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Conserved domains on  [gi|15599963|ref|NP_253457|]
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transcriptional regulator [Pseudomonas aeruginosa PAO1]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
pdhR super family cl32373
pyruvate dehydrogenase complex transcriptional repressor PdhR;
1-241 2.92e-88

pyruvate dehydrogenase complex transcriptional repressor PdhR;


The actual alignment was detected with superfamily member PRK09464:

Pssm-ID: 181879 [Multi-domain]  Cd Length: 254  Bit Score: 262.26  E-value: 2.92e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963    1 MEFGQVRQRRLSDDIVAQLEAMILEGTLKSGERLPAERVLAEQFGVSRPSLREAIQKLVAKGLLVSRQGGGNYVTESLGA 80
Cdd:PRK09464   1 MAYSKIRQPKLSDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGGTFVQSSLWQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963   81 TFSDPLLHLLEGNPEAQRDLLEFRHTLEGSCAYYAALRATSLDHQRLTEAFEALQACYARNDqvSAEEGAADARFHLAIA 160
Cdd:PRK09464  81 SFSDPLVELLSDHPESQFDLLETRHALEGIAAYYAALRGTDEDFERIRECHHAIELAQQSGD--LDAEANAVMQYQIAVT 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963  161 EASHNTVLLHTIKGLFDLLRRNVVTNIGGMYaQRTETRAQLMEQHQRLYDAIISGQAELAREVSNQHIHYVQEVLAEVQE 240
Cdd:PRK09464 159 EAAHNVVLLHLLRCMEPMLEQNVRQNFELLY-RRREMLPKVSSHRARIFEAIVAGKPEKAREASHRHLAFIEEILLDLSR 237


                 .
gi 15599963  241 E 241
Cdd:PRK09464 238 E 238
 
Name Accession Description Interval E-value
pdhR PRK09464
pyruvate dehydrogenase complex transcriptional repressor PdhR;
1-241 2.92e-88

pyruvate dehydrogenase complex transcriptional repressor PdhR;


Pssm-ID: 181879 [Multi-domain]  Cd Length: 254  Bit Score: 262.26  E-value: 2.92e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963    1 MEFGQVRQRRLSDDIVAQLEAMILEGTLKSGERLPAERVLAEQFGVSRPSLREAIQKLVAKGLLVSRQGGGNYVTESLGA 80
Cdd:PRK09464   1 MAYSKIRQPKLSDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGGTFVQSSLWQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963   81 TFSDPLLHLLEGNPEAQRDLLEFRHTLEGSCAYYAALRATSLDHQRLTEAFEALQACYARNDqvSAEEGAADARFHLAIA 160
Cdd:PRK09464  81 SFSDPLVELLSDHPESQFDLLETRHALEGIAAYYAALRGTDEDFERIRECHHAIELAQQSGD--LDAEANAVMQYQIAVT 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963  161 EASHNTVLLHTIKGLFDLLRRNVVTNIGGMYaQRTETRAQLMEQHQRLYDAIISGQAELAREVSNQHIHYVQEVLAEVQE 240
Cdd:PRK09464 159 EAAHNVVLLHLLRCMEPMLEQNVRQNFELLY-RRREMLPKVSSHRARIFEAIVAGKPEKAREASHRHLAFIEEILLDLSR 237


                 .
gi 15599963  241 E 241
Cdd:PRK09464 238 E 238
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
5-242 8.75e-71

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


Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 216.72  E-value: 8.75e-71
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963   5 QVRQRRLSDDIVAQLEAMILEGTLKSGERLPAERVLAEQFGVSRPSLREAIQKLVAKGLLVSRQGGGNYVTESLGATFSD 84
Cdd:COG2186   2 PIRRRSLAEQVAEQLRELILSGELKPGDRLPSERELAEQLGVSRTTVREALRALEALGLVEVRQGGGTFVREPSPWALLD 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963  85 PLLHLLEGNPEAQRDLLEFRHTLEGSCAYYAALRATSLDHQRLTEAFEALQACYARNDqvsaEEGAADARFHLAIAEASH 164
Cdd:COG2186  82 PLALLLALDDASLRDLLEARLALEPEAARLAAERATDEDLARLEAALAEMEAAADDGE----AFAEADLAFHRAIAEASG 157

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15599963 165 NTVLLHTIKGLFDLLRRNVVTNIggmyaQRTETRAQLMEQHQRLYDAIISGQAELAREVSNQHIHYVQEVLAEVQEEA 242
Cdd:COG2186 158 NPLLALLLESLRELLRRSVRLTL-----RSPEARERSLAEHRAILDAIRAGDPEAARAAMRAHLEAVRERLREALAER 230
FCD smart00895
This entry represents the C-terminal ligand binding domain of many members of the GntR family; ...
 99-230 2.12e-22

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


Pssm-ID: 214892 [Multi-domain]  Cd Length: 123  Bit Score: 88.96  E-value: 2.12e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963     99 DLLEFRHTLEGSCAYYAALRATSLDHQRLTEAFEALQACYARNDQVsAEEGAADARFHLAIAEASHNTVLLHTIKGLFDL 178
Cdd:smart00895   1 ELYEVRRALEPLAARLAAERATDEDLAALEALLDAMEAAAAAGDDL-EEFAELDREFHRALAEAAGNPVLLELLESLRAR 79

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 15599963    179 LRRnvvtniggMYAQRTETRAQLMEQHQRLYDAIISGQAELAREVSNQHIHY 230
Cdd:smart00895  80 LRR--------LRRLSLEAARRALDEHRAILDAIRARDAEAARAAMREHLEA 123
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 11-75 2.68e-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: 84.42  E-value: 2.68e-21
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15599963  11 LSDDIVAQLEAMILEGTLKSGERLPAERVLAEQFGVSRPSLREAIQKLVAKGLLVSRQGGGNYVT 75
Cdd:cd07377   2 LYEQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFVA 66
FCD pfam07729
FCD domain; This domain is the C-terminal ligand binding domain of many members of the GntR ...
 99-222 6.71e-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: 6.71e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963    99 DLLEFRHTLEGSCAYYAALRATSLDHQRLTEAFEALQACYARNDQVSAEEgaADARFHLAIAEASHNTVLLHTIKGLFDL 178
Cdd:pfam07729   1 ELYELRAALEPLAARLAAERATDEDLAELEALLEALEAAADAGDLEAFAE--ADREFHLALAEAAGNPVLARMLESLWDR 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 15599963   179 LRRnvvtnIGGMYAQRTETRAQLMEQHQRLYDAIISGQAELARE 222
Cdd:pfam07729  79 LRR-----LRRLLLSSPGRLRASLEEHRAILDAIRARDPEAARA 117
C_P_lyase_phnF TIGR02325
phosphonates metabolism transcriptional regulator PhnF; All members of the seed alignment for ...
 15-74 5.01e-10

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: 57.87  E-value: 5.01e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963    15 IVAQLEAMILEGTLKSGERLPAERVLAEQFGVSRPSLREAIQKLVAKGLLVSRQGGGNYV 74
Cdd:TIGR02325  13 IADKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQGRGTFV 72
 
Name Accession Description Interval E-value
pdhR PRK09464
pyruvate dehydrogenase complex transcriptional repressor PdhR;
1-241 2.92e-88

pyruvate dehydrogenase complex transcriptional repressor PdhR;


Pssm-ID: 181879 [Multi-domain]  Cd Length: 254  Bit Score: 262.26  E-value: 2.92e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963    1 MEFGQVRQRRLSDDIVAQLEAMILEGTLKSGERLPAERVLAEQFGVSRPSLREAIQKLVAKGLLVSRQGGGNYVTESLGA 80
Cdd:PRK09464   1 MAYSKIRQPKLSDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGGTFVQSSLWQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963   81 TFSDPLLHLLEGNPEAQRDLLEFRHTLEGSCAYYAALRATSLDHQRLTEAFEALQACYARNDqvSAEEGAADARFHLAIA 160
Cdd:PRK09464  81 SFSDPLVELLSDHPESQFDLLETRHALEGIAAYYAALRGTDEDFERIRECHHAIELAQQSGD--LDAEANAVMQYQIAVT 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963  161 EASHNTVLLHTIKGLFDLLRRNVVTNIGGMYaQRTETRAQLMEQHQRLYDAIISGQAELAREVSNQHIHYVQEVLAEVQE 240
Cdd:PRK09464 159 EAAHNVVLLHLLRCMEPMLEQNVRQNFELLY-RRREMLPKVSSHRARIFEAIVAGKPEKAREASHRHLAFIEEILLDLSR 237


                 .
gi 15599963  241 E 241
Cdd:PRK09464 238 E 238
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
5-242 8.75e-71

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


Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 216.72  E-value: 8.75e-71
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963   5 QVRQRRLSDDIVAQLEAMILEGTLKSGERLPAERVLAEQFGVSRPSLREAIQKLVAKGLLVSRQGGGNYVTESLGATFSD 84
Cdd:COG2186   2 PIRRRSLAEQVAEQLRELILSGELKPGDRLPSERELAEQLGVSRTTVREALRALEALGLVEVRQGGGTFVREPSPWALLD 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963  85 PLLHLLEGNPEAQRDLLEFRHTLEGSCAYYAALRATSLDHQRLTEAFEALQACYARNDqvsaEEGAADARFHLAIAEASH 164
Cdd:COG2186  82 PLALLLALDDASLRDLLEARLALEPEAARLAAERATDEDLARLEAALAEMEAAADDGE----AFAEADLAFHRAIAEASG 157

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15599963 165 NTVLLHTIKGLFDLLRRNVVTNIggmyaQRTETRAQLMEQHQRLYDAIISGQAELAREVSNQHIHYVQEVLAEVQEEA 242
Cdd:COG2186 158 NPLLALLLESLRELLRRSVRLTL-----RSPEARERSLAEHRAILDAIRAGDPEAARAAMRAHLEAVRERLREALAER 230
PRK10421 PRK10421
DNA-binding transcriptional repressor LldR; Provisional
 9-242 1.08e-70

DNA-binding transcriptional repressor LldR; Provisional


Pssm-ID: 236690 [Multi-domain]  Cd Length: 253  Bit Score: 217.33  E-value: 1.08e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963    9 RRLSDDIVAQLEAMILEGTLKSGERLPAERVLAEQFGVSRPSLREAIQKLVAKGLLVSRQGGGNYVtESLGATFSD---- 84
Cdd:PRK10421   1 RRLSDEVADRVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFI-RWRHETWSEqniv 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963   85 -PLLHLLEGNPEAQRDLLEFRHTLEGSCAYYAALRATSLDHQRLTEAFEALQAcyarndQVSAEEGAADARFHLAIAEAS 163
Cdd:PRK10421  80 qPLKTLMADDPDYSFDILEARHAIEASTAWHAAMRATPGDKEKIQLCFEATLS------EDPDLASQADVRFHLAIAEAS 153

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15599963  164 HNTVLLHTIKGLFDLLRRNVVTNIGGMYAQRTeTRAQLMEQHQRLYDAIISGQAELAREVSNQHIHYVQEVLAEVQEEA 242
Cdd:PRK10421 154 HNVVLLQTMRGFFDVLQSSVKQSRQRMYLVPP-VFSQLTEQHQAVMDAILAGDAEGARKAMMAHLSFVHTTIKRFDEDQ 231
PRK09990 PRK09990
DNA-binding transcriptional regulator GlcC; Provisional
 7-241 4.49e-48

DNA-binding transcriptional regulator GlcC; Provisional


Pssm-ID: 182186 [Multi-domain]  Cd Length: 251  Bit Score: 159.55  E-value: 4.49e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963    7 RQRRLSDDIVAQLEAMILEGTLKSGERLPAERVLAEQFGVSRPSLREAIQKLVAKGLLVSRQGGGNYVTESLGATFSDPL 86
Cdd:PRK09990   4 ERRPIADVVAERIERLIVDGVLKVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQGRGSFVARLNRVQDASPL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963   87 LHLLEGNPEAQRDLLEFRHTLEGSCAYYAALRATSLDHQRLTEAFEALQACYARNDQVSAEEGAA-DARFHLAIAEASHN 165
Cdd:PRK09990  84 MHLFSSQPRTLYDLLEVRALLEGESARLAALRGTQADFVLITRRYEEMLAAHENNKEIDPIEHARlDHAFHLAICEASHN 163

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15599963  166 TVLLHTIKGLFDLLRRNVVTNIGGMYaQRTETRAQLMEQHQRLYDAIISGQAELAREVSNQHIHYVQEVLAEVQEE 241
Cdd:PRK09990 164 PVLVHTLQSLTDLMLSSVFASVNNLY-HRPQQKKQIDRQHARLYNAVLQRLPEQAQRAARDHIRTVRDNLREIEQE 238
GntR COG1802
DNA-binding transcriptional regulator, GntR family [Transcription];
5-242 9.04e-40

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


Pssm-ID: 441407 [Multi-domain]  Cd Length: 222  Bit Score: 136.98  E-value: 9.04e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963   5 QVRQRRLSDDIVAQLEAMILEGTLKSGERLPaERVLAEQFGVSRPSLREAIQKLVAKGLLVSRQGGGNYVTEslgatFSd 84
Cdd:COG1802   6 PLRRESLAEQVYEALREAILSGELPPGERLS-EAELAERLGVSRTPVREALRRLEAEGLVEIRPNRGARVAP-----LS- 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963  85 pllhllegnPEAQRDLLEFRHTLEGSCAYYAALRATSLDHQRLTEAFEALQACYARNDQVSAEEgaADARFHLAIAEASH 164
Cdd:COG1802  79 ---------PEEIRELYEVRAALEGLAARLAAERATPADLARLRALLEELEAAAAAGDVAAYLE--LDREFHRALVEAAG 147

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15599963 165 NTVLLHTIKGLFDLLRRnvvtnIGGMYAQRTETRAQLMEQHQRLYDAIISGQAELAREVSNQHIHYVQEVLAEVQEEA 242
Cdd:COG1802 148 NPRLAELLRRLRARLRR-----YRRLSLRSPGRLEESLAEHRAILDALEAGDAEAAAAALRAHLERARERLLEALAAA 220
PRK03837 PRK03837
transcriptional regulator NanR; Provisional
 5-231 5.20e-30

transcriptional regulator NanR; Provisional


Pssm-ID: 235166 [Multi-domain]  Cd Length: 241  Bit Score: 112.42  E-value: 5.20e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963    5 QVRQRRLSDDIVAQLEAMILEGTLKSGERLPAERVLAEQFGVSRPSLREAIQKLVAKGLLVSRQGGGNYVT----ESLGA 80
Cdd:PRK03837   8 PIARKKLSEEVEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQISHGERARVSrpsaDTIIG 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963   81 TFSDPLLHLLEGNPEAQRDLLEFRHTLEGSCAYYAALRATSLDHQRLTEAFEALQACYARNDQVSaeegAADARFHLAIA 160
Cdd:PRK03837  88 QLSGMAKDFLSQSPDGLAHLKQARLFFESSLARYAAEHATDEQIALLRKALERNSQSLGDNAAFI----RSDMEFHRVIA 163

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15599963  161 EASHNTVLLHTIKGLFDLL---RRNVVTniggmyaqRTETRAQLMEQHQRLYDAIISGQAELAREVSNQHIHYV 231
Cdd:PRK03837 164 EIPGNPIFMAIHEALLDWLieaRPEVVI--------LHGHENVTLQEHIAIVDAIRAHDPDEADRALQSHLNRV 229
PRK10225 PRK10225
Uxu operon transcriptional regulator;
6-237 1.16e-25

Uxu operon transcriptional regulator;


Pssm-ID: 182318 [Multi-domain]  Cd Length: 257  Bit Score: 101.25  E-value: 1.16e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963    6 VRQRRLSDDIVAQLEAMILEGTLKSGERLPAERVLAEQFGVSRPSLREAIQKLVAKGLLVSRQGGGNYVTESLGATFSD- 84
Cdd:PRK10225   5 TSAQRPYQEVGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRRGAGIYVLDSSGSHNTDs 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963   85 PLLHLLegNPEAQRDLLEFRHTLEGSCAYYAALRATSLDHQRLTEAFEALQACYARNDQVSAEEGaaDARFHLAIAEASH 164
Cdd:PRK10225  85 PDANVC--NDAGPFELLQARQLLESNIAEFAALQATREDIVKMRQALQLEERELASSAPGSSESG--DMQFHLAIAEATH 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15599963  165 NTVLLHTIKGLFDLLRRNVVTNIGGMYAQRTETRAQLMEQHQRLYDAIISGQAELAREVSNQHIHYVQEVLAE 237
Cdd:PRK10225 161 NSMLVELFRQSWQWRENNPMWIQLHSHLDDSLYRKEWLGDHKQILAALIKKDARAAKLAMWQHLENVKQRLLE 233
FCD smart00895
This entry represents the C-terminal ligand binding domain of many members of the GntR family; ...
 99-230 2.12e-22

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


Pssm-ID: 214892 [Multi-domain]  Cd Length: 123  Bit Score: 88.96  E-value: 2.12e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963     99 DLLEFRHTLEGSCAYYAALRATSLDHQRLTEAFEALQACYARNDQVsAEEGAADARFHLAIAEASHNTVLLHTIKGLFDL 178
Cdd:smart00895   1 ELYEVRRALEPLAARLAAERATDEDLAALEALLDAMEAAAAAGDDL-EEFAELDREFHRALAEAAGNPVLLELLESLRAR 79

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 15599963    179 LRRnvvtniggMYAQRTETRAQLMEQHQRLYDAIISGQAELAREVSNQHIHY 230
Cdd:smart00895  80 LRR--------LRRLSLEAARRALDEHRAILDAIRARDAEAARAAMREHLEA 123
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 11-75 2.68e-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: 84.42  E-value: 2.68e-21
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15599963  11 LSDDIVAQLEAMILEGTLKSGERLPAERVLAEQFGVSRPSLREAIQKLVAKGLLVSRQGGGNYVT 75
Cdd:cd07377   2 LYEQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFVA 66
FCD pfam07729
FCD domain; This domain is the C-terminal ligand binding domain of many members of the GntR ...
 99-222 6.71e-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: 6.71e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963    99 DLLEFRHTLEGSCAYYAALRATSLDHQRLTEAFEALQACYARNDQVSAEEgaADARFHLAIAEASHNTVLLHTIKGLFDL 178
Cdd:pfam07729   1 ELYELRAALEPLAARLAAERATDEDLAELEALLEALEAAADAGDLEAFAE--ADREFHLALAEAAGNPVLARMLESLWDR 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 15599963   179 LRRnvvtnIGGMYAQRTETRAQLMEQHQRLYDAIISGQAELARE 222
Cdd:pfam07729  79 LRR-----LRRLLLSSPGRLRASLEEHRAILDAIRARDPEAARA 117
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
 11-74 1.16e-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: 79.97  E-value: 1.16e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15599963    11 LSDDIVAQLEAMILEGTLKSGERLPAERVLAEQFGVSRPSLREAIQKLVAKGLLVSRQGGGNYV 74
Cdd:pfam00392   1 LYEQVYARLREDILSGRLRPGDKLPSERELAAEFGVSRTTVREALRRLEAEGLVERRQGRGTFV 64
HTH_GNTR smart00345
helix_turn_helix gluconate operon transcriptional repressor;
15-74 2.43e-19

helix_turn_helix gluconate operon transcriptional repressor;


Pssm-ID: 197669 [Multi-domain]  Cd Length: 60  Bit Score: 79.16  E-value: 2.43e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963     15 IVAQLEAMILEGTLKSGERLPAERVLAEQFGVSRPSLREAIQKLVAKGLLVSRQGGGNYV 74
Cdd:smart00345   1 VAERLREDIVSGELRPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGSGTFV 60
MngR COG2188
DNA-binding transcriptional regulator, GntR family [Transcription];
15-76 1.18e-18

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


Pssm-ID: 441791 [Multi-domain]  Cd Length: 238  Bit Score: 82.22  E-value: 1.18e-18
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15599963  15 IVAQLEAMILEGTLKSGERLPAERVLAEQFGVSRPSLREAIQKLVAKGLLVSRQGGGNYVTE 76
Cdd:COG2188  10 IADALRERIESGELPPGDRLPSERELAEEFGVSRMTVRKALDELVEEGLLERRQGRGTFVAE 71
ARO8 COG1167
DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain ...
 15-85 1.53e-15

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: 75.64  E-value: 1.53e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15599963  15 IVAQLEAMILEGTLKSGERLPAERVLAEQFGVSRPSLREAIQKLVAKGLLVSRQGGGNYVTESLGATFSDP 85
Cdd:COG1167  17 LADALREAILSGRLPPGDRLPSSRELAAQLGVSRSTVVRAYEELEAEGLIESRPGSGTFVAARLPAPAPAP 87
PRK11523 PRK11523
transcriptional regulator ExuR;
9-168 8.06e-14

transcriptional regulator ExuR;


Pssm-ID: 183176 [Multi-domain]  Cd Length: 253  Bit Score: 69.10  E-value: 8.06e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963    9 RRLSDDIVAQLEAMILEGTLKSGERLPAERVLAEQFGVSRPSLREAIQKLVAKGLLVSRQGGGNYVTESLGA--TFSDPL 86
Cdd:PRK11523   7 RRLYQQLAAELKERIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRKGSGIHVVSNQPRhqQAADNN 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963   87 LHLLEGNPeaqRDLLEFRHTLEGSCAYYAALRATSLDHQRLTEAFEalqacYARNDQvSAEEGAADARFHLAIAEASHNT 166
Cdd:PRK11523  87 MEFANYGP---FELLQARQLIESNIAEFAATQVTKQDIMKLMAIQE-----QARGED-CFRDSEWDLQFHVQVALATQNS 157


                 ..
gi 15599963  167 VL 168
Cdd:PRK11523 158 AL 159
PRK11402 PRK11402
transcriptional regulator PhoB;
3-74 3.17e-10

transcriptional regulator PhoB;


Pssm-ID: 183118 [Multi-domain]  Cd Length: 241  Bit Score: 58.69  E-value: 3.17e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15599963    3 FGQVRQRrLSDDIVaqleamilEGTLKSGERLPAERVLAEQFGVSRPSLREAIQKLVAKGLLVSRQGGGNYV 74
Cdd:PRK11402  11 YATVRQR-LLDDIA--------QGVYQAGQQIPTENELCTQYNVSRITIRKAISDLVADGVLIRWQGKGTFV 73
C_P_lyase_phnF TIGR02325
phosphonates metabolism transcriptional regulator PhnF; All members of the seed alignment for ...
 15-74 5.01e-10

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: 57.87  E-value: 5.01e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963    15 IVAQLEAMILEGTLKSGERLPAERVLAEQFGVSRPSLREAIQKLVAKGLLVSRQGGGNYV 74
Cdd:TIGR02325  13 IADKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQGRGTFV 72
PRK09764 PRK09764
GntR family transcriptional regulator;
7-76 1.27e-09

GntR family transcriptional regulator;


Pssm-ID: 182065 [Multi-domain]  Cd Length: 240  Bit Score: 56.76  E-value: 1.27e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963    7 RQRRLSDDIVAQleamILEGTLKSGERLPAERVLAEQFGVSRPSLREAIQKLVAKGLLVSRQGGGNYVTE 76
Cdd:PRK09764   6 LYRQIADRIREQ----IARGELKPGDALPTESALQTEFGVSRVTVRQALRQLVEQQILESIQGSGTYVKE 71
PRK15481 PRK15481
transcriptional regulatory protein PtsJ; Provisional
 14-98 7.56e-08

transcriptional regulatory protein PtsJ; Provisional


Pssm-ID: 185378 [Multi-domain]  Cd Length: 431  Bit Score: 52.36  E-value: 7.56e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963   14 DIVAQLEAMILEGTLKSGERLPAERVLAEQFGVSRPSLREAIQKLVAKGLLVSRQGGGNYVTESL------GATFSDPLL 87
Cdd:PRK15481   9 EIFDSIRQLIQAGRLRPGDSLPPVRELASELGVNRNTVAAAYKRLVTAGLAQSQGRNGTVIRGSPspvaleGGDPGTPLH 88

                         90
                 ....*....|.
gi 15599963   88 HLLEGNPEAQR 98
Cdd:PRK15481  89 DLAGGNPDPQR 99
PRK10079 PRK10079
phosphonate metabolism transcriptional regulator PhnF; Provisional
 15-74 3.35e-07

phosphonate metabolism transcriptional regulator PhnF; Provisional


Pssm-ID: 182227 [Multi-domain]  Cd Length: 241  Bit Score: 49.77  E-value: 3.35e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963   15 IVAQLEAMiLEGTLKSGERLPAERVLAEQFGVSRPSLREAIQKLVAKGLLVSRQGGGNYV 74
Cdd:PRK10079  17 IAAKLEQE-LRQHYRCGDYLPAEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQGVGVLV 75
PRK14999 PRK14999
histidine utilization repressor; Provisional
 23-79 3.20e-05

histidine utilization repressor; Provisional


Pssm-ID: 184961 [Multi-domain]  Cd Length: 241  Bit Score: 44.15  E-value: 3.20e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 15599963   23 ILEGTLKSGERLPAERVLAEQFGVSRPSLREAIQKLVAKGLLVSRQGGGNYVTESLG 79
Cdd:PRK14999  25 IAGGVWQPHDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVRLQGVGTFVAEPKG 81
PRK04984 PRK04984
fatty acid metabolism transcriptional regulator FadR;
23-64 1.04e-04

fatty acid metabolism transcriptional regulator FadR;


Pssm-ID: 179909 [Multi-domain]  Cd Length: 239  Bit Score: 42.55  E-value: 1.04e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 15599963   23 ILEGTLKSGERLPAERVLAEQFGVSRPSLREAIQKLVAKGLL 64
Cdd:PRK04984  20 IWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWL 61
PRK11534 PRK11534
DNA-binding transcriptional regulator CsiR; Provisional
 18-236 8.61e-04

DNA-binding transcriptional regulator CsiR; Provisional


Pssm-ID: 183181 [Multi-domain]  Cd Length: 224  Bit Score: 39.49  E-value: 8.61e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963   18 QLEAMILEGTLKSGERLPAErVLAEQFGVSRPSLREAIQKLVAKGLL-VSRQGGGNYVTESLgatfsDPLLHLLEGNPEA 96
Cdd:PRK11534  15 WLKNDIIRGNFQPDEKLRMS-LLTSRYALGVGPLREALSQLVAERLVtVVNQKGYRVASMSE-----QELLDIFDARANM 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963   97 QRDLLEFRhTLEGSCAYYAALRATSldhqrltEAFEALQACYARNDQVSAEEGAADArFHLAIAEASHNTVLLHTIKGLF 176
Cdd:PRK11534  89 EAMLVSLA-IARGGDEWEADVLAKA-------HLLSKLEACDASEKMLDEWDLRHQA-FHTAIVAGCGSHYLLQMRERLF 159

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15599963  177 DLLRRNVVtniggMYAQRTETRAQLME----QHQRLYDAIISGQAELAREVSNQH----IHYVQEVLA 236
Cdd:PRK11534 160 DLAARYRF-----IWLRRTVLSVEMLEdkhdQHQTLTAAILARDTARASELMRQHlltpIPIIQQAMA 222
MntR COG1321
Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];
40-77 1.27e-03

Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];


Pssm-ID: 440932 [Multi-domain]  Cd Length: 135  Bit Score: 37.88  E-value: 1.27e-03
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 15599963  40 LAEQFGVSRPSLREAIQKLVAKGLLVSRQGGGNYVTES 77
Cdd:COG1321  30 IAERLGVSPPSVTEMLKKLEEKGLVEYEPYGGITLTEE 67
COG3355 COG3355
Predicted transcriptional regulator [Transcription];
18-73 5.51e-03

Predicted transcriptional regulator [Transcription];


Pssm-ID: 442583 [Multi-domain]  Cd Length: 131  Bit Score: 36.10  E-value: 5.51e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599963  18 QLEAMILEGTLKSGERLPAERvLAEQFGVSRPSLREAIQKLVAKGLLVSRQ----GGGNY 73
Cdd:COG3355  27 ETDAEVYLILLENGEPLTVEE-LAEALDRSRSTVYRSLQKLLEAGLVEREKrnleGGGYP 85
 
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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