HEAT repeat [General function prediction only];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664518158 192 VRERAVRTLAALPGDRATPHLRDALAHPDEAVRGCAALALGARGHTEAVPELVGMIvagrNDTD------AADALSVLCD 265
Cdd:COG1413    1 VRRAAARALGRLGDPAAVPALIAALADEDPDVRAAAARALGRLGDPRAVPALLEAL----KDPDpevraaAAEALGRIGD 76

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 664518158 266 apgtaDEITDALVTHLTADAtrPPARGRLTQALGDIPGPRAARALASLTEDGDPAVALTATYLL 329
Cdd:COG1413   77 -----PEAVPALIAALKDED--PEVRRAAAEALGRLGDPAAVPALLEALKDPDWEVRRAAARAL 133

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664518158   3 IGEVARRSGISARMLRHYESLGLVRPSSRTGSGYREYSGADIRRIFHIESLRSLGLSLKETARAL---DDPAFAPTVLVG 79
Cdd:COG0789    1 IGEVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLdllDDGEEEVRELLE 80

                         90       100
                 ....*....|....*....|
gi 664518158  80 DLIDRTRERMAAEERLLTRL 99
Cdd:COG0789   81 EHLAELEAQIAELQALRAEL 100

MerR HTH family regulatory protein;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 664518158    1 MLIGEVARRSGISARMLRHYESLGLVRPSsRTGSGYREYSGADIRRIFHIESLRSLGLSLKETARAL 67
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPP-RTERGRRYYTDEDVERLRLIKALLERGLSLKEIKELL 66

Zn(2+)-responsive transcriptional regulator;

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 664518158   3 IGEVARRSGISARMLRHYESLGLVRPSSRTGSGYREYSGADIRRIFHIESLRSLGLSLKETARALD 68
Cdd:PRK09514   4 IGELAKLAEVTPDTLRFYEKQGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLS 69

HEAT repeats; This family includes multiple HEAT repeats.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664518158  177 VPPLLAQGLDSPLPAVRERAVRTLAALPGDRATPHLRDALAHPDEAVRGCAALALGARGHTEAVPELVGMIVAGRNDTDA 256
Cdd:pfam13646   1 LPALLQALLRDPDPEVRAAAIRALGRIGDPEAVPALLELLKDEDPAVRRAAAEALGKIGDPEALPALLELLRDDDDDVVR 80

                  ....*..
gi 664518158  257 ADALSVL 263
Cdd:pfam13646  81 AAAAEAL 87

fumarate reductase/succinate dehydrogenase flavoprotein subunit;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664518158 134 AALAATGETAPVPADALAEAALNEaDPNVAGALRWALAR--SDDDVPPLLAQGLDSPLPAVRERAVRTLAALPGDRATPH 211
Cdd:PRK13800 764 KGLATLGAGGAPAGDAVRALTGDP-DPLVRAAALAALAElgCPPDDVAAATAALRASAWQVRQGAARALAGAAADVAVPA 842

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 664518158 212 LRDALAHPDEAVRGCAALALGaRGHTEavPELVGMIVAGRNDTDA 256
Cdd:PRK13800 843 LVEALTDPHLDVRKAAVLALT-RWPGD--PAARDALTTALTDSDA 884

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 664518158   3 IGEVARRSGISARMLRHYESLGLVRPSSRTGSGYREYSGADIRRIFHIESLRSLGLSLKETARALDDPAFaptvlvgDLI 82
Cdd:cd01106    3 VGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDPSE-------DLL 75

                         90       100
                 ....*....|....*....|...
gi 664518158  83 DRTRERmaaEERLLTRLSRIDAA 105
Cdd:cd01106   76 EALREQ---KELLEEKKERLDKL 95

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 664518158   1 MLIGEVARRSGISARMLRHYESLGLVRPSsRTGSGYREYSGADIRRIFHIESLRSLGLSLKETARALDDPAFAPTV-LVG 79
Cdd:cd00592    1 YTIGEVAKLLGVSVRTLRYYEEKGLLPPE-RSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDARDEELSLaALL 79

                         90       100
                 ....*....|....*....|
gi 664518158  80 DLIDRTRERMAAEERLLTRL 99
Cdd:cd00592   80 ALLDEKLAELEEKIARLEAL 99

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 664518158   1 MLIGEVARRSGISARMLRHYESLGLVRPsSRTGSGYREYSGADIRRIFHIESLRSLGLSLKETARAL-----DDPAFAPT 75
Cdd:cd01282    1 MRIGELAARTGVSVRSLRYYEEQGLLVP-ERSANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLpclrgGEPTFRPC 79

                         90       100       110
                 ....*....|....*....|....*....|
gi 664518158  76 vlvGDLIDRTRERMAAEERLLTRLSRIDAA 105
Cdd:cd01282   80 ---PDLLAVLRRELARIDRQIADLTRSRDR 106

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 664518158   3 IGEVARRSGISARMLRHYESLGLVRPSSR-TGSGYREYSGADIRRIFHIESLRSLGLSLKETARALD--DPAFAPTVLVG 79
Cdd:cd01107    3 IGEFAKLSNLSIKALRYYDKIGLLKPAYVdPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDadNDDELRKLLRE 82

                         90       100
                 ....*....|....*....|..
gi 664518158  80 dLIDRTRERMAAEERLLTRLSR 101
Cdd:cd01107   83 -KLAELEAEIEELQRILRLLED 103

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 664518158   1 MLIGEVARRSGISARMLRHYESLGLVRPSSRTGSGYREYSGADIRRIFHIESLRSLGLSLKETARalddpaFAPTVLVGD 80
Cdd:cd01109    1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKE------YAELRREGD 74

                         90       100       110
                 ....*....|....*....|....*....|..
gi 664518158  81 --------LIDRTRERMAAEERLLTR-LSRID 103
Cdd:cd01109   75 stiperleLLEEHREELEEQIAELQEtLAYLD 106

MerR HTH family regulatory protein;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 664518158    1 MLIGEVARRSGISARMLRHYESLGLVRPSsRTGSGYREYSGADIRRIFHIESLRSLGLSLKETARAL 67
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPP-RTERGRRYYTDEDVERLRLIKALLERGLSLKEIKELL 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 664518158    1 MLIGEVARRSGISARMLRHYESLGLVRPSSRTGSGYREYSGADIRRIFHIESLRSLGLSLKETaRALDDPAFAPTVLVGD 80
Cdd:TIGR02044   1 MNIGQVAKLTGLSSKMIRYYEEKGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEEC-KELLNLWNDPNRTSAD 79

                          90       100
                  ....*....|....*....|..
gi 664518158   81 LIDRTRERMAAEERLLTRLSRI 102
Cdd:TIGR02044  80 VKARTLEKVAEIERKISELQSM 101

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 664518158   3 IGEVARRSGISARMLRHYESLGLVRPSSRTGSGYREYSGADIRRIFHIESLRSLGLSLKETARALDDP-AFAPTVLVGDL 81
Cdd:cd04790    4 ISQLARQFGLSRSTLLYYERIGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPgDDATDVLRRRL 83

                         90       100
                 ....*....|....*....|
gi 664518158  82 --IDRTRERMAAEERLLTRL 99
Cdd:cd04790   84 aeLNREIQRLRQQQRAIATL 103

MerR family regulatory protein;

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 664518158    3 IGEVARRSGISARMLRHYESLGLVRPSSRTGSGYREY 39
Cdd:pfam00376   2 IGEVAKLLGVSPRTLRYYEKIGLLPPPERTEGGYRRY 38

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 664518158   1 MLIGEVARRSGISARMLRHYESLGLVRpSSRTGSGYREYSGADIRRIFHIESLRSLGLSLKETARALDD 69
Cdd:cd01110    2 LSVGEVAKRSGVAVSALHFYEQKGLIA-SWRNAGNQRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALAT 69

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 664518158   1 MLIGEVARRSGISARMLRHYESLGLVRPsSRTGSGYREYSGADIRRI 47
Cdd:cd04761    1 YTIGELAKLTGVSPSTLRYYERIGLLSP-ARTEGGYRLYSDADLERL 46

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 664518158   3 IGEVARRSGISARMLRHYESLGLVRPSSRTGSGYREYSGADIRRIFHIESLRSLGLSLKETARALDDP 70
Cdd:cd04782    3 TGEFAKLCGISKQTLFHYDKIGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDNR 70

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 664518158   3 IGEVARRSGISARMLRHYESLGLVrPSSRTGSGYREYSGADIRRIFHIESLRSLGLSLKETARALDDP 70
Cdd:cd04775    4 IGQMSRKFGVSRSTLLYYESIGLI-PSARSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLAQP 70

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 664518158   1 MLIGEVARRSGISARMLRHYESLGLVRpSSRTGSGYREYSGADIRRIFHIESLRSLGLSLKETARALD 68
Cdd:cd04789    2 YTISELAEKAGISRSTLLYYEKLGLIT-GTRNANGYRLYPDSDLQRLLLIQQLQAGGLSLKECLACLQ 68

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 664518158   1 MLIGEVARRSGISARMLRHYESLGLVRPSSRTGsGYREYSGADIRRIFHIESLRSLGLSLKETARALDDPAFAPtvlvgd 80
Cdd:cd04781    1 LDIAEVARQSGLPASTLRYYEEKGLIASIGRRG-LRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSHDGKPP------ 73

                         90       100
                 ....*....|....*....|....
gi 664518158  81 lIDRT--RERMAAEERLLTRLSRI 102
Cdd:cd04781   74 -IDRQllKAKAAELDQQIQRLQAM 96

HEAT repeats; This family includes multiple HEAT repeats.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664518158  177 VPPLLAQGLDSPLPAVRERAVRTLAALPGDRATPHLRDALAHPDEAVRGCAALALGARGHTEAVPELVGMIVAGRNDTDA 256
Cdd:pfam13646   1 LPALLQALLRDPDPEVRAAAIRALGRIGDPEAVPALLELLKDEDPAVRRAAAEALGKIGDPEALPALLELLRDDDDDVVR 80

                  ....*..
gi 664518158  257 ADALSVL 263
Cdd:pfam13646  81 AAAAEAL 87

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 664518158   1 MLIGEVARRSGISARMLRHYESLGLVRPSSRTGSGYREYSGADIRRIFHIESLRSLGLSLKETARALddPAFAPTVLVGD 80
Cdd:cd04786    1 MKIGELAKRSGMAASRIRFYEAEGLLSSVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLL--PADASNWQHDE 78

                         90       100
                 ....*....|....*....|.
gi 664518158  81 LIDRTRERMAAEERLLTRLSR 101
Cdd:cd04786   79 LLAALERKVADIEALEARLAQ 99

Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. 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 664518158   3 IGEVARRSGISARMLRHYESLGLVRPsSRTGsGYREYSGADIRRIFHIESLRSLGLSLKETARALD--DPAFAPTVLVGD 80
Cdd:cd04776    3 ISELAREFDVTPRTLRFYEDKGLLSP-ERRG-QTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDlyDPPGGNRKQLEK 80

                         90       100
                 ....*....|....*....|....*
gi 664518158  81 LIDRTRERMAAEERlltRLSRIDAA 105
Cdd:cd04776   81 MLEKIEKRRAELEQ---QRRDIDAA 102

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 664518158   1 MLIGEVARRSGISARMLRHYESLGLVRPSSRTGSGYREYSGADIRRIFHIESLRSLGLSLKETARALDD 69
Cdd:cd04773    1 MTIGELAHLLGVPPSTLRHWEKEGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVEQ 69

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.

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gi 664518158   3 IGEVARRSGISARMLRHYESLGLVRPsSRTGSGYREYSGADIRRIFHIESLRSLGLSLKE 62
Cdd:cd04779    3 IGQLAHLAGVSKRTIDYYTNLGLLTP-ERSDSNYRYYDETALDRLQLIEHLKGQRLSLAE 61

Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.

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gi 664518158   3 IGEVARRSGISARMLRHYE-SLGLVRPssRTGSGYREYSGADIRRIFHIESLRSLGLSLKETARAL 67
Cdd:cd04764    3 IKEVSEIIGVKPHTLRYYEkEFNLYIP--RTENGRRYYTDEDIELLKKIKTLLEKGLSIKEIKEIL 66

mercuric resistance operon transcriptional regulator MerR;