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Conserved domains on  [gi|1523361134|gb|RQL43449|]
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FadR family transcriptional regulator [Neisseria meningitidis]

Protein Classification

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

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
4-239 5.98e-61

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


:

Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 192.07  E-value: 5.98e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134   4 VRPQKISDQVLSVLEERIAEGVYAEGGKIPPERVLAEEFGVSRPSVRSALNVLVARQVLEARQGDGYYVSVKPQQDFLQS 83
Cdd:COG2186     3 IRRRSLAEQVAEQLRELILSGELKPGDRLPSERELAEQLGVSRTTVREALRALEALGLVEVRQGGGTFVREPSPWALLDP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134  84 WQELLGKHSNWEQDVFDFSCHIEGCMAALAAERRTDADLKRIGFWLEKFEEACESGnlEHQSEADVSFHQTIADAAHNLL 163
Cdd:COG2186    83 LALLLALDDASLRDLLEARLALEPEAARLAAERATDEDLARLEAALAEMEAAADDG--EAFAEADLAFHRAIAEASGNPL 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1523361134 164 FSHLSGGLLKMLYRQTRSSLiylnQEEDPRPKLMAQHRVLYEAISNRRPGEASEAAKAHLNYVASSIMKDREYQSR 239
Cdd:COG2186   161 LALLLESLRELLRRSVRLTL----RSPEARERSLAEHRAILDAIRAGDPEAARAAMRAHLEAVRERLREALAERAR 232
 
Name Accession Description Interval E-value
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
4-239 5.98e-61

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


Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 192.07  E-value: 5.98e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134   4 VRPQKISDQVLSVLEERIAEGVYAEGGKIPPERVLAEEFGVSRPSVRSALNVLVARQVLEARQGDGYYVSVKPQQDFLQS 83
Cdd:COG2186     3 IRRRSLAEQVAEQLRELILSGELKPGDRLPSERELAEQLGVSRTTVREALRALEALGLVEVRQGGGTFVREPSPWALLDP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134  84 WQELLGKHSNWEQDVFDFSCHIEGCMAALAAERRTDADLKRIGFWLEKFEEACESGnlEHQSEADVSFHQTIADAAHNLL 163
Cdd:COG2186    83 LALLLALDDASLRDLLEARLALEPEAARLAAERATDEDLARLEAALAEMEAAADDG--EAFAEADLAFHRAIAEASGNPL 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1523361134 164 FSHLSGGLLKMLYRQTRSSLiylnQEEDPRPKLMAQHRVLYEAISNRRPGEASEAAKAHLNYVASSIMKDREYQSR 239
Cdd:COG2186   161 LALLLESLRELLRRSVRLTL----RSPEARERSLAEHRAILDAIRAGDPEAARAAMRAHLEAVRERLREALAERAR 232
pdhR PRK09464
pyruvate dehydrogenase complex transcriptional repressor PdhR;
4-255 2.25e-48

pyruvate dehydrogenase complex transcriptional repressor PdhR;


Pssm-ID: 181879 [Multi-domain]  Cd Length: 254  Bit Score: 160.57  E-value: 2.25e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134   4 VRPQKISDQVLSVLEERIAEGVYAEGGKIPPERVLAEEFGVSRPSVRSALNVLVARQVLEARQGDGYYVSVKPQQDFLQS 83
Cdd:PRK09464    6 IRQPKLSDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGGTFVQSSLWQSFSDP 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134  84 WQELLGKHSNWEQDVFDFSCHIEGCMAALAAERRTDADLKRIGFWLEKFEEACESGNLEHQSEADVSFHQTIADAAHNLL 163
Cdd:PRK09464   86 LVELLSDHPESQFDLLETRHALEGIAAYYAALRGTDEDFERIRECHHAIELAQQSGDLDAEANAVMQYQIAVTEAAHNVV 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134 164 FSHLSGGLLKMLYRQTRSSLIYLNQEEDPRPKLMAQHRVLYEAISNRRPGEASEAAKAHLNYVASSIMKDREYQSRnrha 243
Cdd:PRK09464  166 LLHLLRCMEPMLEQNVRQNFELLYRRREMLPKVSSHRARIFEAIVAGKPEKAREASHRHLAFIEEILLDLSREESR---- 241

                         250
                  ....*....|..
gi 1523361134 244 dtlAQNDLKRVQ 255
Cdd:PRK09464  242 ---RERSLRRLQ 250
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 8-73 2.28e-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: 81.72  E-value: 2.28e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1523361134   8 KISDQVLSVLEERIAEGVYAEGGKIPPERVLAEEFGVSRPSVRSALNVLVARQVLEARQGDGYYVS 73
Cdd:cd07377     1 PLYEQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFVA 66
FCD smart00895
This entry represents the C-terminal ligand binding domain of many members of the GntR family; ...
 97-225 4.53e-19

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: 80.10  E-value: 4.53e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134   97 DVFDFSCHIEGCMAALAAERRTDADLKRIGFWLEKFEEACESGN-LEHQSEADVSFHQTIADAAHNLLFSHLSGGLLKML 175
Cdd:smart00895   1 ELYEVRRALEPLAARLAAERATDEDLAALEALLDAMEAAAAAGDdLEEFAELDREFHRALAEAAGNPVLLELLESLRARL 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 1523361134  176 YRqtrssliYLNQEEDPRPKLMAQHRVLYEAISNRRPGEASEAAKAHLNY 225
Cdd:smart00895  81 RR-------LRRLSLEAARRALDEHRAILDAIRARDAEAARAAMREHLEA 123
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
 10-72 2.89e-16

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: 71.11  E-value: 2.89e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1523361134  10 SDQVLSVLEERIAEGVYAEGGKIPPERVLAEEFGVSRPSVRSALNVLVARQVLEARQGDGYYV 72
Cdd:pfam00392   2 YEQVYARLREDILSGRLRPGDKLPSERELAAEFGVSRTTVREALRRLEAEGLVERRQGRGTFV 64
C_P_lyase_phnF TIGR02325
phosphonates metabolism transcriptional regulator PhnF; All members of the seed alignment for ...
 12-76 2.69e-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: 64.42  E-value: 2.69e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1523361134  12 QVLSVLEERIAEGVYAEGGKIPPERVLAEEFGVSRPSVRSALNVLVARQVLEARQGDGYYVSVKP 76
Cdd:TIGR02325  12 QIADKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQGRGTFVAARR 76
 
Name Accession Description Interval E-value
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
4-239 5.98e-61

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


Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 192.07  E-value: 5.98e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134   4 VRPQKISDQVLSVLEERIAEGVYAEGGKIPPERVLAEEFGVSRPSVRSALNVLVARQVLEARQGDGYYVSVKPQQDFLQS 83
Cdd:COG2186     3 IRRRSLAEQVAEQLRELILSGELKPGDRLPSERELAEQLGVSRTTVREALRALEALGLVEVRQGGGTFVREPSPWALLDP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134  84 WQELLGKHSNWEQDVFDFSCHIEGCMAALAAERRTDADLKRIGFWLEKFEEACESGnlEHQSEADVSFHQTIADAAHNLL 163
Cdd:COG2186    83 LALLLALDDASLRDLLEARLALEPEAARLAAERATDEDLARLEAALAEMEAAADDG--EAFAEADLAFHRAIAEASGNPL 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1523361134 164 FSHLSGGLLKMLYRQTRSSLiylnQEEDPRPKLMAQHRVLYEAISNRRPGEASEAAKAHLNYVASSIMKDREYQSR 239
Cdd:COG2186   161 LALLLESLRELLRRSVRLTL----RSPEARERSLAEHRAILDAIRAGDPEAARAAMRAHLEAVRERLREALAERAR 232
pdhR PRK09464
pyruvate dehydrogenase complex transcriptional repressor PdhR;
4-255 2.25e-48

pyruvate dehydrogenase complex transcriptional repressor PdhR;


Pssm-ID: 181879 [Multi-domain]  Cd Length: 254  Bit Score: 160.57  E-value: 2.25e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134   4 VRPQKISDQVLSVLEERIAEGVYAEGGKIPPERVLAEEFGVSRPSVRSALNVLVARQVLEARQGDGYYVSVKPQQDFLQS 83
Cdd:PRK09464    6 IRQPKLSDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGGTFVQSSLWQSFSDP 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134  84 WQELLGKHSNWEQDVFDFSCHIEGCMAALAAERRTDADLKRIGFWLEKFEEACESGNLEHQSEADVSFHQTIADAAHNLL 163
Cdd:PRK09464   86 LVELLSDHPESQFDLLETRHALEGIAAYYAALRGTDEDFERIRECHHAIELAQQSGDLDAEANAVMQYQIAVTEAAHNVV 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134 164 FSHLSGGLLKMLYRQTRSSLIYLNQEEDPRPKLMAQHRVLYEAISNRRPGEASEAAKAHLNYVASSIMKDREYQSRnrha 243
Cdd:PRK09464  166 LLHLLRCMEPMLEQNVRQNFELLYRRREMLPKVSSHRARIFEAIVAGKPEKAREASHRHLAFIEEILLDLSREESR---- 241

                         250
                  ....*....|..
gi 1523361134 244 dtlAQNDLKRVQ 255
Cdd:PRK09464  242 ---RERSLRRLQ 250
PRK10421 PRK10421
DNA-binding transcriptional repressor LldR; Provisional
 8-252 1.50e-34

DNA-binding transcriptional repressor LldR; Provisional


Pssm-ID: 236690 [Multi-domain]  Cd Length: 253  Bit Score: 124.49  E-value: 1.50e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134   8 KISDQVLSVLEERIAEGVYAEGGKIPPERVLAEEFGVSRPSVRSALNVLVARQVLEARQGDGYYVSVKP----QQDFLQS 83
Cdd:PRK10421    2 RLSDEVADRVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRWRHetwsEQNIVQP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134  84 WQELLGKHSNWEQDVFDFSCHIEGCMAALAAERRTDADLKRIGFWLekfeEACESGNLEHQSEADVSFHQTIADAAHNLL 163
Cdd:PRK10421   82 LKTLMADDPDYSFDILEARHAIEASTAWHAAMRATPGDKEKIQLCF----EATLSEDPDLASQADVRFHLAIAEASHNVV 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134 164 FSHLSGGLLKMLY---RQTRSSLIYLNQEEDprpKLMAQHRVLYEAISNRRPGEASEAAKAHLNYVASSIMKDREYQSRN 240
Cdd:PRK10421  158 LLQTMRGFFDVLQssvKQSRQRMYLVPPVFS---QLTEQHQAVMDAILAGDAEGARKAMMAHLSFVHTTIKRFDEDQARQ 234

                         250
                  ....*....|..
gi 1523361134 241 RHADTLAQNDLK 252
Cdd:PRK10421  235 ARITRLPGDHNE 246
GntR COG1802
DNA-binding transcriptional regulator, GntR family [Transcription];
1-232 1.12e-33

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


Pssm-ID: 441407 [Multi-domain]  Cd Length: 222  Bit Score: 121.57  E-value: 1.12e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134   1 MKLVRPQKISDQVLSVLEERIAEGVYAEGGKIPpERVLAEEFGVSRPSVRSALNVLVARQVLEARQGDGYYVSVKPQQDF 80
Cdd:COG1802     4 PSPLRRESLAEQVYEALREAILSGELPPGERLS-EAELAERLGVSRTPVREALRRLEAEGLVEIRPNRGARVAPLSPEEI 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134  81 LqswqellgkhsnweqDVFDFSCHIEGCMAALAAERRTDADLKRIGFWLEKFEEACESGNLEHQSEADVSFHQTIADAAH 160
Cdd:COG1802    83 R---------------ELYEVRAALEGLAARLAAERATPADLARLRALLEELEAAAAAGDVAAYLELDREFHRALVEAAG 147

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1523361134 161 NLLFSHlsggLLKMLYRQTRSSLIYLNQEEDPRPKLMAQHRVLYEAISNRRPGEASEAAKAHLNYVASSIMK 232
Cdd:COG1802   148 NPRLAE----LLRRLRARLRRYRRLSLRSPGRLEESLAEHRAILDALEAGDAEAAAAALRAHLERARERLLE 215
PRK03837 PRK03837
transcriptional regulator NanR; Provisional
 3-226 2.45e-26

transcriptional regulator NanR; Provisional


Pssm-ID: 235166 [Multi-domain]  Cd Length: 241  Bit Score: 102.79  E-value: 2.45e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134   3 LVRPqKISDQVLSVLEERIAEGVYAEGGKIPPERVLAEEFGVSRPSVRSALNVLVARQVLEARQGDGYYVSVKPQQDFLQ 82
Cdd:PRK03837    9 IARK-KLSEEVEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQISHGERARVSRPSADTIIG 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134  83 ----SWQELLGKHSNWEQDVFDFSCHIEGCMAALAAERRTDADLKRIGFWLEKFEEACesGNLEHQSEADVSFHQTIADA 158
Cdd:PRK03837   88 qlsgMAKDFLSQSPDGLAHLKQARLFFESSLARYAAEHATDEQIALLRKALERNSQSL--GDNAAFIRSDMEFHRVIAEI 165

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1523361134 159 AHNLLFSHLSGGLLKMLYRQTRSSLIYLNQEEdprpKLMAQHRVLYEAISNRRPGEASEAAKAHLNYV 226
Cdd:PRK03837  166 PGNPIFMAIHEALLDWLIEARPEVVILHGHEN----VTLQEHIAIVDAIRAHDPDEADRALQSHLNRV 229
PRK09990 PRK09990
DNA-binding transcriptional regulator GlcC; Provisional
 5-230 7.13e-25

DNA-binding transcriptional regulator GlcC; Provisional


Pssm-ID: 182186 [Multi-domain]  Cd Length: 251  Bit Score: 99.07  E-value: 7.13e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134   5 RPQKISDQVLSVLEERIAEGVYAEGGKIPPERVLAEEFGVSRPSVRSALNVLVARQVLEARQGDGYYVSVKPQQDFLQSW 84
Cdd:PRK09990    4 ERRPIADVVAERIERLIVDGVLKVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQGRGSFVARLNRVQDASPL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134  85 QELLGKHSNWEQDVFDFSCHIEGCMAALAAERRTDADL----KRIGFWLEKFEEACESGNLEHqSEADVSFHQTIADAAH 160
Cdd:PRK09990   84 MHLFSSQPRTLYDLLEVRALLEGESARLAALRGTQADFvlitRRYEEMLAAHENNKEIDPIEH-ARLDHAFHLAICEASH 162

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134 161 NLLFSHLSGGLLKMLYRQTRSSLIYLNQEEDPRPKLMAQHRVLYEAISNRRPGEASEAAKAHLNYVASSI 230
Cdd:PRK09990  163 NPVLVHTLQSLTDLMLSSVFASVNNLYHRPQQKKQIDRQHARLYNAVLQRLPEQAQRAARDHIRTVRDNL 232
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 8-73 2.28e-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: 81.72  E-value: 2.28e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1523361134   8 KISDQVLSVLEERIAEGVYAEGGKIPPERVLAEEFGVSRPSVRSALNVLVARQVLEARQGDGYYVS 73
Cdd:cd07377     1 PLYEQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFVA 66
FCD smart00895
This entry represents the C-terminal ligand binding domain of many members of the GntR family; ...
 97-225 4.53e-19

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: 80.10  E-value: 4.53e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134   97 DVFDFSCHIEGCMAALAAERRTDADLKRIGFWLEKFEEACESGN-LEHQSEADVSFHQTIADAAHNLLFSHLSGGLLKML 175
Cdd:smart00895   1 ELYEVRRALEPLAARLAAERATDEDLAALEALLDAMEAAAAAGDdLEEFAELDREFHRALAEAAGNPVLLELLESLRARL 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 1523361134  176 YRqtrssliYLNQEEDPRPKLMAQHRVLYEAISNRRPGEASEAAKAHLNY 225
Cdd:smart00895  81 RR-------LRRLSLEAARRALDEHRAILDAIRARDAEAARAAMREHLEA 123
MngR COG2188
DNA-binding transcriptional regulator, GntR family [Transcription];
12-85 1.93e-18

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


Pssm-ID: 441791 [Multi-domain]  Cd Length: 238  Bit Score: 81.45  E-value: 1.93e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1523361134  12 QVLSVLEERIAEGVYAEGGKIPPERVLAEEFGVSRPSVRSALNVLVARQVLEARQGDGYYVSVKPQQDFLQSWQ 85
Cdd:COG2188     9 QIADALRERIESGELPPGDRLPSERELAEEFGVSRMTVRKALDELVEEGLLERRQGRGTFVAEPKIEYPLSRLT 82
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
 10-72 2.89e-16

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: 71.11  E-value: 2.89e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1523361134  10 SDQVLSVLEERIAEGVYAEGGKIPPERVLAEEFGVSRPSVRSALNVLVARQVLEARQGDGYYV 72
Cdd:pfam00392   2 YEQVYARLREDILSGRLRPGDKLPSERELAAEFGVSRTTVREALRRLEAEGLVERRQGRGTFV 64
HTH_GNTR smart00345
helix_turn_helix gluconate operon transcriptional repressor;
17-72 4.34e-16

helix_turn_helix gluconate operon transcriptional repressor;


Pssm-ID: 197669 [Multi-domain]  Cd Length: 60  Bit Score: 70.30  E-value: 4.34e-16
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1523361134   17 LEERIAEGVYAEGGKIPPERVLAEEFGVSRPSVRSALNVLVARQVLEARQGDGYYV 72
Cdd:smart00345   5 LREDIVSGELRPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGSGTFV 60
FCD pfam07729
FCD domain; This domain is the C-terminal ligand binding domain of many members of the GntR ...
 97-221 1.72e-15

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: 70.86  E-value: 1.72e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134  97 DVFDFSCHIEGCMAALAAERRTDADLKRIGFWLEKFEEACESGNLEHQSEADVSFHQTIADAAHNLLFSHlsggLLKMLY 176
Cdd:pfam07729   1 ELYELRAALEPLAARLAAERATDEDLAELEALLEALEAAADAGDLEAFAEADREFHLALAEAAGNPVLAR----MLESLW 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1523361134 177 RQTRSSLIYLNQEEDPRPKLMAQHRVLYEAISNRRPGEASEAAKA 221
Cdd:pfam07729  77 DRLRRLRRLLLSSPGRLRASLEEHRAILDAIRARDPEAARAAMRR 121
ARO8 COG1167
DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain ...
 5-125 7.44e-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: 70.63  E-value: 7.44e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134   5 RPQKISDQVLSVLEERIAEGVYAEGGKIPPERVLAEEFGVSRPSVRSALNVLVARQVLEARQGDGYYVS------VKPQQ 78
Cdd:COG1167     9 SSGPLYLQLADALREAILSGRLPPGDRLPSSRELAAQLGVSRSTVVRAYEELEAEGLIESRPGSGTFVAarlpapAPAPR 88

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1523361134  79 DFLQSWQELLGKHSNWEQDVFDFSchiegcMAALAAERRTDADLKRI 125
Cdd:COG1167    89 AAAAVAAPALRRLLEAAPGVIDLG------SGAPDPDLFPLAALRRA 129
PRK10225 PRK10225
Uxu operon transcriptional regulator;
7-179 5.05e-13

Uxu operon transcriptional regulator;


Pssm-ID: 182318 [Multi-domain]  Cd Length: 257  Bit Score: 66.97  E-value: 5.05e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134   7 QKISDQVLSVLEERIAEGVYAEGGKIPPERVLAEEFGVSRPSVRSALNVLVARQVLEARQGDGYYVSVKPQQDflqswqE 86
Cdd:PRK10225    8 QRPYQEVGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRRGAGIYVLDSSGSH------N 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134  87 LLGKHSNWEQDVFDFSC-----HIEGCMAALAAERRTDADLKRIGFWLEKFEEACESGNLEHQSEADVSFHQTIADAAHN 161
Cdd:PRK10225   82 TDSPDANVCNDAGPFELlqarqLLESNIAEFAALQATREDIVKMRQALQLEERELASSAPGSSESGDMQFHLAIAEATHN 161

                         170
                  ....*....|....*...
gi 1523361134 162 llfshlsgGLLKMLYRQT 179
Cdd:PRK10225  162 --------SMLVELFRQS 171
C_P_lyase_phnF TIGR02325
phosphonates metabolism transcriptional regulator PhnF; All members of the seed alignment for ...
 12-76 2.69e-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: 64.42  E-value: 2.69e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1523361134  12 QVLSVLEERIAEGVYAEGGKIPPERVLAEEFGVSRPSVRSALNVLVARQVLEARQGDGYYVSVKP 76
Cdd:TIGR02325  12 QIADKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQGRGTFVAARR 76
PRK11523 PRK11523
transcriptional regulator ExuR;
1-161 1.85e-11

transcriptional regulator ExuR;


Pssm-ID: 183176 [Multi-domain]  Cd Length: 253  Bit Score: 62.56  E-value: 1.85e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134   1 MKLVRPQKISDQVLSVLEERIAEGVYAEGGKIPPERVLAEEFGVSRPSVRSALNVLVARQVLEARQGDGYYVsVKPQQDF 80
Cdd:PRK11523    1 MEITEPRRLYQQLAAELKERIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRKGSGIHV-VSNQPRH 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134  81 LQSWQELLGKHSNWEQDVFDFSCHIEGCMAALAAERRTDADLKRigfwLEKFEEACESGNLEHQSEADVSFHQTIADAAH 160
Cdd:PRK11523   80 QQAADNNMEFANYGPFELLQARQLIESNIAEFAATQVTKQDIMK----LMAIQEQARGEDCFRDSEWDLQFHVQVALATQ 155


                  .
gi 1523361134 161 N 161
Cdd:PRK11523  156 N 156
PRK09764 PRK09764
GntR family transcriptional regulator;
12-72 2.84e-11

GntR family transcriptional regulator;


Pssm-ID: 182065 [Multi-domain]  Cd Length: 240  Bit Score: 61.77  E-value: 2.84e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1523361134  12 QVLSVLEERIAEGVYAEGGKIPPERVLAEEFGVSRPSVRSALNVLVARQVLEARQGDGYYV 72
Cdd:PRK09764    9 QIADRIREQIARGELKPGDALPTESALQTEFGVSRVTVRQALRQLVEQQILESIQGSGTYV 69
PRK11402 PRK11402
transcriptional regulator PhoB;
12-72 2.51e-08

transcriptional regulator PhoB;


Pssm-ID: 183118 [Multi-domain]  Cd Length: 241  Bit Score: 53.30  E-value: 2.51e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1523361134  12 QVLSVLEERIAEGVYAEGGKIPPERVLAEEFGVSRPSVRSALNVLVARQVLEARQGDGYYV 72
Cdd:PRK11402   13 TVRQRLLDDIAQGVYQAGQQIPTENELCTQYNVSRITIRKAISDLVADGVLIRWQGKGTFV 73
PRK11534 PRK11534
DNA-binding transcriptional regulator CsiR; Provisional
 17-223 4.73e-05

DNA-binding transcriptional regulator CsiR; Provisional


Pssm-ID: 183181 [Multi-domain]  Cd Length: 224  Bit Score: 43.34  E-value: 4.73e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134  17 LEERIAEGVYAEGGKIPPErVLAEEFGVSRPSVRSALNVLVARQVLEARQGDGYYVSVkpqqdflQSWQELLgkhsnweq 96
Cdd:PRK11534   16 LKNDIIRGNFQPDEKLRMS-LLTSRYALGVGPLREALSQLVAERLVTVVNQKGYRVAS-------MSEQELL-------- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134  97 DVFDFSCHIEGCMAALAAERRTD---ADLKRIGFWLEKFEEaCESGN--LEHQSEADVSFHQTIADAAHnllfshlSGGL 171
Cdd:PRK11534   80 DIFDARANMEAMLVSLAIARGGDeweADVLAKAHLLSKLEA-CDASEkmLDEWDLRHQAFHTAIVAGCG-------SHYL 151

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1523361134 172 LKM---LYRQT-RSSLIYLNQE-------EDPRpklmAQHRVLYEAISNRRPGEASEAAKAHL 223
Cdd:PRK11534  152 LQMrerLFDLAaRYRFIWLRRTvlsvemlEDKH----DQHQTLTAAILARDTARASELMRQHL 210
PRK11414 PRK11414
GntR family transcriptional regulator;
9-142 1.32e-03

GntR family transcriptional regulator;


Pssm-ID: 183126 [Multi-domain]  Cd Length: 221  Bit Score: 39.08  E-value: 1.32e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1523361134   9 ISDQVLSVLEERIAEGVYAEGGKIPPERvLAEEFGVSRPSVRSALNVLVARQVLearqgdgyyvSVKPQQDFLQ---SWQ 85
Cdd:PRK11414   12 LTLQVENDLKHQLSIGALKPGARLITKN-LAEQLGMSITPVREALLRLVSVNAL----------SVAPAQAFTVpevSKR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1523361134  86 ELLgkhsnweqDVFDFSCHIEGCMAALAAERRTDADLKRIGFWLEKFEEACESGNLE 142
Cdd:PRK11414   81 QLD--------EINRIRYELELMAVALAVENLTPQDLAELQELLEKLQQAQEKGDME 129
PRK10079 PRK10079
phosphonate metabolism transcriptional regulator PhnF; Provisional
 5-76 3.60e-03

phosphonate metabolism transcriptional regulator PhnF; Provisional


Pssm-ID: 182227 [Multi-domain]  Cd Length: 241  Bit Score: 37.83  E-value: 3.60e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1523361134   5 RPQKISDQvlsvLEERIaEGVYAEGGKIPPERVLAEEFGVSRPSVRSALNVLVARQVLEARQGDGYYVSVKP 76
Cdd:PRK10079   13 RYQEIAAK----LEQEL-RQHYRCGDYLPAEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQGVGVLVLMRP 79
PRK14999 PRK14999
histidine utilization repressor; Provisional
 6-73 4.56e-03

histidine utilization repressor; Provisional


Pssm-ID: 184961 [Multi-domain]  Cd Length: 241  Bit Score: 37.60  E-value: 4.56e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1523361134   6 PQKISDQVLSVLEERIAEGVYAEGGKIPPERVLAEEFGVSRPSVRSALNVLVARQVLEARQGDGYYVS 73
Cdd:PRK14999   10 PAPFYETVKQDICKKIAGGVWQPHDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVRLQGVGTFVA 77
 
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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