NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2797051725|ref|WP_373365868|]
View 

GntR family transcriptional regulator [Pseudomonas syringae]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
GntR COG1802
DNA-binding transcriptional regulator, GntR family [Transcription];
96-312 5.75e-28

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


:

Pssm-ID: 441407 [Multi-domain]  Cd Length: 222  Bit Score: 108.47  E-value: 5.75e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2797051725  96 SSEELVDTRPLGERIHDEIGAAlsacIAFGHY----RLDEQSAAQHYGVSRAVVREALMRLRDRGLVEKEPYSQWLAGPL 171
Cdd:COG1802     2 TSPSPLRRESLAEQVYEALREA----ILSGELppgeRLSEAELAERLGVSRTPVREALRRLEAEGLVEIRPNRGARVAPL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2797051725 172 TAREITEDYELRACLEPEALRQTAPQLSRETLEAMLARVIEAQDA-EQCSLEEIERLEDDLHQQCLGGLQNRKIATLISQ 250
Cdd:COG1802    78 SPEEIRELYEVRAALEGLAARLAAERATPADLARLRALLEELEAAaAAGDVAAYLELDREFHRALVEAAGNPRLAELLRR 157

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2797051725 251 AQssMIINRIFYRLLSIGAD-DAMLAEHRLILELLLHGAFDAAALNLKEHLLRARQRMLQRLK 312
Cdd:COG1802   158 LR--ARLRRYRRLSLRSPGRlEESLAEHRAILDALEAGDAEAAAAALRAHLERARERLLEALA 218
MngR super family cl34419
DNA-binding transcriptional regulator, GntR family [Transcription];
10-86 1.42e-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: 60.26  E-value: 1.42e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2797051725  10 SRYAMIREVLRNAIVSGAAANGLVLL-EAPLAELFGTSRVPVRKALNLLHEEGLISRFDGRGYLVNPDAREVEPLRLS 86
Cdd:COG2188     5 PLYLQIADALRERIESGELPPGDRLPsERELAEEFGVSRMTVRKALDELVEEGLLERRQGRGTFVAEPKIEYPLSRLT 82
 
Name Accession Description Interval E-value
GntR COG1802
DNA-binding transcriptional regulator, GntR family [Transcription];
96-312 5.75e-28

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


Pssm-ID: 441407 [Multi-domain]  Cd Length: 222  Bit Score: 108.47  E-value: 5.75e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2797051725  96 SSEELVDTRPLGERIHDEIGAAlsacIAFGHY----RLDEQSAAQHYGVSRAVVREALMRLRDRGLVEKEPYSQWLAGPL 171
Cdd:COG1802     2 TSPSPLRRESLAEQVYEALREA----ILSGELppgeRLSEAELAERLGVSRTPVREALRRLEAEGLVEIRPNRGARVAPL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2797051725 172 TAREITEDYELRACLEPEALRQTAPQLSRETLEAMLARVIEAQDA-EQCSLEEIERLEDDLHQQCLGGLQNRKIATLISQ 250
Cdd:COG1802    78 SPEEIRELYEVRAALEGLAARLAAERATPADLARLRALLEELEAAaAAGDVAAYLELDREFHRALVEAAGNPRLAELLRR 157

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2797051725 251 AQssMIINRIFYRLLSIGAD-DAMLAEHRLILELLLHGAFDAAALNLKEHLLRARQRMLQRLK 312
Cdd:COG1802   158 LR--ARLRRYRRLSLRSPGRlEESLAEHRAILDALEAGDAEAAAAALRAHLERARERLLEALA 218
MngR COG2188
DNA-binding transcriptional regulator, GntR family [Transcription];
10-86 1.42e-10

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


Pssm-ID: 441791 [Multi-domain]  Cd Length: 238  Bit Score: 60.26  E-value: 1.42e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2797051725  10 SRYAMIREVLRNAIVSGAAANGLVLL-EAPLAELFGTSRVPVRKALNLLHEEGLISRFDGRGYLVNPDAREVEPLRLS 86
Cdd:COG2188     5 PLYLQIADALRERIESGELPPGDRLPsERELAEEFGVSRMTVRKALDELVEEGLLERRQGRGTFVAEPKIEYPLSRLT 82
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 10-74 5.42e-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: 54.76  E-value: 5.42e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2797051725  10 SRYAMIREVLRNAIVSGAAANGLVL-LEAPLAELFGTSRVPVRKALNLLHEEGLISRFDGRGYLVN 74
Cdd:cd07377     1 PLYEQIADQLREAILSGELKPGDRLpSERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFVA 66
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
 12-73 1.88e-08

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: 50.31  E-value: 1.88e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2797051725  12 YAMIREVLRNAIVSGAAANGLVLL-EAPLAELFGTSRVPVRKALNLLHEEGLISRFDGRGYLV 73
Cdd:pfam00392   2 YEQVYARLREDILSGRLRPGDKLPsERELAAEFGVSRTTVREALRRLEAEGLVERRQGRGTFV 64
FCD smart00895
This entry represents the C-terminal ligand binding domain of many members of the GntR family; ...
 180-302 4.00e-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: 51.21  E-value: 4.00e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2797051725  180 YELRACLEPEALRQTAPQLSRETLEAMLARV--IEAQDAEQCSLEEIERLEDDLHQQCLGGLQNRKIATLISQAQSSMII 257
Cdd:smart00895   3 YEVRRALEPLAARLAAERATDEDLAALEALLdaMEAAAAAGDDLEEFAELDREFHRALAEAAGNPVLLELLESLRARLRR 82

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 2797051725  258 nrifYRLLSIGADDAMLAEHRLILELLLHGAFDAAALNLKEHLLR 302
Cdd:smart00895  83 ----LRRLSLEAARRALDEHRAILDAIRARDAEAARAAMREHLEA 123
PRK10225 PRK10225
Uxu operon transcriptional regulator;
108-309 1.00e-07

Uxu operon transcriptional regulator;


Pssm-ID: 182318 [Multi-domain]  Cd Length: 257  Bit Score: 52.33  E-value: 1.00e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2797051725 108 ERIHDEIGAALSACIAFGHYRLD-----EQSAAQHYGVSRAVVREALMRLRDRGLVEKEP----YSQWLAGPLTAREIT- 177
Cdd:PRK10225    8 QRPYQEVGAMIRDLIIKTPYNPGerlppEREIAEMLDVTRTVVREALIMLEIKGLVEVRRgagiYVLDSSGSHNTDSPDa 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2797051725 178 ---------EDYELRACLEPEALRQTAPQLSRETLEAML-ARVIEAQDAEQCSLEEIERLEDDLHQQCLGGLQNRKIATL 247
Cdd:PRK10225   88 nvcndagpfELLQARQLLESNIAEFAALQATREDIVKMRqALQLEERELASSAPGSSESGDMQFHLAIAEATHNSMLVEL 167

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2797051725 248 ISQAQSSMIINRIFYRLLSIGAD----DAMLAEHRLILELLLHGAFDAAALNLKEHLLRARQRMLQ 309
Cdd:PRK10225  168 FRQSWQWRENNPMWIQLHSHLDDslyrKEWLGDHKQILAALIKKDARAAKLAMWQHLENVKQRLLE 233
HTH_GNTR smart00345
helix_turn_helix gluconate operon transcriptional repressor;
15-73 2.83e-07

helix_turn_helix gluconate operon transcriptional repressor;


Pssm-ID: 197669 [Multi-domain]  Cd Length: 60  Bit Score: 46.80  E-value: 2.83e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2797051725   15 IREVLRNAIVSGAAANGLVL-LEAPLAELFGTSRVPVRKALNLLHEEGLISRFDGRGYLV 73
Cdd:smart00345   1 VAERLREDIVSGELRPGDKLpSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGSGTFV 60
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 105-164 1.07e-06

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: 45.52  E-value: 1.07e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2797051725 105 PLGERIHDEIGAAlsacIAFGHYRLD-----EQSAAQHYGVSRAVVREALMRLRDRGLVEKEPYS 164
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 ...
 180-293 1.97e-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: 43.51  E-value: 1.97e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2797051725 180 YELRACLEPEALRQTAPQLSRETLEAMLARVIEAQDA-EQCSLEEIERLEDDLHQQCLGGLQNRKIATLISQAQSSMiiN 258
Cdd:pfam07729   3 YELRAALEPLAARLAAERATDEDLAELEALLEALEAAaDAGDLEAFAEADREFHLALAEAAGNPVLARMLESLWDRL--R 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2797051725 259 RIFYRLLSIGAD-DAMLAEHRLILELLLHGAFDAAA 293
Cdd:pfam07729  81 RLRRLLLSSPGRlRASLEEHRAILDAIRARDPEAAR 116
PRK11402 PRK11402
transcriptional regulator PhoB;
12-110 1.55e-04

transcriptional regulator PhoB;


Pssm-ID: 183118 [Multi-domain]  Cd Length: 241  Bit Score: 42.51  E-value: 1.55e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2797051725  12 YAMIREVLRNAIVSGAAANGLVL-LEAPLAELFGTSRVPVRKALNLLHEEGLISRFDGRGYLVNPDAREVEPLRLSlSHK 90
Cdd:PRK11402   11 YATVRQRLLDDIAQGVYQAGQQIpTENELCTQYNVSRITIRKAISDLVADGVLIRWQGKGTFVQSQKVENALLTVS-GFT 89

                          90       100
                  ....*....|....*....|....*....
gi 2797051725  91 QFGLDS---------SEELVDTRPLGERI 110
Cdd:PRK11402   90 DFGVSQgkatkekviEQERVSAAPFCEKL 118
C_P_lyase_phnF TIGR02325
phosphonates metabolism transcriptional regulator PhnF; All members of the seed alignment for ...
 10-73 5.95e-03

phosphonates metabolism transcriptional regulator PhnF; All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond. [Transport and binding proteins, Anions, Regulatory functions, DNA interactions]


Pssm-ID: 131378 [Multi-domain]  Cd Length: 238  Bit Score: 37.84  E-value: 5.95e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2797051725  10 SRYAMIREVLRNAIVSGAAANGLVL-LEAPLAELFGTSRVPVRKALNLLHEEGLISRFDGRGYLV 73
Cdd:TIGR02325   8 ALWRQIADKIEQEIAAGHLRAGDYLpAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQGRGTFV 72
 
Name Accession Description Interval E-value
GntR COG1802
DNA-binding transcriptional regulator, GntR family [Transcription];
96-312 5.75e-28

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


Pssm-ID: 441407 [Multi-domain]  Cd Length: 222  Bit Score: 108.47  E-value: 5.75e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2797051725  96 SSEELVDTRPLGERIHDEIGAAlsacIAFGHY----RLDEQSAAQHYGVSRAVVREALMRLRDRGLVEKEPYSQWLAGPL 171
Cdd:COG1802     2 TSPSPLRRESLAEQVYEALREA----ILSGELppgeRLSEAELAERLGVSRTPVREALRRLEAEGLVEIRPNRGARVAPL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2797051725 172 TAREITEDYELRACLEPEALRQTAPQLSRETLEAMLARVIEAQDA-EQCSLEEIERLEDDLHQQCLGGLQNRKIATLISQ 250
Cdd:COG1802    78 SPEEIRELYEVRAALEGLAARLAAERATPADLARLRALLEELEAAaAAGDVAAYLELDREFHRALVEAAGNPRLAELLRR 157

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2797051725 251 AQssMIINRIFYRLLSIGAD-DAMLAEHRLILELLLHGAFDAAALNLKEHLLRARQRMLQRLK 312
Cdd:COG1802   158 LR--ARLRRYRRLSLRSPGRlEESLAEHRAILDALEAGDAEAAAAALRAHLERARERLLEALA 218
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
108-312 4.74e-16

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


Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 76.13  E-value: 4.74e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2797051725 108 ERIHDEIGAALSACIAFGHYRLD-----EQSAAQHYGVSRAVVREALMRLRDRGLVE---------KEPYSQWLAGPLTA 173
Cdd:COG2186     6 RSLAEQVAEQLRELILSGELKPGdrlpsERELAEQLGVSRTTVREALRALEALGLVEvrqgggtfvREPSPWALLDPLAL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2797051725 174 REITED------YELRACLEPEALRQTAPQLSRETLEAmLARVIEAQDAEQCSLEEIERLEDDLHQQCLGGLQNRKIATL 247
Cdd:COG2186    86 LLALDDaslrdlLEARLALEPEAARLAAERATDEDLAR-LEAALAEMEAAADDGEAFAEADLAFHRAIAEASGNPLLALL 164

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2797051725 248 ISQAqSSMIINRIFYRLLSIGADDAMLAEHRLILELLLHGAFDAAALNLKEHLLRARQRMLQRLK 312
Cdd:COG2186   165 LESL-RELLRRSVRLTLRSPEARERSLAEHRAILDAIRAGDPEAARAAMRAHLEAVRERLREALA 228
MngR COG2188
DNA-binding transcriptional regulator, GntR family [Transcription];
10-86 1.42e-10

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


Pssm-ID: 441791 [Multi-domain]  Cd Length: 238  Bit Score: 60.26  E-value: 1.42e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2797051725  10 SRYAMIREVLRNAIVSGAAANGLVLL-EAPLAELFGTSRVPVRKALNLLHEEGLISRFDGRGYLVNPDAREVEPLRLS 86
Cdd:COG2188     5 PLYLQIADALRERIESGELPPGDRLPsERELAEEFGVSRMTVRKALDELVEEGLLERRQGRGTFVAEPKIEYPLSRLT 82
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 10-74 5.42e-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: 54.76  E-value: 5.42e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2797051725  10 SRYAMIREVLRNAIVSGAAANGLVL-LEAPLAELFGTSRVPVRKALNLLHEEGLISRFDGRGYLVN 74
Cdd:cd07377     1 PLYEQIADQLREAILSGELKPGDRLpSERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFVA 66
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
 12-73 1.88e-08

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: 50.31  E-value: 1.88e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2797051725  12 YAMIREVLRNAIVSGAAANGLVLL-EAPLAELFGTSRVPVRKALNLLHEEGLISRFDGRGYLV 73
Cdd:pfam00392   2 YEQVYARLREDILSGRLRPGDKLPsERELAAEFGVSRTTVREALRRLEAEGLVERRQGRGTFV 64
FCD smart00895
This entry represents the C-terminal ligand binding domain of many members of the GntR family; ...
 180-302 4.00e-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: 51.21  E-value: 4.00e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2797051725  180 YELRACLEPEALRQTAPQLSRETLEAMLARV--IEAQDAEQCSLEEIERLEDDLHQQCLGGLQNRKIATLISQAQSSMII 257
Cdd:smart00895   3 YEVRRALEPLAARLAAERATDEDLAALEALLdaMEAAAAAGDDLEEFAELDREFHRALAEAAGNPVLLELLESLRARLRR 82

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 2797051725  258 nrifYRLLSIGADDAMLAEHRLILELLLHGAFDAAALNLKEHLLR 302
Cdd:smart00895  83 ----LRRLSLEAARRALDEHRAILDAIRARDAEAARAAMREHLEA 123
PRK10225 PRK10225
Uxu operon transcriptional regulator;
108-309 1.00e-07

Uxu operon transcriptional regulator;


Pssm-ID: 182318 [Multi-domain]  Cd Length: 257  Bit Score: 52.33  E-value: 1.00e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2797051725 108 ERIHDEIGAALSACIAFGHYRLD-----EQSAAQHYGVSRAVVREALMRLRDRGLVEKEP----YSQWLAGPLTAREIT- 177
Cdd:PRK10225    8 QRPYQEVGAMIRDLIIKTPYNPGerlppEREIAEMLDVTRTVVREALIMLEIKGLVEVRRgagiYVLDSSGSHNTDSPDa 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2797051725 178 ---------EDYELRACLEPEALRQTAPQLSRETLEAML-ARVIEAQDAEQCSLEEIERLEDDLHQQCLGGLQNRKIATL 247
Cdd:PRK10225   88 nvcndagpfELLQARQLLESNIAEFAALQATREDIVKMRqALQLEERELASSAPGSSESGDMQFHLAIAEATHNSMLVEL 167

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2797051725 248 ISQAQSSMIINRIFYRLLSIGAD----DAMLAEHRLILELLLHGAFDAAALNLKEHLLRARQRMLQ 309
Cdd:PRK10225  168 FRQSWQWRENNPMWIQLHSHLDDslyrKEWLGDHKQILAALIKKDARAAKLAMWQHLENVKQRLLE 233
HTH_GNTR smart00345
helix_turn_helix gluconate operon transcriptional repressor;
15-73 2.83e-07

helix_turn_helix gluconate operon transcriptional repressor;


Pssm-ID: 197669 [Multi-domain]  Cd Length: 60  Bit Score: 46.80  E-value: 2.83e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2797051725   15 IREVLRNAIVSGAAANGLVL-LEAPLAELFGTSRVPVRKALNLLHEEGLISRFDGRGYLV 73
Cdd:smart00345   1 VAERLREDIVSGELRPGDKLpSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGSGTFV 60
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 105-164 1.07e-06

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: 45.52  E-value: 1.07e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2797051725 105 PLGERIHDEIGAAlsacIAFGHYRLD-----EQSAAQHYGVSRAVVREALMRLRDRGLVEKEPYS 164
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 ...
 180-293 1.97e-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: 43.51  E-value: 1.97e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2797051725 180 YELRACLEPEALRQTAPQLSRETLEAMLARVIEAQDA-EQCSLEEIERLEDDLHQQCLGGLQNRKIATLISQAQSSMiiN 258
Cdd:pfam07729   3 YELRAALEPLAARLAAERATDEDLAELEALLEALEAAaDAGDLEAFAEADREFHLALAEAAGNPVLARMLESLWDRL--R 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2797051725 259 RIFYRLLSIGAD-DAMLAEHRLILELLLHGAFDAAA 293
Cdd:pfam07729  81 RLRRLLLSSPGRlRASLEEHRAILDAIRARDPEAAR 116
ARO8 COG1167
DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain ...
 7-82 1.29e-04

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: 43.28  E-value: 1.29e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2797051725   7 RTASRYAMIREVLRNAIVSGAAANGLVLleaP----LAELFGTSRVPVRKALNLLHEEGLISRFDGRGYLVNPDAREVEP 82
Cdd:COG1167     9 SSGPLYLQLADALREAILSGRLPPGDRL---PssreLAAQLGVSRSTVVRAYEELEAEGLIESRPGSGTFVAARLPAPAP 85
PRK11402 PRK11402
transcriptional regulator PhoB;
12-110 1.55e-04

transcriptional regulator PhoB;


Pssm-ID: 183118 [Multi-domain]  Cd Length: 241  Bit Score: 42.51  E-value: 1.55e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2797051725  12 YAMIREVLRNAIVSGAAANGLVL-LEAPLAELFGTSRVPVRKALNLLHEEGLISRFDGRGYLVNPDAREVEPLRLSlSHK 90
Cdd:PRK11402   11 YATVRQRLLDDIAQGVYQAGQQIpTENELCTQYNVSRITIRKAISDLVADGVLIRWQGKGTFVQSQKVENALLTVS-GFT 89

                          90       100
                  ....*....|....*....|....*....
gi 2797051725  91 QFGLDS---------SEELVDTRPLGERI 110
Cdd:PRK11402   90 DFGVSQgkatkekviEQERVSAAPFCEKL 118
PRK09764 PRK09764
GntR family transcriptional regulator;
11-73 4.03e-04

GntR family transcriptional regulator;


Pssm-ID: 182065 [Multi-domain]  Cd Length: 240  Bit Score: 41.35  E-value: 4.03e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2797051725  11 RYAMIREVLRNAIVSGAAANGLVL-LEAPLAELFGTSRVPVRKALNLLHEEGLISRFDGRGYLV 73
Cdd:PRK09764    6 LYRQIADRIREQIARGELKPGDALpTESALQTEFGVSRVTVRQALRQLVEQQILESIQGSGTYV 69
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
 112-162 8.59e-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: 37.21  E-value: 8.59e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2797051725 112 DEIGAALSACIAFGHYRLD-----EQSAAQHYGVSRAVVREALMRLRDRGLVEKEP 162
Cdd:pfam00392   3 EQVYARLREDILSGRLRPGdklpsERELAAEFGVSRTTVREALRRLEAEGLVERRQ 58
MngR COG2188
DNA-binding transcriptional regulator, GntR family [Transcription];
135-162 3.03e-03

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


Pssm-ID: 441791 [Multi-domain]  Cd Length: 238  Bit Score: 38.69  E-value: 3.03e-03
                          10        20
                  ....*....|....*....|....*...
gi 2797051725 135 AQHYGVSRAVVREALMRLRDRGLVEKEP 162
Cdd:COG2188    36 AEEFGVSRMTVRKALDELVEEGLLERRQ 63
PRK10421 PRK10421
DNA-binding transcriptional repressor LldR; Provisional
 96-320 3.50e-03

DNA-binding transcriptional repressor LldR; Provisional


Pssm-ID: 236690 [Multi-domain]  Cd Length: 253  Bit Score: 38.59  E-value: 3.50e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2797051725  96 SSEELVD-TRPLGERIHDEIGAALSAciafghyrldEQSAAQHYGVSRAVVREALMRLRDRGLVEKE----PYSQWLagp 170
Cdd:PRK10421    3 LSDEVADrVRALIEEKNLEAGMKLPA----------ERQLAMQLGVSRNSLREALAKLVSEGVLLSRrgggTFIRWR--- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2797051725 171 ltareiTEDYELRACLEP-EALRQTAPQLSRETLEAMLArvIEAQDAEQCSLEEIERLEDDLHqQCLGGLQNRKiATLIS 249
Cdd:PRK10421   70 ------HETWSEQNIVQPlKTLMADDPDYSFDILEARHA--IEASTAWHAAMRATPGDKEKIQ-LCFEATLSED-PDLAS 139

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2797051725 250 QAQSSmiinriFYrlLSIGAddamlAEHRLILELLLHGAFDAaalnLKEHLLRARQRMLQRLKVLSVLPEQ 320
Cdd:PRK10421  140 QADVR------FH--LAIAE-----ASHNVVLLQTMRGFFDV----LQSSVKQSRQRMYLVPPVFSQLTEQ 193
GlpR COG1349
DNA-binding transcriptional regulator of sugar metabolism, DeoR/GlpR family [Transcription, ...
 14-82 5.17e-03

DNA-binding transcriptional regulator of sugar metabolism, DeoR/GlpR family [Transcription, Carbohydrate transport and metabolism];


Pssm-ID: 440960 [Multi-domain]  Cd Length: 254  Bit Score: 37.81  E-value: 5.17e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2797051725  14 MIREVLRNAIVSGAAANGLVLLEApLAELFGTSRVPVRKALNLLHEEGLISRFdgRGYLVNPDAREVEP 82
Cdd:COG1349     1 MLAEERRQKILELLRERGRVSVEE-LAERLGVSEETIRRDLAELEEQGLLRRV--HGGAVLVSSAAAEP 66
C_P_lyase_phnF TIGR02325
phosphonates metabolism transcriptional regulator PhnF; All members of the seed alignment for ...
 10-73 5.95e-03

phosphonates metabolism transcriptional regulator PhnF; All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond. [Transport and binding proteins, Anions, Regulatory functions, DNA interactions]


Pssm-ID: 131378 [Multi-domain]  Cd Length: 238  Bit Score: 37.84  E-value: 5.95e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2797051725  10 SRYAMIREVLRNAIVSGAAANGLVL-LEAPLAELFGTSRVPVRKALNLLHEEGLISRFDGRGYLV 73
Cdd:TIGR02325   8 ALWRQIADKIEQEIAAGHLRAGDYLpAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQGRGTFV 72
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH