125
Cdd:COG0322   595 AIYEYL 600
uvrC PRK00558
excinuclease ABC subunit UvrC;
85-125 7.26e-03

excinuclease ABC subunit UvrC;


Pssm-ID: 234792 [Multi-domain]  Cd Length: 598  Bit Score: 37.40  E-value: 7.26e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1011019383  85 KALLQRFGSLEDVLNAPTHLLQEVDGMGRSSAldLRIVAAL 125
Cdd:PRK00558  557 KALLKHFGSLKAIKEASVEELAKVPGISKKLA--EAIYEAL 595
MPN_archaeal cd08072
Mov34/MPN/PAD-1 family: archaeal JAB1/MPN/Mov34 metalloenzyme; This family contains only ...
 209-236 7.46e-03

Mov34/MPN/PAD-1 family: archaeal JAB1/MPN/Mov34 metalloenzyme; This family contains only archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These 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: 163703  Cd Length: 117  Bit Score: 35.31  E-value: 7.46e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1011019383 209 VHNHPSGDPAPSNADIEMTK------IIVdtCRP 236
Cdd:cd08072    65 VHSHPSGSPRPSDADLSFFSktglvhIIV--GYP 96
 
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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