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Conserved domains on  [gi|1184711864|ref|WP_085270973|]
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transcriptional regulator NrdR [Mycobacterium parmense]

Protein Classification

transcriptional regulator NrdR( domain architecture ID 11442498)

transcriptional regulator NrdR represses transcription of the class Ib ribonucleotide reductase (RNR) genes nrdHIEF, but has a much smaller effect on the transcription of class Ia RNR genes nrdAB and class III RNR genes nrdDG

Gene Ontology:  GO:0140110|GO:0006355|GO:0003677|GO:0005524|GO:0008270
PubMed:  35577776|15949864

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NrdR COG1327
Transcriptional regulator NrdR, contains Zn-ribbon and ATP-cone domains [Transcription];
1-149 3.13e-69

Transcriptional regulator NrdR, contains Zn-ribbon and ATP-cone domains [Transcription];


:

Pssm-ID: 440938 [Multi-domain]  Cd Length: 153  Bit Score: 205.69  E-value: 3.13e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184711864   1 MHCPFCRHPDSRVIDSRETDEGQAIRRRRSCPECGRRFTT---VETAVLAVVKRSGVTEPFSREKVISGVRRACQGRQVD 77
Cdd:COG1327     1 MRCPFCGHEDTKVIDSRPSEDGTAIRRRRECLACGKRFTTyerVELVPLMVIKKDGRREPFDREKLLRGLLRACEKRPVS 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1184711864  78 DDALNLLAQQVEDTVRAAGSPEVPSHEVGLAILGPLRDLDEVAYLRFASVYRSFSSAEDFEREIQALRAHRE 149
Cdd:COG1327    81 AEQIEAAVDRIERELRASGEREVPSREIGELVMEELKKLDEVAYVRFASVYRSFKDVDDFREELEELLKEKE 152
 
Name Accession Description Interval E-value
NrdR COG1327
Transcriptional regulator NrdR, contains Zn-ribbon and ATP-cone domains [Transcription];
1-149 3.13e-69

Transcriptional regulator NrdR, contains Zn-ribbon and ATP-cone domains [Transcription];


Pssm-ID: 440938 [Multi-domain]  Cd Length: 153  Bit Score: 205.69  E-value: 3.13e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184711864   1 MHCPFCRHPDSRVIDSRETDEGQAIRRRRSCPECGRRFTT---VETAVLAVVKRSGVTEPFSREKVISGVRRACQGRQVD 77
Cdd:COG1327     1 MRCPFCGHEDTKVIDSRPSEDGTAIRRRRECLACGKRFTTyerVELVPLMVIKKDGRREPFDREKLLRGLLRACEKRPVS 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1184711864  78 DDALNLLAQQVEDTVRAAGSPEVPSHEVGLAILGPLRDLDEVAYLRFASVYRSFSSAEDFEREIQALRAHRE 149
Cdd:COG1327    81 AEQIEAAVDRIERELRASGEREVPSREIGELVMEELKKLDEVAYVRFASVYRSFKDVDDFREELEELLKEKE 152
TIGR00244 TIGR00244
transcriptional regulator NrdR; Members of this almost entirely bacterial family contain an ...
 1-144 2.82e-47

transcriptional regulator NrdR; Members of this almost entirely bacterial family contain an ATP cone domain (pfam03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes. [Regulatory functions, DNA interactions]


Pssm-ID: 129347 [Multi-domain]  Cd Length: 147  Bit Score: 149.97  E-value: 2.82e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184711864   1 MHCPFCRHPDSRVIDSRETDEGQAIRRRRSCPECGRRFTTVETA---VLAVVKRSGVTEPFSREKVISGVRRACQGRQVD 77
Cdd:TIGR00244   1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAellPPTVIKQDGVREPFNREKLLRGMVRACEKRPVS 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1184711864  78 DDALNLLAQQVEDTVRAAGSPEVPSHEVGLAILGPLRDLDEVAYLRFASVYRSFSSAEDFEREIQAL 144
Cdd:TIGR00244  81 FDDLEHAINHIEAQLRAQGEREVPSELIGQMVMQYLKKLDEVAYIRFASVYRSFQDIADFVDELEQL 147
ATP-cone pfam03477
ATP cone domain;
48-131 1.13e-16

ATP cone domain;


Pssm-ID: 397513 [Multi-domain]  Cd Length: 86  Bit Score: 69.99  E-value: 1.13e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184711864  48 VVKRSGVTEPFSREKVISGVRRACQGrqvDDDALNLLAQQVEDTVRAAGSPEVPSHEVGLAILGPLRDLDEVAYLRFASV 127
Cdd:pfam03477   3 VIKRDGRREPFDKEKIRRAIEKACEK---SPDQADELASEVEEELEKSLEDGISTEEIQDLVEKTLAEHPDYAVARAYIL 79


                  ....
gi 1184711864 128 YRSF 131
Cdd:pfam03477  80 YRNL 83
nrdA PHA02572
ribonucleoside-diphosphate reductase subunit alpha; Provisional
 48-77 1.21e-05

ribonucleoside-diphosphate reductase subunit alpha; Provisional


Pssm-ID: 222883 [Multi-domain]  Cd Length: 753  Bit Score: 43.94  E-value: 1.21e-05
                          10        20        30
                  ....*....|....*....|....*....|
gi 1184711864  48 VVKRSGVTEPFSREKVISGVRRACQGRQVD 77
Cdd:PHA02572    6 VIKSSGVSQPFDLEKIHKVLEWACEGTGVD 35
 
Name Accession Description Interval E-value
NrdR COG1327
Transcriptional regulator NrdR, contains Zn-ribbon and ATP-cone domains [Transcription];
1-149 3.13e-69

Transcriptional regulator NrdR, contains Zn-ribbon and ATP-cone domains [Transcription];


Pssm-ID: 440938 [Multi-domain]  Cd Length: 153  Bit Score: 205.69  E-value: 3.13e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184711864   1 MHCPFCRHPDSRVIDSRETDEGQAIRRRRSCPECGRRFTT---VETAVLAVVKRSGVTEPFSREKVISGVRRACQGRQVD 77
Cdd:COG1327     1 MRCPFCGHEDTKVIDSRPSEDGTAIRRRRECLACGKRFTTyerVELVPLMVIKKDGRREPFDREKLLRGLLRACEKRPVS 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1184711864  78 DDALNLLAQQVEDTVRAAGSPEVPSHEVGLAILGPLRDLDEVAYLRFASVYRSFSSAEDFEREIQALRAHRE 149
Cdd:COG1327    81 AEQIEAAVDRIERELRASGEREVPSREIGELVMEELKKLDEVAYVRFASVYRSFKDVDDFREELEELLKEKE 152
TIGR00244 TIGR00244
transcriptional regulator NrdR; Members of this almost entirely bacterial family contain an ...
 1-144 2.82e-47

transcriptional regulator NrdR; Members of this almost entirely bacterial family contain an ATP cone domain (pfam03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes. [Regulatory functions, DNA interactions]


Pssm-ID: 129347 [Multi-domain]  Cd Length: 147  Bit Score: 149.97  E-value: 2.82e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184711864   1 MHCPFCRHPDSRVIDSRETDEGQAIRRRRSCPECGRRFTTVETA---VLAVVKRSGVTEPFSREKVISGVRRACQGRQVD 77
Cdd:TIGR00244   1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAellPPTVIKQDGVREPFNREKLLRGMVRACEKRPVS 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1184711864  78 DDALNLLAQQVEDTVRAAGSPEVPSHEVGLAILGPLRDLDEVAYLRFASVYRSFSSAEDFEREIQAL 144
Cdd:TIGR00244  81 FDDLEHAINHIEAQLRAQGEREVPSELIGQMVMQYLKKLDEVAYIRFASVYRSFQDIADFVDELEQL 147
ATP-cone pfam03477
ATP cone domain;
48-131 1.13e-16

ATP cone domain;


Pssm-ID: 397513 [Multi-domain]  Cd Length: 86  Bit Score: 69.99  E-value: 1.13e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184711864  48 VVKRSGVTEPFSREKVISGVRRACQGrqvDDDALNLLAQQVEDTVRAAGSPEVPSHEVGLAILGPLRDLDEVAYLRFASV 127
Cdd:pfam03477   3 VIKRDGRREPFDKEKIRRAIEKACEK---SPDQADELASEVEEELEKSLEDGISTEEIQDLVEKTLAEHPDYAVARAYIL 79


                  ....
gi 1184711864 128 YRSF 131
Cdd:pfam03477  80 YRNL 83
nrdA PHA02572
ribonucleoside-diphosphate reductase subunit alpha; Provisional
 48-77 1.21e-05

ribonucleoside-diphosphate reductase subunit alpha; Provisional


Pssm-ID: 222883 [Multi-domain]  Cd Length: 753  Bit Score: 43.94  E-value: 1.21e-05
                          10        20        30
                  ....*....|....*....|....*....|
gi 1184711864  48 VVKRSGVTEPFSREKVISGVRRACQGRQVD 77
Cdd:PHA02572    6 VIKSSGVSQPFDLEKIHKVLEWACEGTGVD 35
NrdD COG1328
Anaerobic ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]; ...
 48-102 9.33e-05

Anaerobic ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]; Anaerobic ribonucleoside-triphosphate reductase is part of the Pathway/BioSystem: Thymidylate biosynthesis


Pssm-ID: 440939 [Multi-domain]  Cd Length: 671  Bit Score: 41.44  E-value: 9.33e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1184711864  48 VVKRSGVTEPFSREKVISGVRRA---CQGRQVDDDALNLLAQQVEDTVRAAGSPEVPS 102
Cdd:COG1328     5 VIKRDGRVVPFDPEKIANAIKKAakaVGGEDRDEELAEEIADEVEKELERLGGGGTIT 62
PRK08270 PRK08270
ribonucleoside triphosphate reductase;
48-100 9.04e-04

ribonucleoside triphosphate reductase;


Pssm-ID: 236212 [Multi-domain]  Cd Length: 656  Bit Score: 38.29  E-value: 9.04e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1184711864  48 VVKRSGVTEPFSREKVISGVRRACQGRQVDDDAL-NLLAQQVEDTVRAAGSPEV 100
Cdd:PRK08270    5 IIKRDGRIVPFDAEKITEAIAKAFKATGEFDPSEaERLALRVIEKLEDEDIPSV 58
PRK12364 PRK12364
ribonucleoside-diphosphate reductase subunit alpha;
48-92 1.64e-03

ribonucleoside-diphosphate reductase subunit alpha;


Pssm-ID: 237077 [Multi-domain]  Cd Length: 842  Bit Score: 37.81  E-value: 1.64e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1184711864  48 VVKRSGVTEPFSREKVISGVRRA--CQGRQVDDDALNLLAQQVEDTV 92
Cdd:PRK12364    3 IIKRNGTTEPYDREKIEVAIRKAfaSVGKPISDEIIYSLVAEVERFI 49
 
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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