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Conserved domains on  [gi|881090392|ref|WP_048799695|]
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MULTISPECIES: helix-turn-helix domain-containing protein [Bacteroidales]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_17 pfam12728
Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.
 43-88 2.31e-10

Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.


:

Pssm-ID: 463684 [Multi-domain]  Cd Length: 51  Bit Score: 50.92  E-value: 2.31e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 881090392  43 DVCRLLNISKRTLQHYRDTGVLPFAQIGHKCYYKREDVEQLLQTKT 88
Cdd:pfam12728  6 EAAELLGVSRRTVYRLIRSGELPAAKIGRRWRIRKSDLEEWLERRR 51
 
Name Accession Description Interval E-value
HTH_17 pfam12728
Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.
 43-88 2.31e-10

Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.


Pssm-ID: 463684 [Multi-domain]  Cd Length: 51  Bit Score: 50.92  E-value: 2.31e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 881090392  43 DVCRLLNISKRTLQHYRDTGVLPFAQIGHKCYYKREDVEQLLQTKT 88
Cdd:pfam12728  6 EAAELLGVSRRTVYRLIRSGELPAAKIGRRWRIRKSDLEEWLERRR 51
AlpA COG3311
DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];
43-92 2.09e-05

DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];


Pssm-ID: 442540 [Multi-domain]  Cd Length: 64  Bit Score: 38.76  E-value: 2.09e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 881090392 43 DVCRLLNISKRTLQHYRDTGVLPFA-QIGHKC-YYKREDVEQLLQTKTEKSK 92
Cdd:COG3311  13 EVAELLGVSRSTIYRLIKKGEFPKPvKLGGRSvRWRESEVEAWLAARIAASR 64
HTH_TipAL-Mta cd01106
Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; ...
 42-85 5.28e-05

Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Unique to this family, is a TipAL-like, lineage specific Bacilli subgroup, which has five conserved cysteines in the C-terminus of the protein.


Pssm-ID: 133381 [Multi-domain]  Cd Length: 103  Bit Score: 38.62  E-value: 5.28e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 881090392  42 GDVCRLLNISKRTLQHYRDTGVLPFAQI---GHKcYYKREDVEQLLQ 85
Cdd:cd01106    4 GEVAKLTGVSVRTLHYYDEIGLLKPSRRtenGYR-LYTEEDLERLQQ 49
excise TIGR01764
DNA binding domain, excisionase family; An excisionase, or Xis protein, is a small protein ...
 38-84 1.53e-03

DNA binding domain, excisionase family; An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376). [Unknown function, General]


Pssm-ID: 200128  Cd Length: 49  Bit Score: 33.34  E-value: 1.53e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 881090392  38 WLHNGDVCRLLNISKRTLQHYRDTGVLPFAQIGHKCYYKREDVEQLL 84
Cdd:TIGR01764  1 YLTVEEAAEYLGVSKSTVYRLIEEGELPAYRVGRHYRIPREDVDEYL 47
 
Name Accession Description Interval E-value
HTH_17 pfam12728
Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.
 43-88 2.31e-10

Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.


Pssm-ID: 463684 [Multi-domain]  Cd Length: 51  Bit Score: 50.92  E-value: 2.31e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 881090392  43 DVCRLLNISKRTLQHYRDTGVLPFAQIGHKCYYKREDVEQLLQTKT 88
Cdd:pfam12728  6 EAAELLGVSRRTVYRLIRSGELPAAKIGRRWRIRKSDLEEWLERRR 51
AlpA COG3311
DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];
43-92 2.09e-05

DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];


Pssm-ID: 442540 [Multi-domain]  Cd Length: 64  Bit Score: 38.76  E-value: 2.09e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 881090392 43 DVCRLLNISKRTLQHYRDTGVLPFA-QIGHKC-YYKREDVEQLLQTKTEKSK 92
Cdd:COG3311  13 EVAELLGVSRSTIYRLIKKGEFPKPvKLGGRSvRWRESEVEAWLAARIAASR 64
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
42-87 3.68e-05

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 38.73  E-value: 3.68e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 881090392  42 GDVCRLLNISKRTLQHYRDTGVLPFAQI---GHKcYYKREDVEQLLQTK 87
Cdd:COG0789    2 GEVARLTGVSVRTLRYYERIGLLPPPERtegGYR-LYSEEDVERLRFIR 49
HTH_TipAL-Mta cd01106
Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; ...
 42-85 5.28e-05

Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Unique to this family, is a TipAL-like, lineage specific Bacilli subgroup, which has five conserved cysteines in the C-terminus of the protein.


Pssm-ID: 133381 [Multi-domain]  Cd Length: 103  Bit Score: 38.62  E-value: 5.28e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 881090392  42 GDVCRLLNISKRTLQHYRDTGVLPFAQI---GHKcYYKREDVEQLLQ 85
Cdd:cd01106    4 GEVAKLTGVSVRTLHYYDEIGLLKPSRRtenGYR-LYTEEDLERLQQ 49
MerR_1 pfam13411
MerR HTH family regulatory protein;
42-87 6.85e-05

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 37.53  E-value: 6.85e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 881090392  42 GDVCRLLNISKRTLQHYRDTGVLPFAQIGHKC-YYKREDVEQLLQTK 87
Cdd:pfam13411  4 SELARLLGVTPRTLRYWEREGLLPPPRTERGRrYYTDEDVERLRLIK 50
HTH_NolA-AlbR cd04788
Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR; ...
 39-91 1.84e-04

Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR; Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.


Pssm-ID: 133415 [Multi-domain]  Cd Length: 96  Bit Score: 36.97  E-value: 1.84e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 881090392 39 LHNGDVCRLLNISKRTLQHYRDTGVLPFAQI---GHKCyYKREDVEQLLQTKTEKS 91
Cdd:cd04788   1 WKIGELARRTGLSVRTLHHYDHIGLLSPSQRtegGHRL-YDRADIRRLHQIIALRR 55
HTH_MerR-like cd00592
Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators; Helix-turn-helix ...
 42-88 4.66e-04

Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators; Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


Pssm-ID: 133378 [Multi-domain]  Cd Length: 100  Bit Score: 36.07  E-value: 4.66e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 881090392  42 GDVCRLLNISKRTLQHYRDTGVLPFA--QIGHKcYYKREDVEQLLQTKT 88
Cdd:cd00592    4 GEVAKLLGVSVRTLRYYEEKGLLPPErsENGYR-LYSEEDLERLRLIRR 51
excise TIGR01764
DNA binding domain, excisionase family; An excisionase, or Xis protein, is a small protein ...
 38-84 1.53e-03

DNA binding domain, excisionase family; An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376). [Unknown function, General]


Pssm-ID: 200128  Cd Length: 49  Bit Score: 33.34  E-value: 1.53e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 881090392  38 WLHNGDVCRLLNISKRTLQHYRDTGVLPFAQIGHKCYYKREDVEQLL 84
Cdd:TIGR01764  1 YLTVEEAAEYLGVSKSTVYRLIEEGELPAYRVGRHYRIPREDVDEYL 47
HTH_MerR-trunc cd04762
Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family ...
 42-84 1.82e-03

Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.


Pssm-ID: 133390 [Multi-domain]  Cd Length: 49  Bit Score: 33.33  E-value: 1.82e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 881090392 42 GDVCRLLNISKRTLQHYRDTGVLPFAQI--GHKcYYKREDVEQLL 84
Cdd:cd04762   4 KEAAELLGVSPSTLRRWVKEGKLKAIRTpgGHR-RFPEEDLERLL 47
HTH_BmrR cd01107
Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Helix-turn-helix (HTH) ...
 42-85 2.95e-03

Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.


Pssm-ID: 133382 [Multi-domain]  Cd Length: 108  Bit Score: 34.03  E-value: 2.95e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 881090392  42 GDVCRLLNISKRTLQHYRDTGVLPFAQIGHKCYYKREDVEQLLQ 85
Cdd:cd01107    4 GEFAKLSNLSIKALRYYDKIGLLKPAYVDPDTGYRYYSAEQLER 47
 
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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