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Conserved domains on  [gi|556486125|ref|WP_023334043|]
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MULTISPECIES: transcriptional regulator LldR [Enterobacter]

Protein Classification

transcriptional regulator LldR( domain architecture ID 11484713)

transcriptional regulator LldR may be a regulatory protein for the LCT genes

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK10421 PRK10421
DNA-binding transcriptional repressor LldR; Provisional
 6-257 5.49e-167

DNA-binding transcriptional repressor LldR; Provisional


:

Pssm-ID: 236690 [Multi-domain]  Cd Length: 253  Bit Score: 461.54  E-value: 5.49e-167
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125   6 RRLSDEIASRVRALIEEQQLEAGMKLPAERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTFVRWQHDDWSEQNIVQ 85
Cdd:PRK10421   1 RRLSDEVADRVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRWRHETWSEQNIVQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125  86 PLKTLMENDPDYSFDILEARHAIETSTAWHAAMRATDADKEKLIACFEATQSRDPDIASQADVRFHLAIAEASHNVVLLQ 165
Cdd:PRK10421  81 PLKTLMADDPDYSFDILEARHAIEASTAWHAAMRATPGDKEKIQLCFEATLSEDPDLASQADVRFHLAIAEASHNVVLLQ 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125 166 TMRGFFDLLQSSVKQSRQRMYLVPPVFAQLTEQHEAVLNAILAGDAEAARKAMMAHLGFVHTTIKRFDEDQARQARITRL 245
Cdd:PRK10421 161 TMRGFFDVLQSSVKQSRQRMYLVPPVFSQLTEQHQAVMDAILAGDAEGARKAMMAHLSFVHTTIKRFDEDQARQARITRL 240

                        250
                 ....*....|...
gi 556486125 246 PGD-SDISRENKA 257
Cdd:PRK10421 241 PGDhNEHSREKNA 253
 
Name Accession Description Interval E-value
PRK10421 PRK10421
DNA-binding transcriptional repressor LldR; Provisional
 6-257 5.49e-167

DNA-binding transcriptional repressor LldR; Provisional


Pssm-ID: 236690 [Multi-domain]  Cd Length: 253  Bit Score: 461.54  E-value: 5.49e-167
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125   6 RRLSDEIASRVRALIEEQQLEAGMKLPAERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTFVRWQHDDWSEQNIVQ 85
Cdd:PRK10421   1 RRLSDEVADRVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRWRHETWSEQNIVQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125  86 PLKTLMENDPDYSFDILEARHAIETSTAWHAAMRATDADKEKLIACFEATQSRDPDIASQADVRFHLAIAEASHNVVLLQ 165
Cdd:PRK10421  81 PLKTLMADDPDYSFDILEARHAIEASTAWHAAMRATPGDKEKIQLCFEATLSEDPDLASQADVRFHLAIAEASHNVVLLQ 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125 166 TMRGFFDLLQSSVKQSRQRMYLVPPVFAQLTEQHEAVLNAILAGDAEAARKAMMAHLGFVHTTIKRFDEDQARQARITRL 245
Cdd:PRK10421 161 TMRGFFDVLQSSVKQSRQRMYLVPPVFSQLTEQHQAVMDAILAGDAEGARKAMMAHLSFVHTTIKRFDEDQARQARITRL 240

                        250
                 ....*....|...
gi 556486125 246 PGD-SDISRENKA 257
Cdd:PRK10421 241 PGDhNEHSREKNA 253
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
3-238 6.70e-67

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


Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 207.09  E-value: 6.70e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125   3 VMPRRLSDEIASRVRALIEEQQLEAGMKLPAERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTFVRwqhdDWSEQN 82
Cdd:COG2186    3 IRRRSLAEQVAEQLRELILSGELKPGDRLPSERELAEQLGVSRTTVREALRALEALGLVEVRQGGGTFVR----EPSPWA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125  83 IVQPLKTLMENDPDYSFDILEARHAIETSTAWHAAMRATDADKEKLIACFEATQS--RDPDIASQADVRFHLAIAEASHN 160
Cdd:COG2186   79 LLDPLALLLALDDASLRDLLEARLALEPEAARLAAERATDEDLARLEAALAEMEAaaDDGEAFAEADLAFHRAIAEASGN 158

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 556486125 161 VVLLQTMRGFFDLLQssvkQSRQRMYLVPPVFAQLTEQHEAVLNAILAGDAEAARKAMMAHLGFVHTTIKRFDEDQAR 238
Cdd:COG2186  159 PLLALLLESLRELLR----RSVRLTLRSPEARERSLAEHRAILDAIRAGDPEAARAAMRAHLEAVRERLREALAERAR 232
FCD smart00895
This entry represents the C-terminal ligand binding domain of many members of the GntR family; ...
 100-222 2.34e-22

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: 88.96  E-value: 2.34e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125   100 DILEARHAIETSTAWHAAMRATDADKEKLIACFEA-----TQSRDPDIASQADVRFHLAIAEASHNVVLLQTMRGFFDLL 174
Cdd:smart00895   1 ELYEVRRALEPLAARLAAERATDEDLAALEALLDAmeaaaAAGDDLEEFAELDREFHRALAEAAGNPVLLELLESLRARL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 556486125   175 qssvkqsRQRMYLVPPVFAQLTEQHEAVLNAILAGDAEAARKAMMAHL 222
Cdd:smart00895  81 -------RRLRRLSLEAARRALDEHRAILDAIRARDAEAARAAMREHL 121
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 8-72 1.06e-21

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: 85.19  E-value: 1.06e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 556486125   8 LSDEIASRVRALIEEQQLEAGMKLPAERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTFVR 72
Cdd:cd07377    2 LYEQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFVA 66
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
 8-71 4.27e-20

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: 81.12  E-value: 4.27e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 556486125    8 LSDEIASRVRALIEEQQLEAGMKLPAERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTFV 71
Cdd:pfam00392   1 LYEQVYARLREDILSGRLRPGDKLPSERELAAEFGVSRTTVREALRRLEAEGLVERRQGRGTFV 64
C_P_lyase_phnF TIGR02325
phosphonates metabolism transcriptional regulator PhnF; All members of the seed alignment for ...
 11-71 7.46e-12

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: 63.26  E-value: 7.46e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 556486125   11 EIASRVRALIEEQQLEAGMKLPAERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTFV 71
Cdd:TIGR02325  12 QIADKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQGRGTFV 72
 
Name Accession Description Interval E-value
PRK10421 PRK10421
DNA-binding transcriptional repressor LldR; Provisional
 6-257 5.49e-167

DNA-binding transcriptional repressor LldR; Provisional


Pssm-ID: 236690 [Multi-domain]  Cd Length: 253  Bit Score: 461.54  E-value: 5.49e-167
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125   6 RRLSDEIASRVRALIEEQQLEAGMKLPAERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTFVRWQHDDWSEQNIVQ 85
Cdd:PRK10421   1 RRLSDEVADRVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRWRHETWSEQNIVQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125  86 PLKTLMENDPDYSFDILEARHAIETSTAWHAAMRATDADKEKLIACFEATQSRDPDIASQADVRFHLAIAEASHNVVLLQ 165
Cdd:PRK10421  81 PLKTLMADDPDYSFDILEARHAIEASTAWHAAMRATPGDKEKIQLCFEATLSEDPDLASQADVRFHLAIAEASHNVVLLQ 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125 166 TMRGFFDLLQSSVKQSRQRMYLVPPVFAQLTEQHEAVLNAILAGDAEAARKAMMAHLGFVHTTIKRFDEDQARQARITRL 245
Cdd:PRK10421 161 TMRGFFDVLQSSVKQSRQRMYLVPPVFSQLTEQHQAVMDAILAGDAEGARKAMMAHLSFVHTTIKRFDEDQARQARITRL 240

                        250
                 ....*....|...
gi 556486125 246 PGD-SDISRENKA 257
Cdd:PRK10421 241 PGDhNEHSREKNA 253
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
3-238 6.70e-67

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


Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 207.09  E-value: 6.70e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125   3 VMPRRLSDEIASRVRALIEEQQLEAGMKLPAERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTFVRwqhdDWSEQN 82
Cdd:COG2186    3 IRRRSLAEQVAEQLRELILSGELKPGDRLPSERELAEQLGVSRTTVREALRALEALGLVEVRQGGGTFVR----EPSPWA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125  83 IVQPLKTLMENDPDYSFDILEARHAIETSTAWHAAMRATDADKEKLIACFEATQS--RDPDIASQADVRFHLAIAEASHN 160
Cdd:COG2186   79 LLDPLALLLALDDASLRDLLEARLALEPEAARLAAERATDEDLARLEAALAEMEAaaDDGEAFAEADLAFHRAIAEASGN 158

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 556486125 161 VVLLQTMRGFFDLLQssvkQSRQRMYLVPPVFAQLTEQHEAVLNAILAGDAEAARKAMMAHLGFVHTTIKRFDEDQAR 238
Cdd:COG2186  159 PLLALLLESLRELLR----RSVRLTLRSPEARERSLAEHRAILDAIRAGDPEAARAAMRAHLEAVRERLREALAERAR 232
pdhR PRK09464
pyruvate dehydrogenase complex transcriptional repressor PdhR;
7-244 7.22e-58

pyruvate dehydrogenase complex transcriptional repressor PdhR;


Pssm-ID: 181879 [Multi-domain]  Cd Length: 254  Bit Score: 184.84  E-value: 7.22e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125   7 RLSDEIASRVRALIEEQQLEAGMKLPAERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTFVrwQHDDWseQNIVQP 86
Cdd:PRK09464  10 KLSDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGGTFV--QSSLW--QSFSDP 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125  87 LKTLMENDPDYSFDILEARHAIETSTAWHAAMRATDADKEKLIACF----EATQSRDPDIASQADVRFHLAIAEASHNVV 162
Cdd:PRK09464  86 LVELLSDHPESQFDLLETRHALEGIAAYYAALRGTDEDFERIRECHhaieLAQQSGDLDAEANAVMQYQIAVTEAAHNVV 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125 163 LLQTMRGFFDLLQSSVKQSRQRMYLVPPVFAQLTEQHEAVLNAILAGDAEAARKAMMAHLGFVHTTIKRFDEDQARQARI 242
Cdd:PRK09464 166 LLHLLRCMEPMLEQNVRQNFELLYRRREMLPKVSSHRARIFEAIVAGKPEKAREASHRHLAFIEEILLDLSREESRRERS 245


                 ..
gi 556486125 243 TR 244
Cdd:PRK09464 246 LR 247
PRK09990 PRK09990
DNA-binding transcriptional regulator GlcC; Provisional
 5-247 3.89e-42

DNA-binding transcriptional regulator GlcC; Provisional


Pssm-ID: 182186 [Multi-domain]  Cd Length: 251  Bit Score: 144.14  E-value: 3.89e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125   5 PRRLSDEIASRVRALIEEQQLEAGMKLPAERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTFVRwqhdDWSEQNIV 84
Cdd:PRK09990   5 RRPIADVVAERIERLIVDGVLKVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQGRGSFVA----RLNRVQDA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125  85 QPLKTLMENDPDYSFDILEARHAIETSTAWHAAMRATDADK-------EKLIACFEATQSRDPDIASQADVRFHLAIAEA 157
Cdd:PRK09990  81 SPLMHLFSSQPRTLYDLLEVRALLEGESARLAALRGTQADFvlitrryEEMLAAHENNKEIDPIEHARLDHAFHLAICEA 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125 158 SHNVVLLQTMRGFFDLLQSSVKQSRQRMYLVPPVFAQLTEQHEAVLNAILAGDAEAARKAMMAHLGFVHTTIKRFDEDQA 237
Cdd:PRK09990 161 SHNPVLVHTLQSLTDLMLSSVFASVNNLYHRPQQKKQIDRQHARLYNAVLQRLPEQAQRAARDHIRTVRDNLREIEQEEQ 240

                        250
                 ....*....|.
gi 556486125 238 RQARIT-RLPG 247
Cdd:PRK09990 241 RLVRATlRLEG 251
GntR COG1802
DNA-binding transcriptional regulator, GntR family [Transcription];
3-238 1.69e-37

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


Pssm-ID: 441407 [Multi-domain]  Cd Length: 222  Bit Score: 131.20  E-value: 1.69e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125   3 VMPRRLSDEIASRVRALIEEQQLEAGMKLPaERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTFVRwqhdDWSEQN 82
Cdd:COG1802    7 LRRESLAEQVYEALREAILSGELPPGERLS-EAELAERLGVSRTPVREALRRLEAEGLVEIRPNRGARVA----PLSPEE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125  83 IVqplktlmendpdysfDILEARHAIETSTAWHAAMRATDADKEKLIACFE----ATQSRDPDIASQADVRFHLAIAEAS 158
Cdd:COG1802   82 IR---------------ELYEVRAALEGLAARLAAERATPADLARLRALLEeleaAAAAGDVAAYLELDREFHRALVEAA 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125 159 HNVVLLQTMRGFFDLLQSsvkqSRQRMYLVPPVFAQLTEQHEAVLNAILAGDAEAARKAMMAHLGFVHTTIKRFDEDQAR 238
Cdd:COG1802  147 GNPRLAELLRRLRARLRR----YRRLSLRSPGRLEESLAEHRAILDALEAGDAEAAAAALRAHLERARERLLEALAAAAA 222
PRK10225 PRK10225
Uxu operon transcriptional regulator;
6-232 1.78e-27

Uxu operon transcriptional regulator;


Pssm-ID: 182318 [Multi-domain]  Cd Length: 257  Bit Score: 106.26  E-value: 1.78e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125   6 RRLSDEIASRVRALIEEQQLEAGMKLPAERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTFVRwqhdDWSEQNIVQ 85
Cdd:PRK10225   8 QRPYQEVGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRRGAGIYVL----DSSGSHNTD 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125  86 PLKTLMENDPDySFDILEARHAIETSTAWHAAMRATdadKEKLIACFEATQSRDPDIASQA-------DVRFHLAIAEAS 158
Cdd:PRK10225  84 SPDANVCNDAG-PFELLQARQLLESNIAEFAALQAT---REDIVKMRQALQLEERELASSApgssesgDMQFHLAIAEAT 159

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 556486125 159 HNVVLLQTMRGFFDLLQSSVKQSRQRMYLVPPVF-AQLTEQHEAVLNAILAGDAEAARKAMMAHLGFVHTTIKRF 232
Cdd:PRK10225 160 HNSMLVELFRQSWQWRENNPMWIQLHSHLDDSLYrKEWLGDHKQILAALIKKDARAAKLAMWQHLENVKQRLLEF 234
PRK03837 PRK03837
transcriptional regulator NanR; Provisional
 6-237 1.97e-24

transcriptional regulator NanR; Provisional


Pssm-ID: 235166 [Multi-domain]  Cd Length: 241  Bit Score: 97.79  E-value: 1.97e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125   6 RRLSDEIASRVRALIEEQQLEAGMKLPAERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTFVRWQHDDWSEQNIVQ 85
Cdd:PRK03837  12 KKLSEEVEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQISHGERARVSRPSADTIIGQLSG 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125  86 PLKTLMENDPDYSFDILEARHAIETSTAWHAAMRATDADKEKLIACFEA-TQSR-DPDIASQADVRFHLAIAEASHNVVL 163
Cdd:PRK03837  92 MAKDFLSQSPDGLAHLKQARLFFESSLARYAAEHATDEQIALLRKALERnSQSLgDNAAFIRSDMEFHRVIAEIPGNPIF 171

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 556486125 164 LQTMRGFFDLLqssvKQSRQRMYLVPPVFAQLTEQHEAVLNAILAGDAEAARKAMMAHLGFVHTTIKRFDEDQA 237
Cdd:PRK03837 172 MAIHEALLDWL----IEARPEVVILHGHENVTLQEHIAIVDAIRAHDPDEADRALQSHLNRVSALYHALGQTTN 241
FCD smart00895
This entry represents the C-terminal ligand binding domain of many members of the GntR family; ...
 100-222 2.34e-22

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: 88.96  E-value: 2.34e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125   100 DILEARHAIETSTAWHAAMRATDADKEKLIACFEA-----TQSRDPDIASQADVRFHLAIAEASHNVVLLQTMRGFFDLL 174
Cdd:smart00895   1 ELYEVRRALEPLAARLAAERATDEDLAALEALLDAmeaaaAAGDDLEEFAELDREFHRALAEAAGNPVLLELLESLRARL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 556486125   175 qssvkqsRQRMYLVPPVFAQLTEQHEAVLNAILAGDAEAARKAMMAHL 222
Cdd:smart00895  81 -------RRLRRLSLEAARRALDEHRAILDAIRARDAEAARAAMREHL 121
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 8-72 1.06e-21

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: 85.19  E-value: 1.06e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 556486125   8 LSDEIASRVRALIEEQQLEAGMKLPAERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTFVR 72
Cdd:cd07377    2 LYEQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFVA 66
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
 8-71 4.27e-20

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: 81.12  E-value: 4.27e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 556486125    8 LSDEIASRVRALIEEQQLEAGMKLPAERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTFV 71
Cdd:pfam00392   1 LYEQVYARLREDILSGRLRPGDKLPSERELAAEFGVSRTTVREALRRLEAEGLVERRQGRGTFV 64
FCD pfam07729
FCD domain; This domain is the C-terminal ligand binding domain of many members of the GntR ...
 100-220 1.33e-19

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: 81.65  E-value: 1.33e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125  100 DILEARHAIETSTAWHAAMRATDADKEKLIACFE----ATQSRDPDIASQADVRFHLAIAEASHNVVLLQTMRGFFDLLQ 175
Cdd:pfam07729   1 ELYELRAALEPLAARLAAERATDEDLAELEALLEaleaAADAGDLEAFAEADREFHLALAEAAGNPVLARMLESLWDRLR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 556486125  176 ssvkQSRQRMYLVPPVFAQLTEQHEAVLNAILAGDAEAARKAMMA 220
Cdd:pfam07729  81 ----RLRRLLLSSPGRLRASLEEHRAILDAIRARDPEAARAAMRR 121
PRK11523 PRK11523
transcriptional regulator ExuR;
5-222 3.34e-19

transcriptional regulator ExuR;


Pssm-ID: 183176 [Multi-domain]  Cd Length: 253  Bit Score: 83.74  E-value: 3.34e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125   5 PRRLSDEIASRVRALIEEQQLEAGMKLPAERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTfvrwqHDDWSEQNIV 84
Cdd:PRK11523   6 PRRLYQQLAAELKERIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRKGSGI-----HVVSNQPRHQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125  85 QPLKTLMENDPDYSFDILEARHAIETSTAWHAAMRATDADKEKLIACFEATQSRDPDIASQADVRFHLAIAEASHNVVLL 164
Cdd:PRK11523  81 QAADNNMEFANYGPFELLQARQLIESNIAEFAATQVTKQDIMKLMAIQEQARGEDCFRDSEWDLQFHVQVALATQNSALA 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125 165 QTMRgffdllqssvKQSRQRMYlvPPVFAQLTEQ------------HEAVLNAILAGDAEAARKAMMAHL 222
Cdd:PRK11523 161 AIVE----------KMWTQRSH--NPYWKKLHEHiddrtvdnwcddHDQILKALIRKDPHAAKLAMWQHL 218
HTH_GNTR smart00345
helix_turn_helix gluconate operon transcriptional repressor;
12-71 5.13e-19

helix_turn_helix gluconate operon transcriptional repressor;


Pssm-ID: 197669 [Multi-domain]  Cd Length: 60  Bit Score: 78.00  E-value: 5.13e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125    12 IASRVRALIEEQQLEAGMKLPAERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTFV 71
Cdd:smart00345   1 VAERLREDIVSGELRPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGSGTFV 60
MngR COG2188
DNA-binding transcriptional regulator, GntR family [Transcription];
11-128 2.13e-18

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


Pssm-ID: 441791 [Multi-domain]  Cd Length: 238  Bit Score: 81.45  E-value: 2.13e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125  11 EIASRVRALIEEQQLEAGMKLPAERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTFVRwqhddwsEQNIVQPLKTL 90
Cdd:COG2188    9 QIADALRERIESGELPPGDRLPSERELAEEFGVSRMTVRKALDELVEEGLLERRQGRGTFVA-------EPKIEYPLSRL 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 556486125  91 mendpdYSFDILEARHAIETSTAWHAA--MRATDADKEKL 128
Cdd:COG2188   82 ------TSFTEELRARGREPSTRVLSAerVPADEEVAEAL 115
ARO8 COG1167
DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain ...
 1-72 2.10e-16

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: 77.95  E-value: 2.10e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 556486125   1 MIVMPRR----LSDEIASRVRALIEEQQLEAGMKLPAERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTFVR 72
Cdd:COG1167    2 LIRLDRDssgpLYLQLADALREAILSGRLPPGDRLPSSRELAAQLGVSRSTVVRAYEELEAEGLIESRPGSGTFVA 77
YhcF COG1725
DNA-binding transcriptional regulator YhcF, GntR family [Transcription];
12-92 3.65e-13

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


Pssm-ID: 441331 [Multi-domain]  Cd Length: 114  Bit Score: 64.04  E-value: 3.65e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125  12 IASRVRALIEEQQLEAGMKLPAERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTFVRWQHDDWSEQNIVQPLKTLM 91
Cdd:COG1725   15 IADQIKEAIASGELKPGDRLPSVRELAAELGVNPNTVAKAYRELEDEGLIETRRGKGTFVAEDARELLEERREEFLEEAL 94


                 .
gi 556486125  92 E 92
Cdd:COG1725   95 R 95
C_P_lyase_phnF TIGR02325
phosphonates metabolism transcriptional regulator PhnF; All members of the seed alignment for ...
 11-71 7.46e-12

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: 63.26  E-value: 7.46e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 556486125   11 EIASRVRALIEEQQLEAGMKLPAERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTFV 71
Cdd:TIGR02325  12 QIADKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQGRGTFV 72
PRK15481 PRK15481
transcriptional regulatory protein PtsJ; Provisional
 11-72 1.29e-09

transcriptional regulatory protein PtsJ; Provisional


Pssm-ID: 185378 [Multi-domain]  Cd Length: 431  Bit Score: 57.75  E-value: 1.29e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 556486125  11 EIASRVRALIEEQQLEAGMKLPAERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTFVR 72
Cdd:PRK15481   9 EIFDSIRQLIQAGRLRPGDSLPPVRELASELGVNRNTVAAAYKRLVTAGLAQSQGRNGTVIR 70
PRK09764 PRK09764
GntR family transcriptional regulator;
11-72 2.77e-09

GntR family transcriptional regulator;


Pssm-ID: 182065 [Multi-domain]  Cd Length: 240  Bit Score: 55.99  E-value: 2.77e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 556486125  11 EIASRVRALIEEQQLEAGMKLPAERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTFVR 72
Cdd:PRK09764   9 QIADRIREQIARGELKPGDALPTESALQTEFGVSRVTVRQALRQLVEQQILESIQGSGTYVK 70
PRK11402 PRK11402
transcriptional regulator PhoB;
2-74 6.75e-09

transcriptional regulator PhoB;


Pssm-ID: 183118 [Multi-domain]  Cd Length: 241  Bit Score: 54.84  E-value: 6.75e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 556486125   2 IVMPRRLSDEIASRVralieeqqLEAGMKLPAERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTFVRWQ 74
Cdd:PRK11402  12 ATVRQRLLDDIAQGV--------YQAGQQIPTENELCTQYNVSRITIRKAISDLVADGVLIRWQGKGTFVQSQ 76
PRK04984 PRK04984
fatty acid metabolism transcriptional regulator FadR;
27-103 1.13e-04

fatty acid metabolism transcriptional regulator FadR;


Pssm-ID: 179909 [Multi-domain]  Cd Length: 239  Bit Score: 42.16  E-value: 1.13e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 556486125  27 AGMKLPAERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTFVrwqHDDW--SEQNIvqpLKTLMENDPDYSFDILE 103
Cdd:PRK04984  27 PGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGKPTKV---NNFWetSGLNI---LETLARLDHDSVPQLID 99
PRK10079 PRK10079
phosphonate metabolism transcriptional regulator PhnF; Provisional
 11-71 1.31e-04

phosphonate metabolism transcriptional regulator PhnF; Provisional


Pssm-ID: 182227 [Multi-domain]  Cd Length: 241  Bit Score: 42.07  E-value: 1.31e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 556486125  11 EIASRVralieEQQLE----AGMKLPAERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTFV 71
Cdd:PRK10079  16 EIAAKL-----EQELRqhyrCGDYLPAEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQGVGVLV 75
PRK14999 PRK14999
histidine utilization repressor; Provisional
 30-71 5.04e-04

histidine utilization repressor; Provisional


Pssm-ID: 184961 [Multi-domain]  Cd Length: 241  Bit Score: 40.30  E-value: 5.04e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 556486125  30 KLPAERQLAAQLGVSRNSLREALATLVSEGVLLSRRGGGTFV 71
Cdd:PRK14999  35 RIPSEAELVAQYGFSRMTINRALRELTDEGWLVRLQGVGTFV 76
PRK11534 PRK11534
DNA-binding transcriptional regulator CsiR; Provisional
 41-222 1.35e-03

DNA-binding transcriptional regulator CsiR; Provisional


Pssm-ID: 183181 [Multi-domain]  Cd Length: 224  Bit Score: 39.11  E-value: 1.35e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125  41 LGVSrnSLREALATLVSEGVL--LSRRGggtfvrWQHDDWSEQNIVqplktlmendpdysfDILEARHAIET-------- 110
Cdd:PRK11534  42 LGVG--PLREALSQLVAERLVtvVNQKG------YRVASMSEQELL---------------DIFDARANMEAmlvslaia 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556486125 111 --STAWHAAMRATDADKEKLIACFEATQSRDP-DIASQAdvrFHLAIAEASHNVVLLQTMRGFFDLlqssvkQSRQR-MY 186
Cdd:PRK11534  99 rgGDEWEADVLAKAHLLSKLEACDASEKMLDEwDLRHQA---FHTAIVAGCGSHYLLQMRERLFDL------AARYRfIW 169

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 556486125 187 LVPPVF-AQLTE----QHEAVLNAILAGDAEAARKAMMAHL 222
Cdd:PRK11534 170 LRRTVLsVEMLEdkhdQHQTLTAAILARDTARASELMRQHL 210
 
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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