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Conserved domains on  [gi|501390121|ref|WP_012421687|]
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MULTISPECIES: transcriptional regulator LldR [Shigella]

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
 6-258 3.76e-172

DNA-binding transcriptional repressor LldR; Provisional


:

Pssm-ID: 236690 [Multi-domain]  Cd Length: 253  Bit Score: 474.64  E-value: 3.76e-172
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121   6 RRLSDEVADRVRALIDEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRWRHDTWPEQNIVQ 85
Cdd:PRK10421   1 RRLSDEVADRVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRWRHETWSEQNIVQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121  86 PLKTLMADDPDYSFDILEARYAIEASTAWHAAMRATPGDKEKIQLCFEATLSEDPDIASQADVRFHLAIAEASHNIVLLQ 165
Cdd:PRK10421  81 PLKTLMADDPDYSFDILEARHAIEASTAWHAAMRATPGDKEKIQLCFEATLSEDPDLASQADVRFHLAIAEASHNVVLLQ 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121 166 TMRGFFDVLQSSVKHSRQRMYLVPPVFSQLTEQHQAVIDAIFAGDADGARKAMMAHLSFVHTTMKRFDEDQARHARITRL 245
Cdd:PRK10421 161 TMRGFFDVLQSSVKQSRQRMYLVPPVFSQLTEQHQAVMDAILAGDAEGARKAMMAHLSFVHTTIKRFDEDQARQARITRL 240

                        250
                 ....*....|...
gi 501390121 246 PGEHNEHSREKNA 258
Cdd:PRK10421 241 PGDHNEHSREKNA 253
 
Name Accession Description Interval E-value
PRK10421 PRK10421
DNA-binding transcriptional repressor LldR; Provisional
 6-258 3.76e-172

DNA-binding transcriptional repressor LldR; Provisional


Pssm-ID: 236690 [Multi-domain]  Cd Length: 253  Bit Score: 474.64  E-value: 3.76e-172
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121   6 RRLSDEVADRVRALIDEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRWRHDTWPEQNIVQ 85
Cdd:PRK10421   1 RRLSDEVADRVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRWRHETWSEQNIVQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121  86 PLKTLMADDPDYSFDILEARYAIEASTAWHAAMRATPGDKEKIQLCFEATLSEDPDIASQADVRFHLAIAEASHNIVLLQ 165
Cdd:PRK10421  81 PLKTLMADDPDYSFDILEARHAIEASTAWHAAMRATPGDKEKIQLCFEATLSEDPDLASQADVRFHLAIAEASHNVVLLQ 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121 166 TMRGFFDVLQSSVKHSRQRMYLVPPVFSQLTEQHQAVIDAIFAGDADGARKAMMAHLSFVHTTMKRFDEDQARHARITRL 245
Cdd:PRK10421 161 TMRGFFDVLQSSVKQSRQRMYLVPPVFSQLTEQHQAVMDAILAGDAEGARKAMMAHLSFVHTTIKRFDEDQARQARITRL 240

                        250
                 ....*....|...
gi 501390121 246 PGEHNEHSREKNA 258
Cdd:PRK10421 241 PGDHNEHSREKNA 253
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
5-238 3.99e-66

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


Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 205.17  E-value: 3.99e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121   5 PRRLSDEVADRVRALIDEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRWRhdtwPEQNIV 84
Cdd:COG2186    5 RRSLAEQVAEQLRELILSGELKPGDRLPSERELAEQLGVSRTTVREALRALEALGLVEVRQGGGTFVREP----SPWALL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121  85 QPLKTLMADDPDYSFDILEARYAIEASTAWHAAMRATPGDKEKIQLCFEA--TLSEDPDIASQADVRFHLAIAEASHNIV 162
Cdd:COG2186   81 DPLALLLALDDASLRDLLEARLALEPEAARLAAERATDEDLARLEAALAEmeAAADDGEAFAEADLAFHRAIAEASGNPL 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 501390121 163 LLQTMRGFFDVLQSSVKHSRQRmylvPPVFSQLTEQHQAVIDAIFAGDADGARKAMMAHLSFVHTTMKRFDEDQAR 238
Cdd:COG2186  161 LALLLESLRELLRRSVRLTLRS----PEARERSLAEHRAILDAIRAGDPEAARAAMRAHLEAVRERLREALAERAR 232
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
 8-71 2.71e-21

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: 84.20  E-value: 2.71e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 501390121    8 LSDEVADRVRALIDEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFI 71
Cdd:pfam00392   1 LYEQVYARLREDILSGRLRPGDKLPSERELAAEFGVSRTTVREALRRLEAEGLVERRQGRGTFV 64
FCD smart00895
This entry represents the C-terminal ligand binding domain of many members of the GntR family; ...
 100-222 1.62e-20

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: 83.95  E-value: 1.62e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121   100 DILEARYAIEASTAWHAAMRATPGDKEKIQLCFEA-----TLSEDPDIASQADVRFHLAIAEASHNIVLLQTMRGFFDvl 174
Cdd:smart00895   1 ELYEVRRALEPLAARLAAERATDEDLAALEALLDAmeaaaAAGDDLEEFAELDREFHRALAEAAGNPVLLELLESLRA-- 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 501390121   175 qssvkHSRQRMYLVPPVFSQLTEQHQAVIDAIFAGDADGARKAMMAHL 222
Cdd:smart00895  79 -----RLRRLRRLSLEAARRALDEHRAILDAIRARDAEAARAAMREHL 121
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 8-72 1.83e-20

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: 82.11  E-value: 1.83e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 501390121   8 LSDEVADRVRALIDEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIR 72
Cdd:cd07377    2 LYEQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFVA 66
C_P_lyase_phnF TIGR02325
phosphonates metabolism transcriptional regulator PhnF; All members of the seed alignment for ...
 11-79 1.19e-11

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: 62.88  E-value: 1.19e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 501390121   11 EVADRVRALIDEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRWRHDTWP 79
Cdd:TIGR02325  12 QIADKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQGRGTFVAARRIDYP 80
 
Name Accession Description Interval E-value
PRK10421 PRK10421
DNA-binding transcriptional repressor LldR; Provisional
 6-258 3.76e-172

DNA-binding transcriptional repressor LldR; Provisional


Pssm-ID: 236690 [Multi-domain]  Cd Length: 253  Bit Score: 474.64  E-value: 3.76e-172
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121   6 RRLSDEVADRVRALIDEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRWRHDTWPEQNIVQ 85
Cdd:PRK10421   1 RRLSDEVADRVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRWRHETWSEQNIVQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121  86 PLKTLMADDPDYSFDILEARYAIEASTAWHAAMRATPGDKEKIQLCFEATLSEDPDIASQADVRFHLAIAEASHNIVLLQ 165
Cdd:PRK10421  81 PLKTLMADDPDYSFDILEARHAIEASTAWHAAMRATPGDKEKIQLCFEATLSEDPDLASQADVRFHLAIAEASHNVVLLQ 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121 166 TMRGFFDVLQSSVKHSRQRMYLVPPVFSQLTEQHQAVIDAIFAGDADGARKAMMAHLSFVHTTMKRFDEDQARHARITRL 245
Cdd:PRK10421 161 TMRGFFDVLQSSVKQSRQRMYLVPPVFSQLTEQHQAVMDAILAGDAEGARKAMMAHLSFVHTTIKRFDEDQARQARITRL 240

                        250
                 ....*....|...
gi 501390121 246 PGEHNEHSREKNA 258
Cdd:PRK10421 241 PGDHNEHSREKNA 253
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
5-238 3.99e-66

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


Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 205.17  E-value: 3.99e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121   5 PRRLSDEVADRVRALIDEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRWRhdtwPEQNIV 84
Cdd:COG2186    5 RRSLAEQVAEQLRELILSGELKPGDRLPSERELAEQLGVSRTTVREALRALEALGLVEVRQGGGTFVREP----SPWALL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121  85 QPLKTLMADDPDYSFDILEARYAIEASTAWHAAMRATPGDKEKIQLCFEA--TLSEDPDIASQADVRFHLAIAEASHNIV 162
Cdd:COG2186   81 DPLALLLALDDASLRDLLEARLALEPEAARLAAERATDEDLARLEAALAEmeAAADDGEAFAEADLAFHRAIAEASGNPL 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 501390121 163 LLQTMRGFFDVLQSSVKHSRQRmylvPPVFSQLTEQHQAVIDAIFAGDADGARKAMMAHLSFVHTTMKRFDEDQAR 238
Cdd:COG2186  161 LALLLESLRELLRRSVRLTLRS----PEARERSLAEHRAILDAIRAGDPEAARAAMRAHLEAVRERLREALAERAR 232
pdhR PRK09464
pyruvate dehydrogenase complex transcriptional repressor PdhR;
7-251 1.34e-55

pyruvate dehydrogenase complex transcriptional repressor PdhR;


Pssm-ID: 181879 [Multi-domain]  Cd Length: 254  Bit Score: 179.06  E-value: 1.34e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121   7 RLSDEVADRVRALIDEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRwrHDTWpeQNIVQP 86
Cdd:PRK09464  10 KLSDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGGTFVQ--SSLW--QSFSDP 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121  87 LKTLMADDPDYSFDILEARYAIEASTAWHAAMRATPGDKEKIQLCF----EATLSEDPDIASQADVRFHLAIAEASHNIV 162
Cdd:PRK09464  86 LVELLSDHPESQFDLLETRHALEGIAAYYAALRGTDEDFERIRECHhaieLAQQSGDLDAEANAVMQYQIAVTEAAHNVV 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121 163 LLQTMRGFFDVLQSSVKHSRQRMYLVPPVFSQLTEQHQAVIDAIFAGDADGARKAMMAHLSFVHTTMKRFDEDQARHARI 242
Cdd:PRK09464 166 LLHLLRCMEPMLEQNVRQNFELLYRRREMLPKVSSHRARIFEAIVAGKPEKAREASHRHLAFIEEILLDLSREESRRERS 245


                 ....*....
gi 501390121 243 TRLPGEHNE 251
Cdd:PRK09464 246 LRRLQQRKN 254
PRK09990 PRK09990
DNA-binding transcriptional regulator GlcC; Provisional
 5-247 8.23e-37

DNA-binding transcriptional regulator GlcC; Provisional


Pssm-ID: 182186 [Multi-domain]  Cd Length: 251  Bit Score: 130.27  E-value: 8.23e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121   5 PRRLSDEVADRVRALIDEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRwrhDTWPEQNIv 84
Cdd:PRK09990   5 RRPIADVVAERIERLIVDGVLKVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQGRGSFVA---RLNRVQDA- 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121  85 QPLKTLMADDPDYSFDILEARYAIEASTAWHAAMRATPGDKEKIQLCFEATLS-----EDPDIASQA--DVRFHLAIAEA 157
Cdd:PRK09990  81 SPLMHLFSSQPRTLYDLLEVRALLEGESARLAALRGTQADFVLITRRYEEMLAahennKEIDPIEHArlDHAFHLAICEA 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121 158 SHNIVLLQTMRGFFDVLQSSVKHSRQRMYLVPPVFSQLTEQHQAVIDAIFAGDADGARKAMMAHLSFVHTTMKRFDEDQA 237
Cdd:PRK09990 161 SHNPVLVHTLQSLTDLMLSSVFASVNNLYHRPQQKKQIDRQHARLYNAVLQRLPEQAQRAARDHIRTVRDNLREIEQEEQ 240

                        250
                 ....*....|.
gi 501390121 238 RHARIT-RLPG 247
Cdd:PRK09990 241 RLVRATlRLEG 251
GntR COG1802
DNA-binding transcriptional regulator, GntR family [Transcription];
5-238 2.36e-33

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


Pssm-ID: 441407 [Multi-domain]  Cd Length: 222  Bit Score: 120.41  E-value: 2.36e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121   5 PRRLSDEVADRVRALIDEKNLEAGMKLPaERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRwrhdtwpeqniv 84
Cdd:COG1802    9 RESLAEQVYEALREAILSGELPPGERLS-EAELAERLGVSRTPVREALRRLEAEGLVEIRPNRGARVA------------ 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121  85 qPLktlmadDPDYSFDILEARYAIEASTAWHAAMRATPGDKEKIQLCFE----ATLSEDPDIASQADVRFHLAIAEASHN 160
Cdd:COG1802   76 -PL------SPEEIRELYEVRAALEGLAARLAAERATPADLARLRALLEeleaAAAAGDVAAYLELDREFHRALVEAAGN 148

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 501390121 161 IVLLQTMRGffdvLQSSVKHSRQRMYLVPPVFSQLTEQHQAVIDAIFAGDADGARKAMMAHLSFVHTTMKRFDEDQAR 238
Cdd:COG1802  149 PRLAELLRR----LRARLRRYRRLSLRSPGRLEESLAEHRAILDALEAGDAEAAAAALRAHLERARERLLEALAAAAA 222
PRK10225 PRK10225
Uxu operon transcriptional regulator;
6-232 1.08e-24

Uxu operon transcriptional regulator;


Pssm-ID: 182318 [Multi-domain]  Cd Length: 257  Bit Score: 98.94  E-value: 1.08e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121   6 RRLSDEVADRVRALIDEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRwrhdTWPEQNIVQ 85
Cdd:PRK10225   8 QRPYQEVGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRRGAGIYVL----DSSGSHNTD 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121  86 PLKTLMADDPDySFDILEARYAIEASTAWHAAMRATPGD----KEKIQLCFEATLSEDPDIASQADVRFHLAIAEASHNI 161
Cdd:PRK10225  84 SPDANVCNDAG-PFELLQARQLLESNIAEFAALQATREDivkmRQALQLEERELASSAPGSSESGDMQFHLAIAEATHNS 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121 162 VLLQTMRgffdvlQSSVKHSRQRMYLvpPVFSQLTE---------QHQAVIDAIFAGDADGARKAMMAHLSFVHTTMKRF 232
Cdd:PRK10225 163 MLVELFR------QSWQWRENNPMWI--QLHSHLDDslyrkewlgDHKQILAALIKKDARAAKLAMWQHLENVKQRLLEF 234
PRK03837 PRK03837
transcriptional regulator NanR; Provisional
 6-237 1.59e-24

transcriptional regulator NanR; Provisional


Pssm-ID: 235166 [Multi-domain]  Cd Length: 241  Bit Score: 97.79  E-value: 1.59e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121   6 RRLSDEVADRVRALIDEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVL---------LSRRGGGTFIRwrhd 76
Cdd:PRK03837  12 KKLSEEVEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVqishgerarVSRPSADTIIG---- 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121  77 twpeqNIVQPLKTLMADDPDYSFDILEARYAIEASTAWHAAMRATPGDKEKIqlcfEATLSE------DPDIASQADVRF 150
Cdd:PRK03837  88 -----QLSGMAKDFLSQSPDGLAHLKQARLFFESSLARYAAEHATDEQIALL----RKALERnsqslgDNAAFIRSDMEF 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121 151 HLAIAEASHNIVLLQTMRGFFDVLqssvKHSRQRMYLVPPVFSQLTEQHQAVIDAIFAGDADGARKAMMAHLSFVHTTMK 230
Cdd:PRK03837 159 HRVIAEIPGNPIFMAIHEALLDWL----IEARPEVVILHGHENVTLQEHIAIVDAIRAHDPDEADRALQSHLNRVSALYH 234


                 ....*..
gi 501390121 231 RFDEDQA 237
Cdd:PRK03837 235 ALGQTTN 241
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
 8-71 2.71e-21

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: 84.20  E-value: 2.71e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 501390121    8 LSDEVADRVRALIDEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFI 71
Cdd:pfam00392   1 LYEQVYARLREDILSGRLRPGDKLPSERELAAEFGVSRTTVREALRRLEAEGLVERRQGRGTFV 64
FCD smart00895
This entry represents the C-terminal ligand binding domain of many members of the GntR family; ...
 100-222 1.62e-20

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: 83.95  E-value: 1.62e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121   100 DILEARYAIEASTAWHAAMRATPGDKEKIQLCFEA-----TLSEDPDIASQADVRFHLAIAEASHNIVLLQTMRGFFDvl 174
Cdd:smart00895   1 ELYEVRRALEPLAARLAAERATDEDLAALEALLDAmeaaaAAGDDLEEFAELDREFHRALAEAAGNPVLLELLESLRA-- 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 501390121   175 qssvkHSRQRMYLVPPVFSQLTEQHQAVIDAIFAGDADGARKAMMAHL 222
Cdd:smart00895  79 -----RLRRLRRLSLEAARRALDEHRAILDAIRARDAEAARAAMREHL 121
HTH_GNTR smart00345
helix_turn_helix gluconate operon transcriptional repressor;
12-71 1.78e-20

helix_turn_helix gluconate operon transcriptional repressor;


Pssm-ID: 197669 [Multi-domain]  Cd Length: 60  Bit Score: 81.85  E-value: 1.78e-20
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121    12 VADRVRALIDEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFI 71
Cdd:smart00345   1 VAERLREDIVSGELRPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGSGTFV 60
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 8-72 1.83e-20

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: 82.11  E-value: 1.83e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 501390121   8 LSDEVADRVRALIDEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIR 72
Cdd:cd07377    2 LYEQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFVA 66
FCD pfam07729
FCD domain; This domain is the C-terminal ligand binding domain of many members of the GntR ...
 100-220 1.28e-18

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: 78.95  E-value: 1.28e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121  100 DILEARYAIEASTAWHAAMRATPGDKEKIQLCFE----ATLSEDPDIASQADVRFHLAIAEASHNIVLLQTMRGFFDVLQ 175
Cdd:pfam07729   1 ELYELRAALEPLAARLAAERATDEDLAELEALLEaleaAADAGDLEAFAEADREFHLALAEAAGNPVLARMLESLWDRLR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 501390121  176 ssvkHSRQRMYLVPPVFSQLTEQHQAVIDAIFAGDADGARKAMMA 220
Cdd:pfam07729  81 ----RLRRLLLSSPGRLRASLEEHRAILDAIRARDPEAARAAMRR 121
MngR COG2188
DNA-binding transcriptional regulator, GntR family [Transcription];
11-130 5.45e-16

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


Pssm-ID: 441791 [Multi-domain]  Cd Length: 238  Bit Score: 74.90  E-value: 5.45e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121  11 EVADRVRALIDEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRwrhdtwpEQNIVQPLKTL 90
Cdd:COG2188    9 QIADALRERIESGELPPGDRLPSERELAEEFGVSRMTVRKALDELVEEGLLERRQGRGTFVA-------EPKIEYPLSRL 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 501390121  91 maddpdYSFDILEARYAIEASTAWHAAMRATPGDKEKIQL 130
Cdd:COG2188   82 ------TSFTEELRARGREPSTRVLSAERVPADEEVAEAL 115
PRK11523 PRK11523
transcriptional regulator ExuR;
5-222 5.74e-15

transcriptional regulator ExuR;


Pssm-ID: 183176 [Multi-domain]  Cd Length: 253  Bit Score: 72.19  E-value: 5.74e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121   5 PRRLSDEVADRVRALIDEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFI---RWRHDTWPEQ 81
Cdd:PRK11523   6 PRRLYQQLAAELKERIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRKGSGIHVvsnQPRHQQAADN 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121  82 NIvqplkTLMADDPdysFDILEARYAIEASTAWHAAMRATPGDKEKIQLCFEATLSEDPDIASQADVRFHLAIAEASHNI 161
Cdd:PRK11523  86 NM-----EFANYGP---FELLQARQLIESNIAEFAATQVTKQDIMKLMAIQEQARGEDCFRDSEWDLQFHVQVALATQNS 157

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 501390121 162 VLLQTMRgffdvlqssvKHSRQRMYlvPPVFSQLTEQ------------HQAVIDAIFAGDADGARKAMMAHL 222
Cdd:PRK11523 158 ALAAIVE----------KMWTQRSH--NPYWKKLHEHiddrtvdnwcddHDQILKALIRKDPHAAKLAMWQHL 218
ARO8 COG1167
DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain ...
 1-114 2.28e-14

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: 72.17  E-value: 2.28e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121   1 MIVLPRR----LSDEVADRVRALIDEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRWRhd 76
Cdd:COG1167    2 LIRLDRDssgpLYLQLADALREAILSGRLPPGDRLPSSRELAAQLGVSRSTVVRAYEELEAEGLIESRPGSGTFVAAR-- 79

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 501390121  77 twPEQNIVQPLKTLMADDPDYSFDILEARYAIEASTAW 114
Cdd:COG1167   80 --LPAPAPAPRAAAAVAAPALRRLLEAAPGVIDLGSGA 115
YhcF COG1725
DNA-binding transcriptional regulator YhcF, GntR family [Transcription];
12-72 8.22e-12

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


Pssm-ID: 441331 [Multi-domain]  Cd Length: 114  Bit Score: 60.58  E-value: 8.22e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 501390121  12 VADRVRALIDEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIR 72
Cdd:COG1725   15 IADQIKEAIASGELKPGDRLPSVRELAAELGVNPNTVAKAYRELEDEGLIETRRGKGTFVA 75
C_P_lyase_phnF TIGR02325
phosphonates metabolism transcriptional regulator PhnF; All members of the seed alignment for ...
 11-79 1.19e-11

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: 62.88  E-value: 1.19e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 501390121   11 EVADRVRALIDEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRWRHDTWP 79
Cdd:TIGR02325  12 QIADKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQGRGTFVAARRIDYP 80
PRK15481 PRK15481
transcriptional regulatory protein PtsJ; Provisional
 11-96 2.47e-10

transcriptional regulatory protein PtsJ; Provisional


Pssm-ID: 185378 [Multi-domain]  Cd Length: 431  Bit Score: 60.06  E-value: 2.47e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121  11 EVADRVRALIDEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRwRHDTWPEQNIVQP---L 87
Cdd:PRK15481   9 EIFDSIRQLIQAGRLRPGDSLPPVRELASELGVNRNTVAAAYKRLVTAGLAQSQGRNGTVIR-GSPSPVALEGGDPgtpL 87


                 ....*....
gi 501390121  88 KTLMADDPD 96
Cdd:PRK15481  88 HDLAGGNPD 96
PRK09764 PRK09764
GntR family transcriptional regulator;
11-72 8.46e-09

GntR family transcriptional regulator;


Pssm-ID: 182065 [Multi-domain]  Cd Length: 240  Bit Score: 54.45  E-value: 8.46e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 501390121  11 EVADRVRALIDEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIR 72
Cdd:PRK09764   9 QIADRIREQIARGELKPGDALPTESALQTEFGVSRVTVRQALRQLVEQQILESIQGSGTYVK 70
PRK11402 PRK11402
transcriptional regulator PhoB;
2-72 5.46e-08

transcriptional regulator PhoB;


Pssm-ID: 183118 [Multi-domain]  Cd Length: 241  Bit Score: 52.14  E-value: 5.46e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 501390121   2 IVLPRRLSDEVADRVralideknLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIR 72
Cdd:PRK11402  12 ATVRQRLLDDIAQGV--------YQAGQQIPTENELCTQYNVSRITIRKAISDLVADGVLIRWQGKGTFVQ 74
PRK10079 PRK10079
phosphonate metabolism transcriptional regulator PhnF; Provisional
 31-79 5.99e-04

phosphonate metabolism transcriptional regulator PhnF; Provisional


Pssm-ID: 182227 [Multi-domain]  Cd Length: 241  Bit Score: 40.14  E-value: 5.99e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 501390121  31 LPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRWRHDTWP 79
Cdd:PRK10079  35 LPAEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQGVGVLVLMRPYDYP 83
PRK04984 PRK04984
fatty acid metabolism transcriptional regulator FadR;
27-103 1.10e-03

fatty acid metabolism transcriptional regulator FadR;


Pssm-ID: 179909 [Multi-domain]  Cd Length: 239  Bit Score: 39.47  E-value: 1.10e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121  27 AGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIrwrHDTWpEQ---NIvqpLKTLMADDPDYSFDILE 103
Cdd:PRK04984  27 PGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGKPTKV---NNFW-ETsglNI---LETLARLDHDSVPQLID 99
PRK11534 PRK11534
DNA-binding transcriptional regulator CsiR; Provisional
 28-222 2.39e-03

DNA-binding transcriptional regulator CsiR; Provisional


Pssm-ID: 183181 [Multi-domain]  Cd Length: 224  Bit Score: 38.34  E-value: 2.39e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121  28 GMKLPAERqLAMQLGVSRNSL-----REALAKLVSEGVL--LSRRGggtfirWRHDTWPEQNIVqplktlmaddpdysfD 100
Cdd:PRK11534  23 GNFQPDEK-LRMSLLTSRYALgvgplREALSQLVAERLVtvVNQKG------YRVASMSEQELL---------------D 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501390121 101 ILEARYAIEA----------STAWHAAMRATPGDKEKIQlcfEATLSEDP-DIASQADVRFHLAIAEASHNIVLLQTMRG 169
Cdd:PRK11534  81 IFDARANMEAmlvslaiargGDEWEADVLAKAHLLSKLE---ACDASEKMlDEWDLRHQAFHTAIVAGCGSHYLLQMRER 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 501390121 170 FFDvLQSSVKHsrqrMYLVPPVFS-QLTE----QHQAVIDAIFAGDADGARKAMMAHL 222
Cdd:PRK11534 158 LFD-LAARYRF----IWLRRTVLSvEMLEdkhdQHQTLTAAILARDTARASELMRQHL 210
PRK14999 PRK14999
histidine utilization repressor; Provisional
 30-71 3.32e-03

histidine utilization repressor; Provisional


Pssm-ID: 184961 [Multi-domain]  Cd Length: 241  Bit Score: 37.99  E-value: 3.32e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 501390121  30 KLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFI 71
Cdd:PRK14999  35 RIPSEAELVAQYGFSRMTINRALRELTDEGWLVRLQGVGTFV 76
 
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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