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Conserved domains on  [gi|732686639|gb|AIZ93444|]
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GntR family transcriptional regulator [Escherichia coli str. K-12 substr. MG1655]

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];
9-227 1.03e-60

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


:

Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 190.14  E-value: 1.03e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639   9 AAQKNLSYVLAEKLAQRILKGEYEPGTILPGEIELGEQFGVSRTAVREAVKTLTAKGMVLPRPRIGTRVMPQSNWNFLDQ 88
Cdd:COG2186    3 IRRRSLAEQVAEQLRELILSGELKPGDRLPSERELAEQLGVSRTTVREALRALEALGLVEVRQGGGTFVREPSPWALLDP 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639  89 elLTWWMTEEnfHQVIDHFLVMRICLEPQACLLAATVGTAEQKAHLNTLMAEMAALKENfrRERWIEVDMAWHEHIYEMS 168
Cdd:COG2186   83 --LALLLALD--DASLRDLLEARLALEPEAARLAAERATDEDLARLEAALAEMEAAADD--GEAFAEADLAFHRAIAEAS 156

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 732686639 169 ANPFLTSFASLFHSVYHTYFTSITSDTVIK---LDLHQAIVDAIIQSDGDAAFKACQALLRS 227
Cdd:COG2186  157 GNPLLALLLESLRELLRRSVRLTLRSPEARersLAEHRAILDAIRAGDPEAARAAMRAHLEA 218
 
Name Accession Description Interval E-value
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
9-227 1.03e-60

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


Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 190.14  E-value: 1.03e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639   9 AAQKNLSYVLAEKLAQRILKGEYEPGTILPGEIELGEQFGVSRTAVREAVKTLTAKGMVLPRPRIGTRVMPQSNWNFLDQ 88
Cdd:COG2186    3 IRRRSLAEQVAEQLRELILSGELKPGDRLPSERELAEQLGVSRTTVREALRALEALGLVEVRQGGGTFVREPSPWALLDP 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639  89 elLTWWMTEEnfHQVIDHFLVMRICLEPQACLLAATVGTAEQKAHLNTLMAEMAALKENfrRERWIEVDMAWHEHIYEMS 168
Cdd:COG2186   83 --LALLLALD--DASLRDLLEARLALEPEAARLAAERATDEDLARLEAALAEMEAAADD--GEAFAEADLAFHRAIAEAS 156

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 732686639 169 ANPFLTSFASLFHSVYHTYFTSITSDTVIK---LDLHQAIVDAIIQSDGDAAFKACQALLRS 227
Cdd:COG2186  157 GNPLLALLLESLRELLRRSVRLTLRSPEARersLAEHRAILDAIRAGDPEAARAAMRAHLEA 218
PRK03837 PRK03837
transcriptional regulator NanR; Provisional
 7-227 1.13e-23

transcriptional regulator NanR; Provisional


Pssm-ID: 235166 [Multi-domain]  Cd Length: 241  Bit Score: 94.70  E-value: 1.13e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639   7 QLAAQKNLSYVLAEKLAQRILKGEYEPGTILPGEIELGEQFGVSRTAVREAVKTLTAKGMVL----PRPRIgTRVMPQSN 82
Cdd:PRK03837   7 RPIARKKLSEEVEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQishgERARV-SRPSADTI 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639  83 WNFLD---QELLTWWMTEenfhqvIDHFLVMRICLEPQACLLAATVGTAEQKAHL-NTLMAEMAALKENfrrERWIEVDM 158
Cdd:PRK03837  86 IGQLSgmaKDFLSQSPDG------LAHLKQARLFFESSLARYAAEHATDEQIALLrKALERNSQSLGDN---AAFIRSDM 156

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 732686639 159 AWHEHIYEMSANPFLTSFA-SLFH--SVYHTYFTSITSDTVIKLDLHQAIVDAIIQSDGDAAFKACQALLRS 227
Cdd:PRK03837 157 EFHRVIAEIPGNPIFMAIHeALLDwlIEARPEVVILHGHENVTLQEHIAIVDAIRAHDPDEADRALQSHLNR 228
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 14-77 4.14e-22

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: 85.58  E-value: 4.14e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 732686639  14 LSYVLAEKLAQRILKGEYEPGTILPGEIELGEQFGVSRTAVREAVKTLTAKGMVLPRPRIGTRV 77
Cdd:cd07377    2 LYEQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFV 65
FCD smart00895
This entry represents the C-terminal ligand binding domain of many members of the GntR family; ...
 110-227 2.60e-21

This entry represents the C-terminal ligand binding domain of many members of the GntR family; This domain probably binds to a range of effector molecules that regulate the transcription of genes through the action of the N-terminal DNA-binding domain. This domain is found in and that are regulators of sugar biosynthesis operons. Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector binding or oligomerisation domain at the C terminus. The winged-helix DNA-binding domain is well conserved in structure for the whole of the GntR family, and is similar in structure to other transcriptional regulator families. The C-terminal effector-binding and oligomerisation domains are more variable and are consequently used to define the subfamilies. Based on the sequence and structure of the C-terminal domains, the GtnR family can be divided into four major groups, as represented by FadR, HutC, MocR and YtrA, as well as some minor groups such as those represented by AraR and PlmA.


Pssm-ID: 214892 [Multi-domain]  Cd Length: 123  Bit Score: 85.49  E-value: 2.60e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639   110 MRICLEPQACLLAATVGTAEQKAHLNTLMAEM-AALKENFRRERWIEVDMAWHEHIYEMSANPFLTSFASLFHSVYHTYF 188
Cdd:smart00895   5 VRRALEPLAARLAAERATDEDLAALEALLDAMeAAAAAGDDLEEFAELDREFHRALAEAAGNPVLLELLESLRARLRRLR 84

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 732686639   189 TSITSDTVIKLDLHQAIVDAIIQSDGDAAFKACQALLRS 227
Cdd:smart00895  85 RLSLEAARRALDEHRAILDAIRARDAEAARAAMREHLEA 123
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
 18-77 2.39e-19

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: 78.43  E-value: 2.39e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639   18 LAEKLAQRILKGEYEPGTILPGEIELGEQFGVSRTAVREAVKTLTAKGMVLPRPRIGTRV 77
Cdd:pfam00392   5 VYARLREDILSGRLRPGDKLPSERELAAEFGVSRTTVREALRRLEAEGLVERRQGRGTFV 64
C_P_lyase_phnF TIGR02325
phosphonates metabolism transcriptional regulator PhnF; All members of the seed alignment for ...
 18-80 6.38e-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: 60.18  E-value: 6.38e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 732686639   18 LAEKLAQRILKGEYEPGTILPGEIELGEQFGVSRTAVREAVKTLTAKGMVLPRPRIGTRVMPQ 80
Cdd:TIGR02325  13 IADKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQGRGTFVAAR 75
 
Name Accession Description Interval E-value
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
9-227 1.03e-60

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


Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 190.14  E-value: 1.03e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639   9 AAQKNLSYVLAEKLAQRILKGEYEPGTILPGEIELGEQFGVSRTAVREAVKTLTAKGMVLPRPRIGTRVMPQSNWNFLDQ 88
Cdd:COG2186    3 IRRRSLAEQVAEQLRELILSGELKPGDRLPSERELAEQLGVSRTTVREALRALEALGLVEVRQGGGTFVREPSPWALLDP 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639  89 elLTWWMTEEnfHQVIDHFLVMRICLEPQACLLAATVGTAEQKAHLNTLMAEMAALKENfrRERWIEVDMAWHEHIYEMS 168
Cdd:COG2186   83 --LALLLALD--DASLRDLLEARLALEPEAARLAAERATDEDLARLEAALAEMEAAADD--GEAFAEADLAFHRAIAEAS 156

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 732686639 169 ANPFLTSFASLFHSVYHTYFTSITSDTVIK---LDLHQAIVDAIIQSDGDAAFKACQALLRS 227
Cdd:COG2186  157 GNPLLALLLESLRELLRRSVRLTLRSPEARersLAEHRAILDAIRAGDPEAARAAMRAHLEA 218
GntR COG1802
DNA-binding transcriptional regulator, GntR family [Transcription];
4-227 4.19e-38

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


Pssm-ID: 441407 [Multi-domain]  Cd Length: 222  Bit Score: 131.97  E-value: 4.19e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639   4 SAQQLAAQKNLSYVLAEKLAQRILKGEYEPGTILPgEIELGEQFGVSRTAVREAVKTLTAKGMVLPRPRIGTRVMPqsnw 83
Cdd:COG1802    2 TSPSPLRRESLAEQVYEALREAILSGELPPGERLS-EAELAERLGVSRTPVREALRRLEAEGLVEIRPNRGARVAP---- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639  84 nfldqelltwwMTEENFHQVIDhflvMRICLEPQACLLAATVGTAEQKAHLNTLMAEMAALKENFRRERWIEVDMAWHEH 163
Cdd:COG1802   77 -----------LSPEEIRELYE----VRAALEGLAARLAAERATPADLARLRALLEELEAAAAAGDVAAYLELDREFHRA 141

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 732686639 164 IYEMSANPFLTSFASLFHSVYHTY-FTSITSDTVIK--LDLHQAIVDAIIQSDGDAAFKACQALLRS 227
Cdd:COG1802  142 LVEAAGNPRLAELLRRLRARLRRYrRLSLRSPGRLEesLAEHRAILDALEAGDAEAAAAALRAHLER 208
PRK03837 PRK03837
transcriptional regulator NanR; Provisional
 7-227 1.13e-23

transcriptional regulator NanR; Provisional


Pssm-ID: 235166 [Multi-domain]  Cd Length: 241  Bit Score: 94.70  E-value: 1.13e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639   7 QLAAQKNLSYVLAEKLAQRILKGEYEPGTILPGEIELGEQFGVSRTAVREAVKTLTAKGMVL----PRPRIgTRVMPQSN 82
Cdd:PRK03837   7 RPIARKKLSEEVEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQishgERARV-SRPSADTI 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639  83 WNFLD---QELLTWWMTEenfhqvIDHFLVMRICLEPQACLLAATVGTAEQKAHL-NTLMAEMAALKENfrrERWIEVDM 158
Cdd:PRK03837  86 IGQLSgmaKDFLSQSPDG------LAHLKQARLFFESSLARYAAEHATDEQIALLrKALERNSQSLGDN---AAFIRSDM 156

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 732686639 159 AWHEHIYEMSANPFLTSFA-SLFH--SVYHTYFTSITSDTVIKLDLHQAIVDAIIQSDGDAAFKACQALLRS 227
Cdd:PRK03837 157 EFHRVIAEIPGNPIFMAIHeALLDwlIEARPEVVILHGHENVTLQEHIAIVDAIRAHDPDEADRALQSHLNR 228
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 14-77 4.14e-22

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: 85.58  E-value: 4.14e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 732686639  14 LSYVLAEKLAQRILKGEYEPGTILPGEIELGEQFGVSRTAVREAVKTLTAKGMVLPRPRIGTRV 77
Cdd:cd07377    2 LYEQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFV 65
FCD smart00895
This entry represents the C-terminal ligand binding domain of many members of the GntR family; ...
 110-227 2.60e-21

This entry represents the C-terminal ligand binding domain of many members of the GntR family; This domain probably binds to a range of effector molecules that regulate the transcription of genes through the action of the N-terminal DNA-binding domain. This domain is found in and that are regulators of sugar biosynthesis operons. Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector binding or oligomerisation domain at the C terminus. The winged-helix DNA-binding domain is well conserved in structure for the whole of the GntR family, and is similar in structure to other transcriptional regulator families. The C-terminal effector-binding and oligomerisation domains are more variable and are consequently used to define the subfamilies. Based on the sequence and structure of the C-terminal domains, the GtnR family can be divided into four major groups, as represented by FadR, HutC, MocR and YtrA, as well as some minor groups such as those represented by AraR and PlmA.


Pssm-ID: 214892 [Multi-domain]  Cd Length: 123  Bit Score: 85.49  E-value: 2.60e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639   110 MRICLEPQACLLAATVGTAEQKAHLNTLMAEM-AALKENFRRERWIEVDMAWHEHIYEMSANPFLTSFASLFHSVYHTYF 188
Cdd:smart00895   5 VRRALEPLAARLAAERATDEDLAALEALLDAMeAAAAAGDDLEEFAELDREFHRALAEAAGNPVLLELLESLRARLRRLR 84

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 732686639   189 TSITSDTVIKLDLHQAIVDAIIQSDGDAAFKACQALLRS 227
Cdd:smart00895  85 RLSLEAARRALDEHRAILDAIRARDAEAARAAMREHLEA 123
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
 18-77 2.39e-19

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: 78.43  E-value: 2.39e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639   18 LAEKLAQRILKGEYEPGTILPGEIELGEQFGVSRTAVREAVKTLTAKGMVLPRPRIGTRV 77
Cdd:pfam00392   5 VYARLREDILSGRLRPGDKLPSERELAAEFGVSRTTVREALRRLEAEGLVERRQGRGTFV 64
HTH_GNTR smart00345
helix_turn_helix gluconate operon transcriptional repressor;
18-77 3.22e-19

helix_turn_helix gluconate operon transcriptional repressor;


Pssm-ID: 197669 [Multi-domain]  Cd Length: 60  Bit Score: 78.00  E-value: 3.22e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639    18 LAEKLAQRILKGEYEPGTILPGEIELGEQFGVSRTAVREAVKTLTAKGMVLPRPRIGTRV 77
Cdd:smart00345   1 VAERLREDIVSGELRPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGSGTFV 60
MngR COG2188
DNA-binding transcriptional regulator, GntR family [Transcription];
18-80 2.59e-18

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


Pssm-ID: 441791 [Multi-domain]  Cd Length: 238  Bit Score: 80.29  E-value: 2.59e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 732686639  18 LAEKLAQRILKGEYEPGTILPGEIELGEQFGVSRTAVREAVKTLTAKGMVLPRPRIGTRVMPQ 80
Cdd:COG2188   10 IADALRERIESGELPPGDRLPSERELAEEFGVSRMTVRKALDELVEEGLLERRQGRGTFVAEP 72
FCD pfam07729
FCD domain; This domain is the C-terminal ligand binding domain of many members of the GntR ...
 108-223 6.82e-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: 76.64  E-value: 6.82e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639  108 LVMRICLEPQACLLAATVGTAEQKAHLNTLMAEMAALKENFRRERWIEVDMAWHEHIYEMSANPFLTSFASLFHSVYHTY 187
Cdd:pfam07729   3 YELRAALEPLAARLAAERATDEDLAELEALLEALEAAADAGDLEAFAEADREFHLALAEAAGNPVLARMLESLWDRLRRL 82

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 732686639  188 FTSITS---DTVIKLDLHQAIVDAIIQSDGDAAFKACQA 223
Cdd:pfam07729  83 RRLLLSspgRLRASLEEHRAILDAIRARDPEAARAAMRR 121
PRK10421 PRK10421
DNA-binding transcriptional repressor LldR; Provisional
 12-220 1.50e-13

DNA-binding transcriptional repressor LldR; Provisional


Pssm-ID: 236690 [Multi-domain]  Cd Length: 253  Bit Score: 67.87  E-value: 1.50e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639  12 KNLSYVLAEKLAQRILKGEYEPGTILPGEIELGEQFGVSRTAVREAVKTLTAKGMVLPRPRIGTrvmpqsnwnFLDQELL 91
Cdd:PRK10421   1 RRLSDEVADRVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGT---------FIRWRHE 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639  92 TWwmTEENFHQVIDHF-----------LVMRICLEPQACLLAATVGTAEQKAHL----NTLMAEMAALKEnfrrerwiEV 156
Cdd:PRK10421  72 TW--SEQNIVQPLKTLmaddpdysfdiLEARHAIEASTAWHAAMRATPGDKEKIqlcfEATLSEDPDLAS--------QA 141

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 732686639 157 DMAWHEHIYEMSANPFLTS-----FASLFHSVYHTYFTSITSDTVIKL--DLHQAIVDAIIQSDGDAAFKA 220
Cdd:PRK10421 142 DVRFHLAIAEASHNVVLLQtmrgfFDVLQSSVKQSRQRMYLVPPVFSQltEQHQAVMDAILAGDAEGARKA 212
pdhR PRK09464
pyruvate dehydrogenase complex transcriptional repressor PdhR;
11-225 9.06e-13

pyruvate dehydrogenase complex transcriptional repressor PdhR;


Pssm-ID: 181879 [Multi-domain]  Cd Length: 254  Bit Score: 65.43  E-value: 9.06e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639  11 QKNLSYVLAEKLAQRILKGEYEPGTILPGEIELGEQFGVSRTAVREAVKTLTAKGMVLPRPRIGTRVMPQSNWNFLDQ-- 88
Cdd:PRK09464   8 QPKLSDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGGTFVQSSLWQSFSDPlv 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639  89 ELLTwWMTEENFhqvidHFLVMRICLEPQACLLAATVGTAEQKAHLNTLMAEMAALKENFRRERWIEVDMAWHEHIYEMS 168
Cdd:PRK09464  88 ELLS-DHPESQF-----DLLETRHALEGIAAYYAALRGTDEDFERIRECHHAIELAQQSGDLDAEANAVMQYQIAVTEAA 161

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 732686639 169 ANPFL----TSFASLFHSVYHTYFT--SITSDTVIKLDLHQA-IVDAIIQSDGDAAFKACQALL 225
Cdd:PRK09464 162 HNVVLlhllRCMEPMLEQNVRQNFEllYRRREMLPKVSSHRArIFEAIVAGKPEKAREASHRHL 225
C_P_lyase_phnF TIGR02325
phosphonates metabolism transcriptional regulator PhnF; All members of the seed alignment for ...
 18-80 6.38e-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: 60.18  E-value: 6.38e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 732686639   18 LAEKLAQRILKGEYEPGTILPGEIELGEQFGVSRTAVREAVKTLTAKGMVLPRPRIGTRVMPQ 80
Cdd:TIGR02325  13 IADKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQGRGTFVAAR 75
ARO8 COG1167
DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain ...
 18-80 2.70e-10

DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain [Transcription, Amino acid transport and metabolism]; DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain is part of the Pathway/BioSystem: Lysine biosynthesis


Pssm-ID: 440781 [Multi-domain]  Cd Length: 471  Bit Score: 59.46  E-value: 2.70e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 732686639  18 LAEKLAQRILKGEYEPGTILPGEIELGEQFGVSRTAVREAVKTLTAKGMVLPRPRIGTRVMPQ 80
Cdd:COG1167   17 LADALREAILSGRLPPGDRLPSSRELAAQLGVSRSTVVRAYEELEAEGLIESRPGSGTFVAAR 79
PRK09990 PRK09990
DNA-binding transcriptional regulator GlcC; Provisional
 17-185 1.35e-09

DNA-binding transcriptional regulator GlcC; Provisional


Pssm-ID: 182186 [Multi-domain]  Cd Length: 251  Bit Score: 56.70  E-value: 1.35e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639  17 VLAEKLAQRILKGEYEPGTILPGEIELGEQFGVSRTAVREAVKTLTAKGMVLPRPRIGTRVMPQSNwnfldQELLTWWMt 96
Cdd:PRK09990  11 VVAERIERLIVDGVLKVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQGRGSFVARLNR-----VQDASPLM- 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639  97 eenfH------QVIDHFLVMRICLEPQACLLAATVGTAEQKAHLNTLMAEMAALKENFRRERWIE---VDMAWHEHIYEM 167
Cdd:PRK09990  85 ----HlfssqpRTLYDLLEVRALLEGESARLAALRGTQADFVLITRRYEEMLAAHENNKEIDPIEharLDHAFHLAICEA 160

                        170       180       190
                 ....*....|....*....|....*....|
gi 732686639 168 SANPFLTS---------FASLFHSV---YH 185
Cdd:PRK09990 161 SHNPVLVHtlqsltdlmLSSVFASVnnlYH 190
PRK09764 PRK09764
GntR family transcriptional regulator;
10-62 4.76e-08

GntR family transcriptional regulator;


Pssm-ID: 182065 [Multi-domain]  Cd Length: 240  Bit Score: 52.14  E-value: 4.76e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 732686639  10 AQKNLSYVLAEKLAQRILKGEYEPGTILPGEIELGEQFGVSRTAVREAVKTLT 62
Cdd:PRK09764   2 GHKPLYRQIADRIREQIARGELKPGDALPTESALQTEFGVSRVTVRQALRQLV 54
PRK11402 PRK11402
transcriptional regulator PhoB;
4-92 2.39e-07

transcriptional regulator PhoB;


Pssm-ID: 183118 [Multi-domain]  Cd Length: 241  Bit Score: 49.83  E-value: 2.39e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639   4 SAQQLAAQknlsyvLAEKLAQRILKGEYEPGTILPGEIELGEQFGVSRTAVREAVKTLTAKGMVLPRPRIGTRVMPQSnw 83
Cdd:PRK11402   6 SHQLLYAT------VRQRLLDDIAQGVYQAGQQIPTENELCTQYNVSRITIRKAISDLVADGVLIRWQGKGTFVQSQK-- 77


                 ....*....
gi 732686639  84 nfLDQELLT 92
Cdd:PRK11402  78 --VENALLT 84
PRK10225 PRK10225
Uxu operon transcriptional regulator;
21-87 7.42e-07

Uxu operon transcriptional regulator;


Pssm-ID: 182318 [Multi-domain]  Cd Length: 257  Bit Score: 48.48  E-value: 7.42e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 732686639  21 KLAQRILKGEYEPGTILPGEIELGEQFGVSRTAVREAVKTLTAKGMVLPRPRIGTRVMPQSNWNFLD 87
Cdd:PRK10225  17 MIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRRGAGIYVLDSSGSHNTD 83
PRK11523 PRK11523
transcriptional regulator ExuR;
18-217 1.79e-06

transcriptional regulator ExuR;


Pssm-ID: 183176 [Multi-domain]  Cd Length: 253  Bit Score: 47.53  E-value: 1.79e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639  18 LAEKLAQRILKGEYEPGTILPGEIELGEQFGVSRTAVREAVKTLTAKGMVLPRPRIGTRVMPQSNWNFLDQELLTWWMTE 97
Cdd:PRK11523  13 LAAELKERIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRKGSGIHVVSNQPRHQQAADNNMEFANY 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639  98 ENFhqvidHFLVMRICLEPQACLLAATVGTaeqKAHLNTLMA--EMAALKENFRRERWievDMAWHEHIYEMSANPFLTS 175
Cdd:PRK11523  93 GPF-----ELLQARQLIESNIAEFAATQVT---KQDIMKLMAiqEQARGEDCFRDSEW---DLQFHVQVALATQNSALAA 161

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 732686639 176 FASLF--HSVYHTYFTS----ITSDTVIK-LDLHQAIVDAIIQSDGDAA 217
Cdd:PRK11523 162 IVEKMwtQRSHNPYWKKlhehIDDRTVDNwCDDHDQILKALIRKDPHAA 210
PRK15481 PRK15481
transcriptional regulatory protein PtsJ; Provisional
 24-75 5.57e-05

transcriptional regulatory protein PtsJ; Provisional


Pssm-ID: 185378 [Multi-domain]  Cd Length: 431  Bit Score: 43.50  E-value: 5.57e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 732686639  24 QRILKGEYEPGTILPGEIELGEQFGVSRTAVREAVKTLTAKGMVLPRPRIGT 75
Cdd:PRK15481  16 QLIQAGRLRPGDSLPPVRELASELGVNRNTVAAAYKRLVTAGLAQSQGRNGT 67
PRK04984 PRK04984
fatty acid metabolism transcriptional regulator FadR;
1-56 8.31e-05

fatty acid metabolism transcriptional regulator FadR;


Pssm-ID: 179909 [Multi-domain]  Cd Length: 239  Bit Score: 42.55  E-value: 8.31e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 732686639   1 MPLSAQQLAAqknlsyvLAEK-LAQRILKGEYEPGTILPGEIELGEQFGVSRTAVRE 56
Cdd:PRK04984   1 MVIKAQSPAG-------FAEEyIIESIWNNRFPPGSILPAERELSELIGVTRTTLRE 50
PRK14999 PRK14999
histidine utilization repressor; Provisional
 20-77 3.58e-04

histidine utilization repressor; Provisional


Pssm-ID: 184961 [Multi-domain]  Cd Length: 241  Bit Score: 40.69  E-value: 3.58e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 732686639  20 EKLAQRILKGEYEPGTILPGEIELGEQFGVSRTAVREAVKTLTAKGMVLPRPRIGTRV 77
Cdd:PRK14999  19 QDICKKIAGGVWQPHDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVRLQGVGTFV 76
PRK10079 PRK10079
phosphonate metabolism transcriptional regulator PhnF; Provisional
 18-137 9.36e-04

phosphonate metabolism transcriptional regulator PhnF; Provisional


Pssm-ID: 182227 [Multi-domain]  Cd Length: 241  Bit Score: 39.37  E-value: 9.36e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639  18 LAEKLAQRiLKGEYEPGTILPGEIELGEQFGVSRTAVREAVKTLTAKGMVLPRPRIGTRV-MPQSNWNFLDQELLTWWMT 96
Cdd:PRK10079  17 IAAKLEQE-LRQHYRCGDYLPAEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQGVGVLVlMRPYDYPLNAQARFSQNLL 95

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 732686639  97 EENFHQVIDHFL-VMRICLEPQACLLAATVGtaEQKAHLNTL 137
Cdd:PRK10079  96 DQGSHPTSEKLLsVLRPASGHVADALGITEG--ENVIHLRTL 135
HTH_11 pfam08279
HTH domain; This family includes helix-turn-helix domains in a wide variety of proteins.
 42-68 2.02e-03

HTH domain; This family includes helix-turn-helix domains in a wide variety of proteins.


Pssm-ID: 429896 [Multi-domain]  Cd Length: 52  Bit Score: 35.10  E-value: 2.02e-03
                          10        20
                  ....*....|....*....|....*..
gi 732686639   42 ELGEQFGVSRTAVREAVKTLTAKGMVL 68
Cdd:pfam08279  18 ELAEKLGVSRRTIRRDIKILEELGVPI 44
BirA COG1654
Biotin operon repressor [Transcription];
21-107 4.44e-03

Biotin operon repressor [Transcription];


Pssm-ID: 441260 [Multi-domain]  Cd Length: 324  Bit Score: 37.66  E-value: 4.44e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 732686639  21 KLAQRILK----GEYepgtiLPGEiELGEQFGVSRTAVREAVKTLTAKGmvLP---RPRIGTRVMPQSNWnfLDQELLTW 93
Cdd:COG1654    4 STRLKLLRlladGEF-----HSGE-ELAEELGVSRAAVWKHIKALRELG--YEiesVPGKGYRLAEPPDL--LDPEEIRA 73

                         90
                 ....*....|....
gi 732686639  94 WMTEENFHQVIDHF 107
Cdd:COG1654   74 GLSTKRLGREILYV 87
 
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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