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Conserved domains on  [gi|2059228583|ref|WP_217025918|]
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DNA repair protein RadC [Cytobacillus oceanisediminis]

Protein Classification

JAB domain-containing protein( domain architecture ID 11477685)

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK00024 PRK00024
DNA repair protein RadC;
8-229 2.55e-131

DNA repair protein RadC;


:

Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 369.02  E-value: 2.55e-131
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059228583   8 IKDFPQDERPGERFVLNGPQSLSNHELIAILLRTGTKDESVLQLANRLITHFEGLRLLKDASLDEITAIKGIGSAKAIQL 87
Cdd:PRK00024    3 IKDWPEEERPRERLLKYGAAALSDAELLAILLRTGTKGKSVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059228583  88 LAAVEIGRRISTLTYDDRYTIRSPEDGANYVMHDMRFLSQEHFVCLYLNTKNQVLHKKTIFIGSLNASIVHPREVFKEAF 167
Cdd:PRK00024   83 KAALELARRILAERLREREVLLSPEDVADYLMAELRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRAL 162

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2059228583 168 RRSAASIICIHNHPSGDPTPSREDIEVTKRLAESGKIIGIEVLDHLIIGENKFVSLKEKGYL 229
Cdd:PRK00024  163 KLNAAALILAHNHPSGDPEPSQADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGLL 224
 
Name Accession Description Interval E-value
PRK00024 PRK00024
DNA repair protein RadC;
8-229 2.55e-131

DNA repair protein RadC;


Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 369.02  E-value: 2.55e-131
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059228583   8 IKDFPQDERPGERFVLNGPQSLSNHELIAILLRTGTKDESVLQLANRLITHFEGLRLLKDASLDEITAIKGIGSAKAIQL 87
Cdd:PRK00024    3 IKDWPEEERPRERLLKYGAAALSDAELLAILLRTGTKGKSVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059228583  88 LAAVEIGRRISTLTYDDRYTIRSPEDGANYVMHDMRFLSQEHFVCLYLNTKNQVLHKKTIFIGSLNASIVHPREVFKEAF 167
Cdd:PRK00024   83 KAALELARRILAERLREREVLLSPEDVADYLMAELRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRAL 162

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2059228583 168 RRSAASIICIHNHPSGDPTPSREDIEVTKRLAESGKIIGIEVLDHLIIGENKFVSLKEKGYL 229
Cdd:PRK00024  163 KLNAAALILAHNHPSGDPEPSQADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGLL 224
RadC COG2003
DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ...
 8-229 9.96e-124

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: 349.74  E-value: 9.96e-124
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059228583   8 IKDFPQDERPGERFVLNGPQSLSNHELIAILLRTGTKDESVLQLANRLITHFEGLRLLKDASLDEITAIKGIGSAKAIQL 87
Cdd:COG2003     3 IKDLPHRERPRERLLAKGAAALSDAELLAILLRTGTPGKDAVELAKELLARFGSLRGLLRASVEELRKIKGIGEAKAAQL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059228583  88 LAAVEIGRRISTLTYDDRYTIRSPEDGANYVMHDMRFLSQEHFVCLYLNTKNQVLHKKTIFIGSLNASIVHPREVFKEAF 167
Cdd:COG2003    83 KAALELGRRLLREELEERPVISSPEDVADYLRARLAHLPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRAL 162

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2059228583 168 RRSAASIICIHNHPSGDPTPSREDIEVTKRLAESGKIIGIEVLDHLIIGENKFVSLKEKGYL 229
Cdd:COG2003   163 RLNAAAIILAHNHPSGDPEPSRADIELTRRLKEAGELLGIRLLDHIIIGDGGYVSFAEEGLL 224
radc TIGR00608
DNA repair protein radc; The genes in this family for which the functions are known have an as ...
 16-229 3.51e-97

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: 282.41  E-value: 3.51e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059228583  16 RPGERFVLNGPQSLSNHELIAILLRTGT-KDESVLQLANRLITHF---EGLRLLKDASLDEITAIKGIGSAKAIQLLAAV 91
Cdd:TIGR00608   1 MPREKLLKFGAEALSDYELLAIILRTGTpKGLDVLSLSKRLLDVFgrqDSLGHLLSAPPEELSSVPGIGEAKAIQLKAAV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059228583  92 EIGRRISTLTYDDRYTIRSPEDGANYVMHDMRFLSQEHFVCLYLNTKNQVLHKKTIFIGSLNASIVHPREVFKEAFRRSA 171
Cdd:TIGR00608  81 ELAKRYAKSRMLERPVIRSPEAAAEFLHTDLAHETREHFMVLFLDRKNRLIAKEVVFIGTVNHVPVHPREIFKEALKLSA 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2059228583 172 ASIICIHNHPSGDPTPSREDIEVTKRLAESGKIIGIEVLDHLIIGENKFVSLKEKGYL 229
Cdd:TIGR00608 161 SALILAHNHPSGEPSPSQEDILITERLRKAAELLGIELLDHLIIGKGRYVSFREEGLL 218
RadC pfam04002
RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was ...
 108-220 5.99e-64

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: 194.16  E-value: 5.99e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059228583 108 IRSPEDGANYVMHDMRFLSQEHFVCLYLNTKNQVLHKKTIFIGSLNASIVHPREVFKEAFRRSAASIICIHNHPSGDPTP 187
Cdd:pfam04002   1 ITSPEDVAEYLMEELRDLDQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDPEP 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 2059228583 188 SREDIEVTKRLAESGKIIGIEVLDHLIIGENKF 220
Cdd:pfam04002  81 SREDIELTRRLKEAGELLGIRLLDHIIIGDGGY 113
MPN_DUF2466 cd08071
Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of ...
 112-224 2.03e-63

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: 192.98  E-value: 2.03e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059228583 112 EDGANYVMHDMRFLSQEHFVCLYLNTKNQVLHKKTIFIGSLNASIVHPREVFKEAFRRSAASIICIHNHPSGDPTPSRED 191
Cdd:cd08071     1 EDVAEYLREELGDLDQEEFVVLLLDTKNRLIAVETISVGTLNSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSRED 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 2059228583 192 IEVTKRLAESGKIIGIEVLDHLIIGENKFVSLK 224
Cdd:cd08071    81 IELTKRLKEAGELLGIRLLDHIIVGDGGYFSFR 113
 
Name Accession Description Interval E-value
PRK00024 PRK00024
DNA repair protein RadC;
8-229 2.55e-131

DNA repair protein RadC;


Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 369.02  E-value: 2.55e-131
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059228583   8 IKDFPQDERPGERFVLNGPQSLSNHELIAILLRTGTKDESVLQLANRLITHFEGLRLLKDASLDEITAIKGIGSAKAIQL 87
Cdd:PRK00024    3 IKDWPEEERPRERLLKYGAAALSDAELLAILLRTGTKGKSVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059228583  88 LAAVEIGRRISTLTYDDRYTIRSPEDGANYVMHDMRFLSQEHFVCLYLNTKNQVLHKKTIFIGSLNASIVHPREVFKEAF 167
Cdd:PRK00024   83 KAALELARRILAERLREREVLLSPEDVADYLMAELRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRAL 162

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2059228583 168 RRSAASIICIHNHPSGDPTPSREDIEVTKRLAESGKIIGIEVLDHLIIGENKFVSLKEKGYL 229
Cdd:PRK00024  163 KLNAAALILAHNHPSGDPEPSQADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGLL 224
RadC COG2003
DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ...
 8-229 9.96e-124

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: 349.74  E-value: 9.96e-124
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059228583   8 IKDFPQDERPGERFVLNGPQSLSNHELIAILLRTGTKDESVLQLANRLITHFEGLRLLKDASLDEITAIKGIGSAKAIQL 87
Cdd:COG2003     3 IKDLPHRERPRERLLAKGAAALSDAELLAILLRTGTPGKDAVELAKELLARFGSLRGLLRASVEELRKIKGIGEAKAAQL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059228583  88 LAAVEIGRRISTLTYDDRYTIRSPEDGANYVMHDMRFLSQEHFVCLYLNTKNQVLHKKTIFIGSLNASIVHPREVFKEAF 167
Cdd:COG2003    83 KAALELGRRLLREELEERPVISSPEDVADYLRARLAHLPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRAL 162

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2059228583 168 RRSAASIICIHNHPSGDPTPSREDIEVTKRLAESGKIIGIEVLDHLIIGENKFVSLKEKGYL 229
Cdd:COG2003   163 RLNAAAIILAHNHPSGDPEPSRADIELTRRLKEAGELLGIRLLDHIIIGDGGYVSFAEEGLL 224
radc TIGR00608
DNA repair protein radc; The genes in this family for which the functions are known have an as ...
 16-229 3.51e-97

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: 282.41  E-value: 3.51e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059228583  16 RPGERFVLNGPQSLSNHELIAILLRTGT-KDESVLQLANRLITHF---EGLRLLKDASLDEITAIKGIGSAKAIQLLAAV 91
Cdd:TIGR00608   1 MPREKLLKFGAEALSDYELLAIILRTGTpKGLDVLSLSKRLLDVFgrqDSLGHLLSAPPEELSSVPGIGEAKAIQLKAAV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059228583  92 EIGRRISTLTYDDRYTIRSPEDGANYVMHDMRFLSQEHFVCLYLNTKNQVLHKKTIFIGSLNASIVHPREVFKEAFRRSA 171
Cdd:TIGR00608  81 ELAKRYAKSRMLERPVIRSPEAAAEFLHTDLAHETREHFMVLFLDRKNRLIAKEVVFIGTVNHVPVHPREIFKEALKLSA 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2059228583 172 ASIICIHNHPSGDPTPSREDIEVTKRLAESGKIIGIEVLDHLIIGENKFVSLKEKGYL 229
Cdd:TIGR00608 161 SALILAHNHPSGEPSPSQEDILITERLRKAAELLGIELLDHLIIGKGRYVSFREEGLL 218
RadC pfam04002
RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was ...
 108-220 5.99e-64

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: 194.16  E-value: 5.99e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059228583 108 IRSPEDGANYVMHDMRFLSQEHFVCLYLNTKNQVLHKKTIFIGSLNASIVHPREVFKEAFRRSAASIICIHNHPSGDPTP 187
Cdd:pfam04002   1 ITSPEDVAEYLMEELRDLDQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDPEP 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 2059228583 188 SREDIEVTKRLAESGKIIGIEVLDHLIIGENKF 220
Cdd:pfam04002  81 SREDIELTRRLKEAGELLGIRLLDHIIIGDGGY 113
MPN_DUF2466 cd08071
Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of ...
 112-224 2.03e-63

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: 192.98  E-value: 2.03e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059228583 112 EDGANYVMHDMRFLSQEHFVCLYLNTKNQVLHKKTIFIGSLNASIVHPREVFKEAFRRSAASIICIHNHPSGDPTPSRED 191
Cdd:cd08071     1 EDVAEYLREELGDLDQEEFVVLLLDTKNRLIAVETISVGTLNSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSRED 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 2059228583 192 IEVTKRLAESGKIIGIEVLDHLIIGENKFVSLK 224
Cdd:cd08071    81 IELTKRLKEAGELLGIRLLDHIIVGDGGYFSFR 113
UPF0758_N pfam20582
UPF0758 N-terminal; This domain is functionally uncharacterized, found at the N-terminal of ...
 8-79 7.74e-31

UPF0758 N-terminal; This domain is functionally uncharacterized, found at the N-terminal of the uncharacterized UPF0758 proteins from bacteria and archaea, and is approximately 90 amino acids in length. UPF0758 was previously known as the radC family, a name that was assigned according to the radC102 mutant of E. coli which was later demonstrated to be an allele of the transcription-repair-coupling factor recG. UPF0758 has been described as a putative JAMM-family deubiquitinating enzyme, but its function remains to be determined. Structure prediction using Colab notebook from AlphaFold DB suggests that it has an alpha bundle fold. It may contain two helix-hairpin-helix (HhH) motifs. This domain is found in association with pfam04002.


Pssm-ID: 466731 [Multi-domain]  Cd Length: 71  Bit Score: 108.52  E-value: 7.74e-31
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2059228583   8 IKDFPQDERPGERFVLNGPQSLSNHELIAILLRTGTKDESVLQLANRLItHFEGLRLLKDASLDEITAIKGI 79
Cdd:pfam20582   1 IKDWPEDERPREKLLRYGAEALSDAELLAILLGSGTKGESAVDLARRLL-HFGGLRGLLKASVEELMKIKGI 71
MPN_prok_mb cd08059
Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); ...
 128-224 1.62e-11

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: 59.11  E-value: 1.62e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059228583 128 EHFVCLYLNTKNQVLHKKTIFIGSLNASIVHprevFKEAFRRSAASIICIHNHPSGDPTPSREDIEVTKRLAesgkiigi 207
Cdd:cd08059    17 EFCGFLSGSKDNVMDELIFLPFVSGSVSAVI----DLAALEIGMKVVGLVHSHPSGSCRPSEADLSLFTRFG-------- 84

                          90
                  ....*....|....*..
gi 2059228583 208 evLDHLIIGENKFVSLK 224
Cdd:cd08059    85 --LYHVIVCYPYENSWK 99
uvrC PRK00558
excinuclease ABC subunit UvrC;
54-90 3.42e-04

excinuclease ABC subunit UvrC;


Pssm-ID: 234792 [Multi-domain]  Cd Length: 598  Bit Score: 41.26  E-value: 3.42e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 2059228583  54 RLITHFEGLRLLKDASLDEITAIKGIGSAKAIQLLAA 90
Cdd:PRK00558  558 ALLKHFGSLKAIKEASVEELAKVPGISKKLAEAIYEA 594
UvrC COG0322
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];
54-90 7.12e-04

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


Pssm-ID: 440091 [Multi-domain]  Cd Length: 603  Bit Score: 40.11  E-value: 7.12e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 2059228583  54 RLITHFEGLRLLKDASLDEITAIKGIGSAKAIQLLAA 90
Cdd:COG0322   563 ALLKHFGSLKAIKEASVEELAAVPGISKKLAEAIYEY 599
PRK13482 PRK13482
DNA integrity scanning protein DisA; Provisional
 5-84 2.66e-03

DNA integrity scanning protein DisA; Provisional


Pssm-ID: 237395 [Multi-domain]  Cd Length: 352  Bit Score: 38.22  E-value: 2.66e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2059228583   5 TLLIKDFPQDERPGERFVLNGPQSLSNHEL-----IAILLRTGTK----DESV---------------LQLANRLITHFE 60
Cdd:PRK13482  229 ELLIRDYSQEKDEDPEEILEELQELSSEELldlsaIARLLGYPGGsealDTPVsprgyrllskiprlpSAVIENLVEHFG 308

                          90       100
                  ....*....|....*....|....
gi 2059228583  61 GLRLLKDASLDEITAIKGIGSAKA 84
Cdd:PRK13482  309 SLQGLLAASIEDLDEVEGIGEVRA 332
MPN_like cd08070
Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); ...
 159-193 5.23e-03

Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); This family contains archaeal and bacterial 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: 163701  Cd Length: 128  Bit Score: 36.08  E-value: 5.23e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 2059228583 159 PREVFKeAFRRSAA---SIICI-HNHPSGDPTPSREDIE 193
Cdd:cd08070    55 PAEQLA-AQREARErglEVVGIyHSHPDGPARPSETDLR 92
 
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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