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 1268330156   2 YRIGQLAHLAHVSKRTIDYYTNLGILKAERSQSNYRYYDETAFETLQFIEKCKEMHMPLCEIKERIEERKKLFGINEHVS 81
Cdd:cd04779     1 YRIGQLAHLAGVSKRTIDYYTNLGLLTPERSDSNYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLEEVQRSDKEQREVA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1268330156  82 KQVNEVTNHIHRLETELTQLKPLLDGLTDSQREKISKSLSGQTTALIQTLILFL 135
Cdd:cd04779    81 QEVQLVCDQIDGLEHRLKQLKPIASQTDRAQRMKMTKELSQQVLTLIQSLTLLL 134

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 1268330156   2 YRIGQLAHLAHVSKRTIDYYTNLGILKAERSQSNYRYYDETAFETLQFIEKCKEMHMPLCEIKERIEERKKLFGINEHVS 81
Cdd:cd04779     1 YRIGQLAHLAGVSKRTIDYYTNLGLLTPERSDSNYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLEEVQRSDKEQREVA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1268330156  82 KQVNEVTNHIHRLETELTQLKPLLDGLTDSQREKISKSLSGQTTALIQTLILFL 135
Cdd:cd04779    81 QEVQLVCDQIDGLEHRLKQLKPIASQTDRAQRMKMTKELSQQVLTLIQSLTLLL 134

helix_turn_helix, mercury resistance;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1268330156    2 YRIGQLAHLAHVSKRTIDYYTNLGILK-AERSQSNYRYYDETAFETLQFIEKCKEMHMPLCEIKERIE 68
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPpPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLE 68

Zn(2+)-responsive transcriptional regulator;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1268330156   1 MYRIGQLAHLAHVSKRTIDYYTNLGILK-AERSQSNYRYYDETAFETLQFIEKCKEMHMPLCEIKE 65
Cdd:PRK09514    1 MYRIGELAKLAEVTPDTLRFYEKQGLMDpEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRE 66

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 1268330156   2 YRIGQLAHLAHVSKRTIDYYTNLGILKAERSQSNYRYYDETAFETLQFIEKCKEMHMPLCEIKERIEERKKLFGINEHVS 81
Cdd:cd04779     1 YRIGQLAHLAGVSKRTIDYYTNLGLLTPERSDSNYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLEEVQRSDKEQREVA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1268330156  82 KQVNEVTNHIHRLETELTQLKPLLDGLTDSQREKISKSLSGQTTALIQTLILFL 135
Cdd:cd04779    81 QEVQLVCDQIDGLEHRLKQLKPIASQTDRAQRMKMTKELSQQVLTLIQSLTLLL 134

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1268330156   4 IGQLAHLAHVSKRTIDYYTNLGILK-AERSQSNYRYYDETAFETLQFIEKCKEMHMPLCEIKERIEERkklfgiNEHVSK 82
Cdd:COG0789     1 IGEVARLTGVSVRTLRYYERIGLLPpPERTEGGYRLYSEEDVERLRFIRRLRELGFSLAEIRELLDLL------DDGEEE 74

                          90       100
                  ....*....|....*....|....*.
gi 1268330156  83 QVNEVTNHIHRLETELTQLKPLLDGL 108
Cdd:COG0789    75 VRELLEEHLAELEAQIAELQALRAEL 100

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 1268330156   2 YRIGQLAHLAHVSKRTIDYYTNLGIL-KAERSQSNYRYYDETAFETLQFIEKCKEMHMPLCEIKE--RIEERKKL--FGI 76
Cdd:cd04770     1 MKIGELAKAAGVSPDTIRYYERIGLLpPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIREllSLRDDGAApcAEV 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 1268330156  77 NEHVSKQVNEVTNHIHRLETELTQLKPLLD 106
Cdd:cd04770    81 RALLEEKLAEVEAKIAELQALRAELAGLLS 110

helix_turn_helix, mercury resistance;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1268330156    2 YRIGQLAHLAHVSKRTIDYYTNLGILK-AERSQSNYRYYDETAFETLQFIEKCKEMHMPLCEIKERIE 68
Cdd:smart00422   1 YTIGEVAKLAGVSVRTLRYYERIGLLPpPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLE 68

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 1268330156   2 YRIGQLAHLAHVSKRTIDYYTNLGILKAER--SQSNYRYYDETAFETLQFIEKCKEMHMPLCEIKERIEERKKLFgINEH 79
Cdd:cd01107     1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAYvdPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADNDDE-LRKL 79

                          90       100
                  ....*....|....*....|....*....
gi 1268330156  80 VSKQVNEVTNHIHRLETELTQLKPLLDGL 108
Cdd:cd01107    80 LREKLAELEAEIEELQRILRLLEDRLKQI 108

Zn(2+)-responsive transcriptional regulator;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1268330156   1 MYRIGQLAHLAHVSKRTIDYYTNLGILK-AERSQSNYRYYDETAFETLQFIEKCKEMHMPLCEIKE 65
Cdd:PRK09514    1 MYRIGELAKLAEVTPDTLRFYEKQGLMDpEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRE 66

Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1268330156   4 IGQLAHLAHVSKRTIDYYTNLGIL-KAERSQSNYRYYDETAFETLQFIEKCKEMHMPLCEIKERIEerkkLFGINEHVSK 82
Cdd:cd01108     3 IGEAAKLTGLSAKMIRYYEEIGLIpPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLA----LWRDPSRASA 78

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1268330156  83 QVNEVTN-HIHRLE---TELTQLKPLLDGLTDS 111
Cdd:cd01108    79 DVKALALeHIAELErkiAELQAMRRTLQQLADS 111

Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators; Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They 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 HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. 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 1268330156   2 YRIGQLAHLAHVSKRTIDYYTNLGILKAERSQSN-YRYYDETAFETLQFIEKCKEMHMPLCEIKERIEERKklFGINEHV 80
Cdd:cd04768     1 LTIGEFAKLAGVSIRTLRHYDDIGLFKPAKIAENgYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDTEM--EELTAML 78

                          90
                  ....*....|....*
gi 1268330156  81 SKQVNEVTNHIHRLE 95
Cdd:cd04768    79 LEKKQAIQQKIDRLQ 93

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 1268330156   4 IGQLAHLAHVSKRTIDYYTNLGIL-KAERSQSNYRYYDETAFETLQFIEKCKEMHMPLCEIKErieerkkLFGINEHVSK 82
Cdd:cd04785     3 IGELARRTGVNVETIRYYESIGLLpEPARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEIRA-------LLALSDRPDR 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1268330156  83 QVNEV----TNHIHRLETELTQLKPLLDGLTDsqrekISKSLSGQTTA---LIQTL 131
Cdd:cd04785    76 SCAEAdaiaRAHLADVRARIADLRRLEAELKR-----MVAACSGGRVAdcrIIEAL 126

MerR family regulatory protein;

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1268330156   3 RIGQLAHLAHVSKRTIDYYTNLGILK-AERSQSNYRYY 39
Cdd:pfam00376   1 TIGEVAKLLGVSPRTLRYYEKIGLLPpPERTEGGYRRY 38

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1268330156   1 MYRIGQLAHLAHVSKRTIDYYTNLGILKAERSQSNYRYYDETAFETLQFIEKCKEMHMPLCEIKERIEER 70
Cdd:cd04775     1 MYTIGQMSRKFGVSRSTLLYYESIGLIPSARSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLAQP 70

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1268330156   1 MYRIGQLAHLAHVSKRTIDYYTNLGILK-AERSQSNYRYYDETAFETLQFIEKCKEMHMPLCEIK 64
Cdd:cd04790     1 MLTISQLARQFGLSRSTLLYYERIGLLSpSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIR 65

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1268330156   3 RIGQLAHLAHVSKRTIDYYTNLGILKA-ERSQSNYRYYDETAFETLQFIEKCKEMHMPLCEIKERIEER 70
Cdd:cd04788     2 KIGELARRTGLSVRTLHHYDHIGLLSPsQRTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRALDGP 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
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1268330156   1 MYRIGQLAHLAHVSKRTIDYYTNLGILKAERSQSNYRYYDETAFETLQFIE 51
Cdd:cd04789     1 MYTISELAEKAGISRSTLLYYEKLGLITGTRNANGYRLYPDSDLQRLLLIQ 51

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 1268330156   4 IGQLAHLAHVSKRTIDYYTNLGILKAERSQSNYRYYDETAFETLQFIEKCKEMHMPLCEIKE 65
Cdd:cd01110     4 VGEVAKRSGVAVSALHFYEQKGLIASWRNAGNQRRYPRDVLRRIAFIKVAQRLGLSLAEIAE 65

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 1268330156   2 YRIGQLAHLAHVSKRTIDYYTNLGILKAERSQSN-YRYYDETAFETLQFIEKCKEMHMPLCEIKERIE 68
Cdd:cd04773     1 MTIGELAHLLGVPPSTLRHWEKEGLLSPDREPETgYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVE 68

Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators; Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1268330156   2 YRIGQLAHLAHVSKRTIDYYTNLGILKAERS-QSNYRYYDETAFETLQFIEKCKEMHMPLCEIKERIEERKKLFGINEHV 80
Cdd:cd01105     2 IGIGEVSKLTGVSPRQLRYWEEKGLIKSIRSdGGGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLRRRRVQAEVRRRL 81

                  ...
gi 1268330156  81 SKQ 83
Cdd:cd01105    82 MKD 84

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1268330156   2 YRIGQLAHLAHVSKRTID-----YytnlGILKAERSQSNYRYYDETAFETLQFI-EKCKEMHMP 59
Cdd:cd01104     1 YTIGAVARLTGVSPDTLRawerrY----GLPAPQRTDGGHRLYSEADVARLRLIrRLTSEGVRI 60