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        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488314303  16 LIGISELSEIAEVSPRQLRYWEEKGYISSIAKDANGPRKYRLHTVVKVHWIKRFLDEGYTLQSAVEKAEEQHRNVGMTKK 95
Cdd:cd01105    1 VIGIGEVSKLTGVSPRQLRYWEEKGLIKSIRSDGGGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLRRRRVQAEVRRR 80

                 ....*...
gi 488314303  96 IFSQMFHG 103
Cdd:cd01105   81 LMKDGLQG 88

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        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488314303  16 LIGISELSEIAEVSPRQLRYWEEKGYISSIAKDANGPRKYRLHTVVKVHWIKRFLDEGYTLQSAVEKAEEQHRNVGMTKK 95
Cdd:cd01105    1 VIGIGEVSKLTGVSPRQLRYWEEKGLIKSIRSDGGGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLRRRRVQAEVRRR 80

                 ....*...
gi 488314303  96 IFSQMFHG 103
Cdd:cd01105   81 LMKDGLQG 88

helix_turn_helix, mercury resistance;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 488314303    19 ISELSEIAEVSPRQLRYWEEKGYISSIAKDANGPRKYRLHTVVKVHWIKRFLDEGYTLQ 77
Cdd:smart00422   3 IGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLE 61

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        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488314303  16 LIGISELSEIAEVSPRQLRYWEEKGYISSIAKDANGPRKYRLHTVVKVHWIKRFLDEGYTLQSAVEKAEEQHRNVGMTKK 95
Cdd:cd01105    1 VIGIGEVSKLTGVSPRQLRYWEEKGLIKSIRSDGGGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLRRRRVQAEVRRR 80

                 ....*...
gi 488314303  96 IFSQMFHG 103
Cdd:cd01105   81 LMKDGLQG 88

helix_turn_helix, mercury resistance;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 488314303    19 ISELSEIAEVSPRQLRYWEEKGYISSIAKDANGPRKYRLHTVVKVHWIKRFLDEGYTLQ 77
Cdd:smart00422   3 IGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLE 61

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). 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 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        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 488314303  19 ISELSEIAEVSPRQLRYWEEKGYISSiAKDANGPRKYRLHTVVKVHWIKRFLDEGYTLQ 77
Cdd:cd01282    3 IGELAARTGVSVRSLRYYEEQGLLVP-ERSANGYRDYDEAAVDRVRQIRRLLAAGLTLE 60

MerR family regulatory protein;

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 488314303   19 ISELSEIAEVSPRQLRYWEEKGYISSIAKDANGPRKY 55
Cdd:pfam00376   2 IGEVAKLLGVSPRTLRYYEKIGLLPPPERTEGGYRRY 38

Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), 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. 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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488314303  19 ISELSEIAEVSPRQLRYWEEKgyISSIA--KDANGPRKYRLHTVVKVHWIKRFL-DEGYTLQSA 79
Cdd:cd04765    3 IGEVAEILGLPPHVLRYWETE--FPQLKpvKRAGGRRYYRPKDVELLLLIKHLLyEKGYTIEGA 64

Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. 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 winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. 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        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 488314303  19 ISELSEIAEVSPRQLRYWEEKGYISSIAKDANGPRKYRLHTVVKVHWIKRFLDEGYTL 76
Cdd:cd04783    3 IGELAKAAGVNVETIRYYQRRGLLPEPPRPEGGYRRYPEETVTRLRFIKRAQELGFTL 60

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. 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 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        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 488314303  19 ISELSEIAEVSPRQLRYWEEKGYISSIAKDANGPRKYRLHTVVKVHWIKRFLDEGYTLQ 77
Cdd:cd04786    3 IGELAKRSGMAASRIRFYEAEGLLSSVERSANGYRDYPPETVWVLEIISSAQQAGFSLD 61

Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. 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        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 488314303  19 ISELSEIAEVSPRQLRYWEEKGYISSIAKDANGPRKYRLHTVVKVHWIKRFLDEGYTLQ 77
Cdd:cd01108    3 IGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLE 61

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        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 488314303  19 ISELSEIAEVSPRQLRYWeEKGYISSIAKDANGPRKYRLHTVVKVHWIKRFLDEG 73
Cdd:cd04764    3 IKEVSEIIGVKPHTLRYY-EKEFNLYIPRTENGRRYYTDEDIELLKKIKTLLEKG 56

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        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488314303  19 ISELSEIAEVSPRQLRYWEEKGYISSiAKDANGPRKYRLHTVVKVHWIKRFL-DEGYTLQS 78
Cdd:cd01279    4 ISVAAELLGIHPQTLRVYDRLGLVSP-ARTNGGGRRYSNNDLELLRQVQRLSqDEGFNLAG 63

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
                 ....*....|....*....|....*....|....*...
gi 488314303  19 ISELSEIAEVSPRQLRYWEEKGYISSIAKDANGPRKYR 56
Cdd:cd04773    3 IGELAHLLGVPPSTLRHWEKEGLLSPDREPETGYRVYD 40

Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators; Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal 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 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. This subgroup lacks one of the conserved, metal-binding cysteines seen in the MerR1 group.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488314303  19 ISELSEIAEVSPRQLRYWEEKGYISSIAKDANGPRKYRLHTVVKVHWIKRFLDEGYTL---QSAVEKAEEQHRNVGMTKK 95
Cdd:cd04787    3 VKELANAAGVTPDTVRFYTRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQLGFSLkdiKEILSHADQGESPCPMVRR 82

                 ....*..
gi 488314303  96 IFSQMFH 102
Cdd:cd04787   83 LIEQRLA 89