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 1213958018   1 MNIGDVARQSGVPPKTIRYYEDIGLVRPN-RSENGYRAFTEKHVHKLAFLGRARALGFTIEDCRTLLALYEDENRESMQV 79
Cdd:TIGR02044   1 MNIGQVAKLTGLSSKMIRYYEEKGLIPPPlRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLNLWNDPNRTSADV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1213958018  80 KAVAEEHLRQIDEKIGKLQSMKATLSDLIDRCAGDHRPDCPILADLS 126
Cdd:TIGR02044  81 KARTLEKVAEIERKISELQSMRDQLEALAQACPGDDSPDCPIIENLS 127

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213958018   3 IGDVARQSGVPPKTIRYYEDIGLVRPN-RSENGYRAFTEKHVHKLAFLGRARALGFTIEDCRTLLALYEDENREsmqVKA 81
Cdd:COG0789     1 IGEVARLTGVSVRTLRYYERIGLLPPPeRTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLLDDGEEE---VRE 77

                          90       100
                  ....*....|....*....|...
gi 1213958018  82 VAEEHLRQIDEKIGKLQSMKATL 104
Cdd:COG0789    78 LLEEHLAELEAQIAELQALRAEL 100

MerR HTH family regulatory protein;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1213958018   1 MNIGDVARQSGVPPKTIRYYEDIGLVRPNRSENGYRAFTEKHVHKLAFLGRARALGFTIEDCRTLL 66
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPPRTERGRRYYTDEDVERLRLIKALLERGLSLKEIKELL 66

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 1213958018   1 MNIGDVARQSGVPPKTIRYYEDIGLVRPN-RSENGYRAFTEKHVHKLAFLGRARALGFTIEDCRTLLALYEDENRESMQV 79
Cdd:TIGR02044   1 MNIGQVAKLTGLSSKMIRYYEEKGLIPPPlRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLNLWNDPNRTSADV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1213958018  80 KAVAEEHLRQIDEKIGKLQSMKATLSDLIDRCAGDHRPDCPILADLS 126
Cdd:TIGR02044  81 KARTLEKVAEIERKISELQSMRDQLEALAQACPGDDSPDCPIIENLS 127

Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators; Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR 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 comprise 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 1213958018   1 MNIGDVARQSGVPPKTIRYYEDIGLV-RPNRSENGYRAFTEKHVHKLAFLGRARALGFTIEDCRTLLALYEDENRESMQV 79
Cdd:cd04785     1 LSIGELARRTGVNVETIRYYESIGLLpEPARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLALSDRPDRSCAEA 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1213958018  80 KAVAEEHLRQIDEKIGKLQSMKATLSDLIDRCAGDHRPDCPILADL 125
Cdd:cd04785    81 DAIARAHLADVRARIADLRRLEAELKRMVAACSGGRVADCRIIEAL 126

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 1213958018   1 MNIGDVARQSGVPPKTIRYYEDIGLV-RPNRSENGYRAFTEKHVHKLAFLGRARALGFTIEDCRTLLALYEDENRESMQV 79
Cdd:cd04784     1 MKIGELAKKTGCSVETIRYYEKEGLLpAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQLQDDPEASCAEV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1213958018  80 KAVAEEHLRQIDEKIGKLQSMKATLSDLIDRCAGDHRP-DCPILADL 125
Cdd:cd04784    81 NALIDEHLAHVRARIAELQALEKQLQALRERCDGARTIeECGILQGL 127

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        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213958018   1 MNIGDVARQSGVPPKTIRYYEDIGLVRPNRSENGYRAFTEKHVHKLAFLGRARALGFTIEDCRTLLALYEDENRESmQVK 80
Cdd:cd00592     1 YTIGEVAKLLGVSVRTLRYYEEKGLLPPERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDARDEELSLA-ALL 79

                          90       100
                  ....*....|....*....|.
gi 1213958018  81 AVAEEHLRQIDEKIGKLQSMK 101
Cdd:cd00592    80 ALLDEKLAELEEKIARLEALL 100

Zn(2+)-responsive transcriptional regulator;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213958018   3 IGDVARQSGVPPKTIRYYEDIGLVRPN-RSENGYRAFTEKHVHKLAFLGRARALGFTIEDCRTLLALYED-ENRESMQVK 80
Cdd:PRK09514    4 IGELAKLAEVTPDTLRFYEKQGLMDPEvRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSIRLDpEHHTCQEVK 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1213958018  81 AVAEEHLRQIDEKIGKLQSMKATLSDLIDRCAG--DHRPDCPILADL 125
Cdd:PRK09514   84 GIVDEKLAEVEAKIAELQHMRRSLQRLNDACCGtaHSAVYCSILEAL 130

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        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213958018   1 MNIGDVARQSGVPPKTIRYYEDIGLVRP-NRSENGYRAFTEKHVHKLAFLGRARALGFTIEDCRTLLALYEDENRESMQV 79
Cdd:cd01109     1 YTIKEVAEKTGLSADTLRYYEKEGLLPPvKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAELRREGDSTIPER 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 1213958018  80 KAVAEEHLRQIDEKIGKLQSMKATLSDLID 109
Cdd:cd01109    81 LELLEEHREELEEQIAELQETLAYLDYKID 110

Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators; Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. 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 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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213958018   1 MNIGDVARQSGVPPKTIRYYEDIGLV-RPNRSENgYRAFTEKHVHKLAFLGRARALGFTIEDCRTLLALYEDENRESMQV 79
Cdd:cd04769     1 MYIGELAQQTGVTIKAIRLYEEKGLLpSPKRSGN-YRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGHEGRAVLPWPH 79

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1213958018  80 KAVA-EEHLRQIDEKIGKLQSMKATLSDLID 109
Cdd:cd04769    80 LQQAlEDKKQEIRAQITELQQLLARLDAFEA 110

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 1213958018   3 IGDVARQSGVPPKTIRYYEDIGLVRPNR--SENGYRAFTEKHVHKLAFLGRARALGFTIEDCRTLLALYEDENRESMqvk 80
Cdd:cd01107     3 IGEFAKLSNLSIKALRYYDKIGLLKPAYvdPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADNDDELRKL--- 79

                          90       100       110
                  ....*....|....*....|....*....|
gi 1213958018  81 avAEEHLRQIDEKIGKLQSMKATLSDLIDR 110
Cdd:cd01107    80 --LREKLAELEAEIEELQRILRLLEDRLKQ 107

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 1213958018   1 MNIGDVARQSGVPPKTIRYYEDIGLVRPNRSENGYRAFTEKHVHKLAFLGRARALGFTIEDCRTLLA-LYEDENRESM-- 77
Cdd:cd01282     1 MRIGELAARTGVSVRSLRYYEEQGLLVPERSANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLPcLRGGEPTFRPcp 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1213958018  78 QVKAVAEEHLRQIDEKIGKLQSMKATLSDLID 109
Cdd:cd01282    81 DLLAVLRRELARIDRQIADLTRSRDRLDAYLA 112

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 1213958018   1 MNIGDVARQSGVPPKTIRYYEDIGLVRPNRSENGYRAFTEKHVHKLAFLGRARALGFTIEDCRTLLALYEDENRESMQVK 80
Cdd:cd04781     1 LDIAEVARQSGLPASTLRYYEEKGLIASIGRRGLRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSHDGKPPIDRQLLK 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1213958018  81 AVAEEhlrqIDEKIGKLQSMKATLsDLIDRCAGDHRPDCPI 121
Cdd:cd04781    81 AKAAE----LDQQIQRLQAMRELL-RHVAQCPAPSHLDCPT 116

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 1213958018   1 MNIGDVARQSGVPPKTIRYYEDIGLVRPNRS-ENGYRAFTEKHVHKLAFLGRARALGFTIEDCRTLLALYEDENRESMQV 79
Cdd:cd04787     1 MKVKELANAAGVTPDTVRFYTRIGLLRPTRDpVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILSHADQGESPCPMV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1213958018  80 KAVAEEHLRQIDEKIGKLQS----MKATLSDLidRCAGDHRPD 118
Cdd:cd04787    81 RRLIEQRLAETERRIKELLKlrdrMQQAVSQW--QQMPDGAPD 121

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 1213958018   1 MNIGDVARQSGVPPKTIRYYEDIGLVRPNRSENGYRAFTEKHVHKLAFL 49
Cdd:cd04761     1 YTIGELAKLTGVSPSTLRYYERIGLLSPARTEGGYRLYSDADLERLRLI 49

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        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213958018   1 MNIGDVARQSGVPPKTIRYYEDIGLVRPNRSENGYRAFTEKHVHKLAFLGRARA-LGFTIEDCRTLLALYEdENRESMQV 79
Cdd:cd04774     1 YKVDEVAKRLGLTKRTLKYYEEIGLVSPERSEGRYRLYSEEDLKRLERILRLREvLGFSLQEVTHFLERPL-EPVDGGHR 79

                          90
                  ....*....|....*..
gi 1213958018  80 KavAEEHLRQIDEKIGK 96
Cdd:cd04774    80 Y--SAESLREIHDALAQ 94

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 1213958018   3 IGDVARQSGVPPKTIRYYEDIGLVRPN-RSENGYRAFTEKHVHKLAFLGRARALGFTIEDCRTLLalyedENRESMQVKA 81
Cdd:cd04782     3 TGEFAKLCGISKQTLFHYDKIGLFKPEiVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYL-----DNRNPDELIE 77

                          90       100
                  ....*....|....*....|
gi 1213958018  82 VAEEHLRQIDEKIGKLQSMK 101
Cdd:cd04782    78 LLKKQEKEIKEEIEELQKIK 97

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 1213958018   1 MNIGDVARQSGVPPKTIRYYEDIGLVRPNRSENGYRAFTEKHVHKLAFLGRARALGFTIEDCRTLLA-LYEDENRESMQV 79
Cdd:cd01110     2 LSVGEVAKRSGVAVSALHFYEQKGLIASWRNAGNQRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALAtLPEDRTPTKADW 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1213958018  80 KAVAEEHLRQIDEKIGKLQSMKATLSDLI-------DRCA 112
Cdd:cd01110    82 ERLSRAWRDRLDERIAELQQLRDQLDGCIgcgclslKKCP 121

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 1213958018   3 IGDVARQSGVPPKTIRYYEDIGLVRPNRSENGYRAFTEKHVHKLAFLGRARALGFTIEDCRTLLalyedenrESMQVKAV 82
Cdd:cd04775     4 IGQMSRKFGVSRSTLLYYESIGLIPSARSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCL--------AQPHVQAI 75

                          90       100
                  ....*....|....*....|....*.
gi 1213958018  83 AEEHLRQIDEKIGKLQSMKATLSDLI 108
Cdd:cd04775    76 LEERLQSLNREIQRLRQQQQVLAAIL 101

Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR; Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively 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 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 1213958018   1 MNIGDVARQSGVPPKTIRYYEDIGLVRPN-RSENGYRAFTEKHVHKLAFLGRARALGFTIEDCRTLLalyedeNRESMQV 79
Cdd:cd04788     1 WKIGELARRTGLSVRTLHHYDHIGLLSPSqRTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRAL------DGPDFDP 74

                          90
                  ....*....|....*....
gi 1213958018  80 KAVAEEHLRQIDEKIGKLQ 98
Cdd:cd04788    75 LELLRRQLARLEEQLELAT 93

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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213958018   1 MNIGDVARQSGVPPKTIRYYEDIGLVRPNRS-ENGYRAFTEKHVHKLAFLGRARALGFTIEDCRTLLALYEDENRESMQV 79
Cdd:cd04773     1 MTIGELAHLLGVPPSTLRHWEKEGLLSPDREpETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVEQLRHAGGTEALA 80

                  ....*....
gi 1213958018  80 KAVAEEHLR 88
Cdd:cd04773    81 AALEQRRVA 89

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        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1213958018   3 IGDVARQSGVPPKTIRYYE-DIGLVRPNRSENGYRAFTEKHVHKLAFLGRARALGFTIEDCRTLLA 67
Cdd:cd04763     3 IGEVALLTGIKPHVLRAWErEFGLLKPQRSDGGHRLFNDADIDRILEIKRWIDNGVQVSKVKKLLS 68

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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213958018   3 IGDVARQSGVPPKTIRYYED-IGLVRPNRSENGYRAFTEKHVHklaFLGRARAL----GFTIEDCRTLLAlyedENRESM 77
Cdd:cd04765     3 IGEVAEILGLPPHVLRYWETeFPQLKPVKRAGGRRYYRPKDVE---LLLLIKHLlyekGYTIEGAKQALK----EDGAAA 75

                          90       100
                  ....*....|....*....|..
gi 1213958018  78 QVKAVAEEHLRQIDEKIGKLQS 99
Cdd:cd04765    76 IREEEAEERLPSIRAELLDLRD 97

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 1213958018   3 IGDVARQSGVPPKTIRYYEDIGLVRPNRSENGYRAFTEKHVHKLAFLGR-ARALGFTIEDCRTLLALyEDENRE 75
Cdd:cd04766     4 ISVAAELSGMHPQTLRLYERLGLLSPSRTDGGTRRYSERDIERLRRIQRlTQELGVNLAGVKRILEL-EEELAE 76

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 1213958018   1 MNIGDVARQSGVPPKTIRYYEDIGLVRPNRSENGYRAFTEKHVHKLA 47
Cdd:cd04762     1 LTTKEAAELLGVSPSTLRRWVKEGKLKAIRTPGGHRRFPEEDLERLL 47

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 1213958018   3 IGDVARQSGVPPKTIRYYE-DIGLVRPnRSENGYRAFTEKHVHKLAFLGRARALGFTIEDCRTLL 66
Cdd:cd04764     3 IKEVSEIIGVKPHTLRYYEkEFNLYIP-RTENGRRYYTDEDIELLKKIKTLLEKGLSIKEIKEIL 66

Helix-Turn-Helix DNA binding domain of the MerD transcription regulator; Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which 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 N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213958018   3 IGDVARQSGVPPKTIRYYEDIGLVRP-NRSENGYRAFTEKHVHKLAFLGRARALGFTIED----CRTLlalyedENRESM 77
Cdd:cd01111     3 ISQLALDAGVSVHIVRDYLLRGLLHPvARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDElarlCRAL------DAGDGK 76

                          90       100       110
                  ....*....|....*....|....*....|
gi 1213958018  78 QVKAVAEEHLRQIDEKIGKLQSMKATLSDL 107
Cdd:cd01111    77 QPEACLAQLRQKIEVRRAALNALTTQLAEM 106

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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1213958018   2 NIGDVARQSGVPPKTIRYYEDIGLVRPNRsENGYRAFTEKHVHKLAFLGR-ARALGFTIEDCRTLLALY-----EDENRE 75
Cdd:cd04767     3 PIGVVAELLNIHPETLRIWERHGLIKPAR-RNGQRLYSNNDLKRLRFIKKlINEKGLNIAGVKQILSMYpcwsiRDCDEG 81