Conserved Protein Domain Family
HTH_GnyR

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cd04776: HTH_GnyR 
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.
Statistics
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PSSM-Id: 133403
View PSSM: cd04776
Aligned: 36 rows
Threshold Bit Score: 120.328
Threshold Setting Gi: 11498281
Created: 13-Nov-2006
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 15597212    5 YTISDLARELDITTRAIRFYEEQGLLSPERRG-QERIYSpRDKVSLKLILRGKRIGFSLAECRELIELYDpdpssgnqKQ 83
gi 11498281    7 YTISELAREFEISTRTIRYYEEIGLLNPERTPgNQRIFSrKDRAKLKLILRGRRLGFSLEEIREMIEMYDvag---epEQ 83
gi 103487023  33 FSITDLSTEFGVTARALRFYEDEGLISPSRKG-LSRIYSkRDRARLAWILRAKRTGFSLADIREMIDLYDvgd--grkLQ 109
gi 56420025    4 FTISDLAQEFDVSTRTIRYYEERGLLSPIRTEsGQRLYTkKERAKLKLILRGKRFGFSLDEIHEMIALFDedr--tgkKQ 81
gi 49475400    5 YSIGELTKEFSITARTLRYYEEEGLLVPCRHG-SARFYTqTDRHKLKQILRAKRVKFSLSEISEMLSMVGkpp--tdeKK 81
gi 13471368    5 YSITELTREFDVSTRTLRFYEDEGLVQPVRRG-RTRLFRpSDRHLIRQIMRGKRLGFSINEIREIIQMYKepp--gevGQ 81
gi 84514408    6 MNIREMCETFEVTPRTLRFYEAKELLFPIRQG-QKRLFTkRDRARLKLILRGKRFGFSLEEIRQLLDLYHmdd--gqeTQ 82
gi 110632386  25 IRIGELAREFDVTLRTLRFYEDKGLLRPKRKG-LTRLYSeKDRERLRIILRGRKIGFPLRDMKQILDLYGstt--vsaPQ 101
gi 69936456   46 LTIRQMCDAFEVTPRTLRFYEARELLFPQRRG-QHRLYGrSDRARLTLILRGKRFGFSLEQIRQLLELYDpae--rniTQ 122
gi 110681101  10 MTIRQMCDTFDVTPRTLRFYESKELLFPIREG-QKRLFTrRDRARLKLILRGKRFGFSLEELRQLLDLYDmgd--qqqTQ 86
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
Feature 1                                                 
gi 15597212   84 LNTMLEKIAERRAQLEQQLLDIEQMQLELDTAEERCRAALI 124
gi 11498281   84 IRLTLKYGEKKLKEIEEKIRELELLKEDLLNLREMLVKRLE 124
gi 103487023 110 RQVTIEKCEERIALLRRQRDDIDSAVDELSRFIEMVKKVDA 150
gi 56420025   82 LEKTVEYGRRKLKEVSERIEDLLQLKAEMEALLSDFEQRLR 122
gi 49475400   82 LKELIAGVNKKRADLQQMQRDIDDFLHDLERIEETLFESLA 122
gi 13471368   82 LKLMIKRIEEKREDLRQKRRDLEETLAELDQAEESCVERLV 122
gi 84514408   83 LSKTYELAERHLADMQAQKAELDEAIGELKAQMAWGAEKLS 123
gi 110632386 102 VRTFLQKAKKQMDWLEQQHKEIEEAAKELSDMVRDLRNRLG 142
gi 69936456  123 TEATLATARDRLADMERQHRELGEAIAELRQQIAEGEASLQ 163
gi 110681101  87 LSRAVEVARDRLDELIQRRDELNDAIADLTDQLKWGEDMVA 127

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