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Conserved domains on  [gi|446800392|ref|WP_000877648|]
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MULTISPECIES: Rrf2 family transcriptional regulator [Bacillus]

Protein Classification

Rrf2 family transcriptional regulator( domain architecture ID 10489162)

Rrf2 family transcriptional regulator similar to nitric oxide-responsive regulator NsrR

Gene Ontology:  GO:0003700|GO:0003677
PubMed:  15808743

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rrf2 pfam02082
Iron-dependent Transcriptional regulator; Several proteins in this family form iron-sulfur ...
 3-127 7.81e-49

Iron-dependent Transcriptional regulator; Several proteins in this family form iron-sulfur clusters enabling iron dependent DNA transcription regulation. The iron binding is mediated by three conserved cysteine residues. Members of this family can also bind O-acetyl-L-serine, [Fe-S] and nitric oxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


:

Pssm-ID: 396591 [Multi-domain]  Cd Length: 131  Bit Score: 152.71  E-value: 7.81e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446800392    3 YSKATNYALHTMLFLAKATPNKLVSVHQLAEMQNVSPTYLSKILTKLTKEGMIHSSSGPKGGYSLSHNWEDISFLDIIHA 82
Cdd:pfam02082   1 LSTKTDYALHALLYLALHPGGEPVTSEEIAERQNISPVYLEKILAKLRKAGLVESVRGAGGGYRLARPPEEITLLDVVRA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 446800392   83 IEGKTSLFEC-----CLHEKPGCLINEAMLAAEEKMEEELRNQKIVDLAK 127
Cdd:pfam02082  81 VEGPLALFECnnpkcPCGIEIQCALREAWEEAQDAMEDVLDSVTLADLVA 130
 
Name Accession Description Interval E-value
Rrf2 pfam02082
Iron-dependent Transcriptional regulator; Several proteins in this family form iron-sulfur ...
 3-127 7.81e-49

Iron-dependent Transcriptional regulator; Several proteins in this family form iron-sulfur clusters enabling iron dependent DNA transcription regulation. The iron binding is mediated by three conserved cysteine residues. Members of this family can also bind O-acetyl-L-serine, [Fe-S] and nitric oxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 396591 [Multi-domain]  Cd Length: 131  Bit Score: 152.71  E-value: 7.81e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446800392    3 YSKATNYALHTMLFLAKATPNKLVSVHQLAEMQNVSPTYLSKILTKLTKEGMIHSSSGPKGGYSLSHNWEDISFLDIIHA 82
Cdd:pfam02082   1 LSTKTDYALHALLYLALHPGGEPVTSEEIAERQNISPVYLEKILAKLRKAGLVESVRGAGGGYRLARPPEEITLLDVVRA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 446800392   83 IEGKTSLFEC-----CLHEKPGCLINEAMLAAEEKMEEELRNQKIVDLAK 127
Cdd:pfam02082  81 VEGPLALFECnnpkcPCGIEIQCALREAWEEAQDAMEDVLDSVTLADLVA 130
IscR COG1959
DNA-binding transcriptional regulator, IscR family [Transcription];
2-130 2.05e-45

DNA-binding transcriptional regulator, IscR family [Transcription];


Pssm-ID: 441562  Cd Length: 141  Bit Score: 144.21  E-value: 2.05e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446800392   2 KYSKATNYALHTMLFLAKATPNKLVSVHQLAEMQNVSPTYLSKILTKLTKEGMIHSSSGPKGGYSLSHNWEDISFLDIIH 81
Cdd:COG1959    1 RLSTKTDYALRALLYLALHPGGEPVTSKEIAERQGISPSYLEKILQKLRKAGLVESVRGPGGGYRLARPPEEITLGDVVR 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446800392  82 AIEGKTSLFECCLHEK-----PGCLINEAMLAAEEKMEEELRNQKIVDLAKKIK 130
Cdd:COG1959   81 AVEGPLALVECVSGPPdcpveEACALHGVWEEAEDAILEVLDSVTLADLVEDAE 134
rrf2_super TIGR00738
Rrf2 family protein; This model represents a superfamily of probable transcriptional ...
 1-127 2.41e-44

Rrf2 family protein; This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency. [Unknown function, General]


Pssm-ID: 273242  Cd Length: 132  Bit Score: 141.23  E-value: 2.41e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446800392    1 MKYSKATNYALHTMLFLAKATPNKLVSVHQLAEMQNVSPTYLSKILTKLTKEGMIHSSSGPKGGYSLSHNWEDISFLDII 80
Cdd:TIGR00738   1 MKLTKKTEYALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRKAGLVESVRGPGGGYRLARPPEEITVGDVV 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 446800392   81 HAIEGKTSLFEC-----CLHEKPGCLINEAMLAAEEKMEEELRNQKIVDLAK 127
Cdd:TIGR00738  81 RAVEGSLAPVQCiglngCHPGEEVCLLHAVWRELEDAIEDFLREITLADLVK 132
rirA PRK11920
iron-responsive transcriptional regulator RirA;
1-127 1.91e-13

iron-responsive transcriptional regulator RirA;


Pssm-ID: 171344  Cd Length: 153  Bit Score: 62.87  E-value: 1.91e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446800392   1 MKYSKATNYALHTMLFLAkATPNKLVSVHQLAEMQNVSPTYLSKILTKLTKEGMIHSSSGPKGGYSLSHNWEDISFLDII 80
Cdd:PRK11920   1 MRLTKQTNYAIRMLMYCA-ANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVRGRNGGVRLGRPAADISLFDVV 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446800392  81 HAIEGKTSLFECCLHEKP------GCLINEAMLAAEEKMEEELRNQKIVDLAK 127
Cdd:PRK11920  80 RVTEDSFSMAECFENDASecplvdSCGLNSALRKALNAFFAVLSKYSIADLVK 132
HTH_ARSR cd00090
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ...
 27-84 9.61e-03

Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.


Pssm-ID: 238042 [Multi-domain]  Cd Length: 78  Bit Score: 33.04  E-value: 9.61e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 446800392  27 SVHQLAEMQNVSPTYLSKILTKLTKEGMIHS-SSGPKGGYSLSHNWEdisFLDIIHAIE 84
Cdd:cd00090   22 TVSELAERLGLSQSTVSRHLKKLEEAGLVESrREGRRVYYSLTDAER---LLALLESLL 77
 
Name Accession Description Interval E-value
Rrf2 pfam02082
Iron-dependent Transcriptional regulator; Several proteins in this family form iron-sulfur ...
 3-127 7.81e-49

Iron-dependent Transcriptional regulator; Several proteins in this family form iron-sulfur clusters enabling iron dependent DNA transcription regulation. The iron binding is mediated by three conserved cysteine residues. Members of this family can also bind O-acetyl-L-serine, [Fe-S] and nitric oxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 396591 [Multi-domain]  Cd Length: 131  Bit Score: 152.71  E-value: 7.81e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446800392    3 YSKATNYALHTMLFLAKATPNKLVSVHQLAEMQNVSPTYLSKILTKLTKEGMIHSSSGPKGGYSLSHNWEDISFLDIIHA 82
Cdd:pfam02082   1 LSTKTDYALHALLYLALHPGGEPVTSEEIAERQNISPVYLEKILAKLRKAGLVESVRGAGGGYRLARPPEEITLLDVVRA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 446800392   83 IEGKTSLFEC-----CLHEKPGCLINEAMLAAEEKMEEELRNQKIVDLAK 127
Cdd:pfam02082  81 VEGPLALFECnnpkcPCGIEIQCALREAWEEAQDAMEDVLDSVTLADLVA 130
IscR COG1959
DNA-binding transcriptional regulator, IscR family [Transcription];
2-130 2.05e-45

DNA-binding transcriptional regulator, IscR family [Transcription];


Pssm-ID: 441562  Cd Length: 141  Bit Score: 144.21  E-value: 2.05e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446800392   2 KYSKATNYALHTMLFLAKATPNKLVSVHQLAEMQNVSPTYLSKILTKLTKEGMIHSSSGPKGGYSLSHNWEDISFLDIIH 81
Cdd:COG1959    1 RLSTKTDYALRALLYLALHPGGEPVTSKEIAERQGISPSYLEKILQKLRKAGLVESVRGPGGGYRLARPPEEITLGDVVR 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446800392  82 AIEGKTSLFECCLHEK-----PGCLINEAMLAAEEKMEEELRNQKIVDLAKKIK 130
Cdd:COG1959   81 AVEGPLALVECVSGPPdcpveEACALHGVWEEAEDAILEVLDSVTLADLVEDAE 134
rrf2_super TIGR00738
Rrf2 family protein; This model represents a superfamily of probable transcriptional ...
 1-127 2.41e-44

Rrf2 family protein; This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency. [Unknown function, General]


Pssm-ID: 273242  Cd Length: 132  Bit Score: 141.23  E-value: 2.41e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446800392    1 MKYSKATNYALHTMLFLAKATPNKLVSVHQLAEMQNVSPTYLSKILTKLTKEGMIHSSSGPKGGYSLSHNWEDISFLDII 80
Cdd:TIGR00738   1 MKLTKKTEYALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRKAGLVESVRGPGGGYRLARPPEEITVGDVV 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 446800392   81 HAIEGKTSLFEC-----CLHEKPGCLINEAMLAAEEKMEEELRNQKIVDLAK 127
Cdd:TIGR00738  81 RAVEGSLAPVQCiglngCHPGEEVCLLHAVWRELEDAIEDFLREITLADLVK 132
suf_reg_Xantho TIGR02944
FeS assembly SUF system regulator, gammaproteobacterial; The SUF system is an oxygen-resistant ...
 1-93 2.36e-17

FeS assembly SUF system regulator, gammaproteobacterial; The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Regulatory functions, DNA interactions]


Pssm-ID: 131989 [Multi-domain]  Cd Length: 130  Bit Score: 72.53  E-value: 2.36e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446800392    1 MKYSKATNYALHTMLFLAKATPNKLvSVHQLAEMQNVSPTYLSKILTKLTKEGMIHSSSGPKGGYSLSHNWEDISFLDII 80
Cdd:TIGR02944   2 LKISKLTDYATLVLTTLAQNDSQPY-SAAEIAEQTGLNAPTVSKILKQLSLAGIVTSKRGVEGGYTLARAPRDITVADIV 80

                          90
                  ....*....|...
gi 446800392   81 HAIEGKTSLFECC 93
Cdd:TIGR02944  81 KAVEGPVALTECS 93
rirA PRK11920
iron-responsive transcriptional regulator RirA;
1-127 1.91e-13

iron-responsive transcriptional regulator RirA;


Pssm-ID: 171344  Cd Length: 153  Bit Score: 62.87  E-value: 1.91e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446800392   1 MKYSKATNYALHTMLFLAkATPNKLVSVHQLAEMQNVSPTYLSKILTKLTKEGMIHSSSGPKGGYSLSHNWEDISFLDII 80
Cdd:PRK11920   1 MRLTKQTNYAIRMLMYCA-ANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVRGRNGGVRLGRPAADISLFDVV 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446800392  81 HAIEGKTSLFECCLHEKP------GCLINEAMLAAEEKMEEELRNQKIVDLAK 127
Cdd:PRK11920  80 RVTEDSFSMAECFENDASecplvdSCGLNSALRKALNAFFAVLSKYSIADLVK 132
PRK11014 PRK11014
HTH-type transcriptional repressor NsrR;
1-127 4.82e-12

HTH-type transcriptional repressor NsrR;


Pssm-ID: 236820  Cd Length: 141  Bit Score: 58.92  E-value: 4.82e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446800392   1 MKYSKATNYALHTMLFLAKATPNKLVSVHQLAEMQNVSPTYLSKILTKLTKEGMIHSSSGPKGGYSLSHNWEDISFLDII 80
Cdd:PRK11014   1 MQLTSFTDYGLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGIRLGKPASTIRIGDVV 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446800392  81 HAIEgKTSLFEC----ClHEKPGCLINEAMLAAEEKMEEELRNQKIVDLAK 127
Cdd:PRK11014  81 RELE-PLSLVNCssefC-HITPACRLKQALSKAVQSFLKELDNYTLADLVE 129
PRK10857 PRK10857
Fe-S cluster assembly transcriptional regulator IscR;
1-100 8.03e-09

Fe-S cluster assembly transcriptional regulator IscR;


Pssm-ID: 236777  Cd Length: 164  Bit Score: 51.04  E-value: 8.03e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446800392   1 MKYSKATNYALHTMLFLAKATPNKLVSVHQLAEMQNVSPTYLSKILTKLTKEGMIHSSSGPKGGYSLSHNWEDISFLDII 80
Cdd:PRK10857   1 MRLTSKGRYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGYLLGKDASSIAVGEVI 80

                         90       100
                 ....*....|....*....|
gi 446800392  81 HAIEGKTSLFECclHEKPGC 100
Cdd:PRK10857  81 SAVDESVDATRC--QGKGGC 98
Phage_rep_O pfam04492
Bacteriophage replication protein O; Replication protein O is necessary for the initiation of ...
 30-55 4.07e-03

Bacteriophage replication protein O; Replication protein O is necessary for the initiation of bacteriophage DNA replication. Protein O interacts with the lambda replication origin, and also with replication protein P to form an oligomer. It is speculated that the N-terminal half interacts with the replication origin while the C terminal half mediates protein-protein interaction (annotation of Swiss: P14815).


Pssm-ID: 461329  Cd Length: 92  Bit Score: 34.14  E-value: 4.07e-03
                          10        20
                  ....*....|....*....|....*.
gi 446800392   30 QLAEMQNVSPTYLSKILTKLTKEGMI 55
Cdd:pfam04492  51 QLAELTGISRTHVSKALKELIRMNVI 76
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 11-60 4.07e-03

cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms];


Pssm-ID: 440428 [Multi-domain]  Cd Length: 207  Bit Score: 35.73  E-value: 4.07e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446800392  11 LHTMLFLAKATPNKL---VSVHQLAEMQNVSPTYLSKILTKLTKEGMIHSSSG 60
Cdd:COG0664  141 ARFLLELADRLDGRIdlpLTQEEIASYLGLTRETVSRILKKLEKEGLIELERG 193
MarR COG1846
DNA-binding transcriptional regulator, MarR family [Transcription];
11-62 5.49e-03

DNA-binding transcriptional regulator, MarR family [Transcription];


Pssm-ID: 441451 [Multi-domain]  Cd Length: 142  Bit Score: 34.56  E-value: 5.49e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 446800392  11 LHTMLFLAKATPnklVSVHQLAEMQNVSPTYLSKILTKLTKEGMIHSSSGPK 62
Cdd:COG1846   41 FRVLAALAEAGG---LTQSELAERLGLTKSTVSRLLDRLEEKGLVEREPDPE 89
MarR pfam01047
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 27-61 6.35e-03

MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.


Pssm-ID: 426012 [Multi-domain]  Cd Length: 59  Bit Score: 32.90  E-value: 6.35e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 446800392   27 SVHQLAEMQNVSPTYLSKILTKLTKEGMIHSSSGP 61
Cdd:pfam01047  19 TVSELAEKLGVSKSTVTRVLDRLEKKGLIERSRSP 53
HTH_ARSR cd00090
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ...
 27-84 9.61e-03

Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.


Pssm-ID: 238042 [Multi-domain]  Cd Length: 78  Bit Score: 33.04  E-value: 9.61e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 446800392  27 SVHQLAEMQNVSPTYLSKILTKLTKEGMIHS-SSGPKGGYSLSHNWEdisFLDIIHAIE 84
Cdd:cd00090   22 TVSELAERLGLSQSTVSRHLKKLEEAGLVESrREGRRVYYSLTDAER---LLALLESLL 77
 
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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