MerR HTH family regulatory protein;

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 1490454836 13 NIDQVSKLTGVRKSTLRYWEKTFEefLKPKRTESNRREYSLADVEKVNTIKRLIDE 68
Cdd:pfam13411  2 TISELARLLGVTPRTLRYWEREGL--LPPPRTERGRRYYTDEDVERLRLIKALLER 55

helix_turn_helix, mercury resistance;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1490454836  12 LNIDQVSKLTGVRKSTLRYWEKtfEEFLKP-KRTESNRREYSLADVEKVNTIKRLID 67
Cdd:smart00422  1 YTIGEVAKLAGVSVRTLRYYER--IGLLPPpIRTEGGYRLYSDEDLERLRFIKRLKE 55

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 1490454836 14 IDQVSKLTGVRKSTLRYWEKTFEEfLKPKRTESNRREYSLADVEKVNTIKRLIDEEHLTTLGVRLRL 80
Cdd:cd04765    3 IGEVAEILGLPPHVLRYWETEFPQ-LKPVKRAGGRRYYRPKDVELLLLIKHLLYEKGYTIEGAKQAL 68

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
                 ....*....|....*....|....*....|....*....|....*....|.
gi 1490454836 12 LNIDQVSKLTGVRKSTLRYWEKtfEEFLKPKRTESNRREYSLADVEKVNTI 62
Cdd:cd04761    1 YTIGELAKLTGVSPSTLRYYER--IGLLSPARTEGGYRLYSDADLERLRLI 49

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 1490454836  12 LNIDQVSKLTGVRKSTLRYWEKtfEEFLKPKRTESNRREYSLADVEKVNTIKRLID 67
Cdd:cd00592     1 YTIGEVAKLLGVSVRTLRYYEE--KGLLPPERSENGYRLYSEEDLERLRLIRRLRE 54

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 1490454836 12 LNIDQVSKLTGVRKSTLRYWEKTfeEFLKPKRTE-SNRREYSLADVEKVNTIKRLIDE------------EHLTTLGVRL 78
Cdd:cd01105    2 IGIGEVSKLTGVSPRQLRYWEEK--GLIKSIRSDgGGQRKYSLADVDRLLVIKELLDEgftlaaaveklrRRRVQAEVRR 79

                         90
                 ....*....|.
gi 1490454836 79 RLdqFSDDFQG 89
Cdd:cd01105   80 RL--MKDGLQG 88

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        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1490454836 14 IDQVSKLTGVRKSTLRYWEKtfEEFLKPKRTESNRREYSLADVEKVNTIKRLIDEEHLTTLGVR--LRLDQ 82
Cdd:cd04766    4 ISVAAELSGMHPQTLRLYER--LGLLSPSRTDGGTRRYSERDIERLRRIQRLTQELGVNLAGVKriLELEE 72

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 1490454836 14 IDQVSKLTGVRKSTLRYWEKTFEefLKPKRTESNRREYSLADVEKVNTIKRLIDE 68
Cdd:cd04764    3 IKEVSEIIGVKPHTLRYYEKEFN--LYIPRTENGRRYYTDEDIELLKKIKTLLEK 55

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1490454836  11 MLNIDQVSKLTGVRKSTLRYWEKtfEEFLKPKRtESNRREYSLADVEKVNTIKRLIDEEHLTTLGVR 77
Cdd:cd04767     1 LYPIGVVAELLNIHPETLRIWER--HGLIKPAR-RNGQRLYSNNDLKRLRFIKKLINEKGLNIAGVK 64

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 1490454836  12 LNIDQVSKLTGVRKSTLRYWEKtfEEFLKPKRTESNRREYSLADVEKVNTIKRLID 67
Cdd:cd01282     1 MRIGELAARTGVSVRSLRYYEE--QGLLVPERSANGYRDYDEAAVDRVRQIRRLLA 54

HTH-type transcriptional regulator MlrA;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1490454836  11 MLNIDQVSKLTGVRKSTLRYWEKTFEeFLKPKRTESNRREYSLADVEKVNTIKRLID 67
Cdd:PRK15043    3 LYTIGEVALLCDINPVTLRAWQRRYG-LLKPQRTDGGHRLFNDADIDRIREIKRWID 58

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 1490454836 12 LNIDQVSKLTGVRKSTLRYWEKTFEefLKPKRTESNRREYSLADVEK 58
Cdd:cd04762    1 LTTKEAAELLGVSPSTLRRWVKEGK--LKAIRTPGGHRRFPEEDLER 45

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 1490454836  12 LNIDQVSKLTGVRKSTLRYWEKTfeEFLKP-KRTESNRREYSLADVEKVNTIKR 64
Cdd:cd01108     1 MNIGEAAKLTGLSAKMIRYYEEI--GLIPPpSRSDNGYRVYNQRDIEELRFIRR 52

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        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1490454836  14 IDQVSKLTGVRKSTLRYWEKTfeEFLKP-KRTESNRREYSLADVEKVNTI 62
Cdd:cd01106     3 VGEVAKLTGVSVRTLHYYDEI--GLLKPsRRTENGYRLYTEEDLERLQQI 50

Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators; Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, 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        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490454836  11 MLNIDQVSKLTGVRKSTLRYWEKTfeEFLKP-KRTESNRREYSLADVEKVNTIKrLIDEEHLTTLGVRLRLDQFSDDFQG 89
Cdd:cd04790     1 MLTISQLARQFGLSRSTLLYYERI--GLLSPsARSESNYRLYGERDLERLEQIC-AYRSAGVSLEDIRSLLQQPGDDATD 77

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), 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 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        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1490454836 14 IDQVSKLTGVRKSTLRYWEKtfEEFLKP-KRTESNRREYSLADVEKVNTIKRLIDEEHLTTLGVRLRLDQFSDD 86
Cdd:cd04780    3 MSELSKRSGVSVATIKYYLR--EGLLPEgRRLAPNQAEYSEAHVERLRLIRALQQEGGLPISQIKEVLDAIADA 74

Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator; Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1490454836  11 MLNIDQVSKLTGVRKSTLRYWEKtfEEFLKPKRTESNRREYSLADVEKVNTIK 63
Cdd:cd01110     1 ELSVGEVAKRSGVAVSALHFYEQ--KGLIASWRNAGNQRRYPRDVLRRIAFIK 51

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1490454836  12 LNIDQVSKLTGVRKSTLRYWEKtfEEFLKPKRTESNRREYSLADVEK 58
Cdd:COG2452     1 LTPGEAAELLGVSPKTLRRWEK--EGKLPAIRTPGGHRRYPESEVER 45

Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators; Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, 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        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1490454836  11 MLNIDQVSKLTGVRKSTLRYWEKTfeEFLKPKRTESNRREYSLADVEKVNTIKRL 65
Cdd:cd04775     1 MYTIGQMSRKFGVSRSTLLYYESI--GLIPSARSEANYRLYSEADLSRLEKIVFL 53

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). 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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1490454836  12 LNIDQVSKLTGVRKSTLRYWekTFEEFLKPKRTESNRREYSLADVEKVNTIKRLiDEEHLT 72
Cdd:cd04779     1 YRIGQLAHLAGVSKRTIDYY--TNLGLLTPERSDSNYRYYDETALDRLQLIEHL-KGQRLS 58