NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|640184121|ref|WP_024814624|]
View 

MULTISPECIES: transcriptional regulator NrdR [unclassified Acidovorax]

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

 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];
1-149 3.38e-84

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


:

Pssm-ID: 440938 [Multi-domain]  Cd Length: 153  Bit Score: 243.44  E-value: 3.38e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640184121   1 MKCPFCSHQETQVVETRVSEEGDFVRRRRRCSACEKRFTTYERPEVNFPVVVKKDGRRIEYERSKLLASFNLALRKRPVS 80
Cdd:COG1327    1 MRCPFCGHEDTKVIDSRPSEDGTAIRRRRECLACGKRFTTYERVELVPLMVIKKDGRREPFDREKLLRGLLRACEKRPVS 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 640184121  81 TTQIDSSIERIEEKLLNMGQREVLSSHIGELVMRELKKLDKVAYIRFASVYRSFEDIDDFRAMVDEVGK 149
Cdd:COG1327   81 AEQIEAAVDRIERELRASGEREVPSREIGELVMEELKKLDEVAYVRFASVYRSFKDVDDFREELEELLK 149
 
Name Accession Description Interval E-value
NrdR COG1327
Transcriptional regulator NrdR, contains Zn-ribbon and ATP-cone domains [Transcription];
1-149 3.38e-84

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


Pssm-ID: 440938 [Multi-domain]  Cd Length: 153  Bit Score: 243.44  E-value: 3.38e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640184121   1 MKCPFCSHQETQVVETRVSEEGDFVRRRRRCSACEKRFTTYERPEVNFPVVVKKDGRRIEYERSKLLASFNLALRKRPVS 80
Cdd:COG1327    1 MRCPFCGHEDTKVIDSRPSEDGTAIRRRRECLACGKRFTTYERVELVPLMVIKKDGRREPFDREKLLRGLLRACEKRPVS 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 640184121  81 TTQIDSSIERIEEKLLNMGQREVLSSHIGELVMRELKKLDKVAYIRFASVYRSFEDIDDFRAMVDEVGK 149
Cdd:COG1327   81 AEQIEAAVDRIERELRASGEREVPSREIGELVMEELKKLDEVAYVRFASVYRSFKDVDDFREELEELLK 149
TIGR00244 TIGR00244
transcriptional regulator NrdR; Members of this almost entirely bacterial family contain an ...
 1-140 1.63e-51

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: 160.76  E-value: 1.63e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640184121    1 MKCPFCSHQETQVVETRVSEEGDFVRRRRRCSACEKRFTTYERPEVNFPVVVKKDGRRIEYERSKLLASFNLALRKRPVS 80
Cdd:TIGR00244   1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLPPTVIKQDGVREPFNREKLLRGMVRACEKRPVS 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 640184121   81 TTQIDSSIERIEEKLLNMGQREVLSSHIGELVMRELKKLDKVAYIRFASVYRSFEDIDDF 140
Cdd:TIGR00244  81 FDDLEHAINHIEAQLRAQGEREVPSELIGQMVMQYLKKLDEVAYIRFASVYRSFQDIADF 140
ATP-cone pfam03477
ATP cone domain;
49-137 1.64e-15

ATP cone domain;


Pssm-ID: 397513 [Multi-domain]  Cd Length: 86  Bit Score: 66.91  E-value: 1.64e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640184121   49 PVVVKKDGRRIEYERSKLLASFNLALRKRPVsttQIDSSIERIEEKLLNMGQREVLSSHIGELVMRELKKLDKVAYIRFA 128
Cdd:pfam03477   1 MKVIKRDGRREPFDKEKIRRAIEKACEKSPD---QADELASEVEEELEKSLEDGISTEEIQDLVEKTLAEHPDYAVARAY 77


                  ....*....
gi 640184121  129 SVYRSFEDI 137
Cdd:pfam03477  78 ILYRNLRKE 86
 
Name Accession Description Interval E-value
NrdR COG1327
Transcriptional regulator NrdR, contains Zn-ribbon and ATP-cone domains [Transcription];
1-149 3.38e-84

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


Pssm-ID: 440938 [Multi-domain]  Cd Length: 153  Bit Score: 243.44  E-value: 3.38e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640184121   1 MKCPFCSHQETQVVETRVSEEGDFVRRRRRCSACEKRFTTYERPEVNFPVVVKKDGRRIEYERSKLLASFNLALRKRPVS 80
Cdd:COG1327    1 MRCPFCGHEDTKVIDSRPSEDGTAIRRRRECLACGKRFTTYERVELVPLMVIKKDGRREPFDREKLLRGLLRACEKRPVS 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 640184121  81 TTQIDSSIERIEEKLLNMGQREVLSSHIGELVMRELKKLDKVAYIRFASVYRSFEDIDDFRAMVDEVGK 149
Cdd:COG1327   81 AEQIEAAVDRIERELRASGEREVPSREIGELVMEELKKLDEVAYVRFASVYRSFKDVDDFREELEELLK 149
TIGR00244 TIGR00244
transcriptional regulator NrdR; Members of this almost entirely bacterial family contain an ...
 1-140 1.63e-51

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: 160.76  E-value: 1.63e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640184121    1 MKCPFCSHQETQVVETRVSEEGDFVRRRRRCSACEKRFTTYERPEVNFPVVVKKDGRRIEYERSKLLASFNLALRKRPVS 80
Cdd:TIGR00244   1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLPPTVIKQDGVREPFNREKLLRGMVRACEKRPVS 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 640184121   81 TTQIDSSIERIEEKLLNMGQREVLSSHIGELVMRELKKLDKVAYIRFASVYRSFEDIDDF 140
Cdd:TIGR00244  81 FDDLEHAINHIEAQLRAQGEREVPSELIGQMVMQYLKKLDEVAYIRFASVYRSFQDIADF 140
ATP-cone pfam03477
ATP cone domain;
49-137 1.64e-15

ATP cone domain;


Pssm-ID: 397513 [Multi-domain]  Cd Length: 86  Bit Score: 66.91  E-value: 1.64e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640184121   49 PVVVKKDGRRIEYERSKLLASFNLALRKRPVsttQIDSSIERIEEKLLNMGQREVLSSHIGELVMRELKKLDKVAYIRFA 128
Cdd:pfam03477   1 MKVIKRDGRREPFDKEKIRRAIEKACEKSPD---QADELASEVEEELEKSLEDGISTEEIQDLVEKTLAEHPDYAVARAY 77


                  ....*....
gi 640184121  129 SVYRSFEDI 137
Cdd:pfam03477  78 ILYRNLRKE 86
 
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