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Conserved domains on  [gi|818723294|gb|KKT67058|]
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hypothetical protein UW61_C0016G0005 [Candidatus Curtissbacteria bacterium GW2011_GWC1_44_33]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 323)

helix-turn-helix (HTH) domain-containing protein with a MerR family HTH domain may bind DNA and function as a transcriptional regulator

Gene Ontology:  GO:0006355|GO:0003677

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_MerR-SF super family cl02600
Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; ...
 18-67 9.13e-10

Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Helix-turn-helix (HTH) transcription regulator MerR superfamily, 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.


The actual alignment was detected with superfamily member cd04762:

Pssm-ID: 470628 [Multi-domain]  Cd Length: 49  Bit Score: 48.73  E-value: 9.13e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 818723294 18 LTVREVSELLRVSPLTIKRWGKRGKLPAIRINSrGDRRYKKEAVLWLLGM 67
Cdd:cd04762   1 LTTKEAAELLGVSPSTLRRWVKEGKLKAIRTPG-GHRRFPEEDLERLLGI 49
 
Name Accession Description Interval E-value
HTH_MerR-trunc cd04762
Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family ...
 18-67 9.13e-10

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: 48.73  E-value: 9.13e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 818723294 18 LTVREVSELLRVSPLTIKRWGKRGKLPAIRINSrGDRRYKKEAVLWLLGM 67
Cdd:cd04762   1 LTTKEAAELLGVSPSTLRRWVKEGKLKAIRTPG-GHRRFPEEDLERLLGI 49
COG2452 COG2452
Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];
18-62 5.60e-09

Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];


Pssm-ID: 441988 [Multi-domain]  Cd Length: 178  Bit Score: 49.22  E-value: 5.60e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 818723294  18 LTVREVSELLRVSPLTIKRWGKRGKLPAIRINSrGDRRYKKEAVL 62
Cdd:COG2452    1 LTPGEAAELLGVSPKTLRRWEKEGKLPAIRTPG-GHRRYPESEVE 44
HTH_17 pfam12728
Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.
 17-62 4.99e-07

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


Pssm-ID: 463684 [Multi-domain]  Cd Length: 51  Bit Score: 41.68  E-value: 4.99e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 818723294  17 LLTVREVSELLRVSPLTIKRWGKRGKLPAIRINSRgdRRYKKEAVL 62
Cdd:pfam12728  1 LLTVEEAAELLGVSRRTVYRLIRSGELPAAKIGRR--WRIRKSDLE 44
excise TIGR01764
DNA binding domain, excisionase family; An excisionase, or Xis protein, is a small protein ...
 17-61 6.56e-05

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: 36.42  E-value: 6.56e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 818723294  17 LLTVREVSELLRVSPLTIKRWGKRGKLPAIRINSRgdRRYKKEAV 61
Cdd:TIGR01764  1 YLTVEEAAEYLGVSKSTVYRLIEEGELPAYRVGRH--YRIPREDV 43
PRK04841 PRK04841
HTH-type transcriptional regulator MalT;
16-37 9.75e-03

HTH-type transcriptional regulator MalT;


Pssm-ID: 235315 [Multi-domain]  Cd Length: 903  Bit Score: 32.61  E-value: 9.75e-03
                         10        20
                 ....*....|....*....|..
gi 818723294  16 DLLTVREVSELLRVSPLTIKRW 37
Cdd:PRK04841 823 KLLNHPDVPELIRTSPLTQREW 844
 
Name Accession Description Interval E-value
HTH_MerR-trunc cd04762
Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family ...
 18-67 9.13e-10

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: 48.73  E-value: 9.13e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 818723294 18 LTVREVSELLRVSPLTIKRWGKRGKLPAIRINSrGDRRYKKEAVLWLLGM 67
Cdd:cd04762   1 LTTKEAAELLGVSPSTLRRWVKEGKLKAIRTPG-GHRRFPEEDLERLLGI 49
COG2452 COG2452
Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];
18-62 5.60e-09

Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];


Pssm-ID: 441988 [Multi-domain]  Cd Length: 178  Bit Score: 49.22  E-value: 5.60e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 818723294  18 LTVREVSELLRVSPLTIKRWGKRGKLPAIRINSrGDRRYKKEAVL 62
Cdd:COG2452    1 LTPGEAAELLGVSPKTLRRWEKEGKLPAIRTPG-GHRRYPESEVE 44
HTH_17 pfam12728
Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.
 17-62 4.99e-07

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


Pssm-ID: 463684 [Multi-domain]  Cd Length: 51  Bit Score: 41.68  E-value: 4.99e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 818723294  17 LLTVREVSELLRVSPLTIKRWGKRGKLPAIRINSRgdRRYKKEAVL 62
Cdd:pfam12728  1 LLTVEEAAELLGVSRRTVYRLIRSGELPAAKIGRR--WRIRKSDLE 44
MerR pfam00376
MerR family regulatory protein;
19-56 3.50e-06

MerR family regulatory protein;


Pssm-ID: 425647 [Multi-domain]  Cd Length: 38  Bit Score: 39.32  E-value: 3.50e-06
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 818723294  19 TVREVSELLRVSPLTIKRWGKRGKLPAIRINSRGDRRY 56
Cdd:pfam00376  1 TIGEVAKLLGVSPRTLRYYEKIGLLPPPERTEGGYRRY 38
MerR_1 pfam13411
MerR HTH family regulatory protein;
19-69 3.65e-06

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 39.85  E-value: 3.65e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 818723294  19 TVREVSELLRVSPLTIKRWGKRGKLPAIRiNSRGDRRYKKEAVLWLLGMQE 69
Cdd:pfam13411  2 TISELARLLGVTPRTLRYWEREGLLPPPR-TERGRRYYTDEDVERLRLIKA 51
excise TIGR01764
DNA binding domain, excisionase family; An excisionase, or Xis protein, is a small protein ...
 17-61 6.56e-05

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: 36.42  E-value: 6.56e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 818723294  17 LLTVREVSELLRVSPLTIKRWGKRGKLPAIRINSRgdRRYKKEAV 61
Cdd:TIGR01764  1 YLTVEEAAEYLGVSKSTVYRLIEEGELPAYRVGRH--YRIPREDV 43
AlpA COG3311
DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];
17-64 1.22e-04

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


Pssm-ID: 442540 [Multi-domain]  Cd Length: 64  Bit Score: 36.06  E-value: 1.22e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 818723294 17 LLTVREVSELLRVSPLTIKRWGKRGKLP-AIRINSRGdRRYKKEAVL-WL 64
Cdd:COG3311   8 LLRLKEVAELLGVSRSTIYRLIKKGEFPkPVKLGGRS-VRWRESEVEaWL 56
HTH_MlrA-CarA cd01104
Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; ...
 18-72 1.93e-03

Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.


Pssm-ID: 133379  Cd Length: 68  Bit Score: 32.98  E-value: 1.93e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 818723294 18 LTVREVSELLRVSPLTIKRWGKRGKLPAIRINSRGDRRYKKEAVLWLLGMQEKTE 72
Cdd:cd01104   1 YTIGAVARLTGVSPDTLRAWERRYGLPAPQRTDGGHRLYSEADVARLRLIRRLTS 55
SoxR COG0789
DNA-binding transcriptional regulator, MerR family [Transcription];
20-64 4.55e-03

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


Pssm-ID: 440552 [Multi-domain]  Cd Length: 100  Bit Score: 32.57  E-value: 4.55e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 818723294  20 VREVSELLRVSPLTIKRWGKRGKLPAIRINSRGDRRYKKEAVLWL 64
Cdd:COG0789    1 IGEVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVERL 45
PRK04841 PRK04841
HTH-type transcriptional regulator MalT;
16-37 9.75e-03

HTH-type transcriptional regulator MalT;


Pssm-ID: 235315 [Multi-domain]  Cd Length: 903  Bit Score: 32.61  E-value: 9.75e-03
                         10        20
                 ....*....|....*....|..
gi 818723294  16 DLLTVREVSELLRVSPLTIKRW 37
Cdd:PRK04841 823 KLLNHPDVPELIRTSPLTQREW 844
 
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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