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Conserved domains on  [gi|1550003262|gb|RVM96128|]
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Rrf2 family transcriptional regulator [Sinorhizobium meliloti]

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 ...
 3-139 9.79e-42

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: 136.14  E-value: 9.79e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550003262   3 LGDGVEQAIHSVTMLSCLQPGSTLSAAALAEFHGVSTSYLLKHLQAMSGAGLLEAVPGPKGGYRLARAPEKITLLDIVLA 82
Cdd:pfam02082   1 LSTKTDYALHALLYLALHPGGEPVTSEEIAERQNISPVYLEKILAKLRKAGLVESVRGAGGGYRLARPPEEITLLDVVRA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1550003262  83 VEGPEPAFRCNEirlrgpNPYSCKPAAPCTINVAMLRAEQAYRAELRRVTIAAIMAD 139
Cdd:pfam02082  81 VEGPLALFECNN------PKCPCGIEIQCALREAWEEAQDAMEDVLDSVTLADLVAD 131
 
Name Accession Description Interval E-value
Rrf2 pfam02082
Iron-dependent Transcriptional regulator; Several proteins in this family form iron-sulfur ...
 3-139 9.79e-42

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: 136.14  E-value: 9.79e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550003262   3 LGDGVEQAIHSVTMLSCLQPGSTLSAAALAEFHGVSTSYLLKHLQAMSGAGLLEAVPGPKGGYRLARAPEKITLLDIVLA 82
Cdd:pfam02082   1 LSTKTDYALHALLYLALHPGGEPVTSEEIAERQNISPVYLEKILAKLRKAGLVESVRGAGGGYRLARPPEEITLLDVVRA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1550003262  83 VEGPEPAFRCNEirlrgpNPYSCKPAAPCTINVAMLRAEQAYRAELRRVTIAAIMAD 139
Cdd:pfam02082  81 VEGPLALFECNN------PKCPCGIEIQCALREAWEEAQDAMEDVLDSVTLADLVAD 131
IscR COG1959
DNA-binding transcriptional regulator, IscR family [Transcription];
2-142 9.21e-40

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


Pssm-ID: 441562  Cd Length: 141  Bit Score: 131.50  E-value: 9.21e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550003262   2 KLGDGVEQAIHSVTMLSCLQPGSTLSAAALAEFHGVSTSYLLKHLQAMSGAGLLEAVPGPKGGYRLARAPEKITLLDIVL 81
Cdd:COG1959     1 RLSTKTDYALRALLYLALHPGGEPVTSKEIAERQGISPSYLEKILQKLRKAGLVESVRGPGGGYRLARPPEEITLGDVVR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1550003262  82 AVEGPEPAFRCNEirlrgpNPYSCKPAAPCTINVAMLRAEQAYRAELRRVTIAAIMADLKA 142
Cdd:COG1959    81 AVEGPLALVECVS------GPPDCPVEEACALHGVWEEAEDAILEVLDSVTLADLVEDAEA 135
rrf2_super TIGR00738
Rrf2 family protein; This model represents a superfamily of probable transcriptional ...
 1-138 3.67e-29

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: 103.87  E-value: 3.67e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550003262   1 MKLGDGVEQAIHSVTMLSCLQPGSTLSAAALAEFHGVSTSYLLKHLQAMSGAGLLEAVPGPKGGYRLARAPEKITLLDIV 80
Cdd:TIGR00738   1 MKLTKKTEYALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRKAGLVESVRGPGGGYRLARPPEEITVGDVV 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1550003262  81 LAVEGPEPAFRCNEIRlrgpnpySCKPAAPCTINVAMLR-AEQAYRAELRRVTIAAIMA 138
Cdd:TIGR00738  81 RAVEGSLAPVQCIGLN-------GCHPGEEVCLLHAVWReLEDAIEDFLREITLADLVK 132
rirA PRK11920
iron-responsive transcriptional regulator RirA;
31-134 1.50e-10

iron-responsive transcriptional regulator RirA;


Pssm-ID: 171344  Cd Length: 153  Bit Score: 56.33  E-value: 1.50e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550003262  31 LAEFHGVSTSYLLKHLQAMSGAGLLEAVPGPKGGYRLARAPEKITLLDIVLAVEGPEPAFRCNEirlrgPNPYSCKPAAP 110
Cdd:PRK11920   30 IARAYGVSELFLFKILQPLVEAGLVETVRGRNGGVRLGRPAADISLFDVVRVTEDSFSMAECFE-----NDASECPLVDS 104

                          90       100
                  ....*....|....*....|....
gi 1550003262 111 CTINVAMLRAEQAYRAELRRVTIA 134
Cdd:PRK11920  105 CGLNSALRKALNAFFAVLSKYSIA 128
HTH_ARSR cd00090
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ...
 26-78 5.90e-04

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: 36.89  E-value: 5.90e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1550003262  26 LSAAALAEFHGVSTSYLLKHLQAMSGAGLLEAVP-GPKGGYRLARAPEKITLLD 78
Cdd:cd00090    21 LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRReGRRVYYSLTDAERLLALLE 74
 
Name Accession Description Interval E-value
Rrf2 pfam02082
Iron-dependent Transcriptional regulator; Several proteins in this family form iron-sulfur ...
 3-139 9.79e-42

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: 136.14  E-value: 9.79e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550003262   3 LGDGVEQAIHSVTMLSCLQPGSTLSAAALAEFHGVSTSYLLKHLQAMSGAGLLEAVPGPKGGYRLARAPEKITLLDIVLA 82
Cdd:pfam02082   1 LSTKTDYALHALLYLALHPGGEPVTSEEIAERQNISPVYLEKILAKLRKAGLVESVRGAGGGYRLARPPEEITLLDVVRA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1550003262  83 VEGPEPAFRCNEirlrgpNPYSCKPAAPCTINVAMLRAEQAYRAELRRVTIAAIMAD 139
Cdd:pfam02082  81 VEGPLALFECNN------PKCPCGIEIQCALREAWEEAQDAMEDVLDSVTLADLVAD 131
IscR COG1959
DNA-binding transcriptional regulator, IscR family [Transcription];
2-142 9.21e-40

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


Pssm-ID: 441562  Cd Length: 141  Bit Score: 131.50  E-value: 9.21e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550003262   2 KLGDGVEQAIHSVTMLSCLQPGSTLSAAALAEFHGVSTSYLLKHLQAMSGAGLLEAVPGPKGGYRLARAPEKITLLDIVL 81
Cdd:COG1959     1 RLSTKTDYALRALLYLALHPGGEPVTSKEIAERQGISPSYLEKILQKLRKAGLVESVRGPGGGYRLARPPEEITLGDVVR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1550003262  82 AVEGPEPAFRCNEirlrgpNPYSCKPAAPCTINVAMLRAEQAYRAELRRVTIAAIMADLKA 142
Cdd:COG1959    81 AVEGPLALVECVS------GPPDCPVEEACALHGVWEEAEDAILEVLDSVTLADLVEDAEA 135
rrf2_super TIGR00738
Rrf2 family protein; This model represents a superfamily of probable transcriptional ...
 1-138 3.67e-29

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: 103.87  E-value: 3.67e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550003262   1 MKLGDGVEQAIHSVTMLSCLQPGSTLSAAALAEFHGVSTSYLLKHLQAMSGAGLLEAVPGPKGGYRLARAPEKITLLDIV 80
Cdd:TIGR00738   1 MKLTKKTEYALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRKAGLVESVRGPGGGYRLARPPEEITVGDVV 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1550003262  81 LAVEGPEPAFRCNEIRlrgpnpySCKPAAPCTINVAMLR-AEQAYRAELRRVTIAAIMA 138
Cdd:TIGR00738  81 RAVEGSLAPVQCIGLN-------GCHPGEEVCLLHAVWReLEDAIEDFLREITLADLVK 132
suf_reg_Xantho TIGR02944
FeS assembly SUF system regulator, gammaproteobacterial; The SUF system is an oxygen-resistant ...
 25-136 8.86e-15

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: 67.14  E-value: 8.86e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550003262  25 TLSAAALAEFHGVSTSYLLKHLQAMSGAGLLEAVPGPKGGYRLARAPEKITLLDIVLAVEGPEPAFRCNEIRLRgpnpys 104
Cdd:TIGR02944  25 PYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSKRGVEGGYTLARAPRDITVADIVKAVEGPVALTECSDDQKK------ 98

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1550003262 105 CKPAAPC-------TINVAMLRAeqayraeLRRVTIAAI 136
Cdd:TIGR02944  99 CSLGNSCgvrsnwkVINSQVLDL-------LSSVSLADM 130
rirA PRK11920
iron-responsive transcriptional regulator RirA;
31-134 1.50e-10

iron-responsive transcriptional regulator RirA;


Pssm-ID: 171344  Cd Length: 153  Bit Score: 56.33  E-value: 1.50e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550003262  31 LAEFHGVSTSYLLKHLQAMSGAGLLEAVPGPKGGYRLARAPEKITLLDIVLAVEGPEPAFRCNEirlrgPNPYSCKPAAP 110
Cdd:PRK11920   30 IARAYGVSELFLFKILQPLVEAGLVETVRGRNGGVRLGRPAADISLFDVVRVTEDSFSMAECFE-----NDASECPLVDS 104

                          90       100
                  ....*....|....*....|....
gi 1550003262 111 CTINVAMLRAEQAYRAELRRVTIA 134
Cdd:PRK11920  105 CGLNSALRKALNAFFAVLSKYSIA 128
PRK11014 PRK11014
HTH-type transcriptional repressor NsrR;
1-139 4.02e-10

HTH-type transcriptional repressor NsrR;


Pssm-ID: 236820  Cd Length: 141  Bit Score: 55.07  E-value: 4.02e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1550003262   1 MKLGDGVEQAIHSVTMLSCLQPGSTLSAAALAEFHGVSTSYLLKHLQAMSGAGLLEAVPGPKGGYRLARAPEKITLLDIV 80
Cdd:PRK11014    1 MQLTSFTDYGLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGIRLGKPASTIRIGDVV 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1550003262  81 LAVEgPEPAFRCneirlrgpNPYSCKPAAPCTINVAMLRAEQAYRAELRRVTIAAIMAD 139
Cdd:PRK11014   81 RELE-PLSLVNC--------SSEFCHITPACRLKQALSKAVQSFLKELDNYTLADLVEE 130
YobV COG2378
Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains ...
 14-70 1.28e-05

Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains [Transcription];


Pssm-ID: 441945 [Multi-domain]  Cd Length: 314  Bit Score: 43.91  E-value: 1.28e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1550003262  14 VTMLSCLQPGSTLSAAALAEFHGVSTSYLLKHLQAMSGAGL-LEAVPGPKGGYRLARA 70
Cdd:COG2378     8 LALLQLLQSRRGVTAAELAERLEVSERTIYRDIDALRELGVpIEAERGRGGGYRLRDG 65
PRK10857 PRK10857
Fe-S cluster assembly transcriptional regulator IscR;
29-92 2.71e-05

Fe-S cluster assembly transcriptional regulator IscR;


Pssm-ID: 236777  Cd Length: 164  Bit Score: 42.18  E-value: 2.71e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1550003262  29 AALAEFHGVSTSYLLKHLQAMSGAGLLEAVPGPKGGYRLARAPEKITLLDIVLAVEGPEPAFRC 92
Cdd:PRK10857   29 ADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGYLLGKDASSIAVGEVISAVDESVDATRC 92
HTH_ARSR cd00090
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ...
 26-78 5.90e-04

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: 36.89  E-value: 5.90e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1550003262  26 LSAAALAEFHGVSTSYLLKHLQAMSGAGLLEAVP-GPKGGYRLARAPEKITLLD 78
Cdd:cd00090    21 LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRReGRRVYYSLTDAERLLALLE 74
PRK11886 PRK11886
bifunctional biotin--[acetyl-CoA-carboxylase] ligase/biotin operon repressor BirA;
15-78 1.34e-03

bifunctional biotin--[acetyl-CoA-carboxylase] ligase/biotin operon repressor BirA;


Pssm-ID: 237010 [Multi-domain]  Cd Length: 319  Bit Score: 37.84  E-value: 1.34e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1550003262  15 TMLSCLQPGSTLSAAALAEFHGVSTSYLLKHLQAMSGAGL-LEAVPGPkgGYRLArAPekITLLD 78
Cdd:PRK11886    8 QLLSLLADGDFHSGEQLGEELGISRAAIWKHIQTLEEWGLdIFSVKGK--GYRLA-EP--LDLLD 67
HrcA_DNA-bdg pfam03444
Winged helix-turn-helix transcription repressor, HrcA DNA-binding; This domain is always found ...
 46-66 2.66e-03

Winged helix-turn-helix transcription repressor, HrcA DNA-binding; This domain is always found with a pair of CBS domains pfam00571.


Pssm-ID: 281443 [Multi-domain]  Cd Length: 79  Bit Score: 35.00  E-value: 2.66e-03
                          10        20
                  ....*....|....*....|.
gi 1550003262  46 LQAMSGAGLLEAVPGPKGGYR 66
Cdd:pfam03444  44 MQSLKALGLVEGVPGPKGGYK 64
BirA COG1654
Biotin operon repressor [Transcription];
17-78 5.06e-03

Biotin operon repressor [Transcription];


Pssm-ID: 441260 [Multi-domain]  Cd Length: 324  Bit Score: 36.50  E-value: 5.06e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1550003262  17 LSCLQPGSTLSAAALAEFHGVSTSYLLKHLQAMSGAGL-LEAVPGpkGGYRLARAPEkitLLD 78
Cdd:COG1654    10 LRLLADGEFHSGEELAEELGVSRAAVWKHIKALRELGYeIESVPG--KGYRLAEPPD---LLD 67
 
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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