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Conserved domains on  [gi|159890774|gb|ABX03854|]
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transcriptional regulator, BadM/Rrf2 family [Herpetosiphon aurantiacus DSM 785]

Protein Classification

RrF2 family transcriptional regulator( domain architecture ID 11449279)

RrF2 family transcriptional regulator similar to Desulfovibrio vulgaris regulatory protein Rrf2, iron-sulfur cluster assembly regulator IscR, and nitric oxide-responsive regulator NsrR

CATH:  1.10.10.10
Gene Ontology:  GO:0003700|GO:0003677
PubMed:  15808743|11742080
SCOP:  4000177

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
IscR COG1959
DNA-binding transcriptional regulator, IscR family [Transcription];
4-136 1.08e-25

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


:

Pssm-ID: 441562  Cd Length: 141  Bit Score: 94.52  E-value: 1.08e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159890774   4 SLAFSQAIAISLYITYKIEEQiydFVPTHEIADFLGIAKPSVVKVVQSLTNAGLIETREGAKGGVRLTRNSQAINLLDIF 83
Cdd:COG1959    3 STKTDYALRALLYLALHPGGE---PVTSKEIAERQGISPSYLEKILQKLRKAGLVESVRGPGGGYRLARPPEEITLGDVV 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 159890774  84 NAIEQAKPLFRlniHPTEPKIEALAARQRMVASLQRAEAAMKQELQAVTLADL 136
Cdd:COG1959   80 RAVEGPLALVE---CVSGPPDCPVEEACALHGVWEEAEDAILEVLDSVTLADL 129
 
Name Accession Description Interval E-value
IscR COG1959
DNA-binding transcriptional regulator, IscR family [Transcription];
4-136 1.08e-25

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


Pssm-ID: 441562  Cd Length: 141  Bit Score: 94.52  E-value: 1.08e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159890774   4 SLAFSQAIAISLYITYKIEEQiydFVPTHEIADFLGIAKPSVVKVVQSLTNAGLIETREGAKGGVRLTRNSQAINLLDIF 83
Cdd:COG1959    3 STKTDYALRALLYLALHPGGE---PVTSKEIAERQGISPSYLEKILQKLRKAGLVESVRGPGGGYRLARPPEEITLGDVV 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 159890774  84 NAIEQAKPLFRlniHPTEPKIEALAARQRMVASLQRAEAAMKQELQAVTLADL 136
Cdd:COG1959   80 RAVEGPLALVE---CVSGPPDCPVEEACALHGVWEEAEDAILEVLDSVTLADL 129
Rrf2 pfam02082
Iron-dependent Transcriptional regulator; Several proteins in this family form iron-sulfur ...
 7-137 5.09e-21

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: 82.22  E-value: 5.09e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159890774    7 FSQAIAISLYITYKIEEQIydfVPTHEIADFLGIAKPSVVKVVQSLTNAGLIETREGAKGGVRLTRNSQAINLLDIFNAI 86
Cdd:pfam02082   5 TDYALHALLYLALHPGGEP---VTSEEIAERQNISPVYLEKILAKLRKAGLVESVRGAGGGYRLARPPEEITLLDVVRAV 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 159890774   87 EqAKPLFRLNIHPTEPKIEALAARQRMVasLQRAEAAMKQELQAVTLADLY 137
Cdd:pfam02082  82 E-GPLALFECNNPKCPCGIEIQCALREA--WEEAQDAMEDVLDSVTLADLV 129
rrf2_super TIGR00738
Rrf2 family protein; This model represents a superfamily of probable transcriptional ...
 28-138 1.90e-16

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: 70.35  E-value: 1.90e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159890774   28 FVPTHEIADFLGIAKPSVVKVVQSLTNAGLIETREGAKGGVRLTRNSQAINLLDIFNAIEQA-KPLFRLNIHPTEPKIEA 106
Cdd:TIGR00738  25 PVSVKEIAERQGISRSYLEKILRTLRKAGLVESVRGPGGGYRLARPPEEITVGDVVRAVEGSlAPVQCIGLNGCHPGEEV 104

                          90       100       110
                  ....*....|....*....|....*....|..
gi 159890774  107 LAARQRMVaslqRAEAAMKQELQAVTLADLYS 138
Cdd:TIGR00738 105 CLLHAVWR----ELEDAIEDFLREITLADLVK 132
PRK11014 PRK11014
HTH-type transcriptional repressor NsrR;
33-136 1.82e-08

HTH-type transcriptional repressor NsrR;


Pssm-ID: 236820  Cd Length: 141  Bit Score: 49.68  E-value: 1.82e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159890774  33 EIADFLGIAKPSVVKVVQSLTNAGLIETREGAKGGVRLTRNSQAINLLDIFNAIEqakPLFRLNIHPTEPKIEAlAARQR 112
Cdd:PRK11014  30 EVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGIRLGKPASTIRIGDVVRELE---PLSLVNCSSEFCHITP-ACRLK 105

                         90       100
                 ....*....|....*....|....
gi 159890774 113 MVasLQRAEAAMKQELQAVTLADL 136
Cdd:PRK11014 106 QA--LSKAVQSFLKELDNYTLADL 127
HTH_ARSR cd00090
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ...
 33-81 1.09e-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: 35.74  E-value: 1.09e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 159890774  33 EIADFLGIAKPSVVKVVQSLTNAGLIETR-EGAKGGVRLTRNSQAINLLD 81
Cdd:cd00090   25 ELAERLGLSQSTVSRHLKKLEEAGLVESRrEGRRVYYSLTDAERLLALLE 74
HTH_DTXR smart00529
Helix-turn-helix diphteria tox regulatory element; iron dependent repressor
 31-83 8.13e-03

Helix-turn-helix diphteria tox regulatory element; iron dependent repressor


Pssm-ID: 197774 [Multi-domain]  Cd Length: 95  Bit Score: 33.73  E-value: 8.13e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 159890774    31 THEIADFLGIAKPSVVKVVQSLTNAGLIE---------TREGAKGGVRLTRNSqaiNLLDIF 83
Cdd:smart00529   1 TSEIAERLNVSPPTVTEMLKKLEKMGLVEyepyrgitlTEKGRRLARRLLRKH---RLLERF 59
 
Name Accession Description Interval E-value
IscR COG1959
DNA-binding transcriptional regulator, IscR family [Transcription];
4-136 1.08e-25

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


Pssm-ID: 441562  Cd Length: 141  Bit Score: 94.52  E-value: 1.08e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159890774   4 SLAFSQAIAISLYITYKIEEQiydFVPTHEIADFLGIAKPSVVKVVQSLTNAGLIETREGAKGGVRLTRNSQAINLLDIF 83
Cdd:COG1959    3 STKTDYALRALLYLALHPGGE---PVTSKEIAERQGISPSYLEKILQKLRKAGLVESVRGPGGGYRLARPPEEITLGDVV 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 159890774  84 NAIEQAKPLFRlniHPTEPKIEALAARQRMVASLQRAEAAMKQELQAVTLADL 136
Cdd:COG1959   80 RAVEGPLALVE---CVSGPPDCPVEEACALHGVWEEAEDAILEVLDSVTLADL 129
Rrf2 pfam02082
Iron-dependent Transcriptional regulator; Several proteins in this family form iron-sulfur ...
 7-137 5.09e-21

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: 82.22  E-value: 5.09e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159890774    7 FSQAIAISLYITYKIEEQIydfVPTHEIADFLGIAKPSVVKVVQSLTNAGLIETREGAKGGVRLTRNSQAINLLDIFNAI 86
Cdd:pfam02082   5 TDYALHALLYLALHPGGEP---VTSEEIAERQNISPVYLEKILAKLRKAGLVESVRGAGGGYRLARPPEEITLLDVVRAV 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 159890774   87 EqAKPLFRLNIHPTEPKIEALAARQRMVasLQRAEAAMKQELQAVTLADLY 137
Cdd:pfam02082  82 E-GPLALFECNNPKCPCGIEIQCALREA--WEEAQDAMEDVLDSVTLADLV 129
rrf2_super TIGR00738
Rrf2 family protein; This model represents a superfamily of probable transcriptional ...
 28-138 1.90e-16

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: 70.35  E-value: 1.90e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159890774   28 FVPTHEIADFLGIAKPSVVKVVQSLTNAGLIETREGAKGGVRLTRNSQAINLLDIFNAIEQA-KPLFRLNIHPTEPKIEA 106
Cdd:TIGR00738  25 PVSVKEIAERQGISRSYLEKILRTLRKAGLVESVRGPGGGYRLARPPEEITVGDVVRAVEGSlAPVQCIGLNGCHPGEEV 104

                          90       100       110
                  ....*....|....*....|....*....|..
gi 159890774  107 LAARQRMVaslqRAEAAMKQELQAVTLADLYS 138
Cdd:TIGR00738 105 CLLHAVWR----ELEDAIEDFLREITLADLVK 132
PRK11014 PRK11014
HTH-type transcriptional repressor NsrR;
33-136 1.82e-08

HTH-type transcriptional repressor NsrR;


Pssm-ID: 236820  Cd Length: 141  Bit Score: 49.68  E-value: 1.82e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159890774  33 EIADFLGIAKPSVVKVVQSLTNAGLIETREGAKGGVRLTRNSQAINLLDIFNAIEqakPLFRLNIHPTEPKIEAlAARQR 112
Cdd:PRK11014  30 EVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGIRLGKPASTIRIGDVVRELE---PLSLVNCSSEFCHITP-ACRLK 105

                         90       100
                 ....*....|....*....|....
gi 159890774 113 MVasLQRAEAAMKQELQAVTLADL 136
Cdd:PRK11014 106 QA--LSKAVQSFLKELDNYTLADL 127
rirA PRK11920
iron-responsive transcriptional regulator RirA;
33-136 1.56e-07

iron-responsive transcriptional regulator RirA;


Pssm-ID: 171344  Cd Length: 153  Bit Score: 47.47  E-value: 1.56e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159890774  33 EIADFLGIAKPSVVKVVQSLTNAGLIETREGAKGGVRLTRNSQAINLLDIFNAIEQAkplFRL-----NIHPTEPKIEAL 107
Cdd:PRK11920  29 EIARAYGVSELFLFKILQPLVEAGLVETVRGRNGGVRLGRPAADISLFDVVRVTEDS---FSMaecfeNDASECPLVDSC 105

                         90       100
                 ....*....|....*....|....*....
gi 159890774 108 AarqrMVASLQRAEAAMKQELQAVTLADL 136
Cdd:PRK11920 106 G----LNSALRKALNAFFAVLSKYSIADL 130
MntR COG1321
Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];
23-71 4.37e-06

Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];


Pssm-ID: 440932 [Multi-domain]  Cd Length: 135  Bit Score: 43.27  E-value: 4.37e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 159890774  23 EQIYDF------VPTHEIADFLGIAKPSVVKVVQSLTNAGLIETREGakGGVRLT 71
Cdd:COG1321   13 KAIYELseeggpVRTSDIAERLGVSPPSVTEMLKKLEEKGLVEYEPY--GGITLT 65
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
33-137 2.48e-04

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


Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 39.15  E-value: 2.48e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 159890774  33 EIADFLGIAKPSVVKVVQSLTNAGLIETREGakGGVRLTRNSQAiNLLDIFNAIEQAKPL-------FRLNIhptEPKIE 105
Cdd:COG2186   36 ELAEQLGVSRTTVREALRALEALGLVEVRQG--GGTFVREPSPW-ALLDPLALLLALDDAslrdlleARLAL---EPEAA 109

                         90       100       110
                 ....*....|....*....|....*....|..
gi 159890774 106 ALAARQRMVASLQRAEAAMKQELQAVTLADLY 137
Cdd:COG2186  110 RLAAERATDEDLARLEAALAEMEAAADDGEAF 141
MarR_2 pfam12802
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 32-67 6.84e-04

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: 432797 [Multi-domain]  Cd Length: 60  Bit Score: 35.64  E-value: 6.84e-04
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 159890774   32 HEIADFLGIAKPSVVKVVQSLTNAGLIETREGAKGG 67
Cdd:pfam12802  23 AELARRLGISKQTVSRLVKRLEAKGLVEREPSPADR 58
HTH_ARSR cd00090
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ...
 33-81 1.09e-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: 35.74  E-value: 1.09e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 159890774  33 EIADFLGIAKPSVVKVVQSLTNAGLIETR-EGAKGGVRLTRNSQAINLLD 81
Cdd:cd00090   25 ELAERLGLSQSTVSRHLKKLEEAGLVESRrEGRRVYYSLTDAERLLALLE 74
TrmB pfam01978
Sugar-specific transcriptional regulator TrmB; One member of this family, TrmB, has been shown ...
 33-63 4.83e-03

Sugar-specific transcriptional regulator TrmB; One member of this family, TrmB, has been shown to be a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter in Thermococcus litoralis.


Pssm-ID: 396525 [Multi-domain]  Cd Length: 67  Bit Score: 33.65  E-value: 4.83e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 159890774   33 EIADFLGIAKPSVVKVVQSLTNAGLIETREG 63
Cdd:pfam01978  27 EIAEESGVPRSKVYEVLRSLEDKGLVEREKG 57
HTH_DTXR smart00529
Helix-turn-helix diphteria tox regulatory element; iron dependent repressor
 31-83 8.13e-03

Helix-turn-helix diphteria tox regulatory element; iron dependent repressor


Pssm-ID: 197774 [Multi-domain]  Cd Length: 95  Bit Score: 33.73  E-value: 8.13e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 159890774    31 THEIADFLGIAKPSVVKVVQSLTNAGLIE---------TREGAKGGVRLTRNSqaiNLLDIF 83
Cdd:smart00529   1 TSEIAERLNVSPPTVTEMLKKLEKMGLVEyepyrgitlTEKGRRLARRLLRKH---RLLERF 59
COG3355 COG3355
Predicted transcriptional regulator [Transcription];
33-67 9.02e-03

Predicted transcriptional regulator [Transcription];


Pssm-ID: 442583 [Multi-domain]  Cd Length: 131  Bit Score: 34.17  E-value: 9.02e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 159890774  33 EIADFLGIAKPSVVKVVQSLTNAGLI--ETREGAKGG 67
Cdd:COG3355   47 ELAEALDRSRSTVYRSLQKLLEAGLVerEKRNLEGGG 83
 
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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