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: 2-Oct-2020
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:
Feature 1        ###             #                ###                                           
NP_250706     5 YTISDLARELDITTRAIRFYEEQGLLSPERRG-QERIYSpRDKVSLKLILRGKRIGFSLAECRELIELYDpdpssgnqKQ 83  Pseudomonas aeru...
NP_069507     7 YTISELAREFEISTRTIRYYEEIGLLNPERTPgNQRIFSrKDRAKLKLILRGRRLGFSLEEIREMIEMYDvag---epEQ 83  Archaeoglobus fu...
YP_616584    33 FSITDLSTEFGVTARALRFYEDEGLISPSRKG-LSRIYSkRDRARLAWILRAKRTGFSLADIREMIDLYDvgd--grkLQ 109 Sphingopyxis ala...
YP_147343     4 FTISDLAQEFDVSTRTIRYYEERGLLSPIRTEsGQRLYTkKERAKLKLILRGKRFGFSLDEIHEMIALFDedr--tgkKQ 81  Geobacillus kaus...
YP_033441     5 YSIGELTKEFSITARTLRYYEEEGLLVPCRHG-SARFYTqTDRHKLKQILRAKRVKFSLSEISEMLSMVGkpp--tdeKK 81  Bartonella hense...
NP_102934     5 YSITELTREFDVSTRTLRFYEDEGLVQPVRRG-RTRLFRpSDRHLIRQIMRGKRLGFSINEIREIIQMYKepp--gevGQ 81  Mesorhizobium lo...
ZP_01001772   6 MNIREMCETFEVTPRTLRFYEAKELLFPIRQG-QKRLFTkRDRARLKLILRGKRFGFSLEEIRQLLDLYHmdd--gqeTQ 82  Loktanella vestf...
YP_672594    25 IRIGELAREFDVTLRTLRFYEDKGLLRPKRKG-LTRLYSeKDRERLRIILRGRKIGFPLRDMKQILDLYGstt--vsaPQ 101 Mesorhizobium sp...
ZP_00631282  46 LTIRQMCDAFEVTPRTLRFYEARELLFPQRRG-QHRLYGrSDRARLTLILRGKRFGFSLEQIRQLLELYDpae--rniTQ 122 Paracoccus denit...
YP_684108    10 MTIRQMCDTFDVTPRTLRFYESKELLFPIREG-QKRLFTrRDRARLKLILRGKRFGFSLEELRQLLDLYDmgd--qqqTQ 86  Roseobacter deni...
Feature 1                                                
NP_250706    84 LNTMLEKIAERRAQLEQQLLDIEQMQLELDTAEERCRAALI 124 Pseudomonas aeruginosa PAO1
NP_069507    84 IRLTLKYGEKKLKEIEEKIRELELLKEDLLNLREMLVKRLE 124 Archaeoglobus fulgidus DSM 4304
YP_616584   110 RQVTIEKCEERIALLRRQRDDIDSAVDELSRFIEMVKKVDA 150 Sphingopyxis alaskensis RB2256
YP_147343    82 LEKTVEYGRRKLKEVSERIEDLLQLKAEMEALLSDFEQRLR 122 Geobacillus kaustophilus HTA426
YP_033441    82 LKELIAGVNKKRADLQQMQRDIDDFLHDLERIEETLFESLA 122 Bartonella henselae str. Houston-1
NP_102934    82 LKLMIKRIEEKREDLRQKRRDLEETLAELDQAEESCVERLV 122 Mesorhizobium loti MAFF303099
ZP_01001772  83 LSKTYELAERHLADMQAQKAELDEAIGELKAQMAWGAEKLS 123 Loktanella vestfoldensis SKA53
YP_672594   102 VRTFLQKAKKQMDWLEQQHKEIEEAAKELSDMVRDLRNRLG 142 Mesorhizobium sp. BNC1
ZP_00631282 123 TEATLATARDRLADMERQHRELGEAIAELRQQIAEGEASLQ 163 Paracoccus denitrificans PD1222
YP_684108    87 LSRAVEVARDRLDELIQRRDELNDAIADLTDQLKWGEDMVA 127 Roseobacter denitrificans OCh 114

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