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Conserved domains on  [gi|779851706|ref|WP_045348560|]
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MULTISPECIES: LysR substrate-binding domain-containing protein [Enterobacter cloacae complex]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK11482 super family cl32694
DNA-binding transcriptional regulator;
7-294 9.68e-37

DNA-binding transcriptional regulator;


The actual alignment was detected with superfamily member PRK11482:

Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 133.31  E-value: 9.68e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706   7 LKKFDLNLLVIFECIYQHLSISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTTVGTNLHHHLEQNLNQIEQ 86
Cdd:PRK11482  26 LRNIDLNLLTIFEAVYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHEYISQGLESILG 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706  87 TINMMHHSDIKKKFVIYCSQMMspGYMLEP-MKLLMSEENYEIEQRDMLISpeSAEDLLAYRKADLIFTIAPIKNRSVVC 165
Cdd:PRK11482 106 ALDITGSYDKQRTITIATTPSV--GALVMPvIYQAIKTHYPQLLLRNIPIS--DAENQLSQFQTDLIIDTHSCSNRTIQH 181

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706 166 SHFATVPIALICRENHPRLADTVSLEALYREKFTFYQSAHPGVKEFQNRANDLFPERDIAFRTDSISSLISMVSSSDLLG 245
Cdd:PRK11482 182 HVLFTDNVVLVCRQGHPLLSLEDDEETLDNAEHTLLLPEGQNFSGLRQRLQEMFPDRQISFSSYNILTIAALIASSDMLG 261

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 779851706 246 FIPVSIYEAYKETLKIKRIA-APFELPEIHVYMLYSRSSLNSSVFSTFIE 294
Cdd:PRK11482 262 IMPSRFYNLFSRCWPLEKLPfPSLNEEQIDFSLHYNKLSLRDPVLENVID 311
 
Name Accession Description Interval E-value
PRK11482 PRK11482
DNA-binding transcriptional regulator;
7-294 9.68e-37

DNA-binding transcriptional regulator;


Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 133.31  E-value: 9.68e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706   7 LKKFDLNLLVIFECIYQHLSISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTTVGTNLHHHLEQNLNQIEQ 86
Cdd:PRK11482  26 LRNIDLNLLTIFEAVYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHEYISQGLESILG 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706  87 TINMMHHSDIKKKFVIYCSQMMspGYMLEP-MKLLMSEENYEIEQRDMLISpeSAEDLLAYRKADLIFTIAPIKNRSVVC 165
Cdd:PRK11482 106 ALDITGSYDKQRTITIATTPSV--GALVMPvIYQAIKTHYPQLLLRNIPIS--DAENQLSQFQTDLIIDTHSCSNRTIQH 181

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706 166 SHFATVPIALICRENHPRLADTVSLEALYREKFTFYQSAHPGVKEFQNRANDLFPERDIAFRTDSISSLISMVSSSDLLG 245
Cdd:PRK11482 182 HVLFTDNVVLVCRQGHPLLSLEDDEETLDNAEHTLLLPEGQNFSGLRQRLQEMFPDRQISFSSYNILTIAALIASSDMLG 261

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 779851706 246 FIPVSIYEAYKETLKIKRIA-APFELPEIHVYMLYSRSSLNSSVFSTFIE 294
Cdd:PRK11482 262 IMPSRFYNLFSRCWPLEKLPfPSLNEEQIDFSLHYNKLSLRDPVLENVID 311
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
10-182 3.37e-31

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 117.27  E-value: 3.37e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706  10 FDLNLLVIFECIYQHLSISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTTVGTNLHHHLEQNLNQIEQTIN 89
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706  90 MMH--HSDIKKKFVIYCSQMMSPGYMLEPMKLLMSE-ENYEIEQRDMliSPESAEDLLAYRKADLIFTIAPIKNRSVVCS 166
Cdd:COG0583   81 ELRalRGGPRGTLRIGAPPSLARYLLPPLLARFRARhPGVRLELREG--NSDRLVDALLEGELDLAIRLGPPPDPGLVAR 158

                        170
                 ....*....|....*.
gi 779851706 167 HFATVPIALICRENHP 182
Cdd:COG0583  159 PLGEERLVLVASPDHP 174
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
12-70 4.74e-20

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 81.66  E-value: 4.74e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 779851706   12 LNLLVIFECIYQHLSISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTTVG 70
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PBP2_LeuO cd08466
The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an ...
 135-287 1.43e-15

The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold; LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse model of Salmonella. In Vibrio cholerae, LeuO is involved in control of biofilm formation and in the stringent response. 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: 176155 [Multi-domain]  Cd Length: 200  Bit Score: 73.83  E-value: 1.43e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706 135 ISPESAEDLLA---YRKADLIFTIAPIKNRSVVCSHFATVPIALICRENHPRLADTVSLEALYREKFTFYQSAHPGVKEF 211
Cdd:cd08466   33 ESPSSEEDLFEdlrLQEVDLVIDYVPFRDPSFKSELLFEDELVCVARKDHPRIQGSLSLEQYLAEKHVVLSLRRGNLSAL 112

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 779851706 212 QNRANDLFPERDIAFRTDSISSLISMVSSSDLLGFIPVSIYEAYKETLKIKRIAAPFELPEIHVYMLYSRSSLNSS 287
Cdd:cd08466  113 DLLTEEVLPQRNIAYEVSSLLSMLAVVSQTDLIAIAPRWLADQYAEQLNLQILPLPFKTKPIPLYMVWHKSRERDP 188
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 26-151 1.94e-07

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: 51.66  E-value: 1.94e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706  26 SISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTTVGTNLHHHLEQNLNQIEQTINMMHHSDIKKKFVIYCS 105
Cdd:NF041036  17 SFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMDELKSFKGRQRLSICCT 96

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 779851706 106 QMMSPGYMLEPMKLLMSEENYEIEQRDMLISPESAEDLLAYRKADL 151
Cdd:NF041036  97 PTFGMAHLPGVLNRFMLRNADVVDLKFLFHSPAQALEGIQNKEFDL 142
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 10-79 2.12e-07

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: 51.46  E-value: 2.12e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706   10 FDLNLLVIFECIYQHLSISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRsGKGITPTTVGTNLHHHLEQ 79
Cdd:TIGR03298   1 LDYRQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHARQ 69
 
Name Accession Description Interval E-value
PRK11482 PRK11482
DNA-binding transcriptional regulator;
7-294 9.68e-37

DNA-binding transcriptional regulator;


Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 133.31  E-value: 9.68e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706   7 LKKFDLNLLVIFECIYQHLSISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTTVGTNLHHHLEQNLNQIEQ 86
Cdd:PRK11482  26 LRNIDLNLLTIFEAVYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHEYISQGLESILG 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706  87 TINMMHHSDIKKKFVIYCSQMMspGYMLEP-MKLLMSEENYEIEQRDMLISpeSAEDLLAYRKADLIFTIAPIKNRSVVC 165
Cdd:PRK11482 106 ALDITGSYDKQRTITIATTPSV--GALVMPvIYQAIKTHYPQLLLRNIPIS--DAENQLSQFQTDLIIDTHSCSNRTIQH 181

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706 166 SHFATVPIALICRENHPRLADTVSLEALYREKFTFYQSAHPGVKEFQNRANDLFPERDIAFRTDSISSLISMVSSSDLLG 245
Cdd:PRK11482 182 HVLFTDNVVLVCRQGHPLLSLEDDEETLDNAEHTLLLPEGQNFSGLRQRLQEMFPDRQISFSSYNILTIAALIASSDMLG 261

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 779851706 246 FIPVSIYEAYKETLKIKRIA-APFELPEIHVYMLYSRSSLNSSVFSTFIE 294
Cdd:PRK11482 262 IMPSRFYNLFSRCWPLEKLPfPSLNEEQIDFSLHYNKLSLRDPVLENVID 311
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
10-182 3.37e-31

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 117.27  E-value: 3.37e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706  10 FDLNLLVIFECIYQHLSISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTTVGTNLHHHLEQNLNQIEQTIN 89
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706  90 MMH--HSDIKKKFVIYCSQMMSPGYMLEPMKLLMSE-ENYEIEQRDMliSPESAEDLLAYRKADLIFTIAPIKNRSVVCS 166
Cdd:COG0583   81 ELRalRGGPRGTLRIGAPPSLARYLLPPLLARFRARhPGVRLELREG--NSDRLVDALLEGELDLAIRLGPPPDPGLVAR 158

                        170
                 ....*....|....*.
gi 779851706 167 HFATVPIALICRENHP 182
Cdd:COG0583  159 PLGEERLVLVASPDHP 174
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
12-70 4.74e-20

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 81.66  E-value: 4.74e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 779851706   12 LNLLVIFECIYQHLSISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTTVG 70
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PBP2_LeuO cd08466
The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an ...
 135-287 1.43e-15

The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold; LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse model of Salmonella. In Vibrio cholerae, LeuO is involved in control of biofilm formation and in the stringent response. 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: 176155 [Multi-domain]  Cd Length: 200  Bit Score: 73.83  E-value: 1.43e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706 135 ISPESAEDLLA---YRKADLIFTIAPIKNRSVVCSHFATVPIALICRENHPRLADTVSLEALYREKFTFYQSAHPGVKEF 211
Cdd:cd08466   33 ESPSSEEDLFEdlrLQEVDLVIDYVPFRDPSFKSELLFEDELVCVARKDHPRIQGSLSLEQYLAEKHVVLSLRRGNLSAL 112

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 779851706 212 QNRANDLFPERDIAFRTDSISSLISMVSSSDLLGFIPVSIYEAYKETLKIKRIAAPFELPEIHVYMLYSRSSLNSS 287
Cdd:cd08466  113 DLLTEEVLPQRNIAYEVSSLLSMLAVVSQTDLIAIAPRWLADQYAEQLNLQILPLPFKTKPIPLYMVWHKSRERDP 188
PRK10216 PRK10216
HTH-type transcriptional regulator YidZ;
7-93 7.37e-15

HTH-type transcriptional regulator YidZ;


Pssm-ID: 182312 [Multi-domain]  Cd Length: 319  Bit Score: 73.70  E-value: 7.37e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706   7 LKKFDLNLLVIFECIYQHLSISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTTVGTNLHHHLEQNLNQIEQ 86
Cdd:PRK10216   5 LTTLDLNLLLCLQLLMQERSVTKAAKRMNVTPSAVSKSLAKLRAWFDDPLFVNTPLGLSPTPLMVSMEQNLAEWMQMGNQ 84


                 ....*..
gi 779851706  87 TINMMHH 93
Cdd:PRK10216  85 LLDKPHH 91
leuO PRK09508
leucine transcriptional activator; Reviewed
 7-283 1.71e-11

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 63.89  E-value: 1.71e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706   7 LKKFDLNLLVIFECIYQHLSISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTTVGTNLHHHLEQNL----N 82
Cdd:PRK09508  19 LRMVDLNLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARARQLFGPVRQALqlvqN 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706  83 QI----------EQTINMMHHS--DIKKKFVIYCS-QMMSPGYMLepmkLLMSEENYEIEQRdmlispesaedlLAYRKA 149
Cdd:PRK09508  99 ELpgsgfepessERVFNLCICSplDIRLTSQIYNRiEQIAPNIHV----VFKSSLNQNIEHQ------------LRYQET 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706 150 DliFTIAPIKNRSvvcSHFATVPI-----ALICRENHPRLADTVSLEALYREKFTFYqsAHPGVKEFQN---RANDLfpE 221
Cdd:PRK09508 163 E--FVISYEEFDR---PEFTSVPLfkdelVLVASKNHPRIKGPITEEQLYNEQHAVV--SLDRFASFSQpwyDTVDK--Q 233

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 779851706 222 RDIAFRTDSISSLISMVSSSDLLGFIPVSIYEAYKETLKIKRIAAPFELPEIHVYMLYSRSS 283
Cdd:PRK09508 234 ASIAYQGTALSSVLNVVSQTHLVAIAPRWLAEEFAESLELQILPLPLKNNSRTCYLSWHESA 295
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
7-103 1.43e-10

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 61.17  E-value: 1.43e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706   7 LKKFDLNLLVIFECIYQHLSISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTTVGTNLHHHLEQNLNQIEQ 86
Cdd:PRK10086  11 LNGWQLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQ 90

                         90
                 ....*....|....*..
gi 779851706  87 TINMMHHSDIKKKFVIY 103
Cdd:PRK10086  91 EILDIKNQELSGTLTVY 107
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 135-283 2.21e-10

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: 59.15  E-value: 2.21e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706 135 ISPESAEDLLAYRKADLIFTIAPIKNRSVVCSHFATVPIALICRENHPRLADTVSLEALYREK---FTFYQSAHPGVKEF 211
Cdd:cd08417   36 LDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARKDHPLAGGPLTLEDYLAAPhvlVSPRGRGHGLVDDA 115

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 779851706 212 QNRANdlfPERDIAFRTDSISSLISMVSSSDLLGFIPVSIYEAYKETLKIKRIAAPFELPEIHVYMLYSRSS 283
Cdd:cd08417  116 LAELG---LSRRVALTVPHFLAAPALVAGTDLIATVPRRLAEALAERLGLRVLPLPFELPPFTVSLYWHPRR 184
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 136-294 1.09e-09

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: 57.30  E-value: 1.09e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706  136 SPESAEDLLAYRKADLIFTIAPIKNRSVVCSHFATVPIALICRENHPRLA-DTVSLEALYREKFTFYQSAHPGVKEFQNR 214
Cdd:pfam03466  39 NSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAPPDHPLARgEPVSLEDLADEPLILLPPGSGLRDLLDRA 118

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706  215 ANDLFPERDIAFRTDSISSLISMVSSSDLLGFIPVSIYEAYKETLKIKRIAAPFELPEIHVYMLYSRSSLNSSVFSTFIE 294
Cdd:pfam03466 119 LRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIE 198
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 26-86 1.84e-09

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 57.77  E-value: 1.84e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 779851706  26 SISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTTVGTNLHHHLEQNLNQIEQ 86
Cdd:PRK11233  17 SLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQ 77
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 26-151 1.94e-07

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: 51.66  E-value: 1.94e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706  26 SISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTTVGTNLHHHLEQNLNQIEQTINMMHHSDIKKKFVIYCS 105
Cdd:NF041036  17 SFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMDELKSFKGRQRLSICCT 96

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 779851706 106 QMMSPGYMLEPMKLLMSEENYEIEQRDMLISPESAEDLLAYRKADL 151
Cdd:NF041036  97 PTFGMAHLPGVLNRFMLRNADVVDLKFLFHSPAQALEGIQNKEFDL 142
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 10-79 2.12e-07

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: 51.46  E-value: 2.12e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706   10 FDLNLLVIFECIYQHLSISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRsGKGITPTTVGTNLHHHLEQ 79
Cdd:TIGR03298   1 LDYRQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHARQ 69
rbcR CHL00180
LysR transcriptional regulator; Provisional
 10-70 2.49e-07

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 51.17  E-value: 2.49e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 779851706  10 FDLNLLVIFECIYQHLSISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTTVG 70
Cdd:CHL00180   5 FTLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAG 65
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 12-70 2.93e-07

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 51.00  E-value: 2.93e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 779851706  12 LNLLVIFECIYQHLSISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTTVG 70
Cdd:PRK11139   8 LNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEG 66
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
10-79 5.80e-07

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 49.97  E-value: 5.80e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706  10 FDLNLLVIFECIYQHLSISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRsGKGITPTTVGTNLHHHLEQ 79
Cdd:PRK13348   2 LDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQ 70
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 136-294 7.69e-07

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: 48.75  E-value: 7.69e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706 136 SPESAEDLLAYRKADLIFTIAPIKNRSVVCSHFATVPIALICRENHPrLAD--TVSLEALYREKFTFYQSAHPGVKEFQN 213
Cdd:cd05466   37 GSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPDHP-LAKrkSVTLADLADEPLILFERGSGLRRLLDR 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706 214 RANDLFPERDIAFRTDSISSLISMVSSSDLLGFIPVSIYEAYK-ETLKIKRIAAPFelPEIHVYMLYSRSSLNSSVFSTF 292
Cdd:cd05466  116 AFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELAdGGLVVLPLEDPP--LSRTIGLVWRKGRYLSPAARAF 193


                 ..
gi 779851706 293 IE 294
Cdd:cd05466  194 LE 195
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
29-79 1.07e-05

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 46.31  E-value: 1.07e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 779851706  29 KAAETLYITPSAVSQSLQRLRGQLNDPLFIRsGKGITPTTVGTNLHHHLEQ 79
Cdd:PRK03635  21 RAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQ 70
PRK09986 PRK09986
LysR family transcriptional regulator;
7-215 1.75e-05

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 45.48  E-value: 1.75e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706   7 LKKFDLNLLVIFECIYQHLSISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTTVGTNLHHHLEQNLNQIEQ 86
Cdd:PRK09986   4 LYRIDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQ 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706  87 TINMMH----HSDIKKKFVIYCSQMMspGYMLEPMKLLMSEE-NYEIEQRDMliSPESAEDLLAYRKADL-IFTIAPIK- 159
Cdd:PRK09986  84 SLARVEqigrGEAGRIEIGIVGTALW--GRLRPAMRHFLKENpNVEWLLREL--SPSMQMAALERRELDAgIWRMADLEp 159

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 779851706 160 NRSVVCSHFATVPIALICRENHPrLA--DTVSLEALYREKFTFYQSAHPGVKEFQNRA 215
Cdd:PRK09986 160 NPGFTSRRLHESAFAVAVPEEHP-LAsrSSVPLKALRNEYFITLPFVHSDWGKFLQRV 216
nhaR PRK11062
transcriptional activator NhaR; Provisional
 13-70 2.18e-05

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 45.38  E-value: 2.18e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 779851706  13 NLLVIFECIYQHLSISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTTVG 70
Cdd:PRK11062   7 NHLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELG 64
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
10-85 1.38e-04

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 42.87  E-value: 1.38e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 779851706  10 FDLNLLVIFECIYQHLSISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTTVGTNLHHHLEQNLNQIE 85
Cdd:PRK10094   2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLE 77
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 23-85 1.71e-04

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 42.64  E-value: 1.71e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 779851706  23 QHLSISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTTVGTNLHHHLEQNLNQIE 85
Cdd:PRK11242  14 EHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLE 76
PRK09801 PRK09801
LysR family transcriptional regulator;
1-89 3.32e-04

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 41.56  E-value: 3.32e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706   1 MANLYDLKKfDLNLLVifECIYQHlSISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTTVGTNLHHHLEQN 80
Cdd:PRK09801   1 MLNSWPLAK-DLQVLV--EIVHSG-SFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEI 76


                 ....*....
gi 779851706  81 LNQIEQTIN 89
Cdd:PRK09801  77 LTQYQRLVD 85
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 11-73 3.45e-04

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 41.55  E-value: 3.45e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 779851706  11 DLNLLVIFECIYQHLSISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTTVGTNL 73
Cdd:PRK15092  12 DLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQL 74
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
35-105 4.44e-04

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 40.96  E-value: 4.44e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 779851706  35 YITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTTVGTNLHHHLEQNLNQIEQ-TINMMHHSD-IKKKFVIYCS 105
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQlRHTLDQQGPsLSGELSLFCS 74
PRK09791 PRK09791
LysR family transcriptional regulator;
12-76 4.83e-04

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 41.29  E-value: 4.83e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 779851706  12 LNLLVIFECIYQHLSISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTTVGTNLHHH 76
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQH 71
PRK10341 PRK10341
transcriptional regulator TdcA;
15-91 6.45e-04

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 40.62  E-value: 6.45e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 779851706  15 LVIFECIYQHLSISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTTVGTNLHHHLEQNLNQIEQTINMM 91
Cdd:PRK10341  12 LVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEI 88
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 14-68 1.35e-03

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 39.64  E-value: 1.35e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 779851706  14 LLVIFECIYQHLSISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTT 68
Cdd:PRK12683   6 LRIIREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTGLT 60
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
17-68 1.40e-03

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 39.57  E-value: 1.40e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 779851706  17 IFECIYQHLSISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTT 68
Cdd:PRK12684   9 VREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRGLT 60
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 17-86 1.84e-03

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 39.20  E-value: 1.84e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 779851706  17 IFECIYQHLSISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITP-TTVGTNLHHHLEQNLNQIEQ 86
Cdd:PRK12682   9 VREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKGlTEPGKAVLDVIERILREVGN 79
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
29-106 1.87e-03

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 39.23  E-value: 1.87e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 779851706  29 KAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGKGITPTTVGTNLHHHLEqnlnqieqtiNMMHHSDIKKKFVIYCSQ 106
Cdd:PRK03601  20 RAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAE----------TLMNTWQAAKKEVAHTSQ 87
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
 135-287 2.40e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. 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. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate of the oxidative degradation of the aromatic ring in soil bacteria. LinR positively regulates expression of the genes (linD and linE) encoding enzymes for gamma-hexachlorocyclohexane (a haloorganic insecticide) degradation. Expression of linD and linE are induced by their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ) and chlorohydroquinone (CHQ). 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: 176148 [Multi-domain]  Cd Length: 201  Bit Score: 38.33  E-value: 2.40e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 779851706 135 ISPESAEDLLAYRKADLIFTIAPIKNRSVVCSHFATVPIALICRENHPRLADTVSLEALYREKFTFYQSAHPGVKEFQNR 214
Cdd:cd08459   36 LPVDELEEALESGEIDLAIGYLPDLGAGFFQQRLFRERYVCLVRKDHPRIGSTLTLEQFLAARHVVVSASGTGHGLVEQA 115

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 779851706 215 ANDLFPERDIAFRTDSISSLISMVSSSDLLGFIPVSIYEAYKETLKIKRIAAPFELPEIHVYMLYSRSSLNSS 287
Cdd:cd08459  116 LREAGIRRRIALRVPHFLALPLIVAQTDLVATVPERLARLFARAGGLRIVPLPFPLPPFEVKLYWHRRFHRDP 188
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 26-62 4.53e-03

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 38.13  E-value: 4.53e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 779851706  26 SISKAAETLYITPSAVSQSLQRLRGQLNDPLFIRSGK 62
Cdd:PRK10837  19 STTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGK 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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