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Conserved domains on  [gi|814585372|ref|WP_046384581|]
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MULTISPECIES: GntR family transcriptional regulator [Pseudomonas]

Protein Classification

GntR family transcriptional regulator( domain architecture ID 13390121)

GntR-family transcriptional regulator is one of a group of transcriptional regulators with a conserved N-terminal helix-turn-helix DNA-binding domain and a diverse C-terminal effector-binding and oligomerization domain

Gene Ontology:  GO:0003700|GO:0003677
PubMed:  15808743|33509775|26172911

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
GntR COG1802
DNA-binding transcriptional regulator, GntR family [Transcription];
95-311 2.33e-28

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


:

Pssm-ID: 441407 [Multi-domain]  Cd Length: 222  Bit Score: 109.24  E-value: 2.33e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814585372  95 DEDELVDTRPLGERIVEEIGAAlstcIAFGHY----RLDEQAAADHYGVSRAVVREALMRLRDRGLVEKEPYSQWLAGPL 170
Cdd:COG1802    2 TSPSPLRRESLAEQVYEALREA----ILSGELppgeRLSEAELAERLGVSRTPVREALRRLEAEGLVEIRPNRGARVAPL 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814585372 171 TAREVTEDYELRACLEPEALRQSAPNLDRALLEAMLQRVLDAQDSPQC-SLEAIEQIEEDLHQRCLAGLQNRKIAALIRQ 249
Cdd:COG1802   78 SPEEIRELYEVRAALEGLAARLAAERATPADLARLRALLEELEAAAAAgDVAAYLELDREFHRALVEAAGNPRLAELLRR 157

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 814585372 250 GQspMIISRIFYRLLGIGADPA-MLAEHRLILELLLHGAFDAAALNLREHLQRARQRMLQRLK 311
Cdd:COG1802  158 LR--ARLRRYRRLSLRSPGRLEeSLAEHRAILDALEAGDAEAAAAALRAHLERARERLLEALA 218
MngR super family cl34419
DNA-binding transcriptional regulator, GntR family [Transcription];
5-84 2.40e-10

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


The actual alignment was detected with superfamily member COG2188:

Pssm-ID: 441791 [Multi-domain]  Cd Length: 238  Bit Score: 59.88  E-value: 2.40e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814585372   5 SASASRYAMIHQLLRDAIVNGTARHGLVLL-EAPLAELFGTSRVPVRKALDLLHAEGLICRFNGRGYLINPEGVAMEPLR 83
Cdd:COG2188    1 SSPVPLYLQIADALRERIESGELPPGDRLPsERELAEEFGVSRMTVRKALDELVEEGLLERRQGRGTFVAEPKIEYPLSR 80


                 .
gi 814585372  84 L 84
Cdd:COG2188   81 L 81
 
Name Accession Description Interval E-value
GntR COG1802
DNA-binding transcriptional regulator, GntR family [Transcription];
95-311 2.33e-28

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


Pssm-ID: 441407 [Multi-domain]  Cd Length: 222  Bit Score: 109.24  E-value: 2.33e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814585372  95 DEDELVDTRPLGERIVEEIGAAlstcIAFGHY----RLDEQAAADHYGVSRAVVREALMRLRDRGLVEKEPYSQWLAGPL 170
Cdd:COG1802    2 TSPSPLRRESLAEQVYEALREA----ILSGELppgeRLSEAELAERLGVSRTPVREALRRLEAEGLVEIRPNRGARVAPL 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814585372 171 TAREVTEDYELRACLEPEALRQSAPNLDRALLEAMLQRVLDAQDSPQC-SLEAIEQIEEDLHQRCLAGLQNRKIAALIRQ 249
Cdd:COG1802   78 SPEEIRELYEVRAALEGLAARLAAERATPADLARLRALLEELEAAAAAgDVAAYLELDREFHRALVEAAGNPRLAELLRR 157

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 814585372 250 GQspMIISRIFYRLLGIGADPA-MLAEHRLILELLLHGAFDAAALNLREHLQRARQRMLQRLK 311
Cdd:COG1802  158 LR--ARLRRYRRLSLRSPGRLEeSLAEHRAILDALEAGDAEAAAAALRAHLERARERLLEALA 218
MngR COG2188
DNA-binding transcriptional regulator, GntR family [Transcription];
5-84 2.40e-10

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


Pssm-ID: 441791 [Multi-domain]  Cd Length: 238  Bit Score: 59.88  E-value: 2.40e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814585372   5 SASASRYAMIHQLLRDAIVNGTARHGLVLL-EAPLAELFGTSRVPVRKALDLLHAEGLICRFNGRGYLINPEGVAMEPLR 83
Cdd:COG2188    1 SSPVPLYLQIADALRERIESGELPPGDRLPsERELAEEFGVSRMTVRKALDELVEEGLLERRQGRGTFVAEPKIEYPLSR 80


                 .
gi 814585372  84 L 84
Cdd:COG2188   81 L 81
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 9-73 3.17e-10

Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is presumed to result in a conformational change that regulates the DNA-binding affinity of the repressor. The GntR-like proteins bind as dimers, where each monomer recognizes a half-site of 2-fold symmetric DNA sequences.


Pssm-ID: 153418 [Multi-domain]  Cd Length: 66  Bit Score: 55.15  E-value: 3.17e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 814585372   9 SRYAMIHQLLRDAIVNGTARHGLVL-LEAPLAELFGTSRVPVRKALDLLHAEGLICRFNGRGYLIN 73
Cdd:cd07377    1 PLYEQIADQLREAILSGELKPGDRLpSERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFVA 66
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
 11-72 5.76e-09

Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerization domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor.


Pssm-ID: 306822 [Multi-domain]  Cd Length: 64  Bit Score: 51.85  E-value: 5.76e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 814585372   11 YAMIHQLLRDAIVNGTARHGLVLL-EAPLAELFGTSRVPVRKALDLLHAEGLICRFNGRGYLI 72
Cdd:pfam00392   2 YEQVYARLREDILSGRLRPGDKLPsERELAAEFGVSRTTVREALRRLEAEGLVERRQGRGTFV 64
FCD smart00895
This entry represents the C-terminal ligand binding domain of many members of the GntR family; ...
 179-301 2.98e-08

This entry represents the C-terminal ligand binding domain of many members of the GntR family; This domain probably binds to a range of effector molecules that regulate the transcription of genes through the action of the N-terminal DNA-binding domain. This domain is found in and that are regulators of sugar biosynthesis operons. Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector binding or oligomerisation domain at the C terminus. The winged-helix DNA-binding domain is well conserved in structure for the whole of the GntR family, and is similar in structure to other transcriptional regulator families. The C-terminal effector-binding and oligomerisation domains are more variable and are consequently used to define the subfamilies. Based on the sequence and structure of the C-terminal domains, the GtnR family can be divided into four major groups, as represented by FadR, HutC, MocR and YtrA, as well as some minor groups such as those represented by AraR and PlmA.


Pssm-ID: 214892 [Multi-domain]  Cd Length: 123  Bit Score: 51.59  E-value: 2.98e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814585372   179 YELRACLEPEALRQSAPNLDRALLEAMLQRV--LDAQDSPQCSLEAIEQIEEDLHQRCLAGLQNRKIAALIRQGQSPMII 256
Cdd:smart00895   3 YEVRRALEPLAARLAAERATDEDLAALEALLdaMEAAAAAGDDLEEFAELDREFHRALAEAAGNPVLLELLESLRARLRR 82

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 814585372   257 SRIFYRllgiGADPAMLAEHRLILELLLHGAFDAAALNLREHLQR 301
Cdd:smart00895  83 LRRLSL----EAARRALDEHRAILDAIRARDAEAARAAMREHLEA 123
HTH_GNTR smart00345
helix_turn_helix gluconate operon transcriptional repressor;
14-72 1.05e-07

helix_turn_helix gluconate operon transcriptional repressor;


Pssm-ID: 197669 [Multi-domain]  Cd Length: 60  Bit Score: 47.95  E-value: 1.05e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 814585372    14 IHQLLRDAIVNGTARHGLVL-LEAPLAELFGTSRVPVRKALDLLHAEGLICRFNGRGYLI 72
Cdd:smart00345   1 VAERLREDIVSGELRPGDKLpSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGSGTFV 60
PRK10225 PRK10225
Uxu operon transcriptional regulator;
107-308 1.18e-07

Uxu operon transcriptional regulator;


Pssm-ID: 182318 [Multi-domain]  Cd Length: 257  Bit Score: 51.94  E-value: 1.18e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814585372 107 ERIVEEIGAALSTCIAFGHYRLD-----EQAAADHYGVSRAVVREALMRLRDRGLVEKEP----YSQWLAGPLTAREVT- 176
Cdd:PRK10225   8 QRPYQEVGAMIRDLIIKTPYNPGerlppEREIAEMLDVTRTVVREALIMLEIKGLVEVRRgagiYVLDSSGSHNTDSPDa 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814585372 177 ---------EDYELRACLEPEALRQSAPNLDRALLEAMLQRV-LDAQDSPQCSLEAIEQIEEDLHQRCLAGLQNRKIAAL 246
Cdd:PRK10225  88 nvcndagpfELLQARQLLESNIAEFAALQATREDIVKMRQALqLEERELASSAPGSSESGDMQFHLAIAEATHNSMLVEL 167

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 814585372 247 IRQG-----QSPMIIsRIFYRLLGIGADPAMLAEHRLILELLLHGAFDAAALNLREHLQRARQRMLQ 308
Cdd:PRK10225 168 FRQSwqwreNNPMWI-QLHSHLDDSLYRKEWLGDHKQILAALIKKDARAAKLAMWQHLENVKQRLLE 233
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 104-163 4.47e-07

Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is presumed to result in a conformational change that regulates the DNA-binding affinity of the repressor. The GntR-like proteins bind as dimers, where each monomer recognizes a half-site of 2-fold symmetric DNA sequences.


Pssm-ID: 153418 [Multi-domain]  Cd Length: 66  Bit Score: 46.29  E-value: 4.47e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 814585372 104 PLGERIVEEIGAAlstcIAFGHYRLD-----EQAAADHYGVSRAVVREALMRLRDRGLVEKEPYS 163
Cdd:cd07377    1 PLYEQIADQLREA----ILSGELKPGdrlpsERELAEELGVSRTTVREALRELEAEGLVERRPGR 61
FCD pfam07729
FCD domain; This domain is the C-terminal ligand binding domain of many members of the GntR ...
 179-297 5.57e-05

FCD domain; This domain is the C-terminal ligand binding domain of many members of the GntR family. This domain binds to a range of effector molecules, including Lactate, Zn(II), Ni(II), Ca(II), Mg(II), citrate, sugar acids, sialic acid and N-acetylglucosamine-6-P, that regulate the transcription of genes through the action of the N-terminal DNA-binding domain pfam00392 (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). This domain is found in Swiss:P45427 and Swiss:P31460 that are regulators of sugar biosynthesis operons. It is also in the known structure of FadR where it binds to acyl-coA, the domain is alpha helical. This family has been named as FCD for (FadR C-terminal Domain).


Pssm-ID: 429623 [Multi-domain]  Cd Length: 121  Bit Score: 41.97  E-value: 5.57e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814585372  179 YELRACLEPEALRQSAPNLDRALLEAMLQRVLD-AQDSPQCSLEAIEQIEEDLHQRCLAGLQNRKIAALIRQGQSpmIIS 257
Cdd:pfam07729   3 YELRAALEPLAARLAAERATDEDLAELEALLEAlEAAADAGDLEAFAEADREFHLALAEAAGNPVLARMLESLWD--RLR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 814585372  258 RIFYRLLGIGADP-AMLAEHRLILELLLHGAFDAAALNLRE 297
Cdd:pfam07729  81 RLRRLLLSSPGRLrASLEEHRAILDAIRARDPEAARAAMRR 121
PRK11402 PRK11402
transcriptional regulator PhoB;
11-69 2.78e-04

transcriptional regulator PhoB;


Pssm-ID: 183118 [Multi-domain]  Cd Length: 241  Bit Score: 41.74  E-value: 2.78e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 814585372  11 YAMIHQLLRDAIVNGTARHGLVL-LEAPLAELFGTSRVPVRKALDLLHAEGLICRFNGRG 69
Cdd:PRK11402  11 YATVRQRLLDDIAQGVYQAGQQIpTENELCTQYNVSRITIRKAISDLVADGVLIRWQGKG 70
 
Name Accession Description Interval E-value
GntR COG1802
DNA-binding transcriptional regulator, GntR family [Transcription];
95-311 2.33e-28

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


Pssm-ID: 441407 [Multi-domain]  Cd Length: 222  Bit Score: 109.24  E-value: 2.33e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814585372  95 DEDELVDTRPLGERIVEEIGAAlstcIAFGHY----RLDEQAAADHYGVSRAVVREALMRLRDRGLVEKEPYSQWLAGPL 170
Cdd:COG1802    2 TSPSPLRRESLAEQVYEALREA----ILSGELppgeRLSEAELAERLGVSRTPVREALRRLEAEGLVEIRPNRGARVAPL 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814585372 171 TAREVTEDYELRACLEPEALRQSAPNLDRALLEAMLQRVLDAQDSPQC-SLEAIEQIEEDLHQRCLAGLQNRKIAALIRQ 249
Cdd:COG1802   78 SPEEIRELYEVRAALEGLAARLAAERATPADLARLRALLEELEAAAAAgDVAAYLELDREFHRALVEAAGNPRLAELLRR 157

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 814585372 250 GQspMIISRIFYRLLGIGADPA-MLAEHRLILELLLHGAFDAAALNLREHLQRARQRMLQRLK 311
Cdd:COG1802  158 LR--ARLRRYRRLSLRSPGRLEeSLAEHRAILDALEAGDAEAAAAALRAHLERARERLLEALA 218
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
100-311 5.87e-17

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


Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 78.44  E-value: 5.87e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814585372 100 VDTRPLGERIVEEIGAAlstcIAFGHYRLD-----EQAAADHYGVSRAVVREALMRLRDRGLVE---------KEPYSQW 165
Cdd:COG2186    3 IRRRSLAEQVAEQLREL----ILSGELKPGdrlpsERELAEQLGVSRTTVREALRALEALGLVEvrqgggtfvREPSPWA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814585372 166 LAGPLTAREVTED------YELRACLEPEALRQSAPNLDRALLEAmLQRVLDAQDSPQCSLEAIEQIEEDLHQRCLAGLQ 239
Cdd:COG2186   79 LLDPLALLLALDDaslrdlLEARLALEPEAARLAAERATDEDLAR-LEAALAEMEAAADDGEAFAEADLAFHRAIAEASG 157

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 814585372 240 NRKIAALIRQgQSPMIISRIFYRLLGIGADPAMLAEHRLILELLLHGAFDAAALNLREHLQRARQRMLQRLK 311
Cdd:COG2186  158 NPLLALLLES-LRELLRRSVRLTLRSPEARERSLAEHRAILDAIRAGDPEAARAAMRAHLEAVRERLREALA 228
MngR COG2188
DNA-binding transcriptional regulator, GntR family [Transcription];
5-84 2.40e-10

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


Pssm-ID: 441791 [Multi-domain]  Cd Length: 238  Bit Score: 59.88  E-value: 2.40e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814585372   5 SASASRYAMIHQLLRDAIVNGTARHGLVLL-EAPLAELFGTSRVPVRKALDLLHAEGLICRFNGRGYLINPEGVAMEPLR 83
Cdd:COG2188    1 SSPVPLYLQIADALRERIESGELPPGDRLPsERELAEEFGVSRMTVRKALDELVEEGLLERRQGRGTFVAEPKIEYPLSR 80


                 .
gi 814585372  84 L 84
Cdd:COG2188   81 L 81
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 9-73 3.17e-10

Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is presumed to result in a conformational change that regulates the DNA-binding affinity of the repressor. The GntR-like proteins bind as dimers, where each monomer recognizes a half-site of 2-fold symmetric DNA sequences.


Pssm-ID: 153418 [Multi-domain]  Cd Length: 66  Bit Score: 55.15  E-value: 3.17e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 814585372   9 SRYAMIHQLLRDAIVNGTARHGLVL-LEAPLAELFGTSRVPVRKALDLLHAEGLICRFNGRGYLIN 73
Cdd:cd07377    1 PLYEQIADQLREAILSGELKPGDRLpSERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFVA 66
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
 11-72 5.76e-09

Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerization domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor.


Pssm-ID: 306822 [Multi-domain]  Cd Length: 64  Bit Score: 51.85  E-value: 5.76e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 814585372   11 YAMIHQLLRDAIVNGTARHGLVLL-EAPLAELFGTSRVPVRKALDLLHAEGLICRFNGRGYLI 72
Cdd:pfam00392   2 YEQVYARLREDILSGRLRPGDKLPsERELAAEFGVSRTTVREALRRLEAEGLVERRQGRGTFV 64
FCD smart00895
This entry represents the C-terminal ligand binding domain of many members of the GntR family; ...
 179-301 2.98e-08

This entry represents the C-terminal ligand binding domain of many members of the GntR family; This domain probably binds to a range of effector molecules that regulate the transcription of genes through the action of the N-terminal DNA-binding domain. This domain is found in and that are regulators of sugar biosynthesis operons. Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector binding or oligomerisation domain at the C terminus. The winged-helix DNA-binding domain is well conserved in structure for the whole of the GntR family, and is similar in structure to other transcriptional regulator families. The C-terminal effector-binding and oligomerisation domains are more variable and are consequently used to define the subfamilies. Based on the sequence and structure of the C-terminal domains, the GtnR family can be divided into four major groups, as represented by FadR, HutC, MocR and YtrA, as well as some minor groups such as those represented by AraR and PlmA.


Pssm-ID: 214892 [Multi-domain]  Cd Length: 123  Bit Score: 51.59  E-value: 2.98e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814585372   179 YELRACLEPEALRQSAPNLDRALLEAMLQRV--LDAQDSPQCSLEAIEQIEEDLHQRCLAGLQNRKIAALIRQGQSPMII 256
Cdd:smart00895   3 YEVRRALEPLAARLAAERATDEDLAALEALLdaMEAAAAAGDDLEEFAELDREFHRALAEAAGNPVLLELLESLRARLRR 82

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 814585372   257 SRIFYRllgiGADPAMLAEHRLILELLLHGAFDAAALNLREHLQR 301
Cdd:smart00895  83 LRRLSL----EAARRALDEHRAILDAIRARDAEAARAAMREHLEA 123
HTH_GNTR smart00345
helix_turn_helix gluconate operon transcriptional repressor;
14-72 1.05e-07

helix_turn_helix gluconate operon transcriptional repressor;


Pssm-ID: 197669 [Multi-domain]  Cd Length: 60  Bit Score: 47.95  E-value: 1.05e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 814585372    14 IHQLLRDAIVNGTARHGLVL-LEAPLAELFGTSRVPVRKALDLLHAEGLICRFNGRGYLI 72
Cdd:smart00345   1 VAERLREDIVSGELRPGDKLpSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGSGTFV 60
PRK10225 PRK10225
Uxu operon transcriptional regulator;
107-308 1.18e-07

Uxu operon transcriptional regulator;


Pssm-ID: 182318 [Multi-domain]  Cd Length: 257  Bit Score: 51.94  E-value: 1.18e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814585372 107 ERIVEEIGAALSTCIAFGHYRLD-----EQAAADHYGVSRAVVREALMRLRDRGLVEKEP----YSQWLAGPLTAREVT- 176
Cdd:PRK10225   8 QRPYQEVGAMIRDLIIKTPYNPGerlppEREIAEMLDVTRTVVREALIMLEIKGLVEVRRgagiYVLDSSGSHNTDSPDa 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814585372 177 ---------EDYELRACLEPEALRQSAPNLDRALLEAMLQRV-LDAQDSPQCSLEAIEQIEEDLHQRCLAGLQNRKIAAL 246
Cdd:PRK10225  88 nvcndagpfELLQARQLLESNIAEFAALQATREDIVKMRQALqLEERELASSAPGSSESGDMQFHLAIAEATHNSMLVEL 167

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 814585372 247 IRQG-----QSPMIIsRIFYRLLGIGADPAMLAEHRLILELLLHGAFDAAALNLREHLQRARQRMLQ 308
Cdd:PRK10225 168 FRQSwqwreNNPMWI-QLHSHLDDSLYRKEWLGDHKQILAALIKKDARAAKLAMWQHLENVKQRLLE 233
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 104-163 4.47e-07

Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is presumed to result in a conformational change that regulates the DNA-binding affinity of the repressor. The GntR-like proteins bind as dimers, where each monomer recognizes a half-site of 2-fold symmetric DNA sequences.


Pssm-ID: 153418 [Multi-domain]  Cd Length: 66  Bit Score: 46.29  E-value: 4.47e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 814585372 104 PLGERIVEEIGAAlstcIAFGHYRLD-----EQAAADHYGVSRAVVREALMRLRDRGLVEKEPYS 163
Cdd:cd07377    1 PLYEQIADQLREA----ILSGELKPGdrlpsERELAEELGVSRTTVREALRELEAEGLVERRPGR 61
ARO8 COG1167
DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain ...
 5-104 5.54e-05

DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain [Transcription, Amino acid transport and metabolism]; DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain is part of the Pathway/BioSystem: Lysine biosynthesis


Pssm-ID: 440781 [Multi-domain]  Cd Length: 471  Bit Score: 44.43  E-value: 5.54e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814585372   5 SASASRYAMIHQLLRDAIVNGTARHGLVLleaP----LAELFGTSRVPVRKALDLLHAEGLICRFNGRGYLINPEgvAME 80
Cdd:COG1167    8 DSSGPLYLQLADALREAILSGRLPPGDRL---PssreLAAQLGVSRSTVVRAYEELEAEGLIESRPGSGTFVAAR--LPA 82

                         90       100
                 ....*....|....*....|....
gi 814585372  81 PLRLPLSAAHLGLNDEDELVDTRP 104
Cdd:COG1167   83 PAPAPRAAAAVAAPALRRLLEAAP 106
FCD pfam07729
FCD domain; This domain is the C-terminal ligand binding domain of many members of the GntR ...
 179-297 5.57e-05

FCD domain; This domain is the C-terminal ligand binding domain of many members of the GntR family. This domain binds to a range of effector molecules, including Lactate, Zn(II), Ni(II), Ca(II), Mg(II), citrate, sugar acids, sialic acid and N-acetylglucosamine-6-P, that regulate the transcription of genes through the action of the N-terminal DNA-binding domain pfam00392 (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). This domain is found in Swiss:P45427 and Swiss:P31460 that are regulators of sugar biosynthesis operons. It is also in the known structure of FadR where it binds to acyl-coA, the domain is alpha helical. This family has been named as FCD for (FadR C-terminal Domain).


Pssm-ID: 429623 [Multi-domain]  Cd Length: 121  Bit Score: 41.97  E-value: 5.57e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 814585372  179 YELRACLEPEALRQSAPNLDRALLEAMLQRVLD-AQDSPQCSLEAIEQIEEDLHQRCLAGLQNRKIAALIRQGQSpmIIS 257
Cdd:pfam07729   3 YELRAALEPLAARLAAERATDEDLAELEALLEAlEAAADAGDLEAFAEADREFHLALAEAAGNPVLARMLESLWD--RLR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 814585372  258 RIFYRLLGIGADP-AMLAEHRLILELLLHGAFDAAALNLRE 297
Cdd:pfam07729  81 RLRRLLLSSPGRLrASLEEHRAILDAIRARDPEAARAAMRR 121
PRK11402 PRK11402
transcriptional regulator PhoB;
11-69 2.78e-04

transcriptional regulator PhoB;


Pssm-ID: 183118 [Multi-domain]  Cd Length: 241  Bit Score: 41.74  E-value: 2.78e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 814585372  11 YAMIHQLLRDAIVNGTARHGLVL-LEAPLAELFGTSRVPVRKALDLLHAEGLICRFNGRG 69
Cdd:PRK11402  11 YATVRQRLLDDIAQGVYQAGQQIpTENELCTQYNVSRITIRKAISDLVADGVLIRWQGKG 70
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
 111-161 3.60e-04

Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerization domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor.


Pssm-ID: 306822 [Multi-domain]  Cd Length: 64  Bit Score: 38.36  E-value: 3.60e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 814585372  111 EEIGAALSTCIAFGHYRLD-----EQAAADHYGVSRAVVREALMRLRDRGLVEKEP 161
Cdd:pfam00392   3 EQVYARLREDILSGRLRPGdklpsERELAAEFGVSRTTVREALRRLEAEGLVERRQ 58
MngR COG2188
DNA-binding transcriptional regulator, GntR family [Transcription];
101-161 3.36e-03

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


Pssm-ID: 441791 [Multi-domain]  Cd Length: 238  Bit Score: 38.30  E-value: 3.36e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 814585372 101 DTRPLGERIVEEIGAAlstcIAFGHYRLD-----EQAAADHYGVSRAVVREALMRLRDRGLVEKEP 161
Cdd:COG2188    2 SPVPLYLQIADALRER----IESGELPPGdrlpsERELAEEFGVSRMTVRKALDELVEEGLLERRQ 63
PRK09764 PRK09764
GntR family transcriptional regulator;
6-77 4.66e-03

GntR family transcriptional regulator;


Pssm-ID: 182065 [Multi-domain]  Cd Length: 240  Bit Score: 37.89  E-value: 4.66e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 814585372   6 ASASRYAMIHQLLRDAIVNGTARHGLVL-LEAPLAELFGTSRVPVRKALDLLHAEGLICRFNGRGYLINPEGV 77
Cdd:PRK09764   2 GHKPLYRQIADRIREQIARGELKPGDALpTESALQTEFGVSRVTVRQALRQLVEQQILESIQGSGTYVKEERV 74
MntR COG1321
Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];
134-162 8.82e-03

Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];


Pssm-ID: 440932 [Multi-domain]  Cd Length: 135  Bit Score: 35.95  E-value: 8.82e-03
                         10        20
                 ....*....|....*....|....*....
gi 814585372 134 ADHYGVSRAVVREALMRLRDRGLVEKEPY 162
Cdd:COG1321   31 AERLGVSPPSVTEMLKKLEEKGLVEYEPY 59
PRK14999 PRK14999
histidine utilization repressor; Provisional
 5-76 9.24e-03

histidine utilization repressor; Provisional


Pssm-ID: 184961 [Multi-domain]  Cd Length: 241  Bit Score: 37.22  E-value: 9.24e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 814585372   5 SASASRYAMIHQLLRDAIVNGTAR-HGLVLLEAPLAELFGTSRVPVRKALDLLHAEGLICRFNGRG-YLINPEG 76
Cdd:PRK14999   8 SAPAPFYETVKQDICKKIAGGVWQpHDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVRLQGVGtFVAEPKG 81
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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