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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 818694519   2 LKISEAAEILGVSMDTLRRWDENGKLTAIKKEGGtHRYYREKDMEIFAS 50
Cdd:cd04762    1 LTTKEAAELLGVSPSTLRRWVKEGKLKAIRTPGG-HRRFPEEDLERLLG 48

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 818694519   2 LKISEAAEILGVSMDTLRRWDENGKLTAIKKEGGtHRYYREKDMEIFAS 50
Cdd:cd04762    1 LTTKEAAELLGVSPSTLRRWVKEGKLKAIRTPGG-HRRFPEEDLERLLG 48

MerR HTH family regulatory protein;

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 818694519    3 KISEAAEILGVSMDTLRRWDENGKLtAIKKEGGTHRYYREKDMEIFA 49
Cdd:pfam13411   2 TISELARLLGVTPRTLRYWEREGLL-PPPRTERGRRYYTDEDVERLR 47

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]

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 818694519    2 LKISEAAEILGVSMDTLRRWDENGKLTAIkKEGGTHRYYRE 42
Cdd:TIGR01764   2 LTVEEAAEYLGVSKSTVYRLIEEGELPAY-RVGRHYRIPRE 41

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 818694519   2 LKISEAAEILGVSMDTLRRWDENGKLTAIKKEGGtHRYYREKDMEIFAS 50
Cdd:cd04762    1 LTTKEAAELLGVSPSTLRRWVKEGKLKAIRTPGG-HRRFPEEDLERLLG 48

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 818694519   2 LKISEAAEILGVSMDTLRRWDENGKLTAIKKEGGtHRYYREKDME 46
Cdd:cd04761    1 YTIGELAKLTGVSPSTLRYYERIGLLSPARTEGG-YRLYSDADLE 44

MerR family regulatory protein;

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 818694519    3 KISEAAEILGVSMDTLRRWDENGKLTAIKKEGGTHRYY 40
Cdd:pfam00376   1 TIGEVAKLLGVSPRTLRYYEKIGLLPPPERTEGGYRRY 38

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 818694519    1 MLKISEAAEILGVSMDTLRRWDENGKLTAIKKegGTHRYYREKDME 46
Cdd:pfam12728   1 LLTVEEAAELLGVSRRTVYRLIRSGELPAAKI--GRRWRIRKSDLE 44

Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB; Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 818694519   2 LKISEAAEILGVSMDTLRRWDENGKLTAIKKEGGTHRYYREKDME 46
Cdd:cd01109    1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRDENGIRDFTEEDLE 45

Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). 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. 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-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 818694519   3 KISEAAEILGVSMDTLRRWDENGKLTAIKKEGGtHRYYREKDMEIF 48
Cdd:cd04764    2 TIKEVSEIIGVKPHTLRYYEKEFNLYIPRTENG-RRYYTDEDIELL 46

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 818694519   4 ISEAAEILGVSMDTLRRWDENGKLTAIKKEGGTHRYYREKDME 46
Cdd:cd01106    3 VGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLYTEEDLE 45

Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE; Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. 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. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 818694519   2 LKISEAAEILGVSMDTLRRWDENGKLTAIKKEGGTHRYYREKD 44
Cdd:cd04773    1 MTIGELAHLLGVPPSTLRHWEKEGLLSPDREPETGYRVYDPSD 43

Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators; Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. 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. A typical MerR regulator is comprised of two 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 dissimilar C-terminal domains bind specific coactivator molecules.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 818694519   4 ISEAAEILGVSMDTLRRWDENGKLTAIKKEGGTHRYYREKDME 46
Cdd:cd01105    4 IGEVSKLTGVSPRQLRYWEEKGLIKSIRSDGGGQRKYSLADVD 46

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]

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 818694519    2 LKISEAAEILGVSMDTLRRWDENGKLTAIkKEGGTHRYYRE 42
Cdd:TIGR01764   2 LTVEEAAEYLGVSKSTVYRLIEEGELPAY-RVGRHYRIPRE 41

Zn(2+)-responsive transcriptional regulator;

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 818694519   1 MLKISEAAEILGVSMDTLRRWDENGKLT-AIKKEGGtHRYYREKDME 46
Cdd:PRK09514   1 MYRIGELAKLAEVTPDTLRFYEKQGLMDpEVRTEGG-YRLYTEQDLQ 46

Helix-Turn-Helix DNA binding domain of the HspR transcription regulator; Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. 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. A typical MerR regulator is 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 dissimilar C-terminal domains bind specific coactivator molecules.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 818694519   4 ISEAAEILGVSMDTLRRWDENGKLTAIKKEGGThRYYREKDME 46
Cdd:cd04766    4 ISVAAELSGMHPQTLRLYERLGLLSPSRTDGGT-RRYSERDIE 45

Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators; Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. 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. A typical MerR regulator is comprised of two 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 dissimilar C-terminal domains bind specific coactivator molecules.

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 818694519   4 ISEAAEILGVSMDTLRRWDENGKLTAIKKEGGTHRY 39
Cdd:cd01279    4 ISVAAELLGIHPQTLRVYDRLGLVSPARTNGGGRRY 39

Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are 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 have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. 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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 818694519   2 LKISEAAEILGVSMDTLRRWDENGKLTAIKKEGGTHRYYREKDME 46
Cdd:cd04784    1 MKIGELAKKTGCSVETIRYYEKEGLLPAPARSANNYRLYDEEHLE 45