NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|644360139|ref|WP_025303427|]
View 

MULTISPECIES: GntR family transcriptional regulator [Serratia]

Protein Classification

GntR family transcriptional regulator( domain architecture ID 11706244)

GntR family transcriptional regulator binds a specific ligand that modulates DNA binding and the expression of genes encoding fatty acid biosynthetic and degrading enzymes

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];
103-318 4.86e-23

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


:

Pssm-ID: 441407 [Multi-domain]  Cd Length: 222  Bit Score: 95.37  E-value: 4.86e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644360139 103 PQEELVDTRSTSEKVFSDLQEALstcmVFGHYQ----VNEASAAEFYNVSRSAIREALMRLRDQGLVEKEPYAQWLAGPL 178
Cdd:COG1802    2 TSPSPLRRESLAEQVYEALREAI----LSGELPpgerLSEAELAERLGVSRTPVREALRRLEAEGLVEIRPNRGARVAPL 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644360139 179 TAREITDHYEIRACLEPAALLKAAPHLSRQHVLDSLERLTQLEQ--GTFSLASLERVEEDLHIHCLAPAGNKTLLGVLRQ 256
Cdd:COG1802   78 SPEEIRELYEVRAALEGLAARLAAERATPADLARLRALLEELEAaaAAGDVAAYLELDREFHRALVEAAGNPRLAELLRR 157

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 644360139 257 SQSPLIVTRIFYDMLGIKIEEAmLNEHRLVLQMLLQGANDAAALGLQEHLRRAQMRTLQRLK 318
Cdd:COG1802  158 LRARLRRYRRLSLRSPGRLEES-LAEHRAILDALEAGDAEAAAAALRAHLERARERLLEALA 218
HTH_ARSR super family cl46857
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ...
 18-81 2.21e-09

Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.


The actual alignment was detected with superfamily member cd07377:

Pssm-ID: 481197 [Multi-domain]  Cd Length: 66  Bit Score: 52.83  E-value: 2.21e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 644360139  18 RYEMIRQTLDEAIRAGSVPAGLVL-LEGPLADMFGTSRVPVRKALGLLHQEGLIARFEGRGFIVT 81
Cdd:cd07377    2 LYEQIADQLREAILSGELKPGDRLpSERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFVA 66
 
Name Accession Description Interval E-value
GntR COG1802
DNA-binding transcriptional regulator, GntR family [Transcription];
103-318 4.86e-23

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


Pssm-ID: 441407 [Multi-domain]  Cd Length: 222  Bit Score: 95.37  E-value: 4.86e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644360139 103 PQEELVDTRSTSEKVFSDLQEALstcmVFGHYQ----VNEASAAEFYNVSRSAIREALMRLRDQGLVEKEPYAQWLAGPL 178
Cdd:COG1802    2 TSPSPLRRESLAEQVYEALREAI----LSGELPpgerLSEAELAERLGVSRTPVREALRRLEAEGLVEIRPNRGARVAPL 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644360139 179 TAREITDHYEIRACLEPAALLKAAPHLSRQHVLDSLERLTQLEQ--GTFSLASLERVEEDLHIHCLAPAGNKTLLGVLRQ 256
Cdd:COG1802   78 SPEEIRELYEVRAALEGLAARLAAERATPADLARLRALLEELEAaaAAGDVAAYLELDREFHRALVEAAGNPRLAELLRR 157

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 644360139 257 SQSPLIVTRIFYDMLGIKIEEAmLNEHRLVLQMLLQGANDAAALGLQEHLRRAQMRTLQRLK 318
Cdd:COG1802  158 LRARLRRYRRLSLRSPGRLEES-LAEHRAILDALEAGDAEAAAAALRAHLERARERLLEALA 218
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 18-81 2.21e-09

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: 52.83  E-value: 2.21e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 644360139  18 RYEMIRQTLDEAIRAGSVPAGLVL-LEGPLADMFGTSRVPVRKALGLLHQEGLIARFEGRGFIVT 81
Cdd:cd07377    2 LYEQIADQLREAILSGELKPGDRLpSERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFVA 66
MngR COG2188
DNA-binding transcriptional regulator, GntR family [Transcription];
15-82 3.54e-09

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


Pssm-ID: 441791 [Multi-domain]  Cd Length: 238  Bit Score: 56.41  E-value: 3.54e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 644360139  15 AGARYEMIRQTLDEAIRAGSVPAGLVLlegP----LADMFGTSRVPVRKALGLLHQEGLIARFEGRGFIVTP 82
Cdd:COG2188    3 PVPLYLQIADALRERIESGELPPGDRL---PsereLAEEFGVSRMTVRKALDELVEEGLLERRQGRGTFVAE 71
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
 19-80 6.59e-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: 51.46  E-value: 6.59e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 644360139   19 YEMIRQTLDEAIRAGSVPAGLVLL-EGPLADMFGTSRVPVRKALGLLHQEGLIARFEGRGFIV 80
Cdd:pfam00392   2 YEQVYARLREDILSGRLRPGDKLPsERELAAEFGVSRTTVREALRRLEAEGLVERRQGRGTFV 64
FCD smart00895
This entry represents the C-terminal ligand binding domain of many members of the GntR family; ...
 185-308 1.24e-07

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: 49.67  E-value: 1.24e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644360139   185 DHYEIRACLEPAALLKAAPHLSRQHVLDSLERLTQLEQGTFSLASLERVEE---DLHIHCLAPAGNKTLLGVLRQsqspL 261
Cdd:smart00895   1 ELYEVRRALEPLAARLAAERATDEDLAALEALLDAMEAAAAAGDDLEEFAEldrEFHRALAEAAGNPVLLELLES----L 76

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 644360139   262 IVTRIFYDMLGIKIEEAMLNEHRLVLQMLLQGANDAAALGLQEHLRR 308
Cdd:smart00895  77 RARLRRLRRLSLEAARRALDEHRAILDAIRARDAEAARAAMREHLEA 123
PRK10225 PRK10225
Uxu operon transcriptional regulator;
138-315 6.89e-06

Uxu operon transcriptional regulator;


Pssm-ID: 182318 [Multi-domain]  Cd Length: 257  Bit Score: 46.94  E-value: 6.89e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644360139 138 EASAAEFYNVSRSAIREALMRLRDQGLVEKEP----YAQWLAGPLTAREITDHY----------EIRACLEPAALLKAAP 203
Cdd:PRK10225  36 EREIAEMLDVTRTVVREALIMLEIKGLVEVRRgagiYVLDSSGSHNTDSPDANVcndagpfellQARQLLESNIAEFAAL 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644360139 204 HLSRQHVLDSLERLtQLEQGTFSLASLERVEE-DLHIH-CLAPAG-NKTLLGVLRQS-----QSPLIVTriFYDMLGIKI 275
Cdd:PRK10225 116 QATREDIVKMRQAL-QLEERELASSAPGSSESgDMQFHlAIAEAThNSMLVELFRQSwqwreNNPMWIQ--LHSHLDDSL 192

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 644360139 276 -EEAMLNEHRLVLQMLLQGANDAAALGLQEHLRRAQMRTLQ 315
Cdd:PRK10225 193 yRKEWLGDHKQILAALIKKDARAAKLAMWQHLENVKQRLLE 233
HTH_GNTR smart00345
helix_turn_helix gluconate operon transcriptional repressor;
22-80 2.07e-05

helix_turn_helix gluconate operon transcriptional repressor;


Pssm-ID: 197669 [Multi-domain]  Cd Length: 60  Bit Score: 41.79  E-value: 2.07e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 644360139    22 IRQTLDEAIRAGSVPAGLVL-LEGPLADMFGTSRVPVRKALGLLHQEGLIARFEGRGFIV 80
Cdd:smart00345   1 VAERLREDIVSGELRPGDKLpSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGSGTFV 60
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 138-169 2.69e-05

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: 41.28  E-value: 2.69e-05
                         10        20        30
                 ....*....|....*....|....*....|..
gi 644360139 138 EASAAEFYNVSRSAIREALMRLRDQGLVEKEP 169
Cdd:cd07377   28 ERELAEELGVSRTTVREALRELEAEGLVERRP 59
PRK11402 PRK11402
transcriptional regulator PhoB;
19-83 7.46e-05

transcriptional regulator PhoB;


Pssm-ID: 183118 [Multi-domain]  Cd Length: 241  Bit Score: 43.67  E-value: 7.46e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 644360139  19 YEMIRQTLDEAIRAGSVPAGLVL-LEGPLADMFGTSRVPVRKALGLLHQEGLIARFEGRG-FIVTPE 83
Cdd:PRK11402  11 YATVRQRLLDDIAQGVYQAGQQIpTENELCTQYNVSRITIRKAISDLVADGVLIRWQGKGtFVQSQK 77
FCD pfam07729
FCD domain; This domain is the C-terminal ligand binding domain of many members of the GntR ...
 185-304 2.32e-04

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: 40.43  E-value: 2.32e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644360139  185 DHYEIRACLEPAALLKAAPHLSRQHV--LDSLERLTQLEQGTFSLASLERVEEDLHIHCLAPAGNKTLLGVLRQSQSPLI 262
Cdd:pfam07729   1 ELYELRAALEPLAARLAAERATDEDLaeLEALLEALEAAADAGDLEAFAEADREFHLALAEAAGNPVLARMLESLWDRLR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 644360139  263 VTRIFYdMLGIKIEEAMLNEHRLVLQMLLQGANDAAALGLQE 304
Cdd:pfam07729  81 RLRRLL-LSSPGRLRASLEEHRAILDAIRARDPEAARAAMRR 121
 
Name Accession Description Interval E-value
GntR COG1802
DNA-binding transcriptional regulator, GntR family [Transcription];
103-318 4.86e-23

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


Pssm-ID: 441407 [Multi-domain]  Cd Length: 222  Bit Score: 95.37  E-value: 4.86e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644360139 103 PQEELVDTRSTSEKVFSDLQEALstcmVFGHYQ----VNEASAAEFYNVSRSAIREALMRLRDQGLVEKEPYAQWLAGPL 178
Cdd:COG1802    2 TSPSPLRRESLAEQVYEALREAI----LSGELPpgerLSEAELAERLGVSRTPVREALRRLEAEGLVEIRPNRGARVAPL 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644360139 179 TAREITDHYEIRACLEPAALLKAAPHLSRQHVLDSLERLTQLEQ--GTFSLASLERVEEDLHIHCLAPAGNKTLLGVLRQ 256
Cdd:COG1802   78 SPEEIRELYEVRAALEGLAARLAAERATPADLARLRALLEELEAaaAAGDVAAYLELDREFHRALVEAAGNPRLAELLRR 157

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 644360139 257 SQSPLIVTRIFYDMLGIKIEEAmLNEHRLVLQMLLQGANDAAALGLQEHLRRAQMRTLQRLK 318
Cdd:COG1802  158 LRARLRRYRRLSLRSPGRLEES-LAEHRAILDALEAGDAEAAAAALRAHLERARERLLEALA 218
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
108-318 5.04e-13

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


Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 67.65  E-value: 5.04e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644360139 108 VDTRSTSEKVFSDLQEALSTcmvfGHYQV-----NEASAAEFYNVSRSAIREALMRLRDQGLVE---------KEPYAQW 173
Cdd:COG2186    3 IRRRSLAEQVAEQLRELILS----GELKPgdrlpSERELAEQLGVSRTTVREALRALEALGLVEvrqgggtfvREPSPWA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644360139 174 LAGPLTAR------EITDHYEIRACLEPAALLKAAPHLSRQHvLDSLER-LTQLEQGTFSLASLERVEEDLHIHCLAPAG 246
Cdd:COG2186   79 LLDPLALLlalddaSLRDLLEARLALEPEAARLAAERATDED-LARLEAaLAEMEAAADDGEAFAEADLAFHRAIAEASG 157

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 644360139 247 NKTLLGVLRqSQSPLIVTRIFYDMLGIKIEEAMLNEHRLVLQMLLQGANDAAALGLQEHLRRAQMRTLQRLK 318
Cdd:COG2186  158 NPLLALLLE-SLRELLRRSVRLTLRSPEARERSLAEHRAILDAIRAGDPEAARAAMRAHLEAVRERLREALA 228
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 18-81 2.21e-09

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: 52.83  E-value: 2.21e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 644360139  18 RYEMIRQTLDEAIRAGSVPAGLVL-LEGPLADMFGTSRVPVRKALGLLHQEGLIARFEGRGFIVT 81
Cdd:cd07377    2 LYEQIADQLREAILSGELKPGDRLpSERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFVA 66
MngR COG2188
DNA-binding transcriptional regulator, GntR family [Transcription];
15-82 3.54e-09

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


Pssm-ID: 441791 [Multi-domain]  Cd Length: 238  Bit Score: 56.41  E-value: 3.54e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 644360139  15 AGARYEMIRQTLDEAIRAGSVPAGLVLlegP----LADMFGTSRVPVRKALGLLHQEGLIARFEGRGFIVTP 82
Cdd:COG2188    3 PVPLYLQIADALRERIESGELPPGDRL---PsereLAEEFGVSRMTVRKALDELVEEGLLERRQGRGTFVAE 71
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
 19-80 6.59e-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: 51.46  E-value: 6.59e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 644360139   19 YEMIRQTLDEAIRAGSVPAGLVLL-EGPLADMFGTSRVPVRKALGLLHQEGLIARFEGRGFIV 80
Cdd:pfam00392   2 YEQVYARLREDILSGRLRPGDKLPsERELAAEFGVSRTTVREALRRLEAEGLVERRQGRGTFV 64
FCD smart00895
This entry represents the C-terminal ligand binding domain of many members of the GntR family; ...
 185-308 1.24e-07

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: 49.67  E-value: 1.24e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644360139   185 DHYEIRACLEPAALLKAAPHLSRQHVLDSLERLTQLEQGTFSLASLERVEE---DLHIHCLAPAGNKTLLGVLRQsqspL 261
Cdd:smart00895   1 ELYEVRRALEPLAARLAAERATDEDLAALEALLDAMEAAAAAGDDLEEFAEldrEFHRALAEAAGNPVLLELLES----L 76

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 644360139   262 IVTRIFYDMLGIKIEEAMLNEHRLVLQMLLQGANDAAALGLQEHLRR 308
Cdd:smart00895  77 RARLRRLRRLSLEAARRALDEHRAILDAIRARDAEAARAAMREHLEA 123
PRK10225 PRK10225
Uxu operon transcriptional regulator;
138-315 6.89e-06

Uxu operon transcriptional regulator;


Pssm-ID: 182318 [Multi-domain]  Cd Length: 257  Bit Score: 46.94  E-value: 6.89e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644360139 138 EASAAEFYNVSRSAIREALMRLRDQGLVEKEP----YAQWLAGPLTAREITDHY----------EIRACLEPAALLKAAP 203
Cdd:PRK10225  36 EREIAEMLDVTRTVVREALIMLEIKGLVEVRRgagiYVLDSSGSHNTDSPDANVcndagpfellQARQLLESNIAEFAAL 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644360139 204 HLSRQHVLDSLERLtQLEQGTFSLASLERVEE-DLHIH-CLAPAG-NKTLLGVLRQS-----QSPLIVTriFYDMLGIKI 275
Cdd:PRK10225 116 QATREDIVKMRQAL-QLEERELASSAPGSSESgDMQFHlAIAEAThNSMLVELFRQSwqwreNNPMWIQ--LHSHLDDSL 192

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 644360139 276 -EEAMLNEHRLVLQMLLQGANDAAALGLQEHLRRAQMRTLQ 315
Cdd:PRK10225 193 yRKEWLGDHKQILAALIKKDARAAKLAMWQHLENVKQRLLE 233
HTH_GNTR smart00345
helix_turn_helix gluconate operon transcriptional repressor;
22-80 2.07e-05

helix_turn_helix gluconate operon transcriptional repressor;


Pssm-ID: 197669 [Multi-domain]  Cd Length: 60  Bit Score: 41.79  E-value: 2.07e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 644360139    22 IRQTLDEAIRAGSVPAGLVL-LEGPLADMFGTSRVPVRKALGLLHQEGLIARFEGRGFIV 80
Cdd:smart00345   1 VAERLREDIVSGELRPGDKLpSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGSGTFV 60
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 138-169 2.69e-05

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: 41.28  E-value: 2.69e-05
                         10        20        30
                 ....*....|....*....|....*....|..
gi 644360139 138 EASAAEFYNVSRSAIREALMRLRDQGLVEKEP 169
Cdd:cd07377   28 ERELAEELGVSRTTVREALRELEAEGLVERRP 59
ARO8 COG1167
DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain ...
 13-82 4.13e-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: 45.20  E-value: 4.13e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 644360139  13 TRAGARYEMIRQTLDEAIRAGSVPAGLVLlegP----LADMFGTSRVPVRKALGLLHQEGLIARFEGRGFIVTP 82
Cdd:COG1167    8 DSSGPLYLQLADALREAILSGRLPPGDRL---PssreLAAQLGVSRSTVVRAYEELEAEGLIESRPGSGTFVAA 78
PRK11402 PRK11402
transcriptional regulator PhoB;
19-83 7.46e-05

transcriptional regulator PhoB;


Pssm-ID: 183118 [Multi-domain]  Cd Length: 241  Bit Score: 43.67  E-value: 7.46e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 644360139  19 YEMIRQTLDEAIRAGSVPAGLVL-LEGPLADMFGTSRVPVRKALGLLHQEGLIARFEGRG-FIVTPE 83
Cdd:PRK11402  11 YATVRQRLLDDIAQGVYQAGQQIpTENELCTQYNVSRITIRKAISDLVADGVLIRWQGKGtFVQSQK 77
FCD pfam07729
FCD domain; This domain is the C-terminal ligand binding domain of many members of the GntR ...
 185-304 2.32e-04

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: 40.43  E-value: 2.32e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644360139  185 DHYEIRACLEPAALLKAAPHLSRQHV--LDSLERLTQLEQGTFSLASLERVEEDLHIHCLAPAGNKTLLGVLRQSQSPLI 262
Cdd:pfam07729   1 ELYELRAALEPLAARLAAERATDEDLaeLEALLEALEAAADAGDLEAFAEADREFHLALAEAAGNPVLARMLESLWDRLR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 644360139  263 VTRIFYdMLGIKIEEAMLNEHRLVLQMLLQGANDAAALGLQE 304
Cdd:pfam07729  81 RLRRLL-LSSPGRLRASLEEHRAILDAIRARDPEAARAAMRR 121
PRK09764 PRK09764
GntR family transcriptional regulator;
18-83 4.66e-04

GntR family transcriptional regulator;


Pssm-ID: 182065 [Multi-domain]  Cd Length: 240  Bit Score: 40.97  E-value: 4.66e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 644360139  18 RYEMIRQTLDEAIRAGSVPAGLVL-LEGPLADMFGTSRVPVRKALGLLHQEGLIARFEGRGFIVTPE 83
Cdd:PRK09764   6 LYRQIADRIREQIARGELKPGDALpTESALQTEFGVSRVTVRQALRQLVEQQILESIQGSGTYVKEE 72
PRK14999 PRK14999
histidine utilization repressor; Provisional
 19-84 7.95e-04

histidine utilization repressor; Provisional


Pssm-ID: 184961 [Multi-domain]  Cd Length: 241  Bit Score: 40.30  E-value: 7.95e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 644360139  19 YEMIRQTLDEAIRAGS-VPAGLVLLEGPLADMFGTSRVPVRKALGLLHQEGLIARFEGRG-FIVTPEG 84
Cdd:PRK14999  14 YETVKQDICKKIAGGVwQPHDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVRLQGVGtFVAEPKG 81
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
 138-169 9.40e-03

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: 34.13  E-value: 9.40e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 644360139  138 EASAAEFYNVSRSAIREALMRLRDQGLVEKEP 169
Cdd:pfam00392  27 ERELAAEFGVSRTTVREALRRLEAEGLVERRQ 58
 
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