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Conserved domains on  [gi|502669985|ref|WP_012905837|]
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GntR family transcriptional regulator [Citrobacter rodentium]

Protein Classification

PRK11414 family protein( domain architecture ID 11485341)

PRK11414 family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK11414 PRK11414
GntR family transcriptional regulator;
1-221 9.12e-139

GntR family transcriptional regulator;


:

Pssm-ID: 183126 [Multi-domain]  Cd Length: 221  Bit Score: 387.30  E-value: 9.12e-139
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502669985   1 MPGTEKTQHISLTSRVERGLKDRLSIGELRPGARLITKNIAEEMGISITPVREALLRLVSASALTIAPAQAFIVPEISMA 80
Cdd:PRK11414   1 MPGTEKTQHISLTLQVENDLKHQLSIGALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALSVAPAQAFTVPEVSKR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502669985  81 RFAEITRLRCELEGMAVMEATGQITPERMEILEALLANYQWAYENGSVAERLLANRALRFKIYHFSSMPTLVEMIEQLWV 160
Cdd:PRK11414  81 QLDEINRIRYELELMAVALAVENLTPQDLAELQELLEKLQQAQEKGDMEQIINANRLFRLAIYHRSNMPILCEMIEQLWV 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 502669985 161 RMGPSLHFLHGLEKEGAYQHNVDHYRQLFTLIAEGNKEASRSCLLEIINKNVAIVKQQYLN 221
Cdd:PRK11414 161 RMGPSLHYLYEAINPAELREHIENYRLLLAALKAKDKEGCRHCLAEIMQQNVAILYQQYNR 221
 
Name Accession Description Interval E-value
PRK11414 PRK11414
GntR family transcriptional regulator;
1-221 9.12e-139

GntR family transcriptional regulator;


Pssm-ID: 183126 [Multi-domain]  Cd Length: 221  Bit Score: 387.30  E-value: 9.12e-139
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502669985   1 MPGTEKTQHISLTSRVERGLKDRLSIGELRPGARLITKNIAEEMGISITPVREALLRLVSASALTIAPAQAFIVPEISMA 80
Cdd:PRK11414   1 MPGTEKTQHISLTLQVENDLKHQLSIGALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALSVAPAQAFTVPEVSKR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502669985  81 RFAEITRLRCELEGMAVMEATGQITPERMEILEALLANYQWAYENGSVAERLLANRALRFKIYHFSSMPTLVEMIEQLWV 160
Cdd:PRK11414  81 QLDEINRIRYELELMAVALAVENLTPQDLAELQELLEKLQQAQEKGDMEQIINANRLFRLAIYHRSNMPILCEMIEQLWV 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 502669985 161 RMGPSLHFLHGLEKEGAYQHNVDHYRQLFTLIAEGNKEASRSCLLEIINKNVAIVKQQYLN 221
Cdd:PRK11414 161 RMGPSLHYLYEAINPAELREHIENYRLLLAALKAKDKEGCRHCLAEIMQQNVAILYQQYNR 221
GntR COG1802
DNA-binding transcriptional regulator, GntR family [Transcription];
1-206 1.18e-37

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


Pssm-ID: 441407 [Multi-domain]  Cd Length: 222  Bit Score: 130.43  E-value: 1.18e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502669985   1 MPGTEKTQHISLTSRVERGLKDRLSIGELRPGARLITKNIAEEMGISITPVREALLRLVSASALTIAPAQAFIVPEISMA 80
Cdd:COG1802    1 MTSPSPLRRESLAEQVYEALREAILSGELPPGERLSEAELAERLGVSRTPVREALRRLEAEGLVEIRPNRGARVAPLSPE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502669985  81 RFAEITRLRCELEGMAVMEATGQITPERMEILEALLANYQWAYENGSVAERLLANRALRFKIYHFSSMPTLVEMIEQLWV 160
Cdd:COG1802   81 EIRELYEVRAALEGLAARLAAERATPADLARLRALLEELEAAAAAGDVAAYLELDREFHRALVEAAGNPRLAELLRRLRA 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 502669985 161 RMGPSLHFLhgLEKEGAYQHNVDHYRQLFTLIAEGNKEASRSCLLE 206
Cdd:COG1802  161 RLRRYRRLS--LRSPGRLEESLAEHRAILDALEAGDAEAAAAALRA 204
FCD pfam07729
FCD domain; This domain is the C-terminal ligand binding domain of many members of the GntR ...
 84-206 3.56e-13

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: 63.93  E-value: 3.56e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502669985   84 EITRLRCELEGMAVMEATGQITPERMEILEALLANYQWAYENGSVAERLLANRALRFKIYHFSSMPTLVEMIEQLWVRMG 163
Cdd:pfam07729   1 ELYELRAALEPLAARLAAERATDEDLAELEALLEALEAAADAGDLEAFAEADREFHLALAEAAGNPVLARMLESLWDRLR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 502669985  164 PSLHFLhgLEKEGAYQHNVDHYRQLFTLIAEGNKEASRSCLLE 206
Cdd:pfam07729  81 RLRRLL--LSSPGRLRASLEEHRAILDAIRARDPEAARAAMRR 121
HTH_GNTR smart00345
helix_turn_helix gluconate operon transcriptional repressor;
16-74 1.38e-10

helix_turn_helix gluconate operon transcriptional repressor;


Pssm-ID: 197669 [Multi-domain]  Cd Length: 60  Bit Score: 55.27  E-value: 1.38e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 502669985    16 VERGLKDRLSIGELRPGARLIT-KNIAEEMGISITPVREALLRLVSASALTIAPAQAFIV 74
Cdd:smart00345   1 VAERLREDIVSGELRPGDKLPSeRELAAQLGVSRTTVREALSRLEAEGLVQRRPGSGTFV 60
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 11-60 1.87e-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: 43.98  E-value: 1.87e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 502669985  11 SLTSRVERGLKDRLSIGELRPGARLITKN-IAEEMGISITPVREALLRLVS 60
Cdd:cd07377    1 PLYEQIADQLREAILSGELKPGDRLPSEReLAEELGVSRTTVREALRELEA 51
 
Name Accession Description Interval E-value
PRK11414 PRK11414
GntR family transcriptional regulator;
1-221 9.12e-139

GntR family transcriptional regulator;


Pssm-ID: 183126 [Multi-domain]  Cd Length: 221  Bit Score: 387.30  E-value: 9.12e-139
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502669985   1 MPGTEKTQHISLTSRVERGLKDRLSIGELRPGARLITKNIAEEMGISITPVREALLRLVSASALTIAPAQAFIVPEISMA 80
Cdd:PRK11414   1 MPGTEKTQHISLTLQVENDLKHQLSIGALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALSVAPAQAFTVPEVSKR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502669985  81 RFAEITRLRCELEGMAVMEATGQITPERMEILEALLANYQWAYENGSVAERLLANRALRFKIYHFSSMPTLVEMIEQLWV 160
Cdd:PRK11414  81 QLDEINRIRYELELMAVALAVENLTPQDLAELQELLEKLQQAQEKGDMEQIINANRLFRLAIYHRSNMPILCEMIEQLWV 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 502669985 161 RMGPSLHFLHGLEKEGAYQHNVDHYRQLFTLIAEGNKEASRSCLLEIINKNVAIVKQQYLN 221
Cdd:PRK11414 161 RMGPSLHYLYEAINPAELREHIENYRLLLAALKAKDKEGCRHCLAEIMQQNVAILYQQYNR 221
GntR COG1802
DNA-binding transcriptional regulator, GntR family [Transcription];
1-206 1.18e-37

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


Pssm-ID: 441407 [Multi-domain]  Cd Length: 222  Bit Score: 130.43  E-value: 1.18e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502669985   1 MPGTEKTQHISLTSRVERGLKDRLSIGELRPGARLITKNIAEEMGISITPVREALLRLVSASALTIAPAQAFIVPEISMA 80
Cdd:COG1802    1 MTSPSPLRRESLAEQVYEALREAILSGELPPGERLSEAELAERLGVSRTPVREALRRLEAEGLVEIRPNRGARVAPLSPE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502669985  81 RFAEITRLRCELEGMAVMEATGQITPERMEILEALLANYQWAYENGSVAERLLANRALRFKIYHFSSMPTLVEMIEQLWV 160
Cdd:COG1802   81 EIRELYEVRAALEGLAARLAAERATPADLARLRALLEELEAAAAAGDVAAYLELDREFHRALVEAAGNPRLAELLRRLRA 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 502669985 161 RMGPSLHFLhgLEKEGAYQHNVDHYRQLFTLIAEGNKEASRSCLLE 206
Cdd:COG1802  161 RLRRYRRLS--LRSPGRLEESLAEHRAILDALEAGDAEAAAAALRA 204
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
11-208 5.90e-15

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


Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 71.12  E-value: 5.90e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502669985  11 SLTSRVERGLKDRLSIGELRPGARLIT-KNIAEEMGISITPVREALLRL---------------VSASALTIAPAQAFIV 74
Cdd:COG2186    7 SLAEQVAEQLRELILSGELKPGDRLPSeRELAEQLGVSRTTVREALRALealglvevrqgggtfVREPSPWALLDPLALL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502669985  75 PEISMARFAEITRLRCELEGMAVMEATGQITPERMEILEALLANYQWAYENGsvAERLLANRALRFKIYHFSSMPTLVEM 154
Cdd:COG2186   87 LALDDASLRDLLEARLALEPEAARLAAERATDEDLARLEAALAEMEAAADDG--EAFAEADLAFHRAIAEASGNPLLALL 164

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 502669985 155 IEQLWVRMGPSLHflHGLEKEGAYQHNVDHYRQLFTLIAEGNKEASRSCLLEII 208
Cdd:COG2186  165 LESLRELLRRSVR--LTLRSPEARERSLAEHRAILDAIRAGDPEAARAAMRAHL 216
FCD pfam07729
FCD domain; This domain is the C-terminal ligand binding domain of many members of the GntR ...
 84-206 3.56e-13

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: 63.93  E-value: 3.56e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502669985   84 EITRLRCELEGMAVMEATGQITPERMEILEALLANYQWAYENGSVAERLLANRALRFKIYHFSSMPTLVEMIEQLWVRMG 163
Cdd:pfam07729   1 ELYELRAALEPLAARLAAERATDEDLAELEALLEALEAAADAGDLEAFAEADREFHLALAEAAGNPVLARMLESLWDRLR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 502669985  164 PSLHFLhgLEKEGAYQHNVDHYRQLFTLIAEGNKEASRSCLLE 206
Cdd:pfam07729  81 RLRRLL--LSSPGRLRASLEEHRAILDAIRARDPEAARAAMRR 121
HTH_GNTR smart00345
helix_turn_helix gluconate operon transcriptional repressor;
16-74 1.38e-10

helix_turn_helix gluconate operon transcriptional repressor;


Pssm-ID: 197669 [Multi-domain]  Cd Length: 60  Bit Score: 55.27  E-value: 1.38e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 502669985    16 VERGLKDRLSIGELRPGARLIT-KNIAEEMGISITPVREALLRLVSASALTIAPAQAFIV 74
Cdd:smart00345   1 VAERLREDIVSGELRPGDKLPSeRELAAQLGVSRTTVREALSRLEAEGLVQRRPGSGTFV 60
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
 12-74 9.33e-10

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: 53.00  E-value: 9.33e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 502669985   12 LTSRVERGLKDRLSIGELRPGARLITKN-IAEEMGISITPVREALLRLVSASALTIAPAQAFIV 74
Cdd:pfam00392   1 LYEQVYARLREDILSGRLRPGDKLPSEReLAAEFGVSRTTVREALRRLEAEGLVERRQGRGTFV 64
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 11-60 1.87e-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: 43.98  E-value: 1.87e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 502669985  11 SLTSRVERGLKDRLSIGELRPGARLITKN-IAEEMGISITPVREALLRLVS 60
Cdd:cd07377    1 PLYEQIADQLREAILSGELKPGDRLPSEReLAEELGVSRTTVREALRELEA 51
PRK11534 PRK11534
DNA-binding transcriptional regulator CsiR; Provisional
 18-97 2.58e-04

DNA-binding transcriptional regulator CsiR; Provisional


Pssm-ID: 183181 [Multi-domain]  Cd Length: 224  Bit Score: 40.65  E-value: 2.58e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502669985  18 RGLKDRLSIGELRPGARLITKNIAEEMGISITPVREALLRLVSASALTIAPAQAFIVPEISMARFAEITRLRCELEGMAV 97
Cdd:PRK11534  14 RWLKNDIIRGNFQPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQKGYRVASMSEQELLDIFDARANMEAMLV 93
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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