Conserved Protein Domain Family
HTH_MerR-like_sg2

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cd04778: HTH_MerR-like_sg2 
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily
Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 2). 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.
Statistics
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PSSM-Id: 133405
View PSSM: cd04778
Aligned: 10 rows
Threshold Bit Score: 214.949
Threshold Setting Gi: 21221610
Created: 4-Jan-2007
Updated: 17-Jan-2013
Structure
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Aligned Rows:
 
DNA bindingputative dimer
Feature 1:DNA binding residues [nucleic acid binding site]
Evidence:
  • Comment:Based on sequence similarity to BmrR and the structure of Bacillus subtilis BmrR bound to DNA (1EXI).

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1          ###             #                ###                                          
gi 72162732    3 EYRIDELARLANTTVRNVRVYQDRGLLS-PPRREGRVGIYTEVHLARLRLIGQLLKRGYTFANIAELVSVWERGGNLSEV 81
gi 17547799    3 EFTIDELARAAATTVRNVRSYQDRGLID-PPERRGRVGIYTQAHLGRLKLINHLLARGYTLANIQELLKALVEGHDLRSI 81
gi 111019095   3 EYRIDDLAREARVSVRNVRVYQDRGLLP-PPRKQGRTGWYNESHLARLHLIGRMLDRGYTFATISELLTAAHYGLQVKDV 81
gi 29830797    2 TYRIEDLAHRSGATVRTIRAYQDRGLLP-RPERRGRANVYADAHLARLRQIAGLLDRGYTLASIKELLEAWDSGRGLGGV 80
gi 41408299   66 EYRIDDLARLAGTTTRNICVYRDRGLLP-PPLRVGRIALFNDTHLTRLRLITSMLDRGYTIAHVREMLSAWEQGKNLGDV 144
gi 92908307   18 EYRLNELSRISGVSTRNIRAYRERGLLD-PPRRQGRSAYYNDFHLAQLDTINQLLRRGFSSAHIAEFFASMRAGADLADI 96
gi 90203081   19 EYRLEDLARESGISARNIRAYRERGLLD-PPRRVGRSALYDDYHLSQLNTISQLLRKGYNSAHIAEFFASMRQGTDLADI 97
gi 54024830    3 EYRIDDLARAAGTTSRNVRLYQERGLLPqPVRREGRANIYDDSHLARLQIVNGLLERGFTLAHITDFITSWETGKDLTEI 82
gi 21221610    6 EYRMAELARLAGITVRTVRFYRERKLIP-PPRREGRIAWYDDHHLARLRTIAALLERGHTLNGIAELADAFDHGRDVGDL 84
gi 84319903   25 EYSVDELARAAGSSVRNVRAYQDRGLLP-PPERRGRVGVYFDSHLKRLRLISQLLERGYSSANIKELLEAWEQGRDLDHV 103
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
gi 72162732   82 LGFe--------SAVGDPWSDEIPGYMTLEELTDlfgdq-vtpeRVARAVELGLLEPEGk---rYRVPSPRLLHAGAELV 149
gi 17547799   82 LGLe--------AAISSPWSDAFPKHFSLLALAKlfgcs-isrqALARAIGLGLLEPDGl---gYLARNPKLLMAGAQMA 149
gi 111019095  82 LET---------DDPGSRWKKRRRAARLTIAELKrmfgaqtteaNIAKGTELGVLVPAGd---dYSVNDPRLVEAAQVLV 149
gi 29830797   81 LGLv--------AEVDGPWSDEEAGRISRAELSErfggs-pddaAVADALELGVLEPVPghedlFLVPSPQELAVAVELH 151
gi 41408299  145 LGLe--------TAIVGTWTTEKPETMSLAEAQRlvg----dprAFERLVALQVIRVDGs---rATLTRPKLIEAFNEIR 209
gi 92908307   97 LGLqrs----lfTAEDGRDETPSAGRDLDLDPSSe---------EAGELVAYGLAEVVDg---rVVFVDPSIAEIVGRAT 160
gi 90203081   98 LGLq-------rAVLGQTPEPRNRNTAVKIDAKSe---------EARKLVAFGMAEVVDg---eVLMIDCAAADILARSP 158
gi 54024830   83 LGLqkavtdawgARHDPVQLPRDAVVALLADLDAeqa----eekHLDRLADLQLVRTDDd---tVTLLRPDLVEVLLELH 155
gi 21221610   85 LGLge------pTEETPVRLTPEELAARFEGEVTp--------eNLAAAMELGYLGTDGd---eLVHISHRLLEVSSALV 147
gi 84319903  104 LGLd--------QAIIGEWNLETPGSIGFDELQAifgde-lndrVIDKAQALGLLLFDGe---rMKIPSPRLFQGRAGTV 171
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
gi 72162732  150 EIGMSLDAVLDla------------qeLRDRIDAAAEalnrqvsehiiatyape-giihsedlgkvadvirRVRPLAQIA 216
gi 17547799  150 QAGFPLEEVLDii------------erARPHTQAVADdlvsmvvreldkyekg--qlpppedvprlvdviwRIRPLAAVA 215
gi 111019095 150 DAGIPLEAVLEqt------------aaVRRDLSDVAArfvavvadrylaaegep-leldeakvseiarlvdQMRPLAHDA 216
gi 29830797  152 EAGVPLSAIAGhl------------reLRGQVEHIASrflefttehvfarylge-hppnevdateaaslvrRLRPLAQQT 218
gi 41408299  210 GYGVEFDKLIDlheqivpeidkisdmlVRAGAEHVLDri-------------------------------kPGEPLPADA 258
gi 92908307  161 DPMLYIRAIVRiv------------asTRHNVDTLAGvvadalqeciearfg----rdrtpdplemhrmvqDYRELANRL 224
gi 90203081  159 DQLLYVRALLRfv------------eaAEDSVDDLAEafvtslgelyharvgad-ylprpdevdeirqvvqDYRALGEKV 225
gi 54024830  156 GDGIDLATMIDly------------adLRAKLEDVARtlvvaaknrivddhgpgwlpdtdaetaattqmltRWRELGTRI 223
gi 21221610  148 REGIPLGEVLQag------------vrVREHADALAElfadlilr------------------hapepelhRLRPLARSV 197
gi 84319903  172 PQRHPAGGAARs---------------TRRVAQRHRAsgggnrppd-----------------rhppggrpRHRPAARGA 219

                 ....*....
Feature 1                 
gi 72162732  217 VDAILAQAM 225
gi 17547799  216 VEVELMRAL 224
gi 111019095 217 VQSLFEEAM 225
gi 29830797  219 VDAELARAM 227
gi 41408299  259 EIAELITML 267
gi 92908307  225 VARHLDEAL 233
gi 90203081  226 MVARFDQAT 234
gi 54024830  224 VHSGLEQAL 232
gi 21221610  198 VEAELSLAL 206
gi 84319903  220 GPAGAGQGV 228

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