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Conserved domains on  [gi|1828255882|ref|WP_167532747|]
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LysR family transcriptional regulator [Streptomyces alboniger]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

LysR family transcriptional regulator containing an N-terminal HTH (helix-turn-helix) DNA-binding domain and a C-terminal substrate binding domain, which is structurally homologous to the type 2 periplasmic-binding (PBP2) fold proteins

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0003677|GO:0006355
PubMed:  19047729|8257110|15808743
SCOP:  4000316

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-298 3.02e-28

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 109.96  E-value: 3.02e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882   5 LDLALVRSFAITAEELHFRRAAERLFITQQALSQRIRRLELLLGVSLFVRGNRSVALTEEGQRFLAPARRV---MEAADA 81
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRIlaeLEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882  82 AVQAVQPRERRPLRVDVVD--GRLAPLQLVRKLLEEDPELPLNLSMRQSlAAALPALARDEIDTAFGRVHDVQgwsAEFS 159
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPslARYLLPPLLARFRARHPGVRLELREGNS-DRLVDALLEGELDLAIRLGPPPD---PGLV 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882 160 HRLVRLEPLRALVPRTHPLAGRDEvridelrscgiwqprngVASEWEHYVRRLADSFGLslafsgaALSDEHFLEHLWSH 239
Cdd:COG0583   157 ARPLGEERLVLVASPDHPLARRAP-----------------LVNSLEALLAAVAAGLGI-------ALLPRFLAADELAA 212

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882 240 GEmaclagadvsyafspdIRSIPLVDPTPVYPWSMVWR-RQAGHPLVDRLVGLAKRSAGD 298
Cdd:COG0583   213 GR----------------LVALPLPDPPPPRPLYLVWRrRRHLSPAVRAFLDFLREALAE 256
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-298 3.02e-28

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 109.96  E-value: 3.02e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882   5 LDLALVRSFAITAEELHFRRAAERLFITQQALSQRIRRLELLLGVSLFVRGNRSVALTEEGQRFLAPARRV---MEAADA 81
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRIlaeLEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882  82 AVQAVQPRERRPLRVDVVD--GRLAPLQLVRKLLEEDPELPLNLSMRQSlAAALPALARDEIDTAFGRVHDVQgwsAEFS 159
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPslARYLLPPLLARFRARHPGVRLELREGNS-DRLVDALLEGELDLAIRLGPPPD---PGLV 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882 160 HRLVRLEPLRALVPRTHPLAGRDEvridelrscgiwqprngVASEWEHYVRRLADSFGLslafsgaALSDEHFLEHLWSH 239
Cdd:COG0583   157 ARPLGEERLVLVASPDHPLARRAP-----------------LVNSLEALLAAVAAGLGI-------ALLPRFLAADELAA 212

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882 240 GEmaclagadvsyafspdIRSIPLVDPTPVYPWSMVWR-RQAGHPLVDRLVGLAKRSAGD 298
Cdd:COG0583   213 GR----------------LVALPLPDPPPPRPLYLVWRrRRHLSPAVRAFLDFLREALAE 256
PRK09986 PRK09986
LysR family transcriptional regulator;
5-190 9.29e-20

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 87.47  E-value: 9.29e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882   5 LDLALVRSFAITAEELHFRRAAERLFITQQALSQRIRRLELLLGVSLFVRGNRSVALTEEGQRFLAPARRVM---EAADA 81
Cdd:PRK09986    7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLdnaEQSLA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882  82 AVQAVQPRERRPLRVDVVD----GRLAPlqLVRKLLEEDPELPLNLSmRQSLAAALPALARDEIDTAFGRVHDVQGwSAE 157
Cdd:PRK09986   87 RVEQIGRGEAGRIEIGIVGtalwGRLRP--AMRHFLKENPNVEWLLR-ELSPSMQMAALERRELDAGIWRMADLEP-NPG 162

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1828255882 158 FSHRLVRLEPLRALVPRTHPLAGRDEVRIDELR 190
Cdd:PRK09986  163 FTSRRLHESAFAVAVPEEHPLASRSSVPLKALR 195
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-66 5.35e-19

Bacterial regulatory helix-turn-helix protein, lysR family;


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 79.35  E-value: 5.35e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882   7 LALVRSFAITAEELHFRRAAERLFITQQALSQRIRRLELLLGVSLFVRGNRSVALTEEGQ 66
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 138-292 6.82e-12

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176106 [Multi-domain]  Cd Length: 197  Bit Score: 63.68  E-value: 6.82e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882 138 RDEIDTAFGRVHDVqgwSAEFSHRLVRLEPLRALVPRTHPLAGRDEVRIDELRSCGIWQPRNGVASEWEHYVRRLADSFG 217
Cdd:cd08414    47 AGRLDVGFVRPPPD---PPGLASRPLLREPLVVALPADHPLAARESVSLADLADEPFVLFPREPGPGLYDQILALCRRAG 123

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1828255882 218 LSLAFSGAAlSDEHFLEHLWSHGEMACLAGADVSYAFSPDIRSIPLVDPTPVYPWSMVWRRQAGHPLVDRLVGLA 292
Cdd:cd08414   124 FTPRIVQEA-SDLQTLLALVAAGLGVALVPASVARLQRPGVVYRPLADPPPRSELALAWRRDNASPALRAFLELA 197
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 11-76 1.32e-08

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 55.13  E-value: 1.32e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1828255882  11 RSFAITAEELHFRRAAERLFITQQALSQRIRRLELLLGVSLFVRGNRSVALTEEGQRFLAPARRVM 76
Cdd:NF041036    7 KTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRIL 72
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
5-298 3.02e-28

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 109.96  E-value: 3.02e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882   5 LDLALVRSFAITAEELHFRRAAERLFITQQALSQRIRRLELLLGVSLFVRGNRSVALTEEGQRFLAPARRV---MEAADA 81
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRIlaeLEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882  82 AVQAVQPRERRPLRVDVVD--GRLAPLQLVRKLLEEDPELPLNLSMRQSlAAALPALARDEIDTAFGRVHDVQgwsAEFS 159
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPslARYLLPPLLARFRARHPGVRLELREGNS-DRLVDALLEGELDLAIRLGPPPD---PGLV 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882 160 HRLVRLEPLRALVPRTHPLAGRDEvridelrscgiwqprngVASEWEHYVRRLADSFGLslafsgaALSDEHFLEHLWSH 239
Cdd:COG0583   157 ARPLGEERLVLVASPDHPLARRAP-----------------LVNSLEALLAAVAAGLGI-------ALLPRFLAADELAA 212

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882 240 GEmaclagadvsyafspdIRSIPLVDPTPVYPWSMVWR-RQAGHPLVDRLVGLAKRSAGD 298
Cdd:COG0583   213 GR----------------LVALPLPDPPPPRPLYLVWRrRRHLSPAVRAFLDFLREALAE 256
PRK09986 PRK09986
LysR family transcriptional regulator;
5-190 9.29e-20

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 87.47  E-value: 9.29e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882   5 LDLALVRSFAITAEELHFRRAAERLFITQQALSQRIRRLELLLGVSLFVRGNRSVALTEEGQRFLAPARRVM---EAADA 81
Cdd:PRK09986    7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLdnaEQSLA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882  82 AVQAVQPRERRPLRVDVVD----GRLAPlqLVRKLLEEDPELPLNLSmRQSLAAALPALARDEIDTAFGRVHDVQGwSAE 157
Cdd:PRK09986   87 RVEQIGRGEAGRIEIGIVGtalwGRLRP--AMRHFLKENPNVEWLLR-ELSPSMQMAALERRELDAGIWRMADLEP-NPG 162

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1828255882 158 FSHRLVRLEPLRALVPRTHPLAGRDEVRIDELR 190
Cdd:PRK09986  163 FTSRRLHESAFAVAVPEEHPLASRSSVPLKALR 195
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 5-189 3.35e-19

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 85.98  E-value: 3.35e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882   5 LDLALVRSFAITAEELHFRRAAERLFITQQALSQRIRRLELLLGVSLFVRGNRSVALTEEGQRFLAPARRVMEAA--DAA 82
Cdd:PRK09906    1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAekAKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882  83 VQAVQPRERRPLRVDVVDgrLAPLQLVRKLLE----EDPELPLNLSmRQSLAAALPALARDEIDTAFGRvHDVQgwSAEF 158
Cdd:PRK09906   81 RARKIVQEDRQLTIGFVP--SAEVNLLPKVLPmfrlRHPDTLIELV-SLITTQQEEKLRRGELDVGFMR-HPVY--SDEI 154

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1828255882 159 SHRLVRLEPLRALVPRTHPLAGRDEVRIDEL 189
Cdd:PRK09906  155 DYLELLDEPLVVVLPVDHPLAHEKEITAAQL 185
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-66 5.35e-19

Bacterial regulatory helix-turn-helix protein, lysR family;


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 79.35  E-value: 5.35e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882   7 LALVRSFAITAEELHFRRAAERLFITQQALSQRIRRLELLLGVSLFVRGNRSVALTEEGQ 66
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 10-73 1.20e-14

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 72.95  E-value: 1.20e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1828255882  10 VRSFAITAEELHFRRAAERLFITQQALSQRIRRLELLLGVSLFVRGNRSVALTEEGQRFLAPAR 73
Cdd:PRK11139   11 LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIR 74
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
7-77 5.81e-12

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 65.41  E-value: 5.81e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1828255882   7 LALVRSFAITAEELHFRRAAERLFITQQALSQRIRRLELLLGVSLFVRGNRSVALTEEGQRFLAPARRVME 77
Cdd:PRK10086   16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLD 86
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 138-292 6.82e-12

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176106 [Multi-domain]  Cd Length: 197  Bit Score: 63.68  E-value: 6.82e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882 138 RDEIDTAFGRVHDVqgwSAEFSHRLVRLEPLRALVPRTHPLAGRDEVRIDELRSCGIWQPRNGVASEWEHYVRRLADSFG 217
Cdd:cd08414    47 AGRLDVGFVRPPPD---PPGLASRPLLREPLVVALPADHPLAARESVSLADLADEPFVLFPREPGPGLYDQILALCRRAG 123

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1828255882 218 LSLAFSGAAlSDEHFLEHLWSHGEMACLAGADVSYAFSPDIRSIPLVDPTPVYPWSMVWRRQAGHPLVDRLVGLA 292
Cdd:cd08414   124 FTPRIVQEA-SDLQTLLALVAAGLGVALVPASVARLQRPGVVYRPLADPPPRSELALAWRRDNASPALRAFLELA 197
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 2-76 8.07e-12

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 65.05  E-value: 8.07e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1828255882   2 IVDLDLALVRSFAITAEELHFRRAAERLFITQQALSQRIRRLELLLGVSLFVRGNRSVALTEEGQRFLAPARRVM 76
Cdd:PRK15092    8 IINLDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKIL 82
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 10-76 9.75e-12

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 64.59  E-value: 9.75e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1828255882  10 VRSFAITAEELHFRRAAERLFITQQALSQRIRRLELLLGVSLFVRGNRSVALTEEGQRFLAPARRVM 76
Cdd:PRK11242    6 IRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRAL 72
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
4-75 1.68e-11

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 64.02  E-value: 1.68e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1828255882   4 DLDLALVRSFAITAEELHFRRAAERLFITQQALSQRIRRLELLLGVSLFVRGnRSVALTEEGQRFLAPARRV 75
Cdd:PRK03635    1 MLDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQRLLRHARQV 71
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
5-75 1.88e-11

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 63.84  E-value: 1.88e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1828255882   5 LDLALVRSFAITAEELHFRRAAERLFITQQALSQRIRRLELLLGVSLFVRGnRSVALTEEGQRFLAPARRV 75
Cdd:PRK13348    2 LDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHLRQV 71
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 17-293 4.24e-11

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 62.74  E-value: 4.24e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882  17 AEELHFRRAAERLFITQQALSQRIRRLELLLGVSLFVRGNRSVALTEEGQRFLAPARRVMeaadaavqavqpRERR---- 92
Cdd:PRK11151   13 AEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVL------------REVKvlke 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882  93 -----------PLRVDV---VDGRLAPlQLVRKLLEEDPELPLNLSMRQSLAAALPALArDEIDTA-FGRVHDvqgwSAE 157
Cdd:PRK11151   81 masqqgetmsgPLHIGLiptVGPYLLP-HIIPMLHQTFPKLEMYLHEAQTHQLLAQLDS-GKLDCAiLALVKE----SEA 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882 158 FSHRLVRLEPLRALVPRTHPLAGRDEVRIDELRSCGIWQPRNGvaseweHYVRRLAdsfgLSLAFSGAALSDEHF----L 233
Cdd:PRK11151  155 FIEVPLFDEPMLLAVYEDHPWANRDRVPMSDLAGEKLLMLEDG------HCLRDQA----MGFCFEAGADEDTHFratsL 224

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1828255882 234 EHLWShgeMAClAGADVS---YAFSPDIRS------IPLVDPTPVYPWSMVWRrqAGHPLVDRLVGLAK 293
Cdd:PRK11151  225 ETLRN---MVA-AGSGITllpALAVPNERKrdgvcyLPCIKPEPRRTIGLVYR--PGSPLRSRYEQLAE 287
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
5-76 1.03e-10

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 61.19  E-value: 1.03e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1828255882   5 LDLALVRSFAITAEELHFRRAAERLFITQQALSQRIRRLELLLGVSLFVRGNRSVALTEEGQRFLAPARRVM 76
Cdd:PRK03601    1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLM 72
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
5-77 1.70e-10

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 60.98  E-value: 1.70e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1828255882   5 LDLALVRSFAITAEELHFRRAAERLFITQQALSQRIRRLELLLGVSLFVRGNRSVALTEEGQRFLAPARRVME 77
Cdd:PRK10094    2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLS 74
rbcR CHL00180
LysR transcriptional regulator; Provisional
 17-76 3.22e-10

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 60.03  E-value: 3.22e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882  17 AEELHFRRAAERLFITQQALSQRIRRLELLLGVSLFVRGNRSVALTEEGQRFLAPARRVM 76
Cdd:CHL00180   17 ATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRIL 76
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
35-77 5.87e-09

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 55.98  E-value: 5.87e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1828255882  35 ALSQRIRRLELLLGVSLFVRGNRSVALTEEGQRFLAPARRVME 77
Cdd:PRK11716    7 TLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLL 49
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 11-76 1.32e-08

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 55.13  E-value: 1.32e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1828255882  11 RSFAITAEELHFRRAAERLFITQQALSQRIRRLELLLGVSLFVRGNRSVALTEEGQRFLAPARRVM 76
Cdd:NF041036    7 KTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRIL 72
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
25-76 1.93e-07

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 51.90  E-value: 1.93e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1828255882  25 AAERLFITQQALSQRIRRLELLLGVSLFVR-GNRSVALTEEGQRFLAPARRVM 76
Cdd:PRK12684   22 AAKALYTSQPGVSKAIIELEDELGVEIFTRhGKRLRGLTEPGRIILASVERIL 74
PRK09791 PRK09791
LysR family transcriptional regulator;
1-77 3.45e-07

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 50.92  E-value: 3.45e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1828255882   1 MIVDLDLALVRSFAITAEELHFRRAAERLFITQQALSQRIRRLELLLGVSLFVRGNRSVALTEEGQRFLAPARRVME 77
Cdd:PRK09791    1 MAFQVKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILE 77
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 8-76 2.63e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 48.40  E-value: 2.63e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1828255882   8 ALVRSFAITAEELHfrraaeRLfitQQALSQRIRRLELLLGVSLFVRGNRSVALTEEGQRFLAPARRVM 76
Cdd:PRK11074   14 ARTGSFSAAAQELH------RV---PSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVI 73
PRK10341 PRK10341
transcriptional regulator TdcA;
25-70 4.41e-06

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 47.55  E-value: 4.41e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1828255882  25 AAERLFITQQALSQRIRRLELLLGVSLFVRGNRSVALTEEGQRFLA 70
Cdd:PRK10341   27 AAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLS 72
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 25-76 1.47e-05

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 46.14  E-value: 1.47e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1828255882  25 AAERLFITQQALSQRIRRLELLLGVSLFVR-GNRSVALTEEGQRFLAPARRVM 76
Cdd:PRK12682   22 AAKALHTSQPGVSKAIIELEEELGIEIFIRhGKRLKGLTEPGKAVLDVIERIL 74
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
 138-292 1.52e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold; The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176144 [Multi-domain]  Cd Length: 200  Bit Score: 45.04  E-value: 1.52e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882 138 RDEIDTAFGRVHDVQGWSAEFSHRLVRLEPLRALVPRTHPLAGRDEVRIDELRscgiwqprngvASEWEHYVRRLADSF- 216
Cdd:cd08453    47 AGEIDAGIVIPPPGASAPPALAYRPLLSEPLVLAVPAAWAAEGGAPLALAAVA-----------AEPLVIFPRRIAPAFh 115

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882 217 GLSLAFSGAALSDEHFLEH---------LWSHGEMACLAGADVSYAFSPDIRSIPLVDPTPVYPWSMVWRRQAGHPLVDR 287
Cdd:cd08453   116 DAVTGYYRAAGQTPRIAQEaiqmqtiisLVSAGMGVALVPASLRNLARPGVVYRELADPAPVLETGLVWRRDDASPVLAR 195


                  ....*
gi 1828255882 288 LVGLA 292
Cdd:cd08453   196 FLDLV 200
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 107-189 3.97e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold; HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176141 [Multi-domain]  Cd Length: 196  Bit Score: 43.90  E-value: 3.97e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882 107 QLVRKLLEEDPELPLNLSmRQSLAAALPALARDEIDTAFGRvHDVQgwSAEFSHRLVRLEPLRALVPRTHPLAGRDEVRI 186
Cdd:cd08450    17 EVLPILREEHPDLDVELS-SLFSPQLAEALMRGKLDVAFMR-PEIQ--SDGIDYQLLLKEPLIVVLPADHRLAGREKIPP 92


                  ...
gi 1828255882 187 DEL 189
Cdd:cd08450    93 QDL 95
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 25-76 4.41e-05

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 44.65  E-value: 4.41e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1828255882  25 AAERLFITQQALSQRIRRLELLLGVSLFVR-GNRSVALTEEGQRFLAPARRVM 76
Cdd:PRK12683   22 VANALYTSQSGVSKQIKDLEDELGVEIFIRrGKRLTGLTEPGKELLQIVERML 74
PRK12680 PRK12680
LysR family transcriptional regulator;
14-76 5.76e-05

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 44.23  E-value: 5.76e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1828255882  14 AITAEELHFRRAAERLFITQQALSQRIRRLELLLGVSLFVRGNRSV-ALTEEGQRFLAPARRVM 76
Cdd:PRK12680   11 AIADAELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVL 74
cbl PRK12679
HTH-type transcriptional regulator Cbl;
26-76 3.19e-04

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 42.10  E-value: 3.19e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1828255882  26 AERLFITQQALSQRIRRLELLLGVSLFVR-GNRSVALTEEGQRFLAPARRVM 76
Cdd:PRK12679   23 ANMLFTSQSGVSRHIRELEDELGIEIFIRrGKRLLGMTEPGKALLVIAERIL 74
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 106-297 4.54e-04

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 40.74  E-value: 4.54e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882 106 LQLVRKLLEEDPELPLNLSMRQSLAAALPALaRDEIDTAFGRVHDVqgwSAEFSHRLVRLEPLRALVPRTHPLAGRDEVR 185
Cdd:pfam03466  18 PPLLARFRERYPDVELELTEGNSEELLDLLL-EGELDLAIRRGPPD---DPGLEARPLGEEPLVLVAPPDHPLARGEPVS 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882 186 IDELRSCGIWQPRNGVASEWehYVRRLADSFGLSLAfSGAALSDEHFLEHLWSHGEMACLAGADVSYAF--SPDIRSIPL 263
Cdd:pfam03466  94 LEDLADEPLILLPPGSGLRD--LLDRALRAAGLRPR-VVLEVNSLEALLQLVAAGLGIALLPRSAVARElaDGRLVALPL 170

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1828255882 264 VDPTPVYPWSMVWRRQAGH-PLVDRLVGLAKRSAG 297
Cdd:pfam03466 171 PEPPLPRELYLVWRKGRPLsPAVRAFIEFLREALA 205
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
21-77 4.69e-04

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 41.19  E-value: 4.69e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1828255882  21 HFRRAAERLFITQQALSQRIRRLELLLGVSLFVRGNRSVALTEEGQRFLAPARRVME 77
Cdd:PRK10082   27 NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQ 83
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
13-76 4.85e-04

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 41.28  E-value: 4.85e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1828255882  13 FAITAEELHFRRAAERLFITQQALSQRIRRLELLLGVSLFVRGNRSVALTEEGQRFLAPARRVM 76
Cdd:PRK10632   10 FAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRML 73
nhaR PRK11062
transcriptional activator NhaR; Provisional
 24-66 5.72e-04

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 41.15  E-value: 5.72e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1828255882  24 RAAERLFITQQALSQRIRRLELLLGVSLFVRGNRSVALTEEGQ 66
Cdd:PRK11062   23 GAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGE 65
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 156-283 6.74e-04

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 40.28  E-value: 6.74e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882 156 AEFSHRLVRLEPLRALVPRTHPLAGRDEVRIDELRScgiwQPRNGVASEWEhyVRRLADsfglsLAFSGAAL-------- 227
Cdd:cd08436    63 PGLASRELAREPLVAVVAPDHPLAGRRRVALADLAD----EPFVDFPPGTG--ARRQVD-----RAFAAAGVrrrvafev 131

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1828255882 228 SDEHFLEHLWSHGEMACLAGADVSYAFsPDIRSIPLvDPTPVYPWSMVWRRQAGHP 283
Cdd:cd08436   132 SDVDLLLDLVARGLGVALLPASVAARL-PGLAALPL-EPAPRRRLYLAWSAPPPSP 185
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 166-190 6.79e-04

The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold; GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 40.21  E-value: 6.79e-04
                          10        20
                  ....*....|....*....|....*
gi 1828255882 166 EPLRALVPRTHPLAGRDEVRIDELR 190
Cdd:cd08434    72 EELVLVVPKDHPLAGRDSVDLAELA 96
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 138-283 6.98e-04

The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, oxidative stress responses, nodule formation of nitrogen-fixing bacteria, synthesis of virulence factors, toxin production, attachment and secretion, to name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 40.28  E-value: 6.98e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882 138 RDEIDTAFGRVHDVQgwsAEFSHRLVRLEPLRALVPRTHPLAGRDEVRIDELRSCGIWQPRNGvaSEWEHYVRRLADSFG 217
Cdd:cd05466    47 EGELDLAIVALPVDD---PGLESEPLFEEPLVLVVPPDHPLAKRKSVTLADLADEPLILFERG--SGLRRLLDRAFAEAG 121

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1828255882 218 LSLAFSgAALSDEHFLEHLWSHGE-MACLAGADVSYAFSPDIRSIPLVDPTPVYPWSMVWRRQAGHP 283
Cdd:cd05466   122 FTPNIA-LEVDSLEAIKALVAAGLgIALLPESAVEELADGGLVVLPLEDPPLSRTIGLVWRKGRYLS 187
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 138-292 1.01e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176139 [Multi-domain]  Cd Length: 197  Bit Score: 39.56  E-value: 1.01e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1828255882 138 RDEIDTAFGRVHDVqgwSAEFSHRLVRLEPLRALVPRTHPLAGRDEVRIDELRSCG-IWQPRNGVASEWEHYVRRLADSf 216
Cdd:cd08448    47 RGELDLGFVHSRRL---PAGLSARLLHREPFVCCLPAGHPLAARRRIDLRELAGEPfVLFSREVSPDYYDQIIALCMDA- 122

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1828255882 217 GLSLAFSGAAlsdEHFLE--HLWSHGEMACLAGADVSYAFSPDIRSIPLVDPTPVYPWSMVWRRQAGHPLVDRLVGLA 292
Cdd:cd08448   123 GFHPKIRHEV---RHWLTvvALVAAGMGVALVPRSLARAGLAGVRFLPLKGATQRSELYAAWKASAPNPALQAFLAAL 197
PRK09801 PRK09801
LysR family transcriptional regulator;
9-67 1.97e-03

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 39.63  E-value: 1.97e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1828255882   9 LVRSFAITAEELH---FRRAAERLFITQQALSQRIRRLELLLGVSLFVRGNRSVALTEEGQR 67
Cdd:PRK09801    7 LAKDLQVLVEIVHsgsFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQR 68
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 140-192 2.46e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold; In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176140 [Multi-domain]  Cd Length: 197  Bit Score: 38.41  E-value: 2.46e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1828255882 140 EIDTAFGRVHDVQGWSAEFSHRLVRlEPLRALVPRTHPLAGRDEVRIDELRSC 192
Cdd:cd08449    49 RIDLGFVRFADTLNDPPLASELLWR-EPMVVALPEEHPLAGRKSLTLADLRDE 100
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 24-73 4.91e-03

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 38.12  E-value: 4.91e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1828255882  24 RAAERLFITQQALSQRIRRLELLLGVSLFVRGNRSVALTEEGQRFLAPAR 73
Cdd:PRK11233   20 QAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHAR 69
cysB PRK12681
HTH-type transcriptional regulator CysB;
25-76 6.12e-03

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 37.96  E-value: 6.12e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1828255882  25 AAERLFITQQALSQRIRRLELLLGVSLFVR-GNRSVALTEEGQRFLAPARRVM 76
Cdd:PRK12681   22 TAEGLYTSQPGISKQVRMLEDELGIQIFARsGKHLTQVTPAGEEIIRIAREIL 74
 
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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