Conserved Protein Domain Family
HTH_MerR-like_sg5

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cd04780: HTH_MerR-like_sg5 
Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily
Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), 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 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: 133407
View PSSM: cd04780
Aligned: 12 rows
Threshold Bit Score: 101.25
Threshold Setting Gi: 29833868
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 29833868   13 MRMSELSRRSGVSVTTIKYYLREGLLPAGRRLSaTQAGYDeDHLRRLRLIRALTgvRGLPVSAARDVLGala-------- 84
gi 84497146    1 MRLAELSDTTGVAVATLKYYLREGLLHPGRAVSrTQSDYDeTHVERVRLVRALSevGGLSLATIGRVLDvitspgqdwit 80
gi 72160506    1 MRIGELSRRSGVSVPTIKYYLREKMLPEGERIAaNQVRYSeEHLRRLRLIRSLIdvGGLPVPTVREVLAe---------- 70
gi 113944307   1 MRISELSKQSGLSVPTIKFYLREGLLQPGVRTGrNQAEYAeEHLARLWFVKVLTgpGRLGISDVREVLTa---------- 70
gi 88855547    1 MKISELSLETGASLATIKYYLREGLLPAGERSApNQATYSkAHVRRIHMIRALTdvGGLAVSDAKRVIDa---------- 70
gi 116671450   1 MQLKELSERSGVSAASIKYYLREGLLPAGAAVHpTRAQYSaRHVERLELIQALRriVGLTIEQIRGLLRm---------- 70
gi 57233695    1 MRISEVAKAAGVSLPTIHYYTREGLLSPLLKTApNMAYYSpDCVEDIRLIKELQseKFLPLSVIKLVLQarrd------- 73
gi 87199499    1 MRMRELEEKTGVNREVIRILLRKGLLPEPLRLArNQAEYDeTHVRAVAVVRELQkgSRLTLDQIKELLDgngl------- 73
gi 94497950    1 MKMRELEERTGVDREVIRIMIREGLLPEPQRPArNAAEYDeGHVSGIATIRHLQqtSRMTLKEIRSALSgeal------- 73
gi 62425807    1 MKLSALAAESGVSTASIKYYIHVGILPPGRKRNaTTAVYSqAHLDRLALITWLRreLGSPIESIAALTRs---------- 70
gi 78778052    3 YKVSQIVKLTQTPKSTILYYIREGLLPEAKKLKsNVHRYSdIHVEILEYIRYMKqeMGSSNEELKTMLKn---------- 72
gi 109674839   2 LKMNELIQKSDTPKSTILYYVKEGLLPEPDKPKpNLYLYEeKCVQIIEFIKYLQinFNSSIAQIKALFShpsf------- 74
                         90       100
                 ....*....|....*....|....*...
Feature 1                                    
gi 29833868   85 --ehAGDTHSLLGLTLGSIRLAEESADD 110
gi 84497146   81 vlstAQRSLVGGREARVVDNLGRASAWV 108
gi 72160506   71 ----IDASQPSVHHAVALAHRGLPVLTG 94
gi 113944307  71 ---iDSRGRPLRGLCSVISPTVAAMPMV 95
gi 88855547   71 ----IESDLPLTRAFEIAQRTVSEQVDP 94
gi 116671450  71 ----ADDGAPRLDLLAAVQRVVLELDSY 94
gi 57233695   74 gqdiEHLGEMRTLLDDVFQPVVTGEPNP 101
gi 87199499   74 -dsgAGAQTYQHLEELLAIRFGLAETRL 100
gi 94497950   74 -erpGPASAYSHLEALLSRSFGLEQPTS 100
gi 62425807   71 ---iDDESLENIELMGICQRLALEASNV 95
gi 78778052   73 ----KNSSLSSSFSMIAPMMQTLENIPK 96
gi 109674839  75 dinnPYETLFKTLELIMGANFTRIYSID 102

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