NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|556352853|ref|WP_023299382|]
View 

MULTISPECIES: FadR/GntR family transcriptional regulator [Enterobacter]

Protein Classification

FadR/GntR family transcriptional regulator( domain architecture ID 11450686)

helix-turn-helix transcriptional regulator belonging to the GntR family, which contains FadR, HutC, MocR, YtrA, AraR, PlmA, and many other subfamilies

CATH:  1.10.10.10
Gene Ontology:  GO:0003677|GO:0003700
PubMed:  2060763
SCOP:  4000155

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
3-236 1.86e-55

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


:

Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 177.05  E-value: 1.86e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853   3 KPSRVLANSSTALDQLRGLINQHESTPGTPLPTERELSETLGVGRREVRRALDVLEEEGRIWRKQGKGTFIGPAAP---V 79
Cdd:COG2186    1 KPIRRRSLAEQVAEQLRELILSGELKPGDRLPSERELAEQLGVSRTTVREALRALEALGLVEVRQGGGTFVREPSPwalL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853  80 EPLALQGLVQQTNLLEVMEARLQLEPGLARLAALRATRENLALMQRMLERIDKVSPDDRDLNElWDSAFHRAIAEAAGNR 159
Cdd:COG2186   81 DPLALLLALDDASLRDLLEARLALEPEAARLAAERATDEDLARLEAALAEMEAAADDGEAFAE-ADLAFHRAIAEASGNP 159

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 556352853 160 LMLGLFDAIDAVRREPGWQYLrelaRTPERVDNYNDHHHNIMSAIIHRQPNEAAAAMREHLLSLQTALIQAIHLEDD 236
Cdd:COG2186  160 LLALLLESLRELLRRSVRLTL----RSPEARERSLAEHRAILDAIRAGDPEAARAAMRAHLEAVRERLREALAERAR 232
 
Name Accession Description Interval E-value
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
3-236 1.86e-55

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


Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 177.05  E-value: 1.86e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853   3 KPSRVLANSSTALDQLRGLINQHESTPGTPLPTERELSETLGVGRREVRRALDVLEEEGRIWRKQGKGTFIGPAAP---V 79
Cdd:COG2186    1 KPIRRRSLAEQVAEQLRELILSGELKPGDRLPSERELAEQLGVSRTTVREALRALEALGLVEVRQGGGTFVREPSPwalL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853  80 EPLALQGLVQQTNLLEVMEARLQLEPGLARLAALRATRENLALMQRMLERIDKVSPDDRDLNElWDSAFHRAIAEAAGNR 159
Cdd:COG2186   81 DPLALLLALDDASLRDLLEARLALEPEAARLAAERATDEDLARLEAALAEMEAAADDGEAFAE-ADLAFHRAIAEASGNP 159

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 556352853 160 LMLGLFDAIDAVRREPGWQYLrelaRTPERVDNYNDHHHNIMSAIIHRQPNEAAAAMREHLLSLQTALIQAIHLEDD 236
Cdd:COG2186  160 LLALLLESLRELLRRSVRLTL----RSPEARERSLAEHRAILDAIRAGDPEAARAAMRAHLEAVRERLREALAERAR 232
PRK10421 PRK10421
DNA-binding transcriptional repressor LldR; Provisional
 16-220 3.70e-27

DNA-binding transcriptional repressor LldR; Provisional


Pssm-ID: 236690 [Multi-domain]  Cd Length: 253  Bit Score: 104.46  E-value: 3.70e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853  16 DQLRGLINQHESTPGTPLPTERELSETLGVGRREVRRALDVLEEEGRIWRKQGKGTFIGPaaPVEPLALQGLVQQ-TNLL 94
Cdd:PRK10421   9 DRVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRW--RHETWSEQNIVQPlKTLM 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853  95 E--------VMEARLQLEPGLARLAALRATRENLALMQRMLERIdkvSPDDRDLNELWDSAFHRAIAEAAGN----RLML 162
Cdd:PRK10421  87 AddpdysfdILEARHAIEASTAWHAAMRATPGDKEKIQLCFEAT---LSEDPDLASQADVRFHLAIAEASHNvvllQTMR 163

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 556352853 163 GLFDAIDAVRRepgwQYLRELARTPERVDNYNDHHHNIMSAIIHRQPNEAAAAMREHL 220
Cdd:PRK10421 164 GFFDVLQSSVK----QSRQRMYLVPPVFSQLTEQHQAVMDAILAGDAEGARKAMMAHL 217
FCD smart00895
This entry represents the C-terminal ligand binding domain of many members of the GntR family; ...
 95-220 4.38e-21

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: 85.10  E-value: 4.38e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853    95 EVMEARLQLEPGLARLAALRATRENLALMQRMLERIDKVSPDDRDLNELW--DSAFHRAIAEAAGNRLMLGLFDAIDAVR 172
Cdd:smart00895   1 ELYEVRRALEPLAARLAAERATDEDLAALEALLDAMEAAAAAGDDLEEFAelDREFHRALAEAAGNPVLLELLESLRARL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 556352853   173 RepgwqylRELARTPERVDNYNDHHHNIMSAIIHRQPNEAAAAMREHL 220
Cdd:smart00895  81 R-------RLRRLSLEAARRALDEHRAILDAIRARDAEAARAAMREHL 121
FCD pfam07729
FCD domain; This domain is the C-terminal ligand binding domain of many members of the GntR ...
 95-218 1.11e-17

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: 76.25  E-value: 1.11e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853   95 EVMEARLQLEPGLARLAALRATRENLALMQRMLERIDKVsPDDRDLNELW--DSAFHRAIAEAAGNRLMLGLFDAIDAVR 172
Cdd:pfam07729   1 ELYELRAALEPLAARLAAERATDEDLAELEALLEALEAA-ADAGDLEAFAeaDREFHLALAEAAGNPVLARMLESLWDRL 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 556352853  173 RepgwQYLRELARTPERVDNYNDHHHNIMSAIIHRQPNEAAAAMRE 218
Cdd:pfam07729  80 R----RLRRLLLSSPGRLRASLEEHRAILDAIRARDPEAARAAMRR 121
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 16-73 1.39e-16

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: 71.32  E-value: 1.39e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 556352853  16 DQLRGLINQHESTPGTPLPTERELSETLGVGRREVRRALDVLEEEGRIWRKQGKGTFI 73
Cdd:cd07377    8 DQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFV 65
C_P_lyase_phnF TIGR02325
phosphonates metabolism transcriptional regulator PhnF; All members of the seed alignment for ...
 16-113 5.23e-10

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: 57.87  E-value: 5.23e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853   16 DQLRGLINQHESTPGTPLPTERELSETLGVGRREVRRALDVLEEEGRIWRKQGKGTFIGPAAPVEPLALQGLVQQTNLLE 95
Cdd:TIGR02325  15 DKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQGRGTFVAARRIDYPLSARTRFSQNLADQ 94

                          90       100
                  ....*....|....*....|...
gi 556352853   96 VMEARLQL-----EPGLARLAAL 113
Cdd:TIGR02325  95 GREPTGELllsdlEPASAELADA 117
 
Name Accession Description Interval E-value
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
3-236 1.86e-55

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


Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 177.05  E-value: 1.86e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853   3 KPSRVLANSSTALDQLRGLINQHESTPGTPLPTERELSETLGVGRREVRRALDVLEEEGRIWRKQGKGTFIGPAAP---V 79
Cdd:COG2186    1 KPIRRRSLAEQVAEQLRELILSGELKPGDRLPSERELAEQLGVSRTTVREALRALEALGLVEVRQGGGTFVREPSPwalL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853  80 EPLALQGLVQQTNLLEVMEARLQLEPGLARLAALRATRENLALMQRMLERIDKVSPDDRDLNElWDSAFHRAIAEAAGNR 159
Cdd:COG2186   81 DPLALLLALDDASLRDLLEARLALEPEAARLAAERATDEDLARLEAALAEMEAAADDGEAFAE-ADLAFHRAIAEASGNP 159

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 556352853 160 LMLGLFDAIDAVRREPGWQYLrelaRTPERVDNYNDHHHNIMSAIIHRQPNEAAAAMREHLLSLQTALIQAIHLEDD 236
Cdd:COG2186  160 LLALLLESLRELLRRSVRLTL----RSPEARERSLAEHRAILDAIRAGDPEAARAAMRAHLEAVRERLREALAERAR 232
GntR COG1802
DNA-binding transcriptional regulator, GntR family [Transcription];
1-236 2.10e-28

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


Pssm-ID: 441407 [Multi-domain]  Cd Length: 222  Bit Score: 106.93  E-value: 2.10e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853   1 MEKPSRVLANSST--ALDQLRGLINQHESTPGTPLpTERELSETLGVGRREVRRALDVLEEEGRIWRKQGKGTFIgpaAP 78
Cdd:COG1802    1 MTSPSPLRRESLAeqVYEALREAILSGELPPGERL-SEAELAERLGVSRTPVREALRRLEAEGLVEIRPNRGARV---AP 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853  79 VEPlalqglvqqTNLLEVMEARLQLEPGLARLAALRATRENLALMQRMLERIDKV--SPDDRDLNELwDSAFHRAIAEAA 156
Cdd:COG1802   77 LSP---------EEIRELYEVRAALEGLAARLAAERATPADLARLRALLEELEAAaaAGDVAAYLEL-DREFHRALVEAA 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853 157 GNRLmlgLFDAIDAVRREPGWqYLRELARTPERVDNYNDHHHNIMSAIIHRQPNEAAAAMREHLLSLQTALIQAIHLEDD 236
Cdd:COG1802  147 GNPR---LAELLRRLRARLRR-YRRLSLRSPGRLEESLAEHRAILDALEAGDAEAAAAALRAHLERARERLLEALAAAAA 222
PRK10421 PRK10421
DNA-binding transcriptional repressor LldR; Provisional
 16-220 3.70e-27

DNA-binding transcriptional repressor LldR; Provisional


Pssm-ID: 236690 [Multi-domain]  Cd Length: 253  Bit Score: 104.46  E-value: 3.70e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853  16 DQLRGLINQHESTPGTPLPTERELSETLGVGRREVRRALDVLEEEGRIWRKQGKGTFIGPaaPVEPLALQGLVQQ-TNLL 94
Cdd:PRK10421   9 DRVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRW--RHETWSEQNIVQPlKTLM 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853  95 E--------VMEARLQLEPGLARLAALRATRENLALMQRMLERIdkvSPDDRDLNELWDSAFHRAIAEAAGN----RLML 162
Cdd:PRK10421  87 AddpdysfdILEARHAIEASTAWHAAMRATPGDKEKIQLCFEAT---LSEDPDLASQADVRFHLAIAEASHNvvllQTMR 163

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 556352853 163 GLFDAIDAVRRepgwQYLRELARTPERVDNYNDHHHNIMSAIIHRQPNEAAAAMREHL 220
Cdd:PRK10421 164 GFFDVLQSSVK----QSRQRMYLVPPVFSQLTEQHQAVMDAILAGDAEGARKAMMAHL 217
PRK03837 PRK03837
transcriptional regulator NanR; Provisional
 11-220 8.87e-26

transcriptional regulator NanR; Provisional


Pssm-ID: 235166 [Multi-domain]  Cd Length: 241  Bit Score: 100.87  E-value: 8.87e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853  11 SSTALDQLRGLINQHESTPGTPLPTERELSETLGVGRREVRRALDVLEEEGRIWRKQGK---------GTFIgpaAPVEP 81
Cdd:PRK03837  15 SEEVEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQISHGErarvsrpsaDTII---GQLSG 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853  82 LALQGLVQQTNLLEVME-ARLQLEPGLARLAALRATRENLALMQRMLERIDKvSPDDRDLNELWDSAFHRAIAEAAGNRL 160
Cdd:PRK03837  92 MAKDFLSQSPDGLAHLKqARLFFESSLARYAAEHATDEQIALLRKALERNSQ-SLGDNAAFIRSDMEFHRVIAEIPGNPI 170

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 556352853 161 MLGLFDAIdavrrePGW--QYLRELARTPERVDNYNDHHHNIMSAIIHRQPNEAAAAMREHL 220
Cdd:PRK03837 171 FMAIHEAL------LDWliEARPEVVILHGHENVTLQEHIAIVDAIRAHDPDEADRALQSHL 226
PRK10225 PRK10225
Uxu operon transcriptional regulator;
18-235 2.97e-23

Uxu operon transcriptional regulator;


Pssm-ID: 182318 [Multi-domain]  Cd Length: 257  Bit Score: 94.32  E-value: 2.97e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853  18 LRGLINQHESTPGTPLPTERELSETLGVGRREVRRALDVLEEEGRIWRKQGKGTFIGPAApvEPLALQG----LVQQTNL 93
Cdd:PRK10225  18 IRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRRGAGIYVLDSS--GSHNTDSpdanVCNDAGP 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853  94 LEVMEARLQLEPGLARLAALRATRENLALMQRMLE----RIDKVSPDDrdlNELWDSAFHRAIAEAAGNRLMLGLFDAID 169
Cdd:PRK10225  96 FELLQARQLLESNIAEFAALQATREDIVKMRQALQleerELASSAPGS---SESGDMQFHLAIAEATHNSMLVELFRQSW 172

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 556352853 170 AVRRE-PGW-QYLRELARTPERVDNYNDHHHnIMSAIIHRQPNEAAAAMREHLLSLQTALIQAIHLED 235
Cdd:PRK10225 173 QWRENnPMWiQLHSHLDDSLYRKEWLGDHKQ-ILAALIKKDARAAKLAMWQHLENVKQRLLEFSNVDD 239
pdhR PRK09464
pyruvate dehydrogenase complex transcriptional repressor PdhR;
11-220 4.46e-23

pyruvate dehydrogenase complex transcriptional repressor PdhR;


Pssm-ID: 181879 [Multi-domain]  Cd Length: 254  Bit Score: 93.93  E-value: 4.46e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853  11 SSTALDQLRGLINQHESTPGTPLPTERELSETLGVGRREVRRALDVLEEEGRIWRKQGKGTFI------GPAAPVEPLAL 84
Cdd:PRK09464  12 SDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGGTFVqsslwqSFSDPLVELLS 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853  85 QGLVQQTNLLevmEARLQLEPGLARLAALRATRENLALMQRMLERIDKVSpDDRDLNELWDS--AFHRAIAEAAGNRLML 162
Cdd:PRK09464  92 DHPESQFDLL---ETRHALEGIAAYYAALRGTDEDFERIRECHHAIELAQ-QSGDLDAEANAvmQYQIAVTEAAHNVVLL 167

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 556352853 163 GLFDAIDAVRREPGWQYLRELARTPERVDNYNDHHHNIMSAIIHRQPNEAAAAMREHL 220
Cdd:PRK09464 168 HLLRCMEPMLEQNVRQNFELLYRRREMLPKVSSHRARIFEAIVAGKPEKAREASHRHL 225
FCD smart00895
This entry represents the C-terminal ligand binding domain of many members of the GntR family; ...
 95-220 4.38e-21

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: 85.10  E-value: 4.38e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853    95 EVMEARLQLEPGLARLAALRATRENLALMQRMLERIDKVSPDDRDLNELW--DSAFHRAIAEAAGNRLMLGLFDAIDAVR 172
Cdd:smart00895   1 ELYEVRRALEPLAARLAAERATDEDLAALEALLDAMEAAAAAGDDLEEFAelDREFHRALAEAAGNPVLLELLESLRARL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 556352853   173 RepgwqylRELARTPERVDNYNDHHHNIMSAIIHRQPNEAAAAMREHL 220
Cdd:smart00895  81 R-------RLRRLSLEAARRALDEHRAILDAIRARDAEAARAAMREHL 121
PRK09990 PRK09990
DNA-binding transcriptional regulator GlcC; Provisional
 29-227 4.11e-18

DNA-binding transcriptional regulator GlcC; Provisional


Pssm-ID: 182186 [Multi-domain]  Cd Length: 251  Bit Score: 80.58  E-value: 4.11e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853  29 PGTPLPTERELSETLGVGRREVRRALDVLEEEGRIWRKQGKGTFIGP---AAPVEPLALQGLVQQTNLLEVMEARLQLEP 105
Cdd:PRK09990  27 VGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQGRGSFVARlnrVQDASPLMHLFSSQPRTLYDLLEVRALLEG 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853 106 GLARLAALRATRENLALMQR----MLERIDKVSPDDRDLNELWDSAFHRAIAEAAGNRLMLGLFDAIDAVRREPGWQYLR 181
Cdd:PRK09990 107 ESARLAALRGTQADFVLITRryeeMLAAHENNKEIDPIEHARLDHAFHLAICEASHNPVLVHTLQSLTDLMLSSVFASVN 186

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 556352853 182 ELARTPERVDNYNDHHHNIMSAIIHRQPNEAAAAMREHLLSLQTAL 227
Cdd:PRK09990 187 NLYHRPQQKKQIDRQHARLYNAVLQRLPEQAQRAARDHIRTVRDNL 232
FCD pfam07729
FCD domain; This domain is the C-terminal ligand binding domain of many members of the GntR ...
 95-218 1.11e-17

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: 76.25  E-value: 1.11e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853   95 EVMEARLQLEPGLARLAALRATRENLALMQRMLERIDKVsPDDRDLNELW--DSAFHRAIAEAAGNRLMLGLFDAIDAVR 172
Cdd:pfam07729   1 ELYELRAALEPLAARLAAERATDEDLAELEALLEALEAA-ADAGDLEAFAeaDREFHLALAEAAGNPVLARMLESLWDRL 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 556352853  173 RepgwQYLRELARTPERVDNYNDHHHNIMSAIIHRQPNEAAAAMRE 218
Cdd:pfam07729  80 R----RLRRLLLSSPGRLRASLEEHRAILDAIRARDPEAARAAMRR 121
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 16-73 1.39e-16

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: 71.32  E-value: 1.39e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 556352853  16 DQLRGLINQHESTPGTPLPTERELSETLGVGRREVRRALDVLEEEGRIWRKQGKGTFI 73
Cdd:cd07377    8 DQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFV 65
PRK11523 PRK11523
transcriptional regulator ExuR;
30-230 3.46e-16

transcriptional regulator ExuR;


Pssm-ID: 183176 [Multi-domain]  Cd Length: 253  Bit Score: 75.27  E-value: 3.46e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853  30 GTPLPTERELSETLGVGRREVRRALDVLEEEGRIWRKQGKGTFIGPAAPVEPLALQGLVQQTNL--LEVMEARLQLEPGL 107
Cdd:PRK11523  29 GDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRKGSGIHVVSNQPRHQQAADNNMEFANYgpFELLQARQLIESNI 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853 108 ARLAALRATRENLALMQRMLERIDKvspDDRDLNELWDSAFHRAIAEAAGNRLMLGLFDAIDAVR-REPGWQYLRELART 186
Cdd:PRK11523 109 AEFAATQVTKQDIMKLMAIQEQARG---EDCFRDSEWDLQFHVQVALATQNSALAAIVEKMWTQRsHNPYWKKLHEHIDD 185

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 556352853 187 pERVDNYNDHHHNIMSAIIHRQPNEAAAAMREHLLSLQTALIQA 230
Cdd:PRK11523 186 -RTVDNWCDDHDQILKALIRKDPHAAKLAMWQHLENTKQMLFNE 228
MngR COG2188
DNA-binding transcriptional regulator, GntR family [Transcription];
16-100 3.62e-16

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


Pssm-ID: 441791 [Multi-domain]  Cd Length: 238  Bit Score: 74.90  E-value: 3.62e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853  16 DQLRGLINQHESTPGTPLPTERELSETLGVGRREVRRALDVLEEEGRIWRKQGKGTFIgpaapVEPLALQGLVQQTNLLE 95
Cdd:COG2188   12 DALRERIESGELPPGDRLPSERELAEEFGVSRMTVRKALDELVEEGLLERRQGRGTFV-----AEPKIEYPLSRLTSFTE 86


                 ....*
gi 556352853  96 VMEAR 100
Cdd:COG2188   87 ELRAR 91
HTH_GNTR smart00345
helix_turn_helix gluconate operon transcriptional repressor;
16-73 1.46e-13

helix_turn_helix gluconate operon transcriptional repressor;


Pssm-ID: 197669 [Multi-domain]  Cd Length: 60  Bit Score: 63.36  E-value: 1.46e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 556352853    16 DQLRGLINQHESTPGTPLPTERELSETLGVGRREVRRALDVLEEEGRIWRKQGKGTFI 73
Cdd:smart00345   3 ERLREDIVSGELRPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGSGTFV 60
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
 16-73 5.12e-13

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: 61.86  E-value: 5.12e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 556352853   16 DQLRGLINQHESTPGTPLPTERELSETLGVGRREVRRALDVLEEEGRIWRKQGKGTFI 73
Cdd:pfam00392   7 ARLREDILSGRLRPGDKLPSERELAAEFGVSRTTVREALRRLEAEGLVERRQGRGTFV 64
PRK11402 PRK11402
transcriptional regulator PhoB;
22-86 2.55e-10

transcriptional regulator PhoB;


Pssm-ID: 183118 [Multi-domain]  Cd Length: 241  Bit Score: 58.69  E-value: 2.55e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 556352853  22 INQHESTPGTPLPTERELSETLGVGRREVRRALDVLEEEGRIWRKQGKGTFI-GPAAPVEPLALQG 86
Cdd:PRK11402  22 IAQGVYQAGQQIPTENELCTQYNVSRITIRKAISDLVADGVLIRWQGKGTFVqSQKVENALLTVSG 87
C_P_lyase_phnF TIGR02325
phosphonates metabolism transcriptional regulator PhnF; All members of the seed alignment for ...
 16-113 5.23e-10

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: 57.87  E-value: 5.23e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853   16 DQLRGLINQHESTPGTPLPTERELSETLGVGRREVRRALDVLEEEGRIWRKQGKGTFIGPAAPVEPLALQGLVQQTNLLE 95
Cdd:TIGR02325  15 DKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQGRGTFVAARRIDYPLSARTRFSQNLADQ 94

                          90       100
                  ....*....|....*....|...
gi 556352853   96 VMEARLQL-----EPGLARLAAL 113
Cdd:TIGR02325  95 GREPTGELllsdlEPASAELADA 117
ARO8 COG1167
DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain ...
 16-83 7.02e-10

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: 58.30  E-value: 7.02e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 556352853  16 DQLRGLINQHESTPGTPLPTERELSETLGVGRREVRRALDVLEEEGRIWRKQGKGTFIGPAAPVEPLA 83
Cdd:COG1167   19 DALREAILSGRLPPGDRLPSSRELAAQLGVSRSTVVRAYEELEAEGLIESRPGSGTFVAARLPAPAPA 86
PRK11534 PRK11534
DNA-binding transcriptional regulator CsiR; Provisional
 93-232 9.56e-09

DNA-binding transcriptional regulator CsiR; Provisional


Pssm-ID: 183181 [Multi-domain]  Cd Length: 224  Bit Score: 54.13  E-value: 9.56e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853  93 LLEVMEARLQLEPGLARLAALRATRE---NLALMQRMLERIDKVSPDDRDLNElWDS---AFHRAIAEAAGNRLMLG--- 163
Cdd:PRK11534  78 LLDIFDARANMEAMLVSLAIARGGDEweaDVLAKAHLLSKLEACDASEKMLDE-WDLrhqAFHTAIVAGCGSHYLLQmre 156

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853 164 -LFDAidAVRREPGWqyLRELARTPERVDNYNDHHHNIMSAIIHRQPNEAAAAMREHLLSLQTALIQAIH 232
Cdd:PRK11534 157 rLFDL--AARYRFIW--LRRTVLSVEMLEDKHDQHQTLTAAILARDTARASELMRQHLLTPIPIIQQAMA 222
YhcF COG1725
DNA-binding transcriptional regulator YhcF, GntR family [Transcription];
16-78 1.73e-08

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


Pssm-ID: 441331 [Multi-domain]  Cd Length: 114  Bit Score: 50.95  E-value: 1.73e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 556352853  16 DQLRGLINQHESTPGTPLPTERELSETLGVGRREVRRALDVLEEEGRIWRKQGKGTFIGPAAP 78
Cdd:COG1725   17 DQIKEAIASGELKPGDRLPSVRELAAELGVNPNTVAKAYRELEDEGLIETRRGKGTFVAEDAR 79
PRK09764 PRK09764
GntR family transcriptional regulator;
16-73 1.53e-06

GntR family transcriptional regulator;


Pssm-ID: 182065 [Multi-domain]  Cd Length: 240  Bit Score: 47.52  E-value: 1.53e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 556352853  16 DQLRGLINQHESTPGTPLPTERELSETLGVGRREVRRALDVLEEEGRIWRKQGKGTFI 73
Cdd:PRK09764  12 DRIREQIARGELKPGDALPTESALQTEFGVSRVTVRQALRQLVEQQILESIQGSGTYV 69
PRK15481 PRK15481
transcriptional regulatory protein PtsJ; Provisional
 16-120 5.03e-04

transcriptional regulatory protein PtsJ; Provisional


Pssm-ID: 185378 [Multi-domain]  Cd Length: 431  Bit Score: 40.80  E-value: 5.03e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556352853  16 DQLRGLINQHESTPGTPLPTERELSETLGVGRREVRRALDVLEEEGrIWRKQG-KGTFIgpAAPVEPLALQGLVQQTNLL 94
Cdd:PRK15481  12 DSIRQLIQAGRLRPGDSLPPVRELASELGVNRNTVAAAYKRLVTAG-LAQSQGrNGTVI--RGSPSPVALEGGDPGTPLH 88

                         90       100
                 ....*....|....*....|....*...
gi 556352853  95 EVMEAR--LQLEPGLARLAALRATRENL 120
Cdd:PRK15481  89 DLAGGNpdPQRLPDLSRYFARLSRTPRL 116
PRK04984 PRK04984
fatty acid metabolism transcriptional regulator FadR;
29-55 3.05e-03

fatty acid metabolism transcriptional regulator FadR;


Pssm-ID: 179909 [Multi-domain]  Cd Length: 239  Bit Score: 37.93  E-value: 3.05e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 556352853  29 PGTPLPTERELSETLGVGR---REV--RRALD 55
Cdd:PRK04984  27 PGSILPAERELSELIGVTRttlREVlqRLARD 58
PRK14999 PRK14999
histidine utilization repressor; Provisional
 29-73 7.63e-03

histidine utilization repressor; Provisional


Pssm-ID: 184961 [Multi-domain]  Cd Length: 241  Bit Score: 36.83  E-value: 7.63e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 556352853  29 PGTPLPTERELSETLGVGRREVRRALDVLEEEGRIWRKQGKGTFI 73
Cdd:PRK14999  32 PHDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVRLQGVGTFV 76
PRK10079 PRK10079
phosphonate metabolism transcriptional regulator PhnF; Provisional
 30-95 8.59e-03

phosphonate metabolism transcriptional regulator PhnF; Provisional


Pssm-ID: 182227 [Multi-domain]  Cd Length: 241  Bit Score: 36.29  E-value: 8.59e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 556352853  30 GTPLPTERELSETLGVGRREVRRALDVLEEEGRIWRKQGKGTFIGPAAPVEPLALQGLVQQtNLLE 95
Cdd:PRK10079  32 GDYLPAEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQGVGVLVLMRPYDYPLNAQARFSQ-NLLD 96
 
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