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        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1259113792   8 YTPKIVADRLGITPDLLKVWSNEFNIQTERSQGGHRRYSKENIEELKAIKEKIHvQSWSYDQVRAW 73
Cdd:cd04764     1 YTIKEVSEIIGVKPHTLRYYEKEFNLYIPRTENGRRYYTDEDIELLKKIKTLLE-KGLSIKEIKEI 65

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1259113792   8 YTPKIVADRLGITPDLLKVWSNEFNIQTERSQGGHRRYSKENIEELKAIKEKIHvQSWSYDQVRAW 73
Cdd:cd04764     1 YTIKEVSEIIGVKPHTLRYYEKEFNLYIPRTENGRRYYTDEDIELLKKIKTLLE-KGLSIKEIKEI 65

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1259113792   8 YTPKIVADRLGITPDLLKVWSNEFNIQTERSQGGHRRYSKENIEELK 54
Cdd:COG2452     1 LTPGEAAELLGVSPKTLRRWEKEGKLPAIRTPGGHRRYPESEVERLE 47

BldC family transcriptional regulator; BldC, a helix-turn-helix transcription factor with homology to the mercury resistance transcriptional regulator MerR, is a DNA-binding protein. It is considered the founding member of a subfamily of regulators with an asymmetric head-to-tail oligomerization for cooperative DNA binding, rather than classic dimerization.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1259113792   6 EMYTPKIVADRLGITPDLLKVWSNEFNIQTERSQGGHRRYSKENIEEL 53
Cdd:NF033787    1 ELLTPAEVAALFRVDPKTVTRWAKAGKLTSIRTLGGHRRYRESEVRAL 48

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1259113792   8 YTPKIVADRLGITPDLLKVWSNEFNIQTERSQGGHRRYSKENIEELKAIKEKIHvQSWSYDQVRAW 73
Cdd:cd04764     1 YTIKEVSEIIGVKPHTLRYYEKEFNLYIPRTENGRRYYTDEDIELLKKIKTLLE-KGLSIKEIKEI 65

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 1259113792   8 YTPKIVADRLGITPDLLKVWSNEFNIQTERSQGGHRRYSKENIEELKAI 56
Cdd:cd04762     1 LTTKEAAELLGVSPSTLRRWVKEGKLKAIRTPGGHRRFPEEDLERLLGI 49

MerR HTH family regulatory protein;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1259113792   8 YTPKIVADRLGITPDLLKVWSNEFNIQTERSQGGHRRYSKENIEELKAIKE 58
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPPRTERGRRYYTDEDVERLRLIKA 51

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1259113792   8 YTPKIVADRLGITPDLLKVWSNEFNIQTERSQGGHRRYSKENIEELKAIK 57
Cdd:cd00592     1 YTIGEVAKLLGVSVRTLRYYEEKGLLPPERSENGYRLYSEEDLERLRLIR 50

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1259113792  13 VADRLGITPDLLKVWSNEFNIQ-TERSQGGHRRYSKENIEELKAIK 57
Cdd:COG0789     4 VARLTGVSVRTLRYYERIGLLPpPERTEGGYRLYSEEDVERLRFIR 49

helix_turn_helix, mercury resistance;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1259113792    8 YTPKIVADRLGITPDLLKVWSNEFNIQ-TERSQGGHRRYSKENIEELKAIK 57
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPpPIRTEGGYRLYSDEDLERLRFIK 51

Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator; Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. 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 winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1259113792   8 YTPKIVADRLGITPDLLKVWSNEFNIQTERSQGGHRRYSKENIEELKAIKE 58
Cdd:cd04774     1 YKVDEVAKRLGLTKRTLKYYEEIGLVSPERSEGRYRLYSEEDLKRLERILR 51

Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators; Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). 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        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1259113792   7 MYTPKIVADRLGITPDLLKVWSNEFNIQTERsQGGHRRYSKENIEELKAIK 57
Cdd:cd04767     1 LYPIGVVAELLNIHPETLRIWERHGLIKPAR-RNGQRLYSNNDLKRLRFIK 50