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 491560650    1 MNISEVAKLTGLTAKAIRFYESKGIIKEASRGANGYRQYTQHQVDELLLIRRSRLVGFNLDECQELLNLSNNPNRRSADV 80
Cdd:TIGR02044   1 MNIGQVAKLTGLSSKMIRYYEEKGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLNLWNDPNRTSADV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 491560650   81 KQKTLEKVSEIETKIEELERMKKTLLDLADTCPGDDSNDCPIIKGLT 127
Cdd:TIGR02044  81 KARTLEKVAEIERKISELQSMRDQLEALAQACPGDDSPDCPIIENLS 127

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491560650   3 ISEVAKLTGLTAKAIRFYESKGIIKEASRGANGYRQYTQHQVDELLLIRRSRLVGFNLDECQELLNLsnnPNRRSADVKQ 82
Cdd:COG0789    1 IGEVARLTGVSVRTLRYYERIGLLPPPERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDL---LDDGEEEVRE 77

                         90       100
                 ....*....|....*....|...
gi 491560650  83 KTLEKVSEIETKIEELERMKKTL 105
Cdd:COG0789   78 LLEEHLAELEAQIAELQALRAEL 100

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 491560650   44 VDELLLIRRSRLVGFNLDECQELLNLSNNPNRRSADVKQKTLEKVSEIETKIEELERMKKTLLDL 108
Cdd:pfam09278   1 LRRLAFIRRARRLGFSLEEIRELLALYDDPGPPCADVRALLREKLAELEARIAELQALRDELDAL 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 491560650    1 MNISEVAKLTGLTAKAIRFYESKGIIKEASRGANGYRQYTQHQVDELLLIRRSRLVGFNLDECQELLNLSNNPNRRSADV 80
Cdd:TIGR02044   1 MNIGQVAKLTGLSSKMIRYYEEKGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLNLWNDPNRTSADV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 491560650   81 KQKTLEKVSEIETKIEELERMKKTLLDLADTCPGDDSNDCPIIKGLT 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 491560650   1 MNISEVAKLTGLTAKAIRFYESKGIIKEASRGANGYRQYTQHQVDELLLIRRSRLVGFNLDECQELLNLSNNPNRRSADV 80
Cdd:cd04770    1 MKIGELAKAAGVSPDTIRYYERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLRDDGAAPCAEV 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 491560650  81 KQKTLEKVSEIETKIEELERMKKTLLDLADTCPGDDSNDCPII 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 491560650   1 MNISEVAKLTGLTAKAIRFYESKGIIKEASRGANGYRQYTQHQVDELLLIRRSRLVGFNLDECQELLNLSNNPNRRSADV 80
Cdd:cd04784    1 MKIGELAKKTGCSVETIRYYEKEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQLQDDPEASCAEV 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 491560650  81 KQKTLEKVSEIETKIEELERMKKTLLDLADTCPGDD-SNDCPIIKGL 126
Cdd:cd04784   81 NALIDEHLAHVRARIAELQALEKQLQALRERCDGARtIEECGILQGL 127

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 491560650   1 MNISEVAKLTGLTAKAIRFYESKGIIKEASRGANGYRQYTQHQVDELLLIRRSRLVGFNLDECQELLNLSNNPNRRsaDV 80
Cdd:cd04783    1 LTIGELAKAAGVNVETIRYYQRRGLLPEPPRPEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLELDDGTDCS--EA 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 491560650  81 KQKTLEKVSEIETKIEELERMKKTLLDLADTCP-GDDSNDCPII 123
Cdd:cd04783   79 RELAEQKLAEVDEKIADLQRMRASLQELVSQCAaTKNNVSCPII 122

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 491560650   1 MNISEVAKLTGLTAKAIRFYESKGIIKeASRGANGYRQYTQHQVDELLLIRRSRLVGFNLDECQELLNLSNNPNrRSADV 80
Cdd:cd00592    1 YTIGEVAKLLGVSVRTLRYYEEKGLLP-PERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDARDEEL-SLAAL 78

                         90       100
                 ....*....|....*....|..
gi 491560650  81 KQKTLEKVSEIETKIEELERMK 102
Cdd:cd00592   79 LALLDEKLAELEEKIARLEALL 100

Zn(II)-responsive transcriptional regulator; This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc 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-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix. [Regulatory functions, DNA interactions]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491560650    3 ISEVAKLTGLTAKAIRFYESKGIIKEASRGANGYRQYTQHQVDELLLIRRSRLVGFNLDECQELLNLSNNPNRRS-ADVK 81
Cdd:TIGR02043   4 IGELAKLCGVTSDTLRFYEKNGLIKPAGRTDSGYRLYTDEDQKRLRFILKAKELGFTLDEIKELLSIKLDATEHScAEVK 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 491560650   82 QKTLEKVSEIETKIEELERMKKTLLDLADTCPG--DDSNDCPIIKGL 126
Cdd:TIGR02043  84 AIVDAKLELVDEKINELTKIRRSLKKLSDACCGhtNDASHCSILEAL 130

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 491560650   1 MNISEVAKLTGLTAKAIRFYESKGIIKEASRgANGYRQYTQHQVDELLLIRRSRLVGFNLDECQELLNLSNNPNRRSADV 80
Cdd:cd04781    1 LDIAEVARQSGLPASTLRYYEEKGLIASIGR-RGLRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSHDGKPPIDRQLL 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 491560650  81 KQktleKVSEIETKIEELERMKKTLLDLADtCPGDDSNDCPI 122
Cdd:cd04781   80 KA----KAAELDQQIQRLQAMRELLRHVAQ-CPAPSHLDCPT 116

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 491560650   1 MNISEVAKLTGLTAKAIRFYESKGIIKeASRGANGYRQYTQHQVDELLLIRRSRLVGFNLDECQELLNLSNNPN---RRS 77
Cdd:cd01282    1 MRIGELAARTGVSVRSLRYYEEQGLLV-PERSANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLPCLRGGEptfRPC 79

                         90       100
                 ....*....|....*....|...
gi 491560650  78 ADVKQKTLEKVSEIETKIEELER 100
Cdd:cd01282   80 PDLLAVLRRELARIDRQIADLTR 102

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 491560650   1 MNISEVAKLTGLTAKAIRFYESKGIIKEASRGANgYRQYTQHQVDELLLIRRSRLVGFNLDECQELLNLSNNPNRRSADV 80
Cdd:cd04769    1 MYIGELAQQTGVTIKAIRLYEEKGLLPSPKRSGN-YRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGHEGRAVLPWPH 79

                         90       100       110
                 ....*....|....*....|....*....|.
gi 491560650  81 KQKTLE-KVSEIETKIEELERMKKTLLDLAD 110
Cdd:cd04769   80 LQQALEdKKQEIRAQITELQQLLARLDAFEA 110

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 491560650   1 MNISEVAKLTGLTAKAIRFYESKGIIKEASRGANGYRQYTQHQVDELLLIRRSRLVGFNLDECQELLNLSNNPNRRSADV 80
Cdd:cd01109    1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAELRREGDSTIPER 80

                         90       100
                 ....*....|....*....|
gi 491560650  81 KQKTLEKVSEIETKIEELER 100
Cdd:cd01109   81 LELLEEHREELEEQIAELQE 100

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 491560650   3 ISEVAKLTGLTAKAIRFYESKGIIKEASRGANGYRQYTQHQVDELLLIRRSRLVGFNLDECQELLNLsnnpnrRSADVKQ 82
Cdd:cd04782    3 TGEFAKLCGISKQTLFHYDKIGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDN------RNPDELI 76

                         90       100
                 ....*....|....*....|.
gi 491560650  83 KTLEK-VSEIETKIEELERMK 102
Cdd:cd04782   77 ELLKKqEKEIKEEIEELQKIK 97

MerR HTH family regulatory protein;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 491560650    1 MNISEVAKLTGLTAKAIRFYESKGIIKEAsRGANGYRQYTQHQVDELLLIRRSRLVGFNLDECQELL 67
Cdd:pfam13411   1 YTISELARLLGVTPRTLRYWEREGLLPPP-RTERGRRYYTDEDVERLRLIKALLERGLSLKEIKELL 66

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 491560650   1 MNISEVAKLTGLTAKAIRFYESKGIIKEAsRGANGYRQYTQHQVDELLLI 50
Cdd:cd04761    1 YTIGELAKLTGVSPSTLRYYERIGLLSPA-RTEGGYRLYSDADLERLRLI 49

mercuric resistance operon transcriptional regulator MerR;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491560650   1 MNISEVAKLTGLTAKAIRFYESKGIIKEASRGANGYRQYTQHQVDELLLIRRSRLVGFNLDECQELLNLSNNPN-RRSAD 79
Cdd:PRK13752   8 LTIGVFAKAAGVNVETIRFYQRKGLLPEPDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELLRLEDGTHcEEASS 87

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 491560650  80 VKQKTLEKVSEietKIEELERMKKTLLDLADTCPGDDSN-DCPIIKGL 126
Cdd:PRK13752  88 LAEHKLKDVRE---KMADLARMEAVLSELVCACHARKGNvSCPLIASL 132

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 491560650   1 MNISEVAKLTGLTAKAIRFYESKGIIKEASRGANgyRQYTQHQVDELLLIRRSRLVGFNLDECQELLNLSnNPNRRSADV 80
Cdd:cd04776    1 YTISELAREFDVTPRTLRFYEDKGLLSPERRGQT--RVYSRRDRARLKLILRGKRLGFSLEEIRELLDLY-DPPGGNRKQ 77

                         90       100
                 ....*....|....*....|....*...
gi 491560650  81 KQKTLEKvseIETKIEELERMKKTLLDL 108
Cdd:cd04776   78 LEKMLEK---IEKRRAELEQQRRDIDAA 102

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 491560650   1 MNISEVAKLTGLTAKAIRFYESKGIIKeASRGANGYRQYTQHQVDELLLIRRSRLVGFNLDECQELLnlsnnpnrrSADV 80
Cdd:cd04789    2 YTISELAEKAGISRSTLLYYEKLGLIT-GTRNANGYRLYPDSDLQRLLLIQQLQAGGLSLKECLACL---------QGKL 71

                         90       100       110
                 ....*....|....*....|....*....|
gi 491560650  81 KQKTL-EKVSEIETKIEELERMKKTLLDLA 109
Cdd:cd04789   72 TRSLLlERLSSLAEQIARKQQARDLLAALL 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 491560650   1 MNISEVAKLTGLTAKAIRFYESKGIIKEASRGANGYRQYTQHQVDELLLIRRSRLVGFNLDECQELLnlsNNPNRRSADV 80
Cdd:cd04788    1 WKIGELARRTGLSVRTLHHYDHIGLLSPSQRTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRAL---DGPDFDPLEL 77

                         90
                 ....*....|
gi 491560650  81 KQKTLEKVSE 90
Cdd:cd04788   78 LRRQLARLEE 87

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 491560650   1 MNISEVAKLTGLTAKAIRFYESKGIIkEASRGANGYRQYTQHQVDELLLIRRSRLV-GFNLDECQELLNLSnnpnRRSAD 79
Cdd:cd04774    1 YKVDEVAKRLGLTKRTLKYYEEIGLV-SPERSEGRYRLYSEEDLKRLERILRLREVlGFSLQEVTHFLERP----LEPVD 75

                         90
                 ....*....|....*....
gi 491560650  80 VKQK-TLEKVSEIETKIEE 97
Cdd:cd04774   76 GGHRySAESLREIHDALAQ 94

Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), 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- and CarA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 491560650   2 NISEVAKLTGLTAKAIRFYESK-GIIKEAsRGANGYRQYTQHQVDELLLIRR 52
Cdd:cd01104    2 TIGAVARLTGVSPDTLRAWERRyGLPAPQ-RTDGGHRLYSEADVARLRLIRR 52

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 491560650   3 ISEVAKLTGLTAKAIRFYESK--GIIKeasRGANGYRQYTQHQVDELLLIRRSRLVGFNLDECQELLN 68
Cdd:cd04764    3 IKEVSEIIGVKPHTLRYYEKEfnLYIP---RTENGRRYYTDEDIELLKKIKTLLEKGLSIKEIKEILN 67

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 491560650   3 ISEVAKLTGLTAKAIRFYESK-GIIKEAsRGANGYRQYTQHQVDELLLIRrsRLV---GFNLDECQELLNLSNNPNRRSA 78
Cdd:cd04765    3 IGEVAEILGLPPHVLRYWETEfPQLKPV-KRAGGRRYYRPKDVELLLLIK--HLLyekGYTIEGAKQALKEDGAAAIREE 79

                         90
                 ....*....|....
gi 491560650  79 DVKQKTLEKVSEIE 92
Cdd:cd04765   80 EAEERLPSIRAELL 93

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 491560650   3 ISEVAKLTGLTAKAIRFYESKGIIkEASRGANGYRQYTQHQVDELLLIRRSRLVGFNLDECQELL----NLSNNPNRRSA 78
Cdd:cd04779    3 IGQLAHLAGVSKRTIDYYTNLGLL-TPERSDSNYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLeevqRSDKEQREVAQ 81

                         90       100
                 ....*....|....*....|...
gi 491560650  79 DVKQKTlEKVSEIETKIEELERM 101
Cdd:cd04779   82 EVQLVC-DQIDGLEHRLKQLKPI 103

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 491560650   3 ISEVAKLTGLTAKAIRFYESKGIIKEASRGANGYRQYTQHQVDELLLIRRSRLVGFNLDECQELL 67
Cdd:cd04763    3 IGEVALLTGIKPHVLRAWEREFGLLKPQRSDGGHRLFNDADIDRILEIKRWIDNGVQVSKVKKLL 67

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        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 491560650   1 MNISEVAKLTGLTAKAIRFYESKGIIKeASRGANGYRQYTQHQVDELLLI 50
Cdd:cd04762    1 LTTKEAAELLGVSPSTLRRWVKEGKLK-AIRTPGGHRRFPEEDLERLLGI 49