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Conserved domains on  [gi|505946113|ref|WP_015728250|]
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LysR family transcriptional regulator [Vibrio vulnificus]

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];
1-228 5.47e-39

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 136.92  E-value: 5.47e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   1 MDIEALRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAGIRLTSHARQLVSQHDQTLS 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113  81 ELKHFQD--KRPLRLGCPEDYNEKVLPSLIALLHQAQPTCSIQVFSEPSIELRRKLDAGDLDCAILTRAPNSEEGYW--L 156
Cdd:COG0583   81 ELRALRGgpRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVArpL 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 505946113 157 TSDQGVWIASQTFCVEAHSALplalfqadckyhaaaidgltkrgqafqllacCNTASAQRALVEQGLAIGAM 228
Cdd:COG0583  161 GEERLVLVASPDHPLARRAPL-------------------------------VNSLEALLAAVAAGLGIALL 201
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-228 5.47e-39

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 136.92  E-value: 5.47e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   1 MDIEALRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAGIRLTSHARQLVSQHDQTLS 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113  81 ELKHFQD--KRPLRLGCPEDYNEKVLPSLIALLHQAQPTCSIQVFSEPSIELRRKLDAGDLDCAILTRAPNSEEGYW--L 156
Cdd:COG0583   81 ELRALRGgpRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVArpL 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 505946113 157 TSDQGVWIASQTFCVEAHSALplalfqadckyhaaaidgltkrgqafqllacCNTASAQRALVEQGLAIGAM 228
Cdd:COG0583  161 GEERLVLVASPDHPLARRAPL-------------------------------VNSLEALLAAVAAGLGIALL 201
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-273 1.61e-33

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 123.99  E-value: 1.61e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   1 MDIEALRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAGIRLTSHARQLVSQHDQTLS 80
Cdd:PRK15092  11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACS 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113  81 ELKHFQDKRPLRLGCPEDYNEKVLPSLIALLHQAQPTCSIQVFSEPSIELRRKLDAGDLDCAILTRAPNSEEGYWLTSDQ 160
Cdd:PRK15092  91 SLMYSNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTTHRPSSFPALNLRTSP 170

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113 161 GVWIASQTFCVEAHSALPLALFQADCKYHAAAIDGLTKRGQAFQLLACCNTASAQRALVEQGLAIGAMGKLSMGDKVRLL 240
Cdd:PRK15092 171 TLWYCAAEYVLQKGEPIPLVLLDEPSPFRDMALATLNAAGIPWRIAYVASTLSAVRAAVKAGLGVTARPVEMMSPDLRVL 250

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 505946113 241 ---KDFPPLPKVDIVLAVSAKSHPLLSQTWLKQLEQ 273
Cdd:PRK15092 251 gesEGLPPLPDTEYLLCRDPNSNNELAQVIFQAMES 286
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 91-266 1.92e-20

The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold; This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. The 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.


Pssm-ID: 176130  Cd Length: 185  Bit Score: 86.23  E-value: 1.92e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113  91 LRLGCPEDYNEKVLPSLIALLHQAQPTCSIQVFSEPSIELRRKLDAGDLDCAILTRAPNSEEGYWLTSDQGVWIASQTFC 170
Cdd:cd08439    2 LRIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALITHPPPGASATILRRSPTVWYCAAGYI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113 171 VEAHSALPLALFQADCKYHAAAIDGLTKRGQAFQLLACCNTASAQRALVEQGLAIGAMGKLSMGDKVRLLKD---FPPLP 247
Cdd:cd08439   82 LAPGEPLPLALLDEPTLDRRAALAALDAAGIPWRIAYAASSLSGLRAAVRAGLGITARTQEMVPPDLRILGEsegLPPLP 161

                        170
                 ....*....|....*....
gi 505946113 248 KVDIVLAVSAKSHPLLSQT 266
Cdd:cd08439  162 DTGYTLCLDPNRPSELAQA 180
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 4.83e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 73.19  E-value: 4.83e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 505946113    3 IEALRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 1-175 1.10e-14

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: 72.46  E-value: 1.10e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   1 MDIEALRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAGIRLTSHARQLVSQHDQTLS 80
Cdd:NF041036   1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113  81 ELKHFQDKRPLRLGCPEDYNEKVLPSLIA--LLHQAQPTCSIQVFSEPSIELrRKLDAGDLDCAILTRAPNSEEG----Y 154
Cdd:NF041036  81 ELKSFKGRQRLSICCTPTFGMAHLPGVLNrfMLRNADVVDLKFLFHSPAQAL-EGIQNKEFDLAIIEHCADLDLGrfhtY 159

                        170       180
                 ....*....|....*....|.
gi 505946113 155 WLTSDQGVWIASQTFCVEAHS 175
Cdd:NF041036 160 PLPQDELVFVSAPSLGLPTPN 180
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 1-93 4.06e-10

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 59.16  E-value: 4.06e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113    1 MDIEALRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKeGRYLVLSDAGIRLTSHARQLVSQHDQTLS 80
Cdd:TIGR03298   1 LDYRQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHARQVRLLEAELLA 79

                          90
                  ....*....|...
gi 505946113   81 ELKHFQDKRPLRL 93
Cdd:TIGR03298  80 ELPGLAPGAPTRL 92
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-228 5.47e-39

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 136.92  E-value: 5.47e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   1 MDIEALRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAGIRLTSHARQLVSQHDQTLS 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113  81 ELKHFQD--KRPLRLGCPEDYNEKVLPSLIALLHQAQPTCSIQVFSEPSIELRRKLDAGDLDCAILTRAPNSEEGYW--L 156
Cdd:COG0583   81 ELRALRGgpRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVArpL 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 505946113 157 TSDQGVWIASQTFCVEAHSALplalfqadckyhaaaidgltkrgqafqllacCNTASAQRALVEQGLAIGAM 228
Cdd:COG0583  161 GEERLVLVASPDHPLARRAPL-------------------------------VNSLEALLAAVAAGLGIALL 201
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-273 1.61e-33

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 123.99  E-value: 1.61e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   1 MDIEALRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAGIRLTSHARQLVSQHDQTLS 80
Cdd:PRK15092  11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACS 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113  81 ELKHFQDKRPLRLGCPEDYNEKVLPSLIALLHQAQPTCSIQVFSEPSIELRRKLDAGDLDCAILTRAPNSEEGYWLTSDQ 160
Cdd:PRK15092  91 SLMYSNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTTHRPSSFPALNLRTSP 170

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113 161 GVWIASQTFCVEAHSALPLALFQADCKYHAAAIDGLTKRGQAFQLLACCNTASAQRALVEQGLAIGAMGKLSMGDKVRLL 240
Cdd:PRK15092 171 TLWYCAAEYVLQKGEPIPLVLLDEPSPFRDMALATLNAAGIPWRIAYVASTLSAVRAAVKAGLGVTARPVEMMSPDLRVL 250

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 505946113 241 ---KDFPPLPKVDIVLAVSAKSHPLLSQTWLKQLEQ 273
Cdd:PRK15092 251 gesEGLPPLPDTEYLLCRDPNSNNELAQVIFQAMES 286
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 91-266 1.92e-20

The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold; This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. The 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.


Pssm-ID: 176130  Cd Length: 185  Bit Score: 86.23  E-value: 1.92e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113  91 LRLGCPEDYNEKVLPSLIALLHQAQPTCSIQVFSEPSIELRRKLDAGDLDCAILTRAPNSEEGYWLTSDQGVWIASQTFC 170
Cdd:cd08439    2 LRIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALITHPPPGASATILRRSPTVWYCAAGYI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113 171 VEAHSALPLALFQADCKYHAAAIDGLTKRGQAFQLLACCNTASAQRALVEQGLAIGAMGKLSMGDKVRLLKD---FPPLP 247
Cdd:cd08439   82 LAPGEPLPLALLDEPTLDRRAALAALDAAGIPWRIAYAASSLSGLRAAVRAGLGITARTQEMVPPDLRILGEsegLPPLP 161

                        170
                 ....*....|....*....
gi 505946113 248 KVDIVLAVSAKSHPLLSQT 266
Cdd:cd08439  162 DTGYTLCLDPNRPSELAQA 180
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 4.83e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 73.19  E-value: 4.83e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 505946113    3 IEALRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-122 3.54e-15

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 74.07  E-value: 3.54e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   1 MDIEALRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAGIRLTSHARQLVSQHDQTLS 80
Cdd:PRK10094   2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPS 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 505946113  81 ELKHFQDKRPLRLGCPED---YNEKVLPSLIALLHQAQPTCSIQV 122
Cdd:PRK10094  82 ELQQVNDGVERQVNIVINnllYNPQAVAQLLAWLNERYPFTQFHI 126
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-276 4.42e-15

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: 71.94  E-value: 4.42e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   91 LRLGCPEDYNEKVLPSLIALLHQAQPTCSIQVFSEPSIELRRKLDAGDLDCAILTRAPNSEEGYW--LTSDQGVWIASQT 168
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEArpLGEEPLVLVAPPD 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113  169 FCVEAHSAL--------PLALFQADCKYHAAAIDGLTKRGQAFQLLACCNTASAQRALVEQGLAIG-----AMGKLSMGD 235
Cdd:pfam03466  84 HPLARGEPVsledladePLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIAllprsAVARELADG 163

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 505946113  236 KVRLLKDFPPLPKVDIVLAVSAKSH-PLLSQTWLKQLEQQFS 276
Cdd:pfam03466 164 RLVALPLPEPPLPRELYLVWRKGRPlSPAVRAFIEFLREALA 205
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 1-175 1.10e-14

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: 72.46  E-value: 1.10e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   1 MDIEALRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAGIRLTSHARQLVSQHDQTLS 80
Cdd:NF041036   1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113  81 ELKHFQDKRPLRLGCPEDYNEKVLPSLIA--LLHQAQPTCSIQVFSEPSIELrRKLDAGDLDCAILTRAPNSEEG----Y 154
Cdd:NF041036  81 ELKSFKGRQRLSICCTPTFGMAHLPGVLNrfMLRNADVVDLKFLFHSPAQAL-EGIQNKEFDLAIIEHCADLDLGrfhtY 159

                        170       180
                 ....*....|....*....|.
gi 505946113 155 WLTSDQGVWIASQTFCVEAHS 175
Cdd:NF041036 160 PLPQDELVFVSAPSLGLPTPN 180
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-148 5.83e-14

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 70.57  E-value: 5.83e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   1 MDIEALRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAGIRLTSHARQLVSQHDQT-L 79
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAkL 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 505946113  80 SELKHFQDKRPLRLGCPEDYNEKVLPSLIALLHQAQPTCSIQVFSEPSIELRRKLDAGDLDCAiLTRAP 148
Cdd:PRK09906  81 RARKIVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVG-FMRHP 148
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-151 1.62e-13

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 69.29  E-value: 1.62e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   1 MDIEALRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAGIrltsharQLVSQHDQTLS 80
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGL-------LLVDQARTVLR 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113  81 ELKHFQD---------KRPLRLGCPEDYNEKVLPSLIALLHQAQPTCSIQVFSEPSIELRRKLDAGDLDCAILTRAPNSE 151
Cdd:PRK11151  74 EVKVLKEmasqqgetmSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESE 153
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 6-137 2.39e-13

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 68.83  E-value: 2.39e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   6 LRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAGIRLTSHARQLVSQ--------HDq 77
Cdd:PRK11242   6 IRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDleagrraiHD- 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 505946113  78 tLSELKHFQdkrpLRLGCPEDYNEKVLPSLIALLHQAQP--TCSIQVFSEPSIE---LRRKLDAG 137
Cdd:PRK11242  85 -VADLSRGS----LRLAMTPTFTAYLIGPLIDAFHARYPgiTLTIREMSQERIEallADDELDVG 144
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 91-271 3.01e-11

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: 61.08  E-value: 3.01e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113  91 LRLGCPEDYNEKVLPSLIALLHQAQPTCSIQVFSEPSIELRRKLDAGDLDCAILTRAPNSEEGYW--LTSDQGVWIASQT 168
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESepLFEEPLVLVVPPD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113 169 FCVEAHSALPLA--------LFQADCKYHAAAIDGLTKRGQAFQLLACCNTASAQRALVEQGLAIG----AMGKLSMGDK 236
Cdd:cd05466   82 HPLAKRKSVTLAdladepliLFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIAllpeSAVEELADGG 161

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 505946113 237 VRLLKDFPPLPKVDIVLAVSA-KSHPLLSQTWLKQL 271
Cdd:cd05466  162 LVVLPLEDPPLSRTIGLVWRKgRYLSPAARAFLELL 197
PRK12680 PRK12680
LysR family transcriptional regulator;
1-150 3.13e-11

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 62.72  E-value: 3.13e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   1 MDIEALRSFLAFVETG-SFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYL-VLSDAGIRLTSHARQLVSQHD-- 76
Cdd:PRK12680   1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANni 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 505946113  77 QTLSELKHFQDKRPLRLGCPEDYNEKVLPSLIALLHQAQPTCSIQVFSEPSIELRRKLDAGDLDCAILTRAPNS 150
Cdd:PRK12680  81 RTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGE 154
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-152 3.63e-11

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 61.96  E-value: 3.63e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   1 MDIEALRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAGIRLTSHARQLVSQHDQTLS 80
Cdd:PRK03601   1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKK 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 505946113  81 ELKHFQDKRPLRLGCPEDYNEKVLPSLIALLHQAQPTCSIqvfsEPSIELR----RKLDAGDLDCAILTRAPNSEE 152
Cdd:PRK03601  81 EVAHTSQHNELSIGASASLWECMLTPWLGRLYQNQEALQF----EARIAQRqslvKQLHERQLDLLITTEAPKMDE 152
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
6-90 2.15e-10

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 59.98  E-value: 2.15e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   6 LRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKeGRYLVLSDAGIRLTSHARQLVSQHDQTLSELKHF 85
Cdd:PRK13348   7 LEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQVALLEADLLSTLPAE 85


                 ....*
gi 505946113  86 QDKRP 90
Cdd:PRK13348  86 RGSPP 90
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 1-93 4.06e-10

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 59.16  E-value: 4.06e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113    1 MDIEALRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKeGRYLVLSDAGIRLTSHARQLVSQHDQTLS 80
Cdd:TIGR03298   1 LDYRQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHARQVRLLEAELLA 79

                          90
                  ....*....|...
gi 505946113   81 ELKHFQDKRPLRL 93
Cdd:TIGR03298  80 ELPGLAPGAPTRL 92
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
6-141 7.53e-10

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 58.53  E-value: 7.53e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   6 LRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAGIRLTSHARQLVSQHDQTLSELKHF 85
Cdd:PRK10082  16 LYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGG 95

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 505946113  86 QD--KRPLRLGCPEDYNEKVLPSLIAllhQAQPTCSIQVFSEPSIELRRKLDAGDLDC 141
Cdd:PRK10082  96 SDyaQRKIKIAAAHSLSLGLLPSIIS---QMPPLFTWAIEAIDVDEAVDKLREGQSDC 150
PRK09986 PRK09986
LysR family transcriptional regulator;
1-80 7.69e-10

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 58.58  E-value: 7.69e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   1 MDIEALRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAGIRLTSHARQLVSQHDQTLS 80
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 5-74 3.10e-09

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 56.78  E-value: 3.10e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   5 ALRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAGIRLTSHARQLVSQ 74
Cdd:PRK11139  10 ALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQ 79
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-144 3.61e-09

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 56.57  E-value: 3.61e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   3 IEALRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAGIRLTSHARQ---LVSQHDQTL 79
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRilaLCEETCRAL 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 505946113  80 SELKHFQdKRPLRLGCPEDYNEKVLPSLIALLHQAQPTCSIQVFSEPSIELRRKLDAGDLDCAIL 144
Cdd:CHL00180  87 EDLKNLQ-RGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIV 150
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-93 5.66e-09

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 55.94  E-value: 5.66e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   1 MDIEALRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELfIKEGRYLVLSDAGIRLTSHARQLVSQHDQTLS 80
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVL-LVRTQPCRPTEAGQRLLRHARQVRLLEAELLG 80

                         90
                 ....*....|...
gi 505946113  81 ELKHfQDKRPLRL 93
Cdd:PRK03635  81 ELPA-LDGTPLTL 92
PRK09791 PRK09791
LysR family transcriptional regulator;
6-150 4.81e-08

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 53.23  E-value: 4.81e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   6 LRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAGIRLTSHARQLvsqhdqtLSELKHF 85
Cdd:PRK09791  10 IRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLI-------LEELRAA 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 505946113  86 QDKRPLRL---------GCPEDYNEKVLPSLIALLHQAQPTCSIQVFSEPSIELRRKLDAGDLDCAILTRAPNS 150
Cdd:PRK09791  83 QEDIRQRQgqlagqiniGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYYQGP 156
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 15-78 9.21e-08

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 52.25  E-value: 9.21e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 505946113  15 TGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAGIRLTSHARQLVSQHDQT 78
Cdd:PRK11074  16 TGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQET 79
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-83 2.12e-07

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 51.22  E-value: 2.12e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   1 MDIEALRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAGIRLTSHARQLVSQHDQTLS 80
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80


                 ...
gi 505946113  81 ELK 83
Cdd:PRK11233  81 AVH 83
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 6-117 2.18e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 51.23  E-value: 2.18e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   6 LRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAGIRLTSHARQLVSQhdqtLSELKHF 85
Cdd:PRK10837   8 LEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQ----AVEIEQL 83

                         90       100       110
                 ....*....|....*....|....*....|....
gi 505946113  86 --QDKRPLRLGCPEDYNEKVLPSLIALLHQAQPT 117
Cdd:PRK10837  84 frEDNGALRIYASSTIGNYILPAMIARYRRDYPQ 117
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
6-84 4.39e-07

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 50.39  E-value: 4.39e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 505946113   6 LRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAGIRLTSHARQLVSQHDQTLSELKH 84
Cdd:PRK10086  19 LHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDIKN 97
PRK10341 PRK10341
transcriptional regulator TdcA;
9-145 4.46e-07

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 50.25  E-value: 4.46e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   9 FLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAGIRLTSHARQLVSQHDQTLSELKH--FQ 86
Cdd:PRK10341  15 FQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGmsSE 94

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 505946113  87 DKRPLRLGCPEDYNEKVLPSLIALLHQAQPTCSIQVFSEPSIELRRKLDAGDLDCAILT 145
Cdd:PRK10341  95 AVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGT 153
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
30-95 5.13e-07

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 49.82  E-value: 5.13e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 505946113  30 SAFSAQMRKLEEEIGAELFIKEGRYLVLSDAGIRLTSHARQLVSQHDQTLSELKHFQD--KRPLRLGC 95
Cdd:PRK11716   6 STLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPslSGELSLFC 73
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-93 1.32e-06

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 48.86  E-value: 1.32e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   1 MDIEALRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAGIRLTSHARQLVSQHDQTLS 80
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                         90
                 ....*....|...
gi 505946113  81 ELKHFQDKRpLRL 93
Cdd:PRK15421  82 ACNEPQQTR-LRI 93
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
9-120 2.32e-06

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 48.22  E-value: 2.32e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   9 FLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAGIRLTSHARQLVSQHDQTLSELKHFQDK 88
Cdd:PRK10632  10 FAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAFNNT 89

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 505946113  89 rP---LRLGCPEDYNEKVLPSLIALLHQAQPTCSI 120
Cdd:PRK10632  90 -PigtLRIGCSSTMAQNVLAGLTAKMLKEYPGLSV 123
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 90-254 2.51e-05

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is 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 C-terminal domain also contains the redox-active cysteines that mediate the redox-dependent conformational switch. Thus, the interaction between the OxyR-tetramer and DNA is notably different between the oxidized and reduced forms. 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.


Pssm-ID: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 44.05  E-value: 2.51e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113  90 PLRLGC-----PedYnekVLPSLIALLHQAQPTCSIQVFSEPSIELRRKLDAGDLDCAILTrAPNSEEGywLTSDQgvwI 164
Cdd:cd08411    2 PLRLGViptiaP--Y---LLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLA-LPVDEPG--LEEEP---L 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113 165 ASQTFCVEAHSALPLALFQadcKYHAAAIDG----LTKRGQAF--QLLACCNTASAQ-------------RALVEQG--- 222
Cdd:cd08411   71 FDEPFLLAVPKDHPLAKRK---SVTPEDLAGerllLLEEGHCLrdQALELCRLAGAReqtdfeatsletlRQMVAAGlgi 147

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 505946113 223 -----LAIGAMGKLSMGDKVRLLKDfpPLPKVDIVLA 254
Cdd:cd08411  148 tllpeLAVPSEELRGDRLVVRPFAE--PAPSRTIGLV 182
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 19-116 1.84e-04

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 42.29  E-value: 1.84e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113  19 TRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVlsdagiRLTSHARQLVSQHDQTLSELKHF---------QDKR 89
Cdd:PRK12682  20 TEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLK------GLTEPGKAVLDVIERILREVGNIkrigddfsnQDSG 93

                         90       100
                 ....*....|....*....|....*..
gi 505946113  90 PLRLGCPEDYNEKVLPSLIALLHQAQP 116
Cdd:PRK12682  94 TLTIATTHTQARYVLPRVVAAFRKRYP 120
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-153 2.89e-04

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 41.57  E-value: 2.89e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   1 MDIEALRSFLAFVETG-SFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYL----------------VLSDAGiR 63
Cdd:PRK12683   1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLtgltepgkellqiverMLLDAE-N 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113  64 LTSHARQLVSQHDQTLS-ELKHFQDKRPLrlgcPEDYNE--KVLPSLIALLHQAQPTcsiqvfsepsiELRRKLDAGDLD 140
Cdd:PRK12683  80 LRRLAEQFADRDSGHLTvATTHTQARYAL----PKVVRQfkEVFPKVHLALRQGSPQ-----------EIAEMLLNGEAD 144

                        170
                 ....*....|...
gi 505946113 141 CAILTRAPNSEEG 153
Cdd:PRK12683 145 IGIATEALDREPD 157
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 103-148 4.44e-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: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 40.25  E-value: 4.44e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 505946113 103 VLPSLIALLHQAQPTCSIQVFSEPSIELRRKLDAGDLDCAILTRAP 148
Cdd:cd08427   14 LLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPP 59
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 103-180 7.06e-04

The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The 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.


Pssm-ID: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 39.95  E-value: 7.06e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 505946113 103 VLPSLIALLHQAQPTCSIQVFSEPSIELRRKLDAGDLDCAIlTRAPNSEEGYWLTSDQgvwIASQTFCVEAHSALPLA 180
Cdd:cd08435   14 LLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAI-GRLADDEQPPDLASEE---LADEPLVVVARPGHPLA 87
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 92-167 1.53e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. 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. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. 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: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 38.73  E-value: 1.53e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 505946113  92 RLGCPEDYNEKVLPSLIALLHQAQPTCSIQVFSEPSIELRRKLDAGDLDCAIlTRAPNSEEGYW---LTSDQGVWIASQ 167
Cdd:cd08417    3 RIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAI-GVFPELPPGLRsqpLFEDRFVCVARK 80
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-96 4.65e-03

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 38.05  E-value: 4.65e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 505946113   1 MDIEALRSFLAFVETGSFTRAAKQISRTQSAFSAQMRKLEEEIGAELFIKEGRYLVLSDAGIRLTSHARQLV--SQHDQT 78
Cdd:PRK14997   2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLveAQAAQD 81

                         90
                 ....*....|....*...
gi 505946113  79 LSELKHFQDKRPLRLGCP 96
Cdd:PRK14997  82 AIAALQVEPRGIVKLTCP 99
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 90-144 6.54e-03

The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (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 N2 fixing bacteria, and synthesis of virulence factors, to a 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: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 36.75  E-value: 6.54e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 505946113  90 PLRLGCPEDYNEKVLPSLIALLHQAQPTCSIQVFSEPSIELRRKLDAGDLDCAIL 144
Cdd:cd08412    1 TLRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALT 55
 
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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