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Conserved domains on  [gi|1262707550|gb|PFT21867|]
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FadR family transcriptional regulator [Bacillus thuringiensis]

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];
10-224 1.75e-61

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


:

Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 192.07  E-value: 1.75e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  10 SKVSRRKLVDEVLERLQEKIFSGKYEVGDRLPTEPQLMEELGVGRSTLRESIKILVHAGILEVRQGQGTRIVSLNITQD- 88
Cdd:COG2186     1 KPIRRRSLAEQVAEQLRELILSGELKPGDRLPSERELAEQLGVSRTTVREALRALEALGLVEVRQGGGTFVREPSPWALl 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  89 ---SFEKRLQAANINHVYEARNMLDKEVAMLAAQRRSDEDLLYLKGHLNKRKNALQEGnyVAYIDADIQFHLAIAKASKN 165
Cdd:COG2186    81 dplALLLALDDASLRDLLEARLALEPEAARLAAERATDEDLARLEAALAEMEAAADDG--EAFAEADLAFHRAIAEASGN 158

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1262707550 166 EVLLDLYQSFVPALRHILSQFILNTANYEDNSDIHEKLFQAILKQNTEEARKYAVQNLE 224
Cdd:COG2186   159 PLLALLLESLRELLRRSVRLTLRSPEARERSLAEHRAILDAIRAGDPEAARAAMRAHLE 217
 
Name Accession Description Interval E-value
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
10-224 1.75e-61

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


Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 192.07  E-value: 1.75e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  10 SKVSRRKLVDEVLERLQEKIFSGKYEVGDRLPTEPQLMEELGVGRSTLRESIKILVHAGILEVRQGQGTRIVSLNITQD- 88
Cdd:COG2186     1 KPIRRRSLAEQVAEQLRELILSGELKPGDRLPSERELAEQLGVSRTTVREALRALEALGLVEVRQGGGTFVREPSPWALl 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  89 ---SFEKRLQAANINHVYEARNMLDKEVAMLAAQRRSDEDLLYLKGHLNKRKNALQEGnyVAYIDADIQFHLAIAKASKN 165
Cdd:COG2186    81 dplALLLALDDASLRDLLEARLALEPEAARLAAERATDEDLARLEAALAEMEAAADDG--EAFAEADLAFHRAIAEASGN 158

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1262707550 166 EVLLDLYQSFVPALRHILSQFILNTANYEDNSDIHEKLFQAILKQNTEEARKYAVQNLE 224
Cdd:COG2186   159 PLLALLLESLRELLRRSVRLTLRSPEARERSLAEHRAILDAIRAGDPEAARAAMRAHLE 217
PRK10421 PRK10421
DNA-binding transcriptional repressor LldR; Provisional
 15-224 1.71e-32

DNA-binding transcriptional repressor LldR; Provisional


Pssm-ID: 236690 [Multi-domain]  Cd Length: 253  Bit Score: 118.33  E-value: 1.71e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  15 RKLVDEVLERLQEKIFSGKYEVGDRLPTEPQLMEELGVGRSTLRESIKILVHAGILEVRQGQGTRIVSL-------NITQ 87
Cdd:PRK10421    1 RRLSDEVADRVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRWRhetwseqNIVQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  88 DSfeKRLQAANINHVY---EARNMLDKEVAMLAAQRRSDEDllylKGHLNKRKNALQEGNYVAYIDADIQFHLAIAKASK 164
Cdd:PRK10421   81 PL--KTLMADDPDYSFdilEARHAIEASTAWHAAMRATPGD----KEKIQLCFEATLSEDPDLASQADVRFHLAIAEASH 154

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1262707550 165 NEVLL-------DLYQSFVPALRHILsqfILNTANYEDNSDIHEKLFQAILKQNTEEARKYAVQNLE 224
Cdd:PRK10421  155 NVVLLqtmrgffDVLQSSVKQSRQRM---YLVPPVFSQLTEQHQAVMDAILAGDAEGARKAMMAHLS 218
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 16-80 5.27e-21

Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is presumed to result in a conformational change that regulates the DNA-binding affinity of the repressor. The GntR-like proteins bind as dimers, where each monomer recognizes a half-site of 2-fold symmetric DNA sequences.


Pssm-ID: 153418 [Multi-domain]  Cd Length: 66  Bit Score: 82.88  E-value: 5.27e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1262707550  16 KLVDEVLERLQEKIFSGKYEVGDRLPTEPQLMEELGVGRSTLRESIKILVHAGILEVRQGQGTRI 80
Cdd:cd07377     1 PLYEQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFV 65
FCD pfam07729
FCD domain; This domain is the C-terminal ligand binding domain of many members of the GntR ...
 102-216 3.31e-20

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: 82.42  E-value: 3.31e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550 102 VYEARNMLDKEVAMLAAQRRSDEDLLYLKGHLNKRKNALQEGNYVAYIDADIQFHLAIAKASKNEVLLDLYQSFVPALRH 181
Cdd:pfam07729   2 LYELRAALEPLAARLAAERATDEDLAELEALLEALEAAADAGDLEAFAEADREFHLALAEAAGNPVLARMLESLWDRLRR 81

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1262707550 182 ILSQFILNTANYEDNSDIHEKLFQAILKQNTEEAR 216
Cdd:pfam07729  82 LRRLLLSSPGRLRASLEEHRAILDAIRARDPEAAR 116
FCD smart00895
This entry represents the C-terminal ligand binding domain of many members of the GntR family; ...
 101-224 1.52e-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: 80.87  E-value: 1.52e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  101 HVYEARNMLDKEVAMLAAQRRSDEDLLYLKGHLNKRKNALQEGN-YVAYIDADIQFHLAIAKASKNEVLLDLYQSFVPAL 179
Cdd:smart00895   1 ELYEVRRALEPLAARLAAERATDEDLAALEALLDAMEAAAAAGDdLEEFAELDREFHRALAEAAGNPVLLELLESLRARL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1262707550  180 RHIlsqFILNTANYEDNSDIHEKLFQAILKQNTEEARKYAVQNLE 224
Cdd:smart00895  81 RRL---RRLSLEAARRALDEHRAILDAIRARDAEAARAAMREHLE 122
C_P_lyase_phnF TIGR02325
phosphonates metabolism transcriptional regulator PhnF; All members of the seed alignment for ...
 20-80 8.49e-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: 62.49  E-value: 8.49e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1262707550  20 EVLERLQEKIFSGKYEVGDRLPTEPQLMEELGVGRSTLRESIKILVHAGILEVRQGQGTRI 80
Cdd:TIGR02325  12 QIADKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQGRGTFV 72
 
Name Accession Description Interval E-value
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
10-224 1.75e-61

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


Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 192.07  E-value: 1.75e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  10 SKVSRRKLVDEVLERLQEKIFSGKYEVGDRLPTEPQLMEELGVGRSTLRESIKILVHAGILEVRQGQGTRIVSLNITQD- 88
Cdd:COG2186     1 KPIRRRSLAEQVAEQLRELILSGELKPGDRLPSERELAEQLGVSRTTVREALRALEALGLVEVRQGGGTFVREPSPWALl 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  89 ---SFEKRLQAANINHVYEARNMLDKEVAMLAAQRRSDEDLLYLKGHLNKRKNALQEGnyVAYIDADIQFHLAIAKASKN 165
Cdd:COG2186    81 dplALLLALDDASLRDLLEARLALEPEAARLAAERATDEDLARLEAALAEMEAAADDG--EAFAEADLAFHRAIAEASGN 158

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1262707550 166 EVLLDLYQSFVPALRHILSQFILNTANYEDNSDIHEKLFQAILKQNTEEARKYAVQNLE 224
Cdd:COG2186   159 PLLALLLESLRELLRRSVRLTLRSPEARERSLAEHRAILDAIRAGDPEAARAAMRAHLE 217
GntR COG1802
DNA-binding transcriptional regulator, GntR family [Transcription];
10-224 7.11e-37

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


Pssm-ID: 441407 [Multi-domain]  Cd Length: 222  Bit Score: 128.50  E-value: 7.11e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  10 SKVSRRKLVDEVLERLQEKIFSGKYEVGDRLpTEPQLMEELGVGRSTLRESIKILVHAGILEVRQGQGTRIVSLNitqds 89
Cdd:COG1802     5 SPLRRESLAEQVYEALREAILSGELPPGERL-SEAELAERLGVSRTPVREALRRLEAEGLVEIRPNRGARVAPLS----- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  90 fekrlqAANINHVYEARNMLDKEVAMLAAQRRSDEDLLYLKGHLNKRKNALQEGNYVAYIDADIQFHLAIAKASKNEVLL 169
Cdd:COG1802    79 ------PEEIRELYEVRAALEGLAARLAAERATPADLARLRALLEELEAAAAAGDVAAYLELDREFHRALVEAAGNPRLA 152

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1262707550 170 DLYQSFVPALRHILSQFILNTANYEDNSDIHEKLFQAILKQNTEEARKYAVQNLE 224
Cdd:COG1802   153 ELLRRLRARLRRYRRLSLRSPGRLEESLAEHRAILDALEAGDAEAAAAALRAHLE 207
PRK10421 PRK10421
DNA-binding transcriptional repressor LldR; Provisional
 15-224 1.71e-32

DNA-binding transcriptional repressor LldR; Provisional


Pssm-ID: 236690 [Multi-domain]  Cd Length: 253  Bit Score: 118.33  E-value: 1.71e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  15 RKLVDEVLERLQEKIFSGKYEVGDRLPTEPQLMEELGVGRSTLRESIKILVHAGILEVRQGQGTRIVSL-------NITQ 87
Cdd:PRK10421    1 RRLSDEVADRVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRWRhetwseqNIVQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  88 DSfeKRLQAANINHVY---EARNMLDKEVAMLAAQRRSDEDllylKGHLNKRKNALQEGNYVAYIDADIQFHLAIAKASK 164
Cdd:PRK10421   81 PL--KTLMADDPDYSFdilEARHAIEASTAWHAAMRATPGD----KEKIQLCFEATLSEDPDLASQADVRFHLAIAEASH 154

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1262707550 165 NEVLL-------DLYQSFVPALRHILsqfILNTANYEDNSDIHEKLFQAILKQNTEEARKYAVQNLE 224
Cdd:PRK10421  155 NVVLLqtmrgffDVLQSSVKQSRQRM---YLVPPVFSQLTEQHQAVMDAILAGDAEGARKAMMAHLS 218
PRK03837 PRK03837
transcriptional regulator NanR; Provisional
 12-224 3.86e-27

transcriptional regulator NanR; Provisional


Pssm-ID: 235166 [Multi-domain]  Cd Length: 241  Bit Score: 103.95  E-value: 3.86e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  12 VSRRKLVDEVLERLQEKIFSGKYEVGDRLPTEPQLMEELGVGRSTLRESIKILVHAGILEVRQGQGTRIVSLniTQDSFE 91
Cdd:PRK03837    9 IARKKLSEEVEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQISHGERARVSRP--SADTII 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  92 KRLQAA----------NINHVYEARNMLDKEVAMLAAQRRSDEDLLYLKGHLNKRKNALqeGNYVAYIDADIQFHLAIAK 161
Cdd:PRK03837   87 GQLSGMakdflsqspdGLAHLKQARLFFESSLARYAAEHATDEQIALLRKALERNSQSL--GDNAAFIRSDMEFHRVIAE 164

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1262707550 162 ASKNEVLLDLYQSFVPAL----RHILSQFILNTANYEDnsdiHEKLFQAILKQNTEEARKYAVQNLE 224
Cdd:PRK03837  165 IPGNPIFMAIHEALLDWLiearPEVVILHGHENVTLQE----HIAIVDAIRAHDPDEADRALQSHLN 227
PRK09990 PRK09990
DNA-binding transcriptional regulator GlcC; Provisional
 13-219 1.36e-24

DNA-binding transcriptional regulator GlcC; Provisional


Pssm-ID: 182186 [Multi-domain]  Cd Length: 251  Bit Score: 97.53  E-value: 1.36e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  13 SRRKLVDEVLERLQEKIFSGKYEVGDRLPTEPQLMEELGVGRSTLRESIKILVHAGILEVRQGQGTRIVSLNITQDS--- 89
Cdd:PRK09990    4 ERRPIADVVAERIERLIVDGVLKVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQGRGSFVARLNRVQDAspl 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  90 ---FEKrlQAANINHVYEARNMLDKEVAMLAAQRRSDEDLLYLKGHLNKRKNA---LQEGNYVAYIDADIQFHLAIAKAS 163
Cdd:PRK09990   84 mhlFSS--QPRTLYDLLEVRALLEGESARLAALRGTQADFVLITRRYEEMLAAhenNKEIDPIEHARLDHAFHLAICEAS 161

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1262707550 164 KNEVLLDLYQSfvpalrhiLSQFILNTANYEDNS------------DIHEKLFQAILKQNTEEARKYA 219
Cdd:PRK09990  162 HNPVLVHTLQS--------LTDLMLSSVFASVNNlyhrpqqkkqidRQHARLYNAVLQRLPEQAQRAA 221
pdhR PRK09464
pyruvate dehydrogenase complex transcriptional repressor PdhR;
9-216 4.89e-21

pyruvate dehydrogenase complex transcriptional repressor PdhR;


Pssm-ID: 181879 [Multi-domain]  Cd Length: 254  Bit Score: 88.15  E-value: 4.89e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550   9 FSKVSRRKLVDEVLERLQEKIFSGKYEVGDRLPTEPQLMEELGVGRSTLRESIKILVHAGILEVRQGQGTrIVSLNITQd 88
Cdd:PRK09464    3 YSKIRQPKLSDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGGT-FVQSSLWQ- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  89 SFEKRLQAANINH------VYEARNMLDKEVAMLAAQRRSDEDLLYLKGHLNKRKNALQEGNYVAYIDADIQFHLAIAKA 162
Cdd:PRK09464   81 SFSDPLVELLSDHpesqfdLLETRHALEGIAAYYAALRGTDEDFERIRECHHAIELAQQSGDLDAEANAVMQYQIAVTEA 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1262707550 163 SKNEVLLDLYQSFVPAL-RHILSQF-ILNTAN--YEDNSDIHEKLFQAILKQNTEEAR 216
Cdd:PRK09464  161 AHNVVLLHLLRCMEPMLeQNVRQNFeLLYRRRemLPKVSSHRARIFEAIVAGKPEKAR 218
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 16-80 5.27e-21

Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is presumed to result in a conformational change that regulates the DNA-binding affinity of the repressor. The GntR-like proteins bind as dimers, where each monomer recognizes a half-site of 2-fold symmetric DNA sequences.


Pssm-ID: 153418 [Multi-domain]  Cd Length: 66  Bit Score: 82.88  E-value: 5.27e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1262707550  16 KLVDEVLERLQEKIFSGKYEVGDRLPTEPQLMEELGVGRSTLRESIKILVHAGILEVRQGQGTRI 80
Cdd:cd07377     1 PLYEQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFV 65
FCD pfam07729
FCD domain; This domain is the C-terminal ligand binding domain of many members of the GntR ...
 102-216 3.31e-20

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: 82.42  E-value: 3.31e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550 102 VYEARNMLDKEVAMLAAQRRSDEDLLYLKGHLNKRKNALQEGNYVAYIDADIQFHLAIAKASKNEVLLDLYQSFVPALRH 181
Cdd:pfam07729   2 LYELRAALEPLAARLAAERATDEDLAELEALLEALEAAADAGDLEAFAEADREFHLALAEAAGNPVLARMLESLWDRLRR 81

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1262707550 182 ILSQFILNTANYEDNSDIHEKLFQAILKQNTEEAR 216
Cdd:pfam07729  82 LRRLLLSSPGRLRASLEEHRAILDAIRARDPEAAR 116
FCD smart00895
This entry represents the C-terminal ligand binding domain of many members of the GntR family; ...
 101-224 1.52e-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: 80.87  E-value: 1.52e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  101 HVYEARNMLDKEVAMLAAQRRSDEDLLYLKGHLNKRKNALQEGN-YVAYIDADIQFHLAIAKASKNEVLLDLYQSFVPAL 179
Cdd:smart00895   1 ELYEVRRALEPLAARLAAERATDEDLAALEALLDAMEAAAAAGDdLEEFAELDREFHRALAEAAGNPVLLELLESLRARL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1262707550  180 RHIlsqFILNTANYEDNSDIHEKLFQAILKQNTEEARKYAVQNLE 224
Cdd:smart00895  81 RRL---RRLSLEAARRALDEHRAILDAIRARDAEAARAAMREHLE 122
PRK10225 PRK10225
Uxu operon transcriptional regulator;
10-173 1.93e-19

Uxu operon transcriptional regulator;


Pssm-ID: 182318 [Multi-domain]  Cd Length: 257  Bit Score: 83.92  E-value: 1.93e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  10 SKVSRRKLVDEVLERLQEKIFSGKYEVGDRLPTEPQLMEELGVGRSTLRESIKILVHAGILEVRQGQGTRIVslnitQDS 89
Cdd:PRK10225    3 SATSAQRPYQEVGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRRGAGIYVL-----DSS 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  90 FEKRLQAANINH--------VYEARNMLDKEVAMLAAQRRSDEDLLYLKGHLNKRKNALQEGNYVAYIDADIQFHLAIAK 161
Cdd:PRK10225   78 GSHNTDSPDANVcndagpfeLLQARQLLESNIAEFAALQATREDIVKMRQALQLEERELASSAPGSSESGDMQFHLAIAE 157

                         170
                  ....*....|..
gi 1262707550 162 ASKNEVLLDLYQ 173
Cdd:PRK10225  158 ATHNSMLVELFR 169
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
 17-80 8.71e-18

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: 74.19  E-value: 8.71e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1262707550  17 LVDEVLERLQEKIFSGKYEVGDRLPTEPQLMEELGVGRSTLRESIKILVHAGILEVRQGQGTRI 80
Cdd:pfam00392   1 LYEQVYARLREDILSGRLRPGDKLPSERELAAEFGVSRTTVREALRRLEAEGLVERRQGRGTFV 64
MngR COG2188
DNA-binding transcriptional regulator, GntR family [Transcription];
13-88 1.56e-17

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


Pssm-ID: 441791 [Multi-domain]  Cd Length: 238  Bit Score: 78.37  E-value: 1.56e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1262707550  13 SRRKLVDEVLERLQEKIFSGKYEVGDRLPTEPQLMEELGVGRSTLRESIKILVHAGILEVRQGQGTRIVSLNITQD 88
Cdd:COG2188     2 SPVPLYLQIADALRERIESGELPPGDRLPSERELAEEFGVSRMTVRKALDELVEEGLLERRQGRGTFVAEPKIEYP 77
HTH_GNTR smart00345
helix_turn_helix gluconate operon transcriptional repressor;
21-80 9.72e-17

helix_turn_helix gluconate operon transcriptional repressor;


Pssm-ID: 197669 [Multi-domain]  Cd Length: 60  Bit Score: 71.45  E-value: 9.72e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550   21 VLERLQEKIFSGKYEVGDRLPTEPQLMEELGVGRSTLRESIKILVHAGILEVRQGQGTRI 80
Cdd:smart00345   1 VAERLREDIVSGELRPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGSGTFV 60
PRK11523 PRK11523
transcriptional regulator ExuR;
15-168 5.13e-15

transcriptional regulator ExuR;


Pssm-ID: 183176 [Multi-domain]  Cd Length: 253  Bit Score: 71.80  E-value: 5.13e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  15 RKLVDEVLERLQEKIFSGKYEVGDRLPTEPQLMEELGVGRSTLRESIKILVHAGILEVRQGQGTRIVS-----LNITQDS 89
Cdd:PRK11523    7 RRLYQQLAAELKERIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRKGSGIHVVSnqprhQQAADNN 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1262707550  90 FEkrLQAANINHVYEARNMLDKEVAMLAAQRRSDEDLLYLkghLNKRKNALQEGNYVAYiDADIQFHLAIAKASKNEVL 168
Cdd:PRK11523   87 ME--FANYGPFELLQARQLIESNIAEFAATQVTKQDIMKL---MAIQEQARGEDCFRDS-EWDLQFHVQVALATQNSAL 159
C_P_lyase_phnF TIGR02325
phosphonates metabolism transcriptional regulator PhnF; All members of the seed alignment for ...
 20-80 8.49e-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: 62.49  E-value: 8.49e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1262707550  20 EVLERLQEKIFSGKYEVGDRLPTEPQLMEELGVGRSTLRESIKILVHAGILEVRQGQGTRI 80
Cdd:TIGR02325  12 QIADKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQGRGTFV 72
PRK09764 PRK09764
GntR family transcriptional regulator;
12-91 2.07e-11

GntR family transcriptional regulator;


Pssm-ID: 182065 [Multi-domain]  Cd Length: 240  Bit Score: 61.38  E-value: 2.07e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  12 VSRRKLVDEVLERLQEKIFSGKYEVGDRLPTEPQLMEELGVGRSTLRESIKILVHAGILEVRQGQGTRIVSLNITQDSFE 91
Cdd:PRK09764    1 MGHKPLYRQIADRIREQIARGELKPGDALPTESALQTEFGVSRVTVRQALRQLVEQQILESIQGSGTYVKEERVNYDIFQ 80
ARO8 COG1167
DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain ...
 13-80 2.13e-08

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: 53.68  E-value: 2.13e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1262707550  13 SRRKLVDEVLERLQEKIFSGKYEVGDRLPTEPQLMEELGVGRSTLRESIKILVHAGILEVRQGQGTRI 80
Cdd:COG1167     9 SSGPLYLQLADALREAILSGRLPPGDRLPSSRELAAQLGVSRSTVVRAYEELEAEGLIESRPGSGTFV 76
YhcF COG1725
DNA-binding transcriptional regulator YhcF, GntR family [Transcription];
23-93 9.39e-08

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


Pssm-ID: 441331 [Multi-domain]  Cd Length: 114  Bit Score: 49.02  E-value: 9.39e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1262707550  23 ERLQEKIFSGKYEVGDRLPTEPQLMEELGVGRSTLRESIKILVHAGILEVRQGQGTRIVSLNITQDSFEKR 93
Cdd:COG1725    17 DQIKEAIASGELKPGDRLPSVRELAAELGVNPNTVAKAYRELEDEGLIETRRGKGTFVAEDARELLEERRE 87
PRK11402 PRK11402
transcriptional regulator PhoB;
13-82 2.78e-07

transcriptional regulator PhoB;


Pssm-ID: 183118 [Multi-domain]  Cd Length: 241  Bit Score: 49.83  E-value: 2.78e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  13 SRRKLVDEVLERLQEKIFSGKYEVGDRLPTEPQLMEELGVGRSTLRESIKILVHAGILEVRQGQGTRIVS 82
Cdd:PRK11402    6 SHQLLYATVRQRLLDDIAQGVYQAGQQIPTENELCTQYNVSRITIRKAISDLVADGVLIRWQGKGTFVQS 75
PRK10079 PRK10079
phosphonate metabolism transcriptional regulator PhnF; Provisional
 20-78 6.54e-06

phosphonate metabolism transcriptional regulator PhnF; Provisional


Pssm-ID: 182227 [Multi-domain]  Cd Length: 241  Bit Score: 45.54  E-value: 6.54e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1262707550  20 EVLERLQEKIfSGKYEVGDRLPTEPQLMEELGVGRSTLRESIKILVHAGILEVRQGQGT 78
Cdd:PRK10079   16 EIAAKLEQEL-RQHYRCGDYLPAEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQGVGV 73
PRK11414 PRK11414
GntR family transcriptional regulator;
11-223 1.25e-05

GntR family transcriptional regulator;


Pssm-ID: 183126 [Multi-domain]  Cd Length: 221  Bit Score: 44.86  E-value: 1.25e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  11 KVSRRKLVDEVLERLQEKIFSGKYEVGDRLPTEpQLMEELGVGRSTLRESIKILVHAGILEVRQGQGTRIVSLNITqdsf 90
Cdd:PRK11414    6 KTQHISLTLQVENDLKHQLSIGALKPGARLITK-NLAEQLGMSITPVREALLRLVSVNALSVAPAQAFTVPEVSKR---- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  91 ekrlQAANINHVyeaRNMLDKEVAMLAAQRRSDEDLLYLKGHLNKRKNALQEGNYVAYIDADIQFHLAIAKASKNEVLLD 170
Cdd:PRK11414   81 ----QLDEINRI---RYELELMAVALAVENLTPQDLAELQELLEKLQQAQEKGDMEQIINANRLFRLAIYHRSNMPILCE 153

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1262707550 171 ----LYQSFVPALRHILSQFilNTANYEDNSDIHEKLFQAiLKQNTEEARKYAVQNL 223
Cdd:PRK11414  154 mieqLWVRMGPSLHYLYEAI--NPAELREHIENYRLLLAA-LKAKDKEGCRHCLAEI 207
PRK14999 PRK14999
histidine utilization repressor; Provisional
 19-99 8.50e-05

histidine utilization repressor; Provisional


Pssm-ID: 184961 [Multi-domain]  Cd Length: 241  Bit Score: 42.23  E-value: 8.50e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262707550  19 DEVLERLQEKIFSGKYEVGDRLPTEPQLMEELGVGRSTLRESIKILVHAGILEVRQGQGTRIVSLNITQDSFEKRLQAAN 98
Cdd:PRK14999   15 ETVKQDICKKIAGGVWQPHDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVRLQGVGTFVAEPKGQSALFEVRSIAEE 94


                  .
gi 1262707550  99 I 99
Cdd:PRK14999   95 I 95
PRK15481 PRK15481
transcriptional regulatory protein PtsJ; Provisional
 16-80 6.68e-04

transcriptional regulatory protein PtsJ; Provisional


Pssm-ID: 185378 [Multi-domain]  Cd Length: 431  Bit Score: 40.03  E-value: 6.68e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1262707550  16 KLVDEVLERLQEKIFSGKYEVGDRLPTEPQLMEELGVGRSTLRESIKILVHAGILEVRQGQGTRI 80
Cdd:PRK15481    5 KTANEIFDSIRQLIQAGRLRPGDSLPPVRELASELGVNRNTVAAAYKRLVTAGLAQSQGRNGTVI 69
HTH_ARSR cd00090
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ...
 45-84 1.41e-03

Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.


Pssm-ID: 238042 [Multi-domain]  Cd Length: 78  Bit Score: 36.51  E-value: 1.41e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1262707550  45 QLMEELGVGRSTLRESIKILVHAGILEVRQGQGTRIVSLN 84
Cdd:cd00090    25 ELAERLGLSQSTVSRHLKKLEEAGLVESRREGRRVYYSLT 64
PRK04984 PRK04984
fatty acid metabolism transcriptional regulator FadR;
27-85 8.33e-03

fatty acid metabolism transcriptional regulator FadR;


Pssm-ID: 179909 [Multi-domain]  Cd Length: 239  Bit Score: 36.39  E-value: 8.33e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1262707550  27 EKIFSGKYEVGDRLPTEPQLMEELGVGRSTLRESIKILVHAGILEVRQGQGTRI------VSLNI 85
Cdd:PRK04984   18 ESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGKPTKVnnfwetSGLNI 82
 
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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