NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|496507747|ref|WP_009216030|]
View 

transcriptional regulator NrdR [Oribacterium sp. oral taxon 078]

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

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
NrdR COG1327
Transcriptional regulator NrdR, contains Zn-ribbon and ATP-cone domains [Transcription];
1-153 1.82e-88

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


:

Pssm-ID: 440938 [Multi-domain]  Cd Length: 153  Bit Score: 254.62  E-value: 1.82e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496507747   1 MKCPYCSAEGTRVIDSRPADENTAIRRRRQCESCGRRFTTYEKLETMPLMVIKKDQSRVPYERSKIEAGILRSCHKRPIS 80
Cdd:COG1327    1 MRCPFCGHEDTKVIDSRPSEDGTAIRRRRECLACGKRFTTYERVELVPLMVIKKDGRREPFDREKLLRGLLRACEKRPVS 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 496507747  81 TAQIGRMVDAIENEIFSAAEKEICTERIGELVMEKLKETDQVAYVRFASVYREFKDINTFVDEIGKLLKSREG 153
Cdd:COG1327   81 AEQIEAAVDRIERELRASGEREVPSREIGELVMEELKKLDEVAYVRFASVYRSFKDVDDFREELEELLKEKEK 153
 
Name Accession Description Interval E-value
NrdR COG1327
Transcriptional regulator NrdR, contains Zn-ribbon and ATP-cone domains [Transcription];
1-153 1.82e-88

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


Pssm-ID: 440938 [Multi-domain]  Cd Length: 153  Bit Score: 254.62  E-value: 1.82e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496507747   1 MKCPYCSAEGTRVIDSRPADENTAIRRRRQCESCGRRFTTYEKLETMPLMVIKKDQSRVPYERSKIEAGILRSCHKRPIS 80
Cdd:COG1327    1 MRCPFCGHEDTKVIDSRPSEDGTAIRRRRECLACGKRFTTYERVELVPLMVIKKDGRREPFDREKLLRGLLRACEKRPVS 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 496507747  81 TAQIGRMVDAIENEIFSAAEKEICTERIGELVMEKLKETDQVAYVRFASVYREFKDINTFVDEIGKLLKSREG 153
Cdd:COG1327   81 AEQIEAAVDRIERELRASGEREVPSREIGELVMEELKKLDEVAYVRFASVYRSFKDVDDFREELEELLKEKEK 153
TIGR00244 TIGR00244
transcriptional regulator NrdR; Members of this almost entirely bacterial family contain an ...
1-147 3.24e-56

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: 173.08  E-value: 3.24e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496507747    1 MKCPYCSAEGTRVIDSRPADENTAIRRRRQCESCGRRFTTYEKLETMPLMVIKKDQSRVPYERSKIEAGILRSCHKRPIS 80
Cdd:TIGR00244   1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLPPTVIKQDGVREPFNREKLLRGMVRACEKRPVS 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 496507747   81 TAQIGRMVDAIENEIFSAAEKEICTERIGELVMEKLKETDQVAYVRFASVYREFKDINTFVDEIGKL 147
Cdd:TIGR00244  81 FDDLEHAINHIEAQLRAQGEREVPSELIGQMVMQYLKKLDEVAYIRFASVYRSFQDIADFVDELEQL 147
ATP-cone pfam03477
ATP cone domain;
49-137 9.80e-19

ATP cone domain;


Pssm-ID: 397513 [Multi-domain]  Cd Length: 86  Bit Score: 75.38  E-value: 9.80e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496507747   49 LMVIKKDQSRVPYERSKIEAGILRSCHKrpiSTAQIGRMVDAIENEIFSAAEKEICTERIGELVMEKLKETDQVAYVRFA 128
Cdd:pfam03477   1 MKVIKRDGRREPFDKEKIRRAIEKACEK---SPDQADELASEVEEELEKSLEDGISTEEIQDLVEKTLAEHPDYAVARAY 77

                  ....*....
gi 496507747  129 SVYREFKDI 137
Cdd:pfam03477  78 ILYRNLRKE 86
PRK12364 PRK12364
ribonucleoside-diphosphate reductase subunit alpha;
51-133 1.85e-05

ribonucleoside-diphosphate reductase subunit alpha;


Pssm-ID: 237077 [Multi-domain]  Cd Length: 842  Bit Score: 43.59  E-value: 1.85e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496507747  51 VIKKDQSRVPYERSKIEAGILRSCH--KRPISTAQIGRMVDAIENEIFSAAEKE--ICTERIGELVMEKLKETDQVAYVR 126
Cdd:PRK12364   3 IIKRNGTTEPYDREKIEVAIRKAFAsvGKPISDEIIYSLVAEVERFIKEKYPNGhnVSVEEIQDLVEKTLMEHGHYAEVK 82

                 ....*..
gi 496507747 127 FASVYRE 133
Cdd:PRK12364  83 SYILYRA 89
 
Name Accession Description Interval E-value
NrdR COG1327
Transcriptional regulator NrdR, contains Zn-ribbon and ATP-cone domains [Transcription];
1-153 1.82e-88

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


Pssm-ID: 440938 [Multi-domain]  Cd Length: 153  Bit Score: 254.62  E-value: 1.82e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496507747   1 MKCPYCSAEGTRVIDSRPADENTAIRRRRQCESCGRRFTTYEKLETMPLMVIKKDQSRVPYERSKIEAGILRSCHKRPIS 80
Cdd:COG1327    1 MRCPFCGHEDTKVIDSRPSEDGTAIRRRRECLACGKRFTTYERVELVPLMVIKKDGRREPFDREKLLRGLLRACEKRPVS 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 496507747  81 TAQIGRMVDAIENEIFSAAEKEICTERIGELVMEKLKETDQVAYVRFASVYREFKDINTFVDEIGKLLKSREG 153
Cdd:COG1327   81 AEQIEAAVDRIERELRASGEREVPSREIGELVMEELKKLDEVAYVRFASVYRSFKDVDDFREELEELLKEKEK 153
TIGR00244 TIGR00244
transcriptional regulator NrdR; Members of this almost entirely bacterial family contain an ...
1-147 3.24e-56

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: 173.08  E-value: 3.24e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496507747    1 MKCPYCSAEGTRVIDSRPADENTAIRRRRQCESCGRRFTTYEKLETMPLMVIKKDQSRVPYERSKIEAGILRSCHKRPIS 80
Cdd:TIGR00244   1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLPPTVIKQDGVREPFNREKLLRGMVRACEKRPVS 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 496507747   81 TAQIGRMVDAIENEIFSAAEKEICTERIGELVMEKLKETDQVAYVRFASVYREFKDINTFVDEIGKL 147
Cdd:TIGR00244  81 FDDLEHAINHIEAQLRAQGEREVPSELIGQMVMQYLKKLDEVAYIRFASVYRSFQDIADFVDELEQL 147
ATP-cone pfam03477
ATP cone domain;
49-137 9.80e-19

ATP cone domain;


Pssm-ID: 397513 [Multi-domain]  Cd Length: 86  Bit Score: 75.38  E-value: 9.80e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496507747   49 LMVIKKDQSRVPYERSKIEAGILRSCHKrpiSTAQIGRMVDAIENEIFSAAEKEICTERIGELVMEKLKETDQVAYVRFA 128
Cdd:pfam03477   1 MKVIKRDGRREPFDKEKIRRAIEKACEK---SPDQADELASEVEEELEKSLEDGISTEEIQDLVEKTLAEHPDYAVARAY 77

                  ....*....
gi 496507747  129 SVYREFKDI 137
Cdd:pfam03477  78 ILYRNLRKE 86
NrdD COG1328
Anaerobic ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]; ...
47-152 2.55e-07

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: 48.76  E-value: 2.55e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496507747  47 MPLMVIKKDQSRVPYERSKIEAGILR---SCHKRPISTAQIGRMVDAIENEIFSAAEKEICT-ERIGELVMEKLKETDQV 122
Cdd:COG1328    1 MMLKVIKRDGRVVPFDPEKIANAIKKaakAVGGEDRDEELAEEIADEVEKELERLGGGGTITvEEIQDIVEKVLMESGHP 80
                         90       100       110
                 ....*....|....*....|....*....|....*
gi 496507747 123 AYVRFASVYREFKDI-----NTFVDEIGKLLKSRE 152
Cdd:COG1328   81 EVAKAYILYREQRTRlrearTTLVDDIELLDEYDD 115
PRK12364 PRK12364
ribonucleoside-diphosphate reductase subunit alpha;
51-133 1.85e-05

ribonucleoside-diphosphate reductase subunit alpha;


Pssm-ID: 237077 [Multi-domain]  Cd Length: 842  Bit Score: 43.59  E-value: 1.85e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496507747  51 VIKKDQSRVPYERSKIEAGILRSCH--KRPISTAQIGRMVDAIENEIFSAAEKE--ICTERIGELVMEKLKETDQVAYVR 126
Cdd:PRK12364   3 IIKRNGTTEPYDREKIEVAIRKAFAsvGKPISDEIIYSLVAEVERFIKEKYPNGhnVSVEEIQDLVEKTLMEHGHYAEVK 82

                 ....*..
gi 496507747 127 FASVYRE 133
Cdd:PRK12364  83 SYILYRA 89
PRK06406 PRK06406
vitamin B12-dependent ribonucleotide reductase;
45-133 3.75e-03

vitamin B12-dependent ribonucleotide reductase;


Pssm-ID: 235796 [Multi-domain]  Cd Length: 771  Bit Score: 36.75  E-value: 3.75e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496507747  45 ETMPLMVIKKDQSRVPYERSKIEAGILRSCHK-RPISTAQIGRMVDAIENEIfsaAEKEICT-ERIGELVMEKL--KETD 120
Cdd:PRK06406   1 EKMVKEVIKRDGTVVPFDKKKIAMAIYKAMLSvKNGSMEDAEELTDKVVERL---KKYERPTvEQIQDIVEKVLmtKKIN 77
                         90
                 ....*....|....*.
gi 496507747 121 QVAYVRFAS---VYRE 133
Cdd:PRK06406  78 GKDFTDVAKsyiLYRE 93
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH