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Conserved domains on  [gi|491368103|ref|WP_005226004|]
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MULTISPECIES: transcriptional regulator NrdR [Enterococcus]

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];
1-153 8.71e-90

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


:

Pssm-ID: 440938 [Multi-domain]  Cd Length: 153  Bit Score: 258.08  E-value: 8.71e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491368103   1 MQCPKCHHNNSRVVDSRQADDGRVIRRRRECENCGYRFTTFERIEEAPLLVIKKNGAREEFNREKILRGLIRSAEKRPVT 80
Cdd:COG1327    1 MRCPFCGHEDTKVIDSRPSEDGTAIRRRRECLACGKRFTTYERVELVPLMVIKKDGRREPFDREKLLRGLLRACEKRPVS 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 491368103  81 MDQMETIVDHVESRVRALGENEISTTQIGEYVMEDLVDLDEIAYIRFASVYRQFKDMSVFLKELQDIVEKAKE 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 8.71e-90

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


Pssm-ID: 440938 [Multi-domain]  Cd Length: 153  Bit Score: 258.08  E-value: 8.71e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491368103   1 MQCPKCHHNNSRVVDSRQADDGRVIRRRRECENCGYRFTTFERIEEAPLLVIKKNGAREEFNREKILRGLIRSAEKRPVT 80
Cdd:COG1327    1 MRCPFCGHEDTKVIDSRPSEDGTAIRRRRECLACGKRFTTYERVELVPLMVIKKDGRREPFDREKLLRGLLRACEKRPVS 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 491368103  81 MDQMETIVDHVESRVRALGENEISTTQIGEYVMEDLVDLDEIAYIRFASVYRQFKDMSVFLKELQDIVEKAKE 153
Cdd:COG1327   81 AEQIEAAVDRIERELRASGEREVPSREIGELVMEELKKLDEVAYVRFASVYRSFKDVDDFREELEELLKEKEK 153
TIGR00244 TIGR00244
transcriptional regulator NrdR; Members of this almost entirely bacterial family contain an ...
 1-147 2.88e-61

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: 185.80  E-value: 2.88e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491368103    1 MQCPKCHHNNSRVVDSRQADDGRVIRRRRECENCGYRFTTFERIEEAPLLVIKKNGAREEFNREKILRGLIRSAEKRPVT 80
Cdd:TIGR00244   1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLPPTVIKQDGVREPFNREKLLRGMVRACEKRPVS 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 491368103   81 MDQMETIVDHVESRVRALGENEISTTQIGEYVMEDLVDLDEIAYIRFASVYRQFKDMSVFLKELQDI 147
Cdd:TIGR00244  81 FDDLEHAINHIEAQLRAQGEREVPSELIGQMVMQYLKKLDEVAYIRFASVYRSFQDIADFVDELEQL 147
ATP-cone pfam03477
ATP cone domain;
49-137 5.24e-19

ATP cone domain;


Pssm-ID: 397513 [Multi-domain]  Cd Length: 86  Bit Score: 76.15  E-value: 5.24e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491368103   49 LLVIKKNGAREEFNREKILRGLIRSAEKrpvTMDQMETIVDHVESRVRALGENEISTTQIGEYVMEDLVDLDEIAYIRFA 128
Cdd:pfam03477   1 MKVIKRDGRREPFDKEKIRRAIEKACEK---SPDQADELASEVEEELEKSLEDGISTEEIQDLVEKTLAEHPDYAVARAY 77


                  ....*....
gi 491368103  129 SVYRQFKDM 137
Cdd:pfam03477  78 ILYRNLRKE 86
PRK09263 PRK09263
anaerobic ribonucleoside triphosphate reductase; Provisional
 48-136 1.10e-03

anaerobic ribonucleoside triphosphate reductase; Provisional


Pssm-ID: 236436 [Multi-domain]  Cd Length: 711  Bit Score: 38.32  E-value: 1.10e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491368103  48 PLLVIKKNGAREEFNREKILRGLIRSAEK-RPVTMDQMETIVDHVESRVraLGENEISTTQIGEYVMEDLVDLDEIAYIR 126
Cdd:PRK09263   2 MPKVIKRDGRKVPFDSEKIKNAIEKAAKAvEVDDEDYCATVAAEIASRV--EGRDEVDIEEIQDAVENQLMAGPYKALAR 79

                         90
                 ....*....|
gi 491368103 127 FASVYRQFKD 136
Cdd:PRK09263  80 AYIEYRHDRD 89
ZnF_C2C2 smart00440
C2C2 Zinc finger; Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and ...
 2-39 3.03e-03

C2C2 Zinc finger; Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.


Pssm-ID: 128717 [Multi-domain]  Cd Length: 40  Bit Score: 33.84  E-value: 3.03e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 491368103     2 QCPKCHHNNS--RVVDSRQADDGRVIRRRreCENCGYRFT 39
Cdd:smart00440   2 ECPKCGNREAtfYQLQTRSADEPMTVFYV--CTKCGHHWR 39
Zn-ribbon_RPA12 cd10507
C-terminal zinc ribbon domain of RPA12 subunit of RNA polymerase I; The C-terminal zinc ribbon ...
 3-40 3.10e-03

C-terminal zinc ribbon domain of RPA12 subunit of RNA polymerase I; The C-terminal zinc ribbon domain (C-ribbon) of subunit A12 (Zn-ribbon_RPA12) in RNA polymerase (Pol) I is involved in intrinsic transcript cleavage. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPA12 in Pol I, RPB9 in Pol II, RPC11 in Pol III and TFS in archaea are distantly related to each other and to the TFIIS elongation factor of Pol II. RPA12 has two zinc-binding domains separated by a flexible linker.


Pssm-ID: 259792  Cd Length: 47  Bit Score: 34.10  E-value: 3.10e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 491368103   3 CPKCHHNNSRV--VDSRQADDGRVIRRrrECENCGYRFTT 40
Cdd:cd10507    9 CPKCGHDEMTYstLQLRSADEGQTVFY--ECPKCGHRFSE 46
 
Name Accession Description Interval E-value
NrdR COG1327
Transcriptional regulator NrdR, contains Zn-ribbon and ATP-cone domains [Transcription];
1-153 8.71e-90

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


Pssm-ID: 440938 [Multi-domain]  Cd Length: 153  Bit Score: 258.08  E-value: 8.71e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491368103   1 MQCPKCHHNNSRVVDSRQADDGRVIRRRRECENCGYRFTTFERIEEAPLLVIKKNGAREEFNREKILRGLIRSAEKRPVT 80
Cdd:COG1327    1 MRCPFCGHEDTKVIDSRPSEDGTAIRRRRECLACGKRFTTYERVELVPLMVIKKDGRREPFDREKLLRGLLRACEKRPVS 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 491368103  81 MDQMETIVDHVESRVRALGENEISTTQIGEYVMEDLVDLDEIAYIRFASVYRQFKDMSVFLKELQDIVEKAKE 153
Cdd:COG1327   81 AEQIEAAVDRIERELRASGEREVPSREIGELVMEELKKLDEVAYVRFASVYRSFKDVDDFREELEELLKEKEK 153
TIGR00244 TIGR00244
transcriptional regulator NrdR; Members of this almost entirely bacterial family contain an ...
 1-147 2.88e-61

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: 185.80  E-value: 2.88e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491368103    1 MQCPKCHHNNSRVVDSRQADDGRVIRRRRECENCGYRFTTFERIEEAPLLVIKKNGAREEFNREKILRGLIRSAEKRPVT 80
Cdd:TIGR00244   1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLPPTVIKQDGVREPFNREKLLRGMVRACEKRPVS 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 491368103   81 MDQMETIVDHVESRVRALGENEISTTQIGEYVMEDLVDLDEIAYIRFASVYRQFKDMSVFLKELQDI 147
Cdd:TIGR00244  81 FDDLEHAINHIEAQLRAQGEREVPSELIGQMVMQYLKKLDEVAYIRFASVYRSFQDIADFVDELEQL 147
ATP-cone pfam03477
ATP cone domain;
49-137 5.24e-19

ATP cone domain;


Pssm-ID: 397513 [Multi-domain]  Cd Length: 86  Bit Score: 76.15  E-value: 5.24e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491368103   49 LLVIKKNGAREEFNREKILRGLIRSAEKrpvTMDQMETIVDHVESRVRALGENEISTTQIGEYVMEDLVDLDEIAYIRFA 128
Cdd:pfam03477   1 MKVIKRDGRREPFDKEKIRRAIEKACEK---SPDQADELASEVEEELEKSLEDGISTEEIQDLVEKTLAEHPDYAVARAY 77


                  ....*....
gi 491368103  129 SVYRQFKDM 137
Cdd:pfam03477  78 ILYRNLRKE 86
NrdD COG1328
Anaerobic ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]; ...
 47-154 2.33e-06

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: 46.06  E-value: 2.33e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491368103  47 APLLVIKKNGAREEFNREKILRGLIRSA---EKRPVTMDQMETIVDHVESRVRALGENE-ISTTQIGEYVMEDLVDLDEI 122
Cdd:COG1328    1 MMLKVIKRDGRVVPFDPEKIANAIKKAAkavGGEDRDEELAEEIADEVEKELERLGGGGtITVEEIQDIVEKVLMESGHP 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 491368103 123 ----AYIrfasVYRQFKDM-----SVFLKELQDIVEKAKEP 154
Cdd:COG1328   81 evakAYI----LYREQRTRlrearTTLVDDIELLDEYDDWR 117
PRK09263 PRK09263
anaerobic ribonucleoside triphosphate reductase; Provisional
 48-136 1.10e-03

anaerobic ribonucleoside triphosphate reductase; Provisional


Pssm-ID: 236436 [Multi-domain]  Cd Length: 711  Bit Score: 38.32  E-value: 1.10e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491368103  48 PLLVIKKNGAREEFNREKILRGLIRSAEK-RPVTMDQMETIVDHVESRVraLGENEISTTQIGEYVMEDLVDLDEIAYIR 126
Cdd:PRK09263   2 MPKVIKRDGRKVPFDSEKIKNAIEKAAKAvEVDDEDYCATVAAEIASRV--EGRDEVDIEEIQDAVENQLMAGPYKALAR 79

                         90
                 ....*....|
gi 491368103 127 FASVYRQFKD 136
Cdd:PRK09263  80 AYIEYRHDRD 89
nrdA PHA02572
ribonucleoside-diphosphate reductase subunit alpha; Provisional
 51-150 1.57e-03

ribonucleoside-diphosphate reductase subunit alpha; Provisional


Pssm-ID: 222883 [Multi-domain]  Cd Length: 753  Bit Score: 37.78  E-value: 1.57e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491368103  51 VIKKNGAREEFNREKILRGLIRSAEKRPVTMDQmetivdhVESRVRALGENEISTTQIGEYVME---DLVDLDEIAYIRF 127
Cdd:PHA02572   6 VIKSSGVSQPFDLEKIHKVLEWACEGTGVDPSE-------LEENSKIQLRDGMTTKDIQEILIKsaaDLISVEEPDYQYV 78

                         90       100       110
                 ....*....|....*....|....*....|...
gi 491368103 128 AS----------VYRQFKDMSVFlkelqDIVEK 150
Cdd:PHA02572  79 AArllmfalrkqVYGQFEPPSFI-----DHISK 106
ZnF_C2C2 smart00440
C2C2 Zinc finger; Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and ...
 2-39 3.03e-03

C2C2 Zinc finger; Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.


Pssm-ID: 128717 [Multi-domain]  Cd Length: 40  Bit Score: 33.84  E-value: 3.03e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 491368103     2 QCPKCHHNNS--RVVDSRQADDGRVIRRRreCENCGYRFT 39
Cdd:smart00440   2 ECPKCGNREAtfYQLQTRSADEPMTVFYV--CTKCGHHWR 39
Zn-ribbon_RPA12 cd10507
C-terminal zinc ribbon domain of RPA12 subunit of RNA polymerase I; The C-terminal zinc ribbon ...
 3-40 3.10e-03

C-terminal zinc ribbon domain of RPA12 subunit of RNA polymerase I; The C-terminal zinc ribbon domain (C-ribbon) of subunit A12 (Zn-ribbon_RPA12) in RNA polymerase (Pol) I is involved in intrinsic transcript cleavage. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPA12 in Pol I, RPB9 in Pol II, RPC11 in Pol III and TFS in archaea are distantly related to each other and to the TFIIS elongation factor of Pol II. RPA12 has two zinc-binding domains separated by a flexible linker.


Pssm-ID: 259792  Cd Length: 47  Bit Score: 34.10  E-value: 3.10e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 491368103   3 CPKCHHNNSRV--VDSRQADDGRVIRRrrECENCGYRFTT 40
Cdd:cd10507    9 CPKCGHDEMTYstLQLRSADEGQTVFY--ECPKCGHRFSE 46
TFIIS_C pfam01096
Transcription factor S-II (TFIIS);
2-39 5.74e-03

Transcription factor S-II (TFIIS);


Pssm-ID: 426046  Cd Length: 39  Bit Score: 32.96  E-value: 5.74e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 491368103    2 QCPKCHHNNS--RVVDSRQADDGrvIRRRRECENCGYRFT 39
Cdd:pfam01096   2 KCPKCGNREAyfFQLQTRSADEP--MTVFYVCTKCGHRWR 39
 
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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