Cu(I)-responsive transcriptional regulator; This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue. [Regulatory functions, DNA interactions]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544825622    1 MNISDVAKKTGLTSKAIRFYEEKGLVTPPLRSENGYRSYTQLHLDELTLLRQARQVGFNLEECGELVNLFNDPKRHSADV 80
Cdd:TIGR02044   1 MNIGQVAKLTGLSSKMIRYYEEKGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLNLWNDPNRTSADV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 544825622   81 KKRTLEKVAEIERHIVELQAMREQLLQLADSCPGDDSADCPIIDNLA 127
Cdd:TIGR02044  81 KARTLEKVAEIERKISELQSMRDQLEALAQACPGDDSPDCPIIENLS 127

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544825622   3 ISDVAKKTGLTSKAIRFYEEKGLVTPPLRSENGYRSYTQLHLDELTLLRQARQVGFNLEECGELVNLFNDPkrhSADVKK 82
Cdd:COG0789    1 IGEVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDG---EEEVRE 77

                         90       100
                 ....*....|....*....|...
gi 544825622  83 RTLEKVAEIERHIVELQAMREQL 105
Cdd:COG0789   78 LLEEHLAELEAQIAELQALRAEL 100

MerR HTH family regulatory protein;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 544825622    1 MNISDVAKKTGLTSKAIRFYEEKGLVTPPlRSENGYRSYTQLHLDELTLLRQARQVGFNLEECGEL 66
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPP-RTERGRRYYTDEDVERLRLIKALLERGLSLKEIKEL 65

Cu(I)-responsive transcriptional regulator; This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue. [Regulatory functions, DNA interactions]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544825622    1 MNISDVAKKTGLTSKAIRFYEEKGLVTPPLRSENGYRSYTQLHLDELTLLRQARQVGFNLEECGELVNLFNDPKRHSADV 80
Cdd:TIGR02044   1 MNIGQVAKLTGLSSKMIRYYEEKGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLNLWNDPNRTSADV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 544825622   81 KKRTLEKVAEIERHIVELQAMREQLLQLADSCPGDDSADCPIIDNLA 127
Cdd:TIGR02044  81 KARTLEKVAEIERKISELQSMRDQLEALAQACPGDDSPDCPIIENLS 127

Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544825622   1 MNISDVAKKTGLTSKAIRFYEEKGLVTPPLRSENGYRSYTQLHLDELTLLRQARQVGFNLEECGELVNLFNDPKRHSADV 80
Cdd:cd04770    1 MKIGELAKAAGVSPDTIRYYERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLRDDGAAPCAEV 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 544825622  81 KKRTLEKVAEIERHIVELQAMREQLLQLADSCPGDDSADCPII 123
Cdd:cd04770   81 RALLEEKLAEVEAKIAELQALRAELAGLLSACDGDESVICPIL 123

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        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544825622   1 MNISDVAKKTGLTSKAIRFYEEKGLVTPPLRSENGYRSYTQLHLDELTLLRQARQVGFNLEECGELVNLFNDPKRHSADV 80
Cdd:cd04784    1 MKIGELAKKTGCSVETIRYYEKEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQLQDDPEASCAEV 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 544825622  81 KKRTLEKVAEIERHIVELQAMREQLLQLADSCPGDDSA-DCPIIDNL 126
Cdd:cd04784   81 NALIDEHLAHVRARIAELQALEKQLQALRERCDGARTIeECGILQGL 127

Zn(2+)-responsive transcriptional regulator;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544825622   3 ISDVAKKTGLTSKAIRFYEEKGLVTPPLRSENGYRSYTQLHLDELTLLRQARQVGFNLEECGELVNLFNDPKRHS-ADVK 81
Cdd:PRK09514   4 IGELAKLAEVTPDTLRFYEKQGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSIRLDPEHHTcQEVK 83

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 544825622  82 KRTLEKVAEIERHIVELQAMREQLLQLADSCPG--DDSADCPIIDNLA-GCCHRKTH 135
Cdd:PRK09514  84 GIVDEKLAEVEAKIAELQHMRRSLQRLNDACCGtaHSAVYCSILEALEqGASGVKSG 140

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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544825622   1 MNISDVAKKTGLTSKAIRFYEEKGLVTPPLRSENGYRSYTQLHLDELTLLRQARQVGFNLEECGELVNLfnDPKRHSADV 80
Cdd:cd04783    1 LTIGELAKAAGVNVETIRYYQRRGLLPEPPRPEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLEL--DDGTDCSEA 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 544825622  81 KKRTLEKVAEIERHIVELQAMREQLLQLADSCP-GDDSADCPIIDNL 126
Cdd:cd04783   79 RELAEQKLAEVDEKIADLQRMRASLQELVSQCAaTKNNVSCPIIAAL 125

Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines 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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544825622   1 MNISDVAKKTGLTSKAIRFYEEKGLVTPPLRsENGYRSYTQLHLDELTLLRQARQVGFNLEECGELVNLFNDPKRHSADV 80
Cdd:cd04781    1 LDIAEVARQSGLPASTLRYYEEKGLIASIGR-RGLRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSHDGKPPIDRQLL 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 544825622  81 KKrtleKVAEIERHIVELQAMReQLLQLADSCPGDDSADCPI 122
Cdd:cd04781   80 KA----KAAELDQQIQRLQAMR-ELLRHVAQCPAPSHLDCPT 116

Hg(II)-responsive transcriptional regulator; This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix. [Cellular processes, Detoxification, Regulatory functions, DNA interactions]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544825622    3 ISDVAKKTGLTSKAIRFYEEKGLVTPPLRSENGYRSYTQLHLDELTLLRQARQVGFNLEECGELVNLfnDPKRHSADVKK 82
Cdd:TIGR02051   2 IGELAKAAGVNVETIRYYERKGLLPEPDRPEGGYRRYPEETVKRLRFIKRAQELGFSLEEIGGLLGL--VDGTHCREMYE 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 544825622   83 RTLEKVAEIERHIVELQAMREQLLQLADSCP-GDDSADCPIIDNL 126
Cdd:TIGR02051  80 LASRKLKSVQAKMADLLRIERLLEELLEQCPaNKGNTSCPIIESL 124

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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544825622   1 MNISDVAKKTGLTSKAIRFYEEKGLVTPPLRSENGYRSYTQLHLDELTLLRQARQVGFNLEECGELVNLFNDPKRHSADV 80
Cdd:cd04786    1 MKIGELAKRSGMAASRIRFYEAEGLLSSVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLLPADASNWQHDELL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 544825622  81 KkrTLE-KVAEIERHIVELQAMREQLLQLADSCPGD-DSADC 120
Cdd:cd04786   81 A--ALErKVADIEALEARLAQNKAQLLVLIDLIESKpDEMDC 120

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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544825622   1 MNISDVAKKTGLTSKAIRFYEEKGLVTPPlRSENGYRSYTQLHLDELTLLRQARQVGFNLEECGELVNLFNDPK---RHS 77
Cdd:cd01282    1 MRIGELAARTGVSVRSLRYYEEQGLLVPE-RSANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLPCLRGGEptfRPC 79

                         90       100
                 ....*....|....*....|....*...
gi 544825622  78 ADVKKRTLEKVAEIERHIVELQAMREQL 105
Cdd:cd01282   80 PDLLAVLRRELARIDRQIADLTRSRDRL 107

MerR, DNA binding; Members of this family of DNA-binding domains are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 544825622   44 LDELTLLRQARQVGFNLEECGELVNLFNDPKRHSADVKKRTLEKVAEIERHIVELQAMREQLLQL 108
Cdd:pfam09278   1 LRRLAFIRRARRLGFSLEEIRELLALYDDPGPPCADVRALLREKLAELEARIAELQALRDELDAL 65

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 544825622   1 MNISDVAKKTGLTSKAIRFYEEKGLVTPPlRSENGYRSYTQLHLDELTLL 50
Cdd:cd04761    1 YTIGELAKLTGVSPSTLRYYERIGLLSPA-RTEGGYRLYSDADLERLRLI 49

Helix-Turn-Helix DNA binding domain of the BltR transcription regulator; Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators 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 predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They 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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544825622   3 ISDVAKKTGLTSKAIRFYEEKGLVTPPLRSENGYRSYTQLHLDELTLLRQARQVGFNLEECGELVNlfndpKRHSADVKK 82
Cdd:cd04782    3 TGEFAKLCGISKQTLFHYDKIGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLD-----NRNPDELIE 77

                         90       100
                 ....*....|....*....|
gi 544825622  83 RTLEKVAEIERHIVELQAMR 102
Cdd:cd04782   78 LLKKQEKEIKEEIEELQKIK 97

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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544825622   1 MNISDVAKKTGLTSKAIRFYEEKGLVTPPLRSENGYRSYTQLHLDELTLLRQARQVGFNLEECGELVnlfndpKRHSADV 80
Cdd:cd01106    1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELL------KDPSEDL 74

                         90       100
                 ....*....|....*....|....*
gi 544825622  81 KKRTLEKVAEIERHIVELQAMREQL 105
Cdd:cd01106   75 LEALREQKELLEEKKERLDKLIKTI 99

Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares 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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544825622   3 ISDVAKKTGLTSKAIRFYEEKGLVTPPLR-SENGYRSYTQLHLDELTLLRQARQVGFNLEECGELVNLFNDpkrhsADVK 81
Cdd:cd01107    3 IGEFAKLSNLSIKALRYYDKIGLLKPAYVdPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADND-----DELR 77

                         90       100
                 ....*....|....*....|....*..
gi 544825622  82 KRTLEKVAEIERHIVELQAMREQLLQL 108
Cdd:cd01107   78 KLLREKLAELEAEIEELQRILRLLEDR 104

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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544825622   1 MNISDVAKKTGLTSKAIRFYEEKGLVtPPLRSENGYRSYTQLHLDELTLLRQARQVGFNLEECGE-LVNLfndPKRHSAD 79
Cdd:cd01110    2 LSVGEVAKRSGVAVSALHFYEQKGLI-ASWRNAGNQRRYPRDVLRRIAFIKVAQRLGLSLAEIAEaLATL---PEDRTPT 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 544825622  80 vkKRTLEKVA-----EIERHIVELQAMREQLlqlaDSCPG 114
Cdd:cd01110   78 --KADWERLSrawrdRLDERIAELQQLRDQL----DGCIG 111

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 544825622   3 ISDVAKKTGLTSKAIRFYEEKGLVTPPLRSENGYRSYTQLHLDELTLLRQARQVGFNLEECGELVNLFNDPkrhSADVKK 82
Cdd:cd04790    4 ISQLARQFGLSRSTLLYYERIGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPGDD---ATDVLR 80

                         90       100
                 ....*....|....*....|....*.
gi 544825622  83 RTLekvAEIERHIVELQAMREQLLQL 108
Cdd:cd04790   81 RRL---AELNREIQRLRQQQRAIATL 103

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        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 544825622   1 MNISDVAKKTGLTSKAIRFYEEKGLVTPPLRSENGYRSYTQLHLDELTLLRQARQVGFNLEECGELV 67
Cdd:cd04773    1 MTIGELAHLLGVPPSTLRHWEKEGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVV 67

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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544825622   3 ISDVAKKTGLTSKAIRFYEEKGLVtPPLRSENGYRSYTQLHLDELTLLRQARQVGFNLEECGELVNlfndpKRHsadVKK 82
Cdd:cd04775    4 IGQMSRKFGVSRSTLLYYESIGLI-PSARSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLA-----QPH---VQA 74

                         90       100
                 ....*....|....*....|....*
gi 544825622  83 RTLEKVAEIERHIVELQAMReQLLQ 107
Cdd:cd04775   75 ILEERLQSLNREIQRLRQQQ-QVLA 98

Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator; Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. 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        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544825622   1 MNISDVAKKTGLTSKAIRFYEEKGLVTPpLRSENGYRSYTQLHLDELTLLRQARQVGFNLEECGELVNLFNDPkrhsadv 80
Cdd:cd04789    2 YTISELAEKAGISRSTLLYYEKLGLITG-TRNANGYRLYPDSDLQRLLLIQQLQAGGLSLKECLACLQGKLTR------- 73

                         90       100
                 ....*....|....*....|....*....
gi 544825622  81 kKRTLEKVAEIERHIVELQAMREQLLQLA 109
Cdd:cd04789   74 -SLLLERLSSLAEQIARKQQARDLLAALL 101

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 544825622   3 ISDVAKKTGLTSKAIRFYEEK-GLVTPplRSENGYRSYTQLHLDELTLLRQARQVGFNLEECGELVN 68
Cdd:cd04764    3 IKEVSEIIGVKPHTLRYYEKEfNLYIP--RTENGRRYYTDEDIELLKKIKTLLEKGLSIKEIKEILN 67

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        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544825622   3 ISDVAKKTGLTSKAIRFYEEKGLVTPPlRSENGYRSYTQLHLDELTLLRQARQVGFNLEEC-GELVNLFNDPKRHSADVK 81
Cdd:cd04779    3 IGQLAHLAGVSKRTIDYYTNLGLLTPE-RSDSNYRYYDETALDRLQLIEHLKGQRLSLAEIkDQLEEVQRSDKEQREVAQ 81

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 544825622  82 krtleKVAEIERHIVELQAmreQLLQLADSCPGDDSA 118
Cdd:cd04779   82 -----EVQLVCDQIDGLEH---RLKQLKPIASQTDRA 110

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
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 544825622   1 MNISDVAKKTGLTSKAIRFYEEKGLVTPPLR-SENGYRsYTQLHLDELTLLRQARQVGF 58
Cdd:cd04780    1 MRMSELSKRSGVSVATIKYYLREGLLPEGRRlAPNQAE-YSEAHVERLRLIRALQQEGG 58

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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544825622   3 ISDVAKKTGLTSKAIRFYEEKGLVTpPLRSENGYRSYTQlhlDELTLLRQARQVgfnLEECGelVNlfndpkrhsadvkk 82
Cdd:cd04766    4 ISVAAELSGMHPQTLRLYERLGLLS-PSRTDGGTRRYSE---RDIERLRRIQRL---TQELG--VN-------------- 60

                         90       100
                 ....*....|....*....|....*...
gi 544825622  83 rtLEKVAEIERHIVELQAMREQLLQLAD 110
Cdd:cd04766   61 --LAGVKRILELEEELAELRAELDELRA 86

Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators; Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, 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-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 544825622   3 ISDVAKKTGLTSKAIRFYE-EKGLVTPPlRSENGYRSYTQLHLD 45
Cdd:cd04763    3 IGEVALLTGIKPHVLRAWErEFGLLKPQ-RSDGGHRLFNDADID 45

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
                 ....*....|....*....|....*....|....*....|....*....|
gi 544825622   3 ISDVAKKTGLTSKAIRFYEEKGLVTPPLRSENGYRSYTQLHLDELTLLRQ 52
Cdd:cd04765    3 IGEVAEILGLPPHVLRYWETEFPQLKPVKRAGGRRYYRPKDVELLLLIKH 52