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Conserved domains on  [gi|742398502|ref|WP_038877627|]
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MULTISPECIES: phosphonate utilization transcriptional regulator PhnR [Serratia]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
phnR super family cl31335
phosphonate utilization transcriptional regulator PhnR; This family of proteins are members of ...
 9-238 4.57e-133

phosphonate utilization transcriptional regulator PhnR; This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii. [Regulatory functions, DNA interactions]


The actual alignment was detected with superfamily member TIGR03337:

Pssm-ID: 132380 [Multi-domain]  Cd Length: 231  Bit Score: 374.16  E-value: 4.57e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502    9 PHYLQIKDQLQARITRGALQAGDKLPSERELCAIFSTTRVTIRESLAQLEATGAIYRADRRGWFVTPERLWLDPTQNTNF 88
Cdd:TIGR03337   1 PQYLYIKDHLSYQIRAGALLPGDKLPSERDLGERFNTTRVTIREALQQLEAEGLIYREDRRGWFVSPPRLRYNPTRTQNF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502   89 HRLCQEQGRTPRTALLSGEKTTVPLDVMQPLALEPFDQVYLLRRVRYADGRAICYCENHCLPQRVPALLSHDLNGSLTEV 168
Cdd:TIGR03337  81 HEYVREQGREPKTELIGVTVTPAPARMAELLQLQPFDRLFLLQRLRYADGRPVCYCENYILPARVPGLLKEDLNGSLTEI 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502  169 YQQHYALIYSNMHLSFYPTALPYRAANALGAMVGLPALLLRRLNYDQHGRILDFDIEYWRHDSLRIEVDT 238
Cdd:TIGR03337 161 YRNHYGLVYHSMNLRFKPTALLEEAAQALGATAGLPALHLERTNYDQHGRVLDLDIEYWRHDALTIEVDT 230
 
Name Accession Description Interval E-value
phnR TIGR03337
phosphonate utilization transcriptional regulator PhnR; This family of proteins are members of ...
 9-238 4.57e-133

phosphonate utilization transcriptional regulator PhnR; This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii. [Regulatory functions, DNA interactions]


Pssm-ID: 132380 [Multi-domain]  Cd Length: 231  Bit Score: 374.16  E-value: 4.57e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502    9 PHYLQIKDQLQARITRGALQAGDKLPSERELCAIFSTTRVTIRESLAQLEATGAIYRADRRGWFVTPERLWLDPTQNTNF 88
Cdd:TIGR03337   1 PQYLYIKDHLSYQIRAGALLPGDKLPSERDLGERFNTTRVTIREALQQLEAEGLIYREDRRGWFVSPPRLRYNPTRTQNF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502   89 HRLCQEQGRTPRTALLSGEKTTVPLDVMQPLALEPFDQVYLLRRVRYADGRAICYCENHCLPQRVPALLSHDLNGSLTEV 168
Cdd:TIGR03337  81 HEYVREQGREPKTELIGVTVTPAPARMAELLQLQPFDRLFLLQRLRYADGRPVCYCENYILPARVPGLLKEDLNGSLTEI 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502  169 YQQHYALIYSNMHLSFYPTALPYRAANALGAMVGLPALLLRRLNYDQHGRILDFDIEYWRHDSLRIEVDT 238
Cdd:TIGR03337 161 YRNHYGLVYHSMNLRFKPTALLEEAAQALGATAGLPALHLERTNYDQHGRVLDLDIEYWRHDALTIEVDT 230
MngR COG2188
DNA-binding transcriptional regulator, GntR family [Transcription];
5-237 2.26e-66

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


Pssm-ID: 441791 [Multi-domain]  Cd Length: 238  Bit Score: 205.10  E-value: 2.26e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502   5 QGDMPHYLQIKDQLQARITRGALQAGDKLPSERELCAIFSTTRVTIRESLAQLEATGAIYRADRRGWFVTPERLWLDPTQ 84
Cdd:COG2188    1 SSPVPLYLQIADALRERIESGELPPGDRLPSERELAEEFGVSRMTVRKALDELVEEGLLERRQGRGTFVAEPKIEYPLSR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502  85 NTNFHRLCQEQGRTPRTALLSGEKTTVPLDVMQPLALEPFDQVYLLRRVRYADGRAICYCENHCLPQRVPALLSHDL-NG 163
Cdd:COG2188   81 LTSFTEELRARGREPSTRVLSAERVPADEEVAEALGLPPGAPVLRIERLRLADGEPVALETSYLPAALFPGLLEEDLeTG 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 742398502 164 SLTEVYQQHYALIYSNMHLSFYPTALPYRAANALGAMVGLPALLLRRLNYDQHGRILDFDIEYWRHDSLRIEVD 237
Cdd:COG2188  161 SLYELLEERYGLRITRAEQRIEAVLADAEEAELLGVPPGAPVLVIERVTYDADGRPVEYSRSYYRGDRYRFVVE 234
UTRA pfam07702
UTRA domain; The UbiC transcription regulator-associated (UTRA) domain is a conserved ...
 94-233 2.22e-32

UTRA domain; The UbiC transcription regulator-associated (UTRA) domain is a conserved ligand-binding domain that has a similar fold to pfam04345. It is believed to modulate activity of bacterial transcription factors in response to binding small molecules sugar phosphates and urocanate, Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 429607 [Multi-domain]  Cd Length: 141  Bit Score: 115.00  E-value: 2.22e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502   94 EQGRTPRTALLSGEKTTVPLDVMQPLALEPFDQVYLLRRVRYADGRAICYCENHCLPQRVPALLSHDL-NGSLTEVYQQH 172
Cdd:pfam07702   1 AQGREPKTEVLSLEEVPASAEIAEALGLPPGEPVYRIERLRYADGEPVALEEDYLPAELVPDLLEEDLeEGSLYDYLEER 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 742398502  173 YALIYSNMHLSFYPTALPYRAANALGAMVGLPALLLRRLNYDQHGRILDFDIEYWRHDSLR 233
Cdd:pfam07702  81 YGLPITRAEQTIEAVLADAEEAELLGISPGAPVLLIERVTYDQDGRPVEYSRSYYRGDRYR 141
UTRA smart00866
The UbiC transcription regulator-associated (UTRA) domain is a conserved ligand-binding domain; ...
 94-230 6.13e-29

The UbiC transcription regulator-associated (UTRA) domain is a conserved ligand-binding domain; It has a similar fold to HutC/FarR-like bacterial transcription factors of the GntR family. It is believed to modulate activity of bacterial transcription factors in response to binding small molecules.


Pssm-ID: 214869 [Multi-domain]  Cd Length: 143  Bit Score: 106.22  E-value: 6.13e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502    94 EQGRTPRTALLSGEKTTVPLDVMQPLALEPFDQVYLLRRVRYADGRAICYCENHCLPQRVPALLSHDLNGSLTEVYQQHY 173
Cdd:smart00866   1 AQGRKPTTKVLSFERVPADEELAEALGLPPGDPVYRIERLRLADGEPVALETTYLPAALFPGLLEEDLSGSLYEYLEERL 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502   174 AL---IYSNMHLSFYPTALPYRAANALGAMVGLPALLLRRLNYDQHGRILDFDIEYWRHD 230
Cdd:smart00866  81 GLkivRSTRAEQTITAVLADEEEAELLGLPPGAPLLVVERVTYDDDGRPVEYSRSYYRGD 140
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 11-74 3.08e-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: 86.35  E-value: 3.08e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 742398502  11 YLQIKDQLQARITRGALQAGDKLPSERELCAIFSTTRVTIRESLAQLEATGAIYRADRRGWFVT 74
Cdd:cd07377    3 YEQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFVA 66
PRK11402 PRK11402
transcriptional regulator PhoB;
9-173 4.54e-20

transcriptional regulator PhoB;


Pssm-ID: 183118 [Multi-domain]  Cd Length: 241  Bit Score: 85.66  E-value: 4.54e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502   9 PHYLQIKDQLQARITRGALQAGDKLPSERELCAIFSTTRVTIRESLAQLEATGAIYRADRRGWFVTPERLWLDPTQNTNF 88
Cdd:PRK11402   9 LLYATVRQRLLDDIAQGVYQAGQQIPTENELCTQYNVSRITIRKAISDLVADGVLIRWQGKGTFVQSQKVENALLTVSGF 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502  89 HRLCQEQGRTPRTALLSGEKtTVPLDVMQPLALEPFDQVYLLRRVRYADGRAICYCENHCLPQRVPALLSHDLNG-SLTE 167
Cdd:PRK11402  89 TDFGVSQGKATKEKVIEQER-VSAAPFCEKLNIPGNSEVFHLCRVMYLDKEPLFIDSSWIPLSRYPDFDEIYVEGsSTYQ 167


                 ....*.
gi 742398502 168 VYQQHY 173
Cdd:PRK11402 168 LFQERF 173
 
Name Accession Description Interval E-value
phnR TIGR03337
phosphonate utilization transcriptional regulator PhnR; This family of proteins are members of ...
 9-238 4.57e-133

phosphonate utilization transcriptional regulator PhnR; This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii. [Regulatory functions, DNA interactions]


Pssm-ID: 132380 [Multi-domain]  Cd Length: 231  Bit Score: 374.16  E-value: 4.57e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502    9 PHYLQIKDQLQARITRGALQAGDKLPSERELCAIFSTTRVTIRESLAQLEATGAIYRADRRGWFVTPERLWLDPTQNTNF 88
Cdd:TIGR03337   1 PQYLYIKDHLSYQIRAGALLPGDKLPSERDLGERFNTTRVTIREALQQLEAEGLIYREDRRGWFVSPPRLRYNPTRTQNF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502   89 HRLCQEQGRTPRTALLSGEKTTVPLDVMQPLALEPFDQVYLLRRVRYADGRAICYCENHCLPQRVPALLSHDLNGSLTEV 168
Cdd:TIGR03337  81 HEYVREQGREPKTELIGVTVTPAPARMAELLQLQPFDRLFLLQRLRYADGRPVCYCENYILPARVPGLLKEDLNGSLTEI 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502  169 YQQHYALIYSNMHLSFYPTALPYRAANALGAMVGLPALLLRRLNYDQHGRILDFDIEYWRHDSLRIEVDT 238
Cdd:TIGR03337 161 YRNHYGLVYHSMNLRFKPTALLEEAAQALGATAGLPALHLERTNYDQHGRVLDLDIEYWRHDALTIEVDT 230
MngR COG2188
DNA-binding transcriptional regulator, GntR family [Transcription];
5-237 2.26e-66

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


Pssm-ID: 441791 [Multi-domain]  Cd Length: 238  Bit Score: 205.10  E-value: 2.26e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502   5 QGDMPHYLQIKDQLQARITRGALQAGDKLPSERELCAIFSTTRVTIRESLAQLEATGAIYRADRRGWFVTPERLWLDPTQ 84
Cdd:COG2188    1 SSPVPLYLQIADALRERIESGELPPGDRLPSERELAEEFGVSRMTVRKALDELVEEGLLERRQGRGTFVAEPKIEYPLSR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502  85 NTNFHRLCQEQGRTPRTALLSGEKTTVPLDVMQPLALEPFDQVYLLRRVRYADGRAICYCENHCLPQRVPALLSHDL-NG 163
Cdd:COG2188   81 LTSFTEELRARGREPSTRVLSAERVPADEEVAEALGLPPGAPVLRIERLRLADGEPVALETSYLPAALFPGLLEEDLeTG 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 742398502 164 SLTEVYQQHYALIYSNMHLSFYPTALPYRAANALGAMVGLPALLLRRLNYDQHGRILDFDIEYWRHDSLRIEVD 237
Cdd:COG2188  161 SLYELLEERYGLRITRAEQRIEAVLADAEEAELLGVPPGAPVLVIERVTYDADGRPVEYSRSYYRGDRYRFVVE 234
UTRA pfam07702
UTRA domain; The UbiC transcription regulator-associated (UTRA) domain is a conserved ...
 94-233 2.22e-32

UTRA domain; The UbiC transcription regulator-associated (UTRA) domain is a conserved ligand-binding domain that has a similar fold to pfam04345. It is believed to modulate activity of bacterial transcription factors in response to binding small molecules sugar phosphates and urocanate, Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 429607 [Multi-domain]  Cd Length: 141  Bit Score: 115.00  E-value: 2.22e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502   94 EQGRTPRTALLSGEKTTVPLDVMQPLALEPFDQVYLLRRVRYADGRAICYCENHCLPQRVPALLSHDL-NGSLTEVYQQH 172
Cdd:pfam07702   1 AQGREPKTEVLSLEEVPASAEIAEALGLPPGEPVYRIERLRYADGEPVALEEDYLPAELVPDLLEEDLeEGSLYDYLEER 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 742398502  173 YALIYSNMHLSFYPTALPYRAANALGAMVGLPALLLRRLNYDQHGRILDFDIEYWRHDSLR 233
Cdd:pfam07702  81 YGLPITRAEQTIEAVLADAEEAELLGISPGAPVLLIERVTYDQDGRPVEYSRSYYRGDRYR 141
UTRA smart00866
The UbiC transcription regulator-associated (UTRA) domain is a conserved ligand-binding domain; ...
 94-230 6.13e-29

The UbiC transcription regulator-associated (UTRA) domain is a conserved ligand-binding domain; It has a similar fold to HutC/FarR-like bacterial transcription factors of the GntR family. It is believed to modulate activity of bacterial transcription factors in response to binding small molecules.


Pssm-ID: 214869 [Multi-domain]  Cd Length: 143  Bit Score: 106.22  E-value: 6.13e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502    94 EQGRTPRTALLSGEKTTVPLDVMQPLALEPFDQVYLLRRVRYADGRAICYCENHCLPQRVPALLSHDLNGSLTEVYQQHY 173
Cdd:smart00866   1 AQGRKPTTKVLSFERVPADEELAEALGLPPGDPVYRIERLRLADGEPVALETTYLPAALFPGLLEEDLSGSLYEYLEERL 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502   174 AL---IYSNMHLSFYPTALPYRAANALGAMVGLPALLLRRLNYDQHGRILDFDIEYWRHD 230
Cdd:smart00866  81 GLkivRSTRAEQTITAVLADEEEAELLGLPPGAPLLVVERVTYDDDGRPVEYSRSYYRGD 140
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 11-74 3.08e-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: 86.35  E-value: 3.08e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 742398502  11 YLQIKDQLQARITRGALQAGDKLPSERELCAIFSTTRVTIRESLAQLEATGAIYRADRRGWFVT 74
Cdd:cd07377    3 YEQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFVA 66
PRK11402 PRK11402
transcriptional regulator PhoB;
9-173 4.54e-20

transcriptional regulator PhoB;


Pssm-ID: 183118 [Multi-domain]  Cd Length: 241  Bit Score: 85.66  E-value: 4.54e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502   9 PHYLQIKDQLQARITRGALQAGDKLPSERELCAIFSTTRVTIRESLAQLEATGAIYRADRRGWFVTPERLWLDPTQNTNF 88
Cdd:PRK11402   9 LLYATVRQRLLDDIAQGVYQAGQQIPTENELCTQYNVSRITIRKAISDLVADGVLIRWQGKGTFVQSQKVENALLTVSGF 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502  89 HRLCQEQGRTPRTALLSGEKtTVPLDVMQPLALEPFDQVYLLRRVRYADGRAICYCENHCLPQRVPALLSHDLNG-SLTE 167
Cdd:PRK11402  89 TDFGVSQGKATKEKVIEQER-VSAAPFCEKLNIPGNSEVFHLCRVMYLDKEPLFIDSSWIPLSRYPDFDEIYVEGsSTYQ 167


                 ....*.
gi 742398502 168 VYQQHY 173
Cdd:PRK11402 168 LFQERF 173
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
 11-73 5.05e-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: 75.34  E-value: 5.05e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 742398502   11 YLQIKDQLQARITRGALQAGDKLPSERELCAIFSTTRVTIRESLAQLEATGAIYRADRRGWFV 73
Cdd:pfam00392   2 YEQVYARLREDILSGRLRPGDKLPSERELAAEFGVSRTTVREALRRLEAEGLVERRQGRGTFV 64
C_P_lyase_phnF TIGR02325
phosphonates metabolism transcriptional regulator PhnF; All members of the seed alignment for ...
 11-235 1.24e-17

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: 79.06  E-value: 1.24e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502   11 YLQIKDQLQARITRGALQAGDKLPSERELCAIFSTTRVTIRESLAQLEATGAIYRADRRGWFVTPERLWLDPTQNTNFHR 90
Cdd:TIGR02325  10 WRQIADKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQGRGTFVAARRIDYPLSARTRFSQ 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502   91 LCQEQGRTPRTALLSGEKTTVPLDVMQPLALEPFDQVYLLRRVRYADGRAICYCENHCLPQRVPALLS-HDLNGSLTEVY 169
Cdd:TIGR02325  90 NLADQGREPTGELLLSDLEPASAELADALGLTVGAPLVRLETLRKADGRPLCRATTWFPAARFPGIGQaYAASGSITDAL 169

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 742398502  170 QQHYALIYSNMHlsfypTALPYRAANA-----LGAMVGLPALLLRRLNYDQHGRILDFDIEYWRHDslRIE 235
Cdd:TIGR02325 170 REQGVADYRRSS-----TRISARHADAkdcarLELPPGRPLLVVQALNHDGEGRPVQYSVSRFRAD--RVE 233
HTH_GNTR smart00345
helix_turn_helix gluconate operon transcriptional repressor;
14-73 2.14e-17

helix_turn_helix gluconate operon transcriptional repressor;


Pssm-ID: 197669 [Multi-domain]  Cd Length: 60  Bit Score: 73.38  E-value: 2.14e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502    14 IKDQLQARITRGALQAGDKLPSERELCAIFSTTRVTIRESLAQLEATGAIYRADRRGWFV 73
Cdd:smart00345   1 VAERLREDIVSGELRPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGSGTFV 60
PRK09764 PRK09764
GntR family transcriptional regulator;
6-233 2.20e-16

GntR family transcriptional regulator;


Pssm-ID: 182065 [Multi-domain]  Cd Length: 240  Bit Score: 75.63  E-value: 2.20e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502   6 GDMPHYLQIKDQLQARITRGALQAGDKLPSERELCAIFSTTRVTIRESLAQLEATGAIYRADRRGWFVTPERLWLDPTQN 85
Cdd:PRK09764   2 GHKPLYRQIADRIREQIARGELKPGDALPTESALQTEFGVSRVTVRQALRQLVEQQILESIQGSGTYVKEERVNYDIFQL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502  86 TNFHRLCQEQGRTPRTALLSGEKTTVPLDVMQPLALEPFDQVYLLRRVRYADGRAICYCENHclpqrVPALLSHDLNGSL 165
Cdd:PRK09764  82 TSFDEKLSDRHVDTHSEVLIFEVIPADDFLQQQLQITAQDRVWHVKRVRYRKQKPMALEETW-----MPLALFPDLTWQV 156

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 742398502 166 TEVYQQHY-----ALIYSNMHLSFYPTALPYRAANALGAMVGLPALLLRRLNYDQHGRILDFDIEYWRHDSLR 233
Cdd:PRK09764 157 MENSKYHFieevkKMVIDRSEQEIIPLMPTEEMSRLLNISQTKPILEKVSRGYLVDGRVFEYSRNAFNTDDYK 229
ARO8 COG1167
DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain ...
 3-77 1.94e-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: 74.87  E-value: 1.94e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 742398502   3 EHQGDMPHYLQIKDQLQARITRGALQAGDKLPSERELCAIFSTTRVTIRESLAQLEATGAIYRADRRGWFVTPER 77
Cdd:COG1167    6 DRDSSGPLYLQLADALREAILSGRLPPGDRLPSSRELAAQLGVSRSTVVRAYEELEAEGLIESRPGSGTFVAARL 80
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
11-79 8.43e-15

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


Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 71.12  E-value: 8.43e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 742398502  11 YLQIKDQLQARITRGALQAGDKLPSERELCAIFSTTRVTIRESLAQLEATGAIYRADRRGWFVTPERLW 79
Cdd:COG2186    9 AEQVAEQLRELILSGELKPGDRLPSERELAEQLGVSRTTVREALRALEALGLVEVRQGGGTFVREPSPW 77
YhcF COG1725
DNA-binding transcriptional regulator YhcF, GntR family [Transcription];
7-75 1.47e-14

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


Pssm-ID: 441331 [Multi-domain]  Cd Length: 114  Bit Score: 67.51  E-value: 1.47e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 742398502   7 DMPHYLQIKDQLQARITRGALQAGDKLPSERELCAIFSTTRVTIRESLAQLEATGAIYRADRRGWFVTP 75
Cdd:COG1725    8 GVPIYEQIADQIKEAIASGELKPGDRLPSVRELAAELGVNPNTVAKAYRELEDEGLIETRRGKGTFVAE 76
GntR COG1802
DNA-binding transcriptional regulator, GntR family [Transcription];
13-75 6.51e-10

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


Pssm-ID: 441407 [Multi-domain]  Cd Length: 222  Bit Score: 57.24  E-value: 6.51e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 742398502  13 QIKDQLQARITRGALQAGDKLpSERELCAIFSTTRVTIRESLAQLEATGAIYRADRRGWFVTP 75
Cdd:COG1802   15 QVYEALREAILSGELPPGERL-SEAELAERLGVSRTPVREALRRLEAEGLVEIRPNRGARVAP 76
pdhR PRK09464
pyruvate dehydrogenase complex transcriptional repressor PdhR;
14-79 4.34e-09

pyruvate dehydrogenase complex transcriptional repressor PdhR;


Pssm-ID: 181879 [Multi-domain]  Cd Length: 254  Bit Score: 55.41  E-value: 4.34e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 742398502  14 IKDQLQARITRGALQAGDKLPSERELCAIFSTTRVTIRESLAQLEATGAIYRADRRGWFVTpERLW 79
Cdd:PRK09464  15 IEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGGTFVQ-SSLW 79
PRK03837 PRK03837
transcriptional regulator NanR; Provisional
 16-63 6.33e-09

transcriptional regulator NanR; Provisional


Pssm-ID: 235166 [Multi-domain]  Cd Length: 241  Bit Score: 54.64  E-value: 6.33e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 742398502  16 DQLQARITRGALQAGDKLPSERELCAIFSTTRVTIRESLAQLEATGAI 63
Cdd:PRK03837  20 ERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLV 67
PRK09990 PRK09990
DNA-binding transcriptional regulator GlcC; Provisional
 13-107 4.47e-07

DNA-binding transcriptional regulator GlcC; Provisional


Pssm-ID: 182186 [Multi-domain]  Cd Length: 251  Bit Score: 49.38  E-value: 4.47e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502  13 QIKDQLQARITR----GALQAGDKLPSERELCAIFSTTRVTIRESLAQLEATGAIYRADRRGWFVTpeRLWLDPTQNTNF 88
Cdd:PRK09990   7 PIADVVAERIERlivdGVLKVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQGRGSFVA--RLNRVQDASPLM 84

                         90       100
                 ....*....|....*....|....*..
gi 742398502  89 HRLcqeqGRTPRT--------ALLSGE 107
Cdd:PRK09990  85 HLF----SSQPRTlydllevrALLEGE 107
PRK10421 PRK10421
DNA-binding transcriptional repressor LldR; Provisional
 13-70 5.41e-07

DNA-binding transcriptional repressor LldR; Provisional


Pssm-ID: 236690 [Multi-domain]  Cd Length: 253  Bit Score: 49.00  E-value: 5.41e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 742398502  13 QIKDQLQARITRGALQAGDKLPSERELCAIFSTTRVTIRESLAQLEATGAIyrADRRG 70
Cdd:PRK10421   6 EVADRVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVL--LSRRG 61
PRK14999 PRK14999
histidine utilization repressor; Provisional
 9-73 1.35e-05

histidine utilization repressor; Provisional


Pssm-ID: 184961 [Multi-domain]  Cd Length: 241  Bit Score: 44.92  E-value: 1.35e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 742398502   9 PHYLQIKDQLQARITRGALQAGDKLPSERELCAIFSTTRVTIRESLAQLEATGAIYRADRRGWFV 73
Cdd:PRK14999  12 PFYETVKQDICKKIAGGVWQPHDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVRLQGVGTFV 76
PRK10079 PRK10079
phosphonate metabolism transcriptional regulator PhnF; Provisional
 11-172 5.81e-05

phosphonate metabolism transcriptional regulator PhnF; Provisional


Pssm-ID: 182227 [Multi-domain]  Cd Length: 241  Bit Score: 42.84  E-value: 5.81e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502  11 YLQIKDQLQARItRGALQAGDKLPSERELCAIFSTTRVTIRESLAQLEATGAIYRADRRGWFVTPERLWLDPTQNTNFHR 90
Cdd:PRK10079  14 YQEIAAKLEQEL-RQHYRCGDYLPAEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQGVGVLVLMRPYDYPLNAQARFSQ 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502  91 LCQEQGRTPRTALLSGEKTTVPLDVMQPLALEPFDQVYLLRRVRYADGRAICYCeNHCLPQ-RVPALLSHDLNGSLTEVY 169
Cdd:PRK10079  93 NLLDQGSHPTSEKLLSVLRPASGHVADALGITEGENVIHLRTLRRVNGVALCLI-DHYFADlTWWPTLQRFDSGSLHDFL 171


                 ...
gi 742398502 170 QQH 172
Cdd:PRK10079 172 REQ 174
PRK11523 PRK11523
transcriptional regulator ExuR;
11-70 1.58e-04

transcriptional regulator ExuR;


Pssm-ID: 183176 [Multi-domain]  Cd Length: 253  Bit Score: 41.75  E-value: 1.58e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502  11 YLQIKDQLQARITRGALQAGDKLPSERELCAIFSTTRVTIRESLAQLEATGaiYRADRRG 70
Cdd:PRK11523  10 YQQLAAELKERIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEG--YVEVRKG 67
PRK10225 PRK10225
Uxu operon transcriptional regulator;
1-70 1.73e-04

Uxu operon transcriptional regulator;


Pssm-ID: 182318 [Multi-domain]  Cd Length: 257  Bit Score: 41.54  E-value: 1.73e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742398502   1 MKEHQGDMPHYLQIKDQLQARITRGALQAGDKLPSERELCAIFSTTRVTIRESLAQLEATGAIyrADRRG 70
Cdd:PRK10225   1 MKSATSAQRPYQEVGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLV--EVRRG 68
HTH_41 pfam14502
Helix-turn-helix domain;
28-70 2.13e-03

Helix-turn-helix domain;


Pssm-ID: 433997 [Multi-domain]  Cd Length: 48  Bit Score: 35.16  E-value: 2.13e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 742398502   28 QAGDKLPSERELCAIFSTTRVTIRESLAQLEATGAIYrADRRG 70
Cdd:pfam14502   1 KAGERLPTISEYSHKFELSVGTVQKALKKLEDMKAIQ-LERRG 42
 
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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