NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|504694821|ref|WP_014881923|]
View 

MULTISPECIES: DNA-binding transcriptional regulator DsdC [Enterobacter]

Protein Classification

DNA-binding transcriptional regulator DsdC( domain architecture ID 11484572)

DNA-binding transcriptional regulator DsdC regulates the expression of the dsdX-dsdA operon

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
2-307 0e+00

DNA-binding transcriptional regulator DsdC;


:

Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 605.84  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821   2 TDANEARNRLLNGWQLSKMYTFEVAARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGKRVYWT 81
Cdd:PRK10086   1 EPLREMRNRLLNGWQLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  82 LKSSLDTLNQEILDIKNQALSGTLTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGNDYVNMQRTGIDLALYFDDTPA 161
Cdd:PRK10086  81 LKSSLDTLNQEILDIKNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPS 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 162 NHLSHHFLMDEEILPVCSPAYAREHQLVKNPHNLSHCTLLHDRQAWSNDSGTDEWLSWAQHFAINM-PPSSGIGFDRSDL 240
Cdd:PRK10086 161 AQLTHHFLMDEEILPVCSPEYAERHALTGNPDNLRHCTLLHDRQAWSNDSGTDEWHSWAQHFGVNLlPPSSGIGFDRSDL 240

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 504694821 241 AIIAAINDVGVAMGRKRLVQKRLEKGELIAPFGEKTLKCHQHYYISTLPGRQWPKIDAFISWLRERA 307
Cdd:PRK10086 241 AVIAAMNHIGVAMGRKRLVQKRLASGELVAPFGDMEVKCHQHYYVTTLPGRQWPKIEAFIDWLKEQV 307
 
Name Accession Description Interval E-value
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
2-307 0e+00

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 605.84  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821   2 TDANEARNRLLNGWQLSKMYTFEVAARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGKRVYWT 81
Cdd:PRK10086   1 EPLREMRNRLLNGWQLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  82 LKSSLDTLNQEILDIKNQALSGTLTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGNDYVNMQRTGIDLALYFDDTPA 161
Cdd:PRK10086  81 LKSSLDTLNQEILDIKNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPS 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 162 NHLSHHFLMDEEILPVCSPAYAREHQLVKNPHNLSHCTLLHDRQAWSNDSGTDEWLSWAQHFAINM-PPSSGIGFDRSDL 240
Cdd:PRK10086 161 AQLTHHFLMDEEILPVCSPEYAERHALTGNPDNLRHCTLLHDRQAWSNDSGTDEWHSWAQHFGVNLlPPSSGIGFDRSDL 240

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 504694821 241 AIIAAINDVGVAMGRKRLVQKRLEKGELIAPFGEKTLKCHQHYYISTLPGRQWPKIDAFISWLRERA 307
Cdd:PRK10086 241 AVIAAMNHIGVAMGRKRLVQKRLASGELVAPFGDMEVKCHQHYYVTTLPGRQWPKIEAFIDWLKEQV 307
dsdC TIGR02036
D-serine deaminase transcriptional activator; This family, part of the LysR family of ...
 8-308 0e+00

D-serine deaminase transcriptional activator; This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea. [Regulatory functions, DNA interactions]


Pssm-ID: 131091 [Multi-domain]  Cd Length: 302  Bit Score: 533.71  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821    8 RNRLLNGWQLSKMYTFEVAARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGKRVYWTLKSSLD 87
Cdd:TIGR02036   1 RNRRLNSFQLSKMHTFEVAARHQSFSLAAEELSLTPSAISHRINQLEEELGIQLFVRSHRKVELTHEGKRIYWALKSSLD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821   88 TLNQEILDIKNQALSGTLTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGNDYVNMQRTGIDLALYFDDTPANHLSHH 167
Cdd:TIGR02036  81 TLNQEILDIKNQELSGTLTLYSRPSFAQCWLVPRIGDFTRRYPSISLTVLTGNENINFQGAGIDVAIYFDDAPPAKLTCH 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  168 FLMDEEILPVCSPAYAREHQLVKNPHNLSHCTLLHDRQAWSNDSGTDEWLSWAQHFAIN-MPPSSGIGFDRSDLAIIAAI 246
Cdd:TIGR02036 161 FIMDETILPVCSPEYAQRHALTNTVINLCHCTLLHDNQAWSYDSGTDEWHSWANHYAVNnLPTSSGIGFDRSDLAVIAAM 240

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 504694821  247 NDVGVAMGRKRLVQKRLEKGELIAPFGEKTLKCHQHYYISTLPGRQWPKIDAFISWLRERAR 308
Cdd:TIGR02036 241 NNAGVAMGRKSLVQKRLASGELVAPFGDMTVKCHQRYYVATLPNRQNPKIELFIIWLREQVK 302
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 104-303 7.76e-55

The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. 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: 176123 [Multi-domain]  Cd Length: 194  Bit Score: 176.62  E-value: 7.76e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 104 TLTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGNDYVNMQRTGIDLALYFDDTPANHLSHHFLMDEEILPVCSPAYA 183
Cdd:cd08432    1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 184 REHQLVKnPHNLSHCTLLHDRQAWsndsgtDEWLSWAQHFAINMP-PSSGIGFDRSDLAIIAAINDVGVAMGRKRLVQKR 262
Cdd:cd08432   81 AGLPLLS-PADLARHTLLHDATRP------EAWQWWLWAAGVADVdARRGPRFDDSSLALQAAVAGLGVALAPRALVADD 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 504694821 263 LEKGELIAPFGEkTLKCHQHYYISTLPGR-QWPKIDAFISWL 303
Cdd:cd08432  154 LAAGRLVRPFDL-PLPSGGAYYLVYPPGRaESPAVAAFRDWL 194
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
17-308 2.36e-46

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 156.95  E-value: 2.36e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  17 LSKMYTFEVAARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGKRVYWTLKSSLDTLNQEILDI 96
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  97 KN--QALSGTLTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGN--DYVNMQRTG-IDLALYFDDTPANHLSHHFLMD 171
Cdd:COG0583   83 RAlrGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNsdRLVDALLEGeLDLAIRLGPPPDPGLVARPLGE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 172 EEILPVCSPAYArehqlvknphnlshctlLHDRQAWSNDsgtdewlswaqhfainmppssgigfdrSDLAIIAAINDVGV 251
Cdd:COG0583  163 ERLVLVASPDHP-----------------LARRAPLVNS---------------------------LEALLAAVAAGLGI 198

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 504694821 252 AMGRKRLVQKRLEKGELIA-PFGEKTLkcHQHYYISTLPGRQW-PKIDAFISWLRERAR 308
Cdd:COG0583  199 ALLPRFLAADELAAGRLVAlPLPDPPP--PRPLYLVWRRRRHLsPAVRAFLDFLREALA 255
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
17-76 2.03e-21

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 85.51  E-value: 2.03e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821   17 LSKMYTFEVAARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGK 76
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 27-188 3.67e-17

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 79.97  E-value: 3.67e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  27 ARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGKRVYWTLKSSLDTLNQEILDIKN--QALSGT 104
Cdd:NF040786  13 AEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDRygKESKGV 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 105 LTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTG--NDYVNMQRTG-IDLALYFDDTPANHLSHHFLMDEEILPVCSPA 181
Cdd:NF040786  93 LRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISdsIKVIELLLEGeVDIGFTGTKLEKKRLVYTPFYKDRLVLITPNG 172


                 ....*..
gi 504694821 182 YAREHQL 188
Cdd:NF040786 173 TEKYRML 179
HTH_ARSR smart00418
helix_turn_helix, Arsenical Resistance Operon Repressor;
36-85 3.97e-03

helix_turn_helix, Arsenical Resistance Operon Repressor;


Pssm-ID: 197713 [Multi-domain]  Cd Length: 66  Bit Score: 35.26  E-value: 3.97e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 504694821    36 AEELSLSPSAVSHRINLLEEElGIqlfvrshrkVELTQEGKRVYWTLKSS 85
Cdd:smart00418  17 AEILGLSQSTVSHHLKKLREA-GL---------VESRREGKRVYYSLTDE 56
 
Name Accession Description Interval E-value
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
2-307 0e+00

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 605.84  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821   2 TDANEARNRLLNGWQLSKMYTFEVAARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGKRVYWT 81
Cdd:PRK10086   1 EPLREMRNRLLNGWQLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  82 LKSSLDTLNQEILDIKNQALSGTLTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGNDYVNMQRTGIDLALYFDDTPA 161
Cdd:PRK10086  81 LKSSLDTLNQEILDIKNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENVNFQRAGIDLAIYFDDAPS 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 162 NHLSHHFLMDEEILPVCSPAYAREHQLVKNPHNLSHCTLLHDRQAWSNDSGTDEWLSWAQHFAINM-PPSSGIGFDRSDL 240
Cdd:PRK10086 161 AQLTHHFLMDEEILPVCSPEYAERHALTGNPDNLRHCTLLHDRQAWSNDSGTDEWHSWAQHFGVNLlPPSSGIGFDRSDL 240

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 504694821 241 AIIAAINDVGVAMGRKRLVQKRLEKGELIAPFGEKTLKCHQHYYISTLPGRQWPKIDAFISWLRERA 307
Cdd:PRK10086 241 AVIAAMNHIGVAMGRKRLVQKRLASGELVAPFGDMEVKCHQHYYVTTLPGRQWPKIEAFIDWLKEQV 307
dsdC TIGR02036
D-serine deaminase transcriptional activator; This family, part of the LysR family of ...
 8-308 0e+00

D-serine deaminase transcriptional activator; This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea. [Regulatory functions, DNA interactions]


Pssm-ID: 131091 [Multi-domain]  Cd Length: 302  Bit Score: 533.71  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821    8 RNRLLNGWQLSKMYTFEVAARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGKRVYWTLKSSLD 87
Cdd:TIGR02036   1 RNRRLNSFQLSKMHTFEVAARHQSFSLAAEELSLTPSAISHRINQLEEELGIQLFVRSHRKVELTHEGKRIYWALKSSLD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821   88 TLNQEILDIKNQALSGTLTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGNDYVNMQRTGIDLALYFDDTPANHLSHH 167
Cdd:TIGR02036  81 TLNQEILDIKNQELSGTLTLYSRPSFAQCWLVPRIGDFTRRYPSISLTVLTGNENINFQGAGIDVAIYFDDAPPAKLTCH 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  168 FLMDEEILPVCSPAYAREHQLVKNPHNLSHCTLLHDRQAWSNDSGTDEWLSWAQHFAIN-MPPSSGIGFDRSDLAIIAAI 246
Cdd:TIGR02036 161 FIMDETILPVCSPEYAQRHALTNTVINLCHCTLLHDNQAWSYDSGTDEWHSWANHYAVNnLPTSSGIGFDRSDLAVIAAM 240

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 504694821  247 NDVGVAMGRKRLVQKRLEKGELIAPFGEKTLKCHQHYYISTLPGRQWPKIDAFISWLRERAR 308
Cdd:TIGR02036 241 NNAGVAMGRKSLVQKRLASGELVAPFGDMTVKCHQRYYVATLPNRQNPKIELFIIWLREQVK 302
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 23-308 7.21e-72

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 223.95  E-value: 7.21e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  23 FEVAARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGKRVYWTLKSSLDTLNQEILDIKNQALS 102
Cdd:PRK11139  14 FEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRARSAK 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 103 GTLTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGNDYVNMQRTGIDLALYFDDT--PANHLSHhfLMDEEILPVCSP 180
Cdd:PRK11139  94 GALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLKAVDRLEDFLRDDVDVAIRYGRGnwPGLRVEK--LLDEYLLPVCSP 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 181 AYAREHQLVKNPHNLSHCTLLHdrqawsnDSGTDEWLSWAQHFAI-NMPPSSGIGFDRSDLAIIAAINDVGVAMGRKRLV 259
Cdd:PRK11139 172 ALLNGGKPLKTPEDLARHTLLH-------DDSREDWRAWFRAAGLdDLNVQQGPIFSHSSMALQAAIHGQGVALGNRVLA 244

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 504694821 260 QKRLEKGELIAPFGEkTLKCHQHYYISTLPGR-QWPKIDAFISWLRERAR 308
Cdd:PRK11139 245 QPEIEAGRLVCPFDT-VLPSPNAFYLVCPDSQaELPKVAAFRQWLLAEAA 293
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 104-303 7.76e-55

The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. 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: 176123 [Multi-domain]  Cd Length: 194  Bit Score: 176.62  E-value: 7.76e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 104 TLTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGNDYVNMQRTGIDLALYFDDTPANHLSHHFLMDEEILPVCSPAYA 183
Cdd:cd08432    1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 184 REHQLVKnPHNLSHCTLLHDRQAWsndsgtDEWLSWAQHFAINMP-PSSGIGFDRSDLAIIAAINDVGVAMGRKRLVQKR 262
Cdd:cd08432   81 AGLPLLS-PADLARHTLLHDATRP------EAWQWWLWAAGVADVdARRGPRFDDSSLALQAAVAGLGVALAPRALVADD 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 504694821 263 LEKGELIAPFGEkTLKCHQHYYISTLPGR-QWPKIDAFISWL 303
Cdd:cd08432  154 LAAGRLVRPFDL-PLPSGGAYYLVYPPGRaESPAVAAFRDWL 194
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
17-308 2.36e-46

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 156.95  E-value: 2.36e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  17 LSKMYTFEVAARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGKRVYWTLKSSLDTLNQEILDI 96
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  97 KN--QALSGTLTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGN--DYVNMQRTG-IDLALYFDDTPANHLSHHFLMD 171
Cdd:COG0583   83 RAlrGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNsdRLVDALLEGeLDLAIRLGPPPDPGLVARPLGE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 172 EEILPVCSPAYArehqlvknphnlshctlLHDRQAWSNDsgtdewlswaqhfainmppssgigfdrSDLAIIAAINDVGV 251
Cdd:COG0583  163 ERLVLVASPDHP-----------------LARRAPLVNS---------------------------LEALLAAVAAGLGI 198

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 504694821 252 AMGRKRLVQKRLEKGELIA-PFGEKTLkcHQHYYISTLPGRQW-PKIDAFISWLRERAR 308
Cdd:COG0583  199 ALLPRFLAADELAAGRLVAlPLPDPPP--PRPLYLVWRRRRHLsPAVRAFLDFLREALA 255
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 104-303 1.06e-32

The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold; GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar 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: 176170 [Multi-domain]  Cd Length: 194  Bit Score: 119.32  E-value: 1.06e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 104 TLTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGNDYVNMQRTGIDLALYF-DDTPANHLShHFLMDEEILPVCSPAY 182
Cdd:cd08481    1 TLELAVLPTFGTRWLIPRLPDFLARHPDITVNLVTRDEPFDFSQGSFDAAIHFgDPVWPGAES-EYLMDEEVVPVCSPAL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 183 AREHQLVKnPHNLSHCTLLH--DR-QAWSNdsgtdewlsWAQHFAINMP-PSSGIGFDRSDLAIIAAINDVGVAMGRKRL 258
Cdd:cd08481   80 LAGRALAA-PADLAHLPLLQqtTRpEAWRD---------WFEEVGLEVPtAYRGMRFEQFSMLAQAAVAGLGVALLPRFL 149

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 504694821 259 VQKRLEKGELIAPFGeKTLKCHQHYYISTLPGR-QWPKIDAFISWL 303
Cdd:cd08481  150 IEEELARGRLVVPFN-LPLTSDKAYYLVYPEDKaESPPVQAFRDWL 194
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 105-303 2.83e-25

The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase genes, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators, BlaA and AmpR, that are involved in control of the expression of beta-lactamase genes. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. BlaA (a constitutive class A penicillinase) belongs to the LysR family of transcriptional regulators, while BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin-binding protein, but it does not act as a beta-lactamase. AmpR regulates the expression of beta-lactamases in many enterobacterial strains and many other gram-negative bacilli. In contrast to BlaA, AmpR acts an activator only in the presence of the beta-lactam inducer. In the absence of the inducer, AmpR acts as a repressor. 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: 176173 [Multi-domain]  Cd Length: 189  Bit Score: 99.75  E-value: 2.83e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 105 LTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGNDYVNMQRTGIDLALYFDDTpANHLSHH-FLMDEEILPVCSPAYA 183
Cdd:cd08484    2 LTVGAVGTFAVGWLLPRLAEFRQLHPFIDLRLSTNNNRVDIAAEGLDFAIRFGEG-AWPGTDAtRLFEAPLSPLCTPELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 184 REhqlVKNPHNLSHCTLLHDRQawsndsgTDEWLSWAQHFAINMPPSSGIGFDRSDLAIIAAINDVGVAMGRKRLVQKRL 263
Cdd:cd08484   81 RR---LSEPADLANETLLRSYR-------ADEWPQWFEAAGVPPPPINGPVFDSSLLMVEAALQGAGVALAPPSMFSREL 150

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 504694821 264 EKGELIAPFGeKTLKCHQhYYISTLPGRQW-PKIDAFISWL 303
Cdd:cd08484  151 ASGALVQPFK-ITVSTGS-YWLTRLKSKPEtPAMSAFSQWL 189
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 105-303 2.31e-23

The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in control of the expression of beta-lactamase gene ampC, contains the type 2 periplasmic binding fold; AmpR acts as a transcriptional activator by binding to a DNA region immediately upstream of the ampC promoter. In the absence of a beta-lactam inducer, AmpR represses the synthesis of beta-lactamase, whereas expression is induced in the presence of a beta-lactam inducer. The AmpD, AmpG, and AmpR proteins are involved in the induction of AmpC-type beta-lactamase (class C) which produced by enterobacterial strains and many other gram-negative bacilli. The activation of ampC by AmpR requires ampG for induction or high-level expression of AmpC. It is probable that the AmpD and AmpG work together to modulate the ability of AmpR to activate ampC expression. 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: 176177 [Multi-domain]  Cd Length: 191  Bit Score: 94.91  E-value: 2.31e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 105 LTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGNDYVNMQRTGIDLALYFDDTPANHLSHHFLMDEEILPVCSPAYAR 184
Cdd:cd08488    2 LHVGAVGTFAVGWLLPRLADFQNRHPFIDLRLSTNNNRVDIAAEGLDYAIRFGSGAWHGIDATRLFEAPLSPLCTPELAR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 185 EhqlVKNPHNLSHCTLLHDRQAwsndsgtDEWLSW--AQHFAINMPPSSGIGFDRSDLAIIAAINDVGVAMGRKRLVQKR 262
Cdd:cd08488   82 Q---LREPADLARHTLLRSYRA-------DEWPQWfeAAGVGHPCGLPNSIMFDSSLGMMEAALQGLGVALAPPSMFSRQ 151

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 504694821 263 LEKGELIAPFgEKTLKCHQhYYISTLPGR-QWPKIDAFISWL 303
Cdd:cd08488  152 LASGALVQPF-ATTLSTGS-YWLTRLQSRpETPAMSAFSAWL 191
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 111-303 1.65e-22

The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is involved in control of tryptophan synthesis, contains type 2 periplasmic binding fold; TrpI and indoleglycerol phosphate (InGP), are required to activate transcription of the trpBA, the genes for tryptophan synthase. The trpBA is induced by the InGp substrate, rather than by tryptophan, but the exact mechanism of the activation event is not known. This substrate-binding domain of TrpI 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: 176171 [Multi-domain]  Cd Length: 195  Bit Score: 92.46  E-value: 1.65e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 111 PSIAQCWLVPMLGDFTRRYPSISLTVLTGNDYVNMQRTGIDLALYFDDTPANHLSHHF-LMDEEILPVCSPAYAREHQLV 189
Cdd:cd08482    8 GSLLMRWLIPRLPAFQAALPDIDLQLSASDGPVDSLRDGIDAAIRFNDAPWPAGMQVIeLFPERVGPVCSPSLAPTVPLR 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 190 KNP-HNLSHCTLLHDRqawsndSGTDEWLSWAQHFAINMPPSS-GIGFDRSDLAIIAAINDVGVAMGRKRLVQKRLEKGE 267
Cdd:cd08482   88 QAPaAALLGAPLLHTR------SRPQAWPDWAAAQGLAPEKLGtGQSFEHFYYLLEAAVAGLGVAIAPWPLVRDDLASGR 161

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 504694821 268 LIAPFGekTLKCHQHYYISTLPGRQWPKIDAFISWL 303
Cdd:cd08482  162 LVAPWG--FIETGSHYVLLRPARLRDSRAGALADWL 195
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 105-303 4.84e-22

The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold; The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine and homocysteine, and orf5, a gene of unknown. The topology of this C-terminal domain of HvrB 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: 176172 [Multi-domain]  Cd Length: 190  Bit Score: 91.25  E-value: 4.84e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 105 LTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGNDYVNMQRTGIDLALYF--DDTPANHLShhFLMDEEILPVCSPAY 182
Cdd:cd08483    2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYgnGDWPGLESE--PLTAAPFVVVAAPGL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 183 AREhQLVKNPHNLSHCTllhdrqaWSNDSGTDEWLSWAQHFAINMPPSSGIGFDRSDLAIIAAINDVGVAMGRKRLVQKR 262
Cdd:cd08483   80 LGD-RKVDSLADLAGLP-------WLQERGTNEQRVWLASMGVVPDLERGVTFLPGQLVLEAARAGLGLSIQARALVEPD 151

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 504694821 263 LEKGELIAPFGEKTLKchQHYYISTLPGRQWPKIDAFISWL 303
Cdd:cd08483  152 IAAGRLTVLFEEEEEG--LGYHIVTRPGVLRPAAKAFVRWL 190
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
17-76 2.03e-21

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 85.51  E-value: 2.03e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821   17 LSKMYTFEVAARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGK 76
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 105-303 2.28e-21

The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which involved in control of the beta-lactamase gene expression; contains the type 2 periplasmic binding fold; This CD represents the C-terminal substrate binding domain of LysR-type transcriptional regulator, BlaA, that involved in control of the expression of beta-lactamase genes, blaA and blaB. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. The blaA gene is located just upstream of blaB in the opposite direction and regulates the expression of the blaB. BlaA also negatively auto-regulates the expression of its own gene, blaA. BlaA (a constitutive class A penicllinase) belongs to the LysR family of transcriptional regulators, whereas BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin binding protein but it does not act as a beta-lactamase. 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: 176176 [Multi-domain]  Cd Length: 189  Bit Score: 89.53  E-value: 2.28e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 105 LTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGNDYVNMQRTGIDLALYFDDT--PANHLSHhfLMDEEILPVCSPAY 182
Cdd:cd08487    2 LTVGAVGTFAVGWLLPRLAEFRQLHPFIELRLRTNNNVVDLATEGLDFAIRFGEGlwPATHNER--LLDAPLSVLCSPEI 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 183 AREhqlVKNPHNLSHCTLLHDRQawsndsgTDEWLSWAQHFAINMPPSSGIGFDRSDLAIIAAINDVGVAMGRKRLVQKR 262
Cdd:cd08487   80 AKR---LSHPADLINETLLRSYR-------TDEWLQWFEAANMPPIKIRGPVFDSSRLMVEAAMQGAGVALAPAKMFSRE 149

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 504694821 263 LEKGELIAPFgeKTLKCHQHYYISTLPGRQW-PKIDAFISWL 303
Cdd:cd08487  150 IENGQLVQPF--KIEVETGSYWLTWLKSKPMtPAMELFRQWI 189
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 102-308 1.01e-20

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: 88.11  E-value: 1.01e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  102 SGTLTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGN--DYVNMQRTG-IDLALYFDDTPANHLSHHFLMDEEILPVC 178
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNseELLDLLLEGeLDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  179 SPAYAREHQLVKNPHNLSHCTLLHDRQAWSNDSGTDEWLSwaqhfAINMPPSSGIGFDRSDLAIIAAINDVGVAMGRKRL 258
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALR-----AAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSA 155

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 504694821  259 VQKRLEKGELIA-PFGEKTLkcHQHYYISTLPGR-QWPKIDAFISWLRERAR 308
Cdd:pfam03466 156 VARELADGRLVAlPLPEPPL--PRELYLVWRKGRpLSPAVRAFIEFLREALA 205
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 27-188 3.67e-17

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 79.97  E-value: 3.67e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  27 ARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGKRVYWTLKSSLDTLNQEILDIKN--QALSGT 104
Cdd:NF040786  13 AEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDRygKESKGV 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 105 LTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTG--NDYVNMQRTG-IDLALYFDDTPANHLSHHFLMDEEILPVCSPA 181
Cdd:NF040786  93 LRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISdsIKVIELLLEGeVDIGFTGTKLEKKRLVYTPFYKDRLVLITPNG 172


                 ....*..
gi 504694821 182 YAREHQL 188
Cdd:NF040786 173 TEKYRML 179
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 103-303 7.50e-17

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 77.10  E-value: 7.50e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 103 GTLTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGNDYVNMQRTGIDLALYFDDTPANHLSHHFLMDEEILPVCSPAY 182
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 183 AREHQLVKNPHNLSHctllHDRQAWSNDSGTDEWLSWAQHFAINMPPSSGIGFDRSDLAIIAAINDVGVAMGRKRLVQKR 262
Cdd:cd08422   81 LARHGTPQTPEDLAR----HRCLGYRLPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAED 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 504694821 263 LEKGELIAPFGEKTLKCHQHYYIstLPGRQW--PKIDAFISWL 303
Cdd:cd08422  157 LASGRLVRVLPDWRPPPLPIYAV--YPSRRHlpAKVRAFIDFL 197
PRK09801 PRK09801
LysR family transcriptional regulator;
11-204 1.15e-14

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 73.15  E-value: 1.15e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  11 LLNGWQLSKMYTFEVAARHE-SFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGKRVYwtlKSSLDTL 89
Cdd:PRK09801   1 MLNSWPLAKDLQVLVEIVHSgSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCY---EHALEIL 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  90 NQ------EILDIKNQAlSGTLTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGNDYVNMQRTGIDLALYFDDTPANH 163
Cdd:PRK09801  78 TQyqrlvdDVTQIKTRP-EGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDY 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 504694821 164 LSHHFLMDEEILPVCSPAYAREHQLVKNPHNLSH--CTLLHDR 204
Cdd:PRK09801 157 YIAHLLTKNKRILCAAPEYLQKYPQPQSLQELSRhdCLVTKER 199
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
41-139 1.70e-14

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 72.16  E-value: 1.70e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  41 LSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGKRVywtLKSSLDTLNQ-----EILDIKNQALSGTLTVYSRPSIAQ 115
Cdd:PRK11716   3 VSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEEL---RPFAQQTLLQwqqlrHTLDQQGPSLSGELSLFCSVTAAY 79

                         90       100
                 ....*....|....*....|....
gi 504694821 116 CWLVPMLGDFTRRYPSISLTVLTG 139
Cdd:PRK11716  80 SHLPPILDRFRAEHPLVEIKLTTG 103
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 21-136 1.61e-13

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 69.59  E-value: 1.61e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  21 YTFEV---AARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGKrvyWTLKSSLDTLNQeILDIK 97
Cdd:PRK11074   5 YSLEVvdaVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGE---WFVKEARSVIKK-MQETR 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 504694821  98 NQAL------SGTLtvysrpSIAQCWLV------PMLGDFTRRYPSISLTV 136
Cdd:PRK11074  81 RQCQqvangwRGQL------SIAVDNIVrpdrtrQLIVDFYRHFDDVELII 125
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
16-154 3.07e-13

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 69.02  E-value: 3.07e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  16 QLSKMYTFEVAARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGKRVYWTLKSSLDTLNQ--EI 93
Cdd:PRK10632   3 RLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDvhEQ 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 504694821  94 LDIKNQALSGTLTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGNDYVNMQRTGIDLAL 154
Cdd:PRK10632  83 LYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVI 143
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
21-140 5.01e-13

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 68.46  E-value: 5.01e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  21 YTFEVAARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVR-SHRKVELTQEGKRVYwtlkSSLDTLNQEILDIK-- 97
Cdd:PRK12684   8 FVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRhGKRLRGLTEPGRIIL----ASVERILQEVENLKrv 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 504694821  98 -----NQAlSGTLTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGN 140
Cdd:PRK12684  84 gkefaAQD-QGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGS 130
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 27-136 3.19e-12

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 65.75  E-value: 3.19e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  27 ARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEG-------KRVYwtlkSSLDTLNQEILDIKNq 99
Cdd:PRK11242  13 AEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGevylryaRRAL----QDLEAGRRAIHDVAD- 87

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 504694821 100 aLS-GTLTVYSRPSIAqCWLV-PMLGDFTRRYPSISLTV 136
Cdd:PRK11242  88 -LSrGSLRLAMTPTFT-AYLIgPLIDAFHARYPGITLTI 124
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
31-201 1.50e-11

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 63.88  E-value: 1.50e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  31 SFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGKRVywtlkssLDTLNQEILDIKNQALSGTLTVYSR 110
Cdd:PRK15421  18 SLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEIL-------LQLANQVLPQISQALQACNEPQQTR 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 111 PSIA-QC-----WLVPMLGDFTRRYPSISLTVLTGNDY---VNMQRTGIDLALYFDDTPANHLSHHFLMDEEILPVCSPA 181
Cdd:PRK15421  91 LRIAiEChsciqWLTPALENFHKNWPQVEMDFKSGVTFdpqPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAPD 170

                        170       180
                 ....*....|....*....|
gi 504694821 182 YAREHQLVKNPHNLSHCTLL 201
Cdd:PRK15421 171 HPLAAKTRITPEDLASETLL 190
rbcR CHL00180
LysR transcriptional regulator; Provisional
 27-136 4.92e-11

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 62.34  E-value: 4.92e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  27 ARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGKRVywtLKSSLDTLN------QEILDIKNQA 100
Cdd:CHL00180  17 ATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELL---LRYGNRILAlceetcRALEDLKNLQ 93

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 504694821 101 lSGTLTVYSRPSIAQcWLVP-MLGDFTRRYPSISLTV 136
Cdd:CHL00180  94 -RGTLIIGASQTTGT-YLMPrLIGLFRQRYPQINVQL 128
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 29-197 1.17e-10

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 61.16  E-value: 1.17e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  29 HESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGKRVYWTLKSSL--DTLNQEILDIKNQALSGTLT 106
Cdd:PRK14997  16 EGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLveAQAAQDAIAALQVEPRGIVK 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 107 VYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGNDYVNMQRTGIDLALY-----FDDTpanHLSHHFLMDEEILPVCSPA 181
Cdd:PRK14997  96 LTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRvrprpFEDS---DLVMRVLADRGHRLFASPD 172

                        170
                 ....*....|....*.
gi 504694821 182 YAREHQLVKNPHNLSH 197
Cdd:PRK14997 173 LIARMGIPSAPAELSH 188
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
22-75 3.55e-10

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 59.82  E-value: 3.55e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 504694821  22 TFEVAARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEG 75
Cdd:PRK10094   9 TFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAG 62
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 35-189 6.64e-10

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 58.85  E-value: 6.64e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  35 AAEELSLSPSAVSHRINLLEEELGIQLFVRS-HRKVELTQEGKRVywtLKSSLDTLNqEILDIKNQAL------SGTLTV 107
Cdd:PRK12682  22 AAKALHTSQPGVSKAIIELEEELGIEIFIRHgKRLKGLTEPGKAV---LDVIERILR-EVGNIKRIGDdfsnqdSGTLTI 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 108 YSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGN--DYVNMQRTGI-DLALYFDDtpanhlshhfLMDEEILpVCSPAYAR 184
Cdd:PRK12682  98 ATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSpdEIARMVISGEaDIGIATES----------LADDPDL-ATLPCYDW 166


                 ....*
gi 504694821 185 EHQLV 189
Cdd:PRK12682 167 QHAVI 171
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 31-178 7.34e-10

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 58.93  E-value: 7.34e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  31 SFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGKRVYWTLKSSLDTLNQEILDIKN--QALSGTLTVY 108
Cdd:PRK11233  17 SLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAVHNvgQALSGQVSIG 96

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504694821 109 SRP-SIAQCWLVPMLGDFTRRYPSISL-------TVLtgNDYVNMQRtgIDLALYFDDTPANHLSHHFLMDEEILPVC 178
Cdd:PRK11233  97 LAPgTAASSLTMPLLQAVRAEFPGIVLylhensgATL--NEKLMNGQ--LDMAVIYEHSPVAGLSSQPLLKEDLFLVG 170
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 102-281 1.30e-09

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 4. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176162 [Multi-domain]  Cd Length: 202  Bit Score: 56.79  E-value: 1.30e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 102 SGTLTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGNDYVNMQRTGIDLALYFDDTP-------ANHLSHHflmdEEI 174
Cdd:cd08473    2 RGTVRVSCPPALAQELLAPLLPRFMAAYPQVRLQLEATNRRVDLIEEGIDVALRVRFPPledsslvMRVLGQS----RQR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 175 LpVCSPAYAREHQLVKNPHNLSHctllHDRQAWSNDSGTDEW-LSWAQ--HFAINMPPssgigfdR---SDLAII--AAI 246
Cdd:cd08473   78 L-VASPALLARLGRPRSPEDLAG----LPTLSLGDVDGRHSWrLEGPDgeSITVRHRP-------RlvtDDLLTLrqAAL 145

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 504694821 247 NDVGVAMGRKRLVQKRLEKGELIAPFGEKTLKCHQ 281
Cdd:cd08473  146 AGVGIALLPDHLCREALRAGRLVRVLPDWTPPRGI 180
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
22-79 1.35e-09

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 58.06  E-value: 1.35e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 504694821  22 TFEVAARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRShRKVELTQEGKRVY 79
Cdd:PRK13348   9 ALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLL 65
PRK09791 PRK09791
LysR family transcriptional regulator;
16-186 7.83e-09

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 55.92  E-value: 7.83e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  16 QLSKMYTFEVAARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGKRVYWTLKSSLDTLN--QEI 93
Cdd:PRK09791   6 KIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRaaQED 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  94 LDIKNQALSGTLTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGN--DYVNMQRTG-IDLAL--YFDDTPANHLSHHF 168
Cdd:PRK09791  86 IRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQlvSMINELRQGeLDFTIntYYQGPYDHEFTFEK 165

                        170
                 ....*....|....*...
gi 504694821 169 LMDEEILPVCSPAYAREH 186
Cdd:PRK09791 166 LLEKQFAVFCRPGHPAIG 183
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 104-303 1.13e-08

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: 54.14  E-value: 1.13e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 104 TLTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGNDY--VNMQRTG-IDLALYFDDTPANHLSHHFLMDEEILPVCSP 180
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSelLEALLEGeLDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 181 AYAREHQLVKNPHNLSHCTL-LHDRqawsnDSGTDEWLSWAQHFAiNMPPSSGIGFDRSDLAIIAAINDVGVAM------ 253
Cdd:cd05466   81 DHPLAKRKSVTLADLADEPLiLFER-----GSGLRRLLDRAFAEA-GFTPNIALEVDSLEAIKALVAAGLGIALlpesav 154

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 504694821 254 ---GRKRLVQKRLEKGELIAPFGektLKCHQHYYIStlpgrqwPKIDAFISWL 303
Cdd:cd05466  155 eelADGGLVVLPLEDPPLSRTIG---LVWRKGRYLS-------PAARAFLELL 197
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 118-303 3.22e-08

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 8. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176166  Cd Length: 197  Bit Score: 52.62  E-value: 3.22e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 118 LVPMLGDFTRRYPSISLTVLTGNDYVNMQRTGIDLALYFDDTPANHLSHHFLMDEEILPVCSPAYAREHQLVKNPHNLSH 197
Cdd:cd08477   16 LTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPLAPYRMVLCASPDYLARHGTPTTPEDLAR 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 198 ctllHDRQAWSNDSGTDEWLSWAQHFAINMPPSSGIGFDRSDLAIIAAINDVGVAMGRKRLVQKRLEKGELIAPFGEKTL 277
Cdd:cd08477   96 ----HECLGFSYWRARNRWRLEGPGGEVKVPVSGRLTVNSGQALRVAALAGLGIVLQPEALLAEDLASGRLVELLPDYLP 171

                        170       180
                 ....*....|....*....|....*.
gi 504694821 278 KCHQHYYISTLPGRQWPKIDAFISWL 303
Cdd:cd08477  172 PPRPMHLLYPPDRRPTPKLRSFIDFL 197
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 35-134 3.35e-08

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 53.89  E-value: 3.35e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  35 AAEELSLSPSAVSHRINLLEEELGIQLFVRS-HRKVELTQEGKRVywtlkssLDTLNQEILDIKN---------QALSGT 104
Cdd:PRK12683  22 VANALYTSQSGVSKQIKDLEDELGVEIFIRRgKRLTGLTEPGKEL-------LQIVERMLLDAENlrrlaeqfaDRDSGH 94

                         90       100       110
                 ....*....|....*....|....*....|
gi 504694821 105 LTVYSRPSIAQCWLVPMLGDFTRRYPSISL 134
Cdd:PRK12683  95 LTVATTHTQARYALPKVVRQFKEVFPKVHL 124
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
27-78 1.01e-07

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 52.47  E-value: 1.01e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 504694821  27 ARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRShRKVELTQEGKRV 78
Cdd:PRK03635  14 VREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQRL 64
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 120-270 1.34e-07

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 6. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176164 [Multi-domain]  Cd Length: 199  Bit Score: 51.02  E-value: 1.34e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 120 PMLGDFTRRYPSISLTvLTGND-YVNMQRTGIDLALYFDDTP-ANHLSHHFLmDEEILPVC-SPAYAREHQLVKNPHNL- 195
Cdd:cd08475   18 PLLLELARRHPELELE-LSFSDrFVDLIEEGIDLAVRIGELAdSTGLVARRL-GTQRMVLCaSPAYLARHGTPRTLEDLa 95

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504694821 196 SHCTLLHDR----QAWsndsgtdeWLSWAQHFAINMPPSSGIGFDRSDLAIIAAINDVGVAMGRKRLVQKRLEKGELIA 270
Cdd:cd08475   96 EHQCIAYGRggqpLPW--------RLADEQGRLVRFRPAPRLQFDDGEAIADAALAGLGIAQLPTWLVADHLQRGELVE 166
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 35-269 2.61e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 51.23  E-value: 2.61e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  35 AAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGKRVYwtlKSSLDTLNQ--EILDIKNQALsGTLTVYSRPS 112
Cdd:PRK10837  23 ASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLY---PRALALLEQavEIEQLFREDN-GALRIYASST 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 113 IAQCWLVPMLGDFTRRYPSISLTVLTGN--DYVN-MQRTGIDLALYfdDTPANH---LSHHFLMDEEILpVCSPayarEH 186
Cdd:PRK10837  99 IGNYILPAMIARYRRDYPQLPLELSVGNsqDVINaVLDFRVDIGLI--EGPCHSpelISEPWLEDELVV-FAAP----DS 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 187 QLVKNPHNLSHctlLHDrQAW---SNDSGTDE-----WLSWAQHFAINMPpssgigFDRSDlAIIAAI-NDVGVAMGRKR 257
Cdd:PRK10837 172 PLARGPVTLEQ---LAA-APWilrERGSGTREivdylLLSHLPRFELAME------LGNSE-AIKHAVrHGLGISCLSRR 240

                        250
                 ....*....|..
gi 504694821 258 LVQKRLEKGELI 269
Cdd:PRK10837 241 VIADQLQAGTLV 252
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
22-134 2.76e-07

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 50.79  E-value: 2.76e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  22 TF-EVA-ARHesFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGKRVYWTLKSSLDTLNQEILDIKNQ 99
Cdd:PRK03601   8 TFlEVSrTRH--FGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKKEVAHT 85

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 504694821 100 ALSGTLTVYSRPSIAQCWLVPMLGDFTRRYPSISL 134
Cdd:PRK03601  86 SQHNELSIGASASLWECMLTPWLGRLYQNQEALQF 120
cysB PRK12681
HTH-type transcriptional regulator CysB;
21-134 5.04e-07

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 50.28  E-value: 5.04e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  21 YTFEVAARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRS--HRKvELTQEGKRVYwtlkssldTLNQEIL---- 94
Cdd:PRK12681   8 YIVEVVNHNLNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSgkHLT-QVTPAGEEII--------RIAREILskve 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 504694821  95 DIKNQALS------GTLTVYSRPSIAQCWLVPMLGDFTRRYPSISL 134
Cdd:PRK12681  79 SIKSVAGEhtwpdkGSLYIATTHTQARYALPPVIKGFIERYPRVSL 124
PRK09986 PRK09986
LysR family transcriptional regulator;
23-102 6.60e-07

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 49.72  E-value: 6.60e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  23 FEVAARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGKrvywTLKSSLDTLnqeiLDIKNQALS 102
Cdd:PRK09986  15 FLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGK----ILMEESRRL----LDNAEQSLA 86
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 102-300 1.00e-06

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 5. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176163 [Multi-domain]  Cd Length: 202  Bit Score: 48.61  E-value: 1.00e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 102 SGTLTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGNDYVNMQRTGIDLALYFDDTPANHlshhflM-------DEEI 174
Cdd:cd08474    2 AGTLRINAPRVAARLLLAPLLARFLARYPDIRLELVVDDGLVDIVAEGFDAGIRLGESVEKD------MvavplgpPLRM 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 175 LPVCSPAYAREHQLVKNPHNLSHctllHD--RQAWSNDSGTDEWlswaqHF-----AINMPPSSGIGFDRSDLAIIAAIN 247
Cdd:cd08474   76 AVVASPAYLARHGTPEHPRDLLN----HRciRYRFPTSGALYRW-----EFerggrELEVDVEGPLILNDSDLMLDAALD 146

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 504694821 248 DVGVAMGRKRLVQKRLEKGELI--------APFGektlkcHQHYYIstlPGRQWP-KIDAFI 300
Cdd:cd08474  147 GLGIAYLFEDLVAEHLASGRLVrvledwspPFPG------GYLYYP---SRRRVPpALRAFI 199
nhaR PRK11062
transcriptional activator NhaR; Provisional
 20-98 3.57e-06

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 47.70  E-value: 3.57e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504694821  20 MYTFEVAARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGKRVYwTLKSSLDTLNQEILDIKN 98
Cdd:PRK11062   9 LYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVF-RYADKMFTLSQEMLDIVN 86
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 103-216 4.37e-06

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 9. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176168 [Multi-domain]  Cd Length: 198  Bit Score: 46.44  E-value: 4.37e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 103 GTLTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGNDYVNMQRTGIDLALYFDDTPANHLSHHFLMDEEILPVCSPAY 182
Cdd:cd08479    1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCASPAY 80

                         90       100       110
                 ....*....|....*....|....*....|....
gi 504694821 183 AREHQLVKNPHNLSHCTLLHDRQawsNDSGTDEW 216
Cdd:cd08479   81 LERHGAPASPEDLARHDCLVIRE---NDEDFGLW 111
cbl PRK12679
HTH-type transcriptional regulator Cbl;
24-149 5.84e-06

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 47.11  E-value: 5.84e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  24 EVAARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVR-SHRKVELTQEGKRVYWTLKSSLDTLN--QEILDIKNQA 100
Cdd:PRK12679  11 EAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRrGKRLLGMTEPGKALLVIAERILNEASnvRRLADLFTND 90

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 504694821 101 LSGTLTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGN--DYVNMQRTG 149
Cdd:PRK12679  91 TSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTpqEIATLLQNG 141
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 103-306 6.46e-06

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 3. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176161  Cd Length: 202  Bit Score: 45.97  E-value: 6.46e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 103 GTLTVYSRPSIAQCWLVPMLGDFTRRYPSISLtVLTGNDY-VNMQRTGIDLALYFDDTPANHLSHHFLMDEEILPVCSPA 181
Cdd:cd08472    1 GRLRVDVPGSLARLLLIPALPDFLARYPDIEL-DLGVSDRpVDLIREGVDCVIRVGELADSSLVARRLGELRMVTCASPA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 182 YAREHQLVKNPHNLSHCTLLHDRQAWSNDSGTDEWLSWAQHFAINMPpsSGIGFDRSDLAIIAAINDVGVAMGRKRLVQK 261
Cdd:cd08472   80 YLARHGTPRHPEDLERHRAVGYFSARTGRVLPWEFQRDGEEREVKLP--SRVSVNDSEAYLAAALAGLGIIQVPRFMVRP 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 504694821 262 RLEKGELIapfgektlKCHQHYYISTLP-------GRQW-PKIDAFISWLRER 306
Cdd:cd08472  158 HLASGRLV--------EVLPDWRPPPLPvsllyphRRHLsPRVRVFVDWVAEL 202
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 27-75 1.61e-05

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 45.79  E-value: 1.61e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 504694821  27 ARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEG 75
Cdd:PRK11151  13 AEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAG 61
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 23-75 1.62e-05

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 45.53  E-value: 1.62e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 504694821  23 FEVAARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEG 75
Cdd:PRK09906   9 FVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAG 61
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
20-179 4.03e-05

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 44.66  E-value: 4.03e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  20 MYTFEVAARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGKRVYWTLKSSLDTLNQEILDIKNQ 99
Cdd:PRK10082  16 LYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGG 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 100 ----------ALSGTLTVYSRPSIaqcwLVPMLGDFTRRYPSISLtvltgNDYVNMQRTG-IDLALYFDD-----TPANH 163
Cdd:PRK10082  96 sdyaqrkikiAAAHSLSLGLLPSI----ISQMPPLFTWAIEAIDV-----DEAVDKLREGqSDCIFSFHDedlleAPFDH 166

                        170
                 ....*....|....*.
gi 504694821 164 LShhfLMDEEILPVCS 179
Cdd:PRK10082 167 IR---LFESQLFPVCA 179
PRK10341 PRK10341
transcriptional regulator TdcA;
23-154 5.66e-05

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 44.08  E-value: 5.66e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  23 FEVAARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGKRVYWTLKSSLDTLNQEILDIKNQALS 102
Cdd:PRK10341  15 FQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGMSSE 94

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 504694821 103 GTLTV-YSRPS-IAQCWLVPMLGDFTRRYPSISLTVLTG--NDYVNMQRTG-IDLAL 154
Cdd:PRK10341  95 AVVDVsFGFPSlIGFTFMSDMINKFKEVFPKAQVSMYEAqlSSFLPAIRDGrLDFAI 151
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 113-268 1.73e-04

C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. 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: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 41.71  E-value: 1.73e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 113 IAQCWLVPMLGDFTRRYPSISLTVLTGN--DYVNMQRTG-IDLALYFDDTPANHLSHHFLMDEEILPVCSPayarEHQLV 189
Cdd:cd08420   10 IGEYLLPRLLARFRKRYPEVRVSLTIGNteEIAERVLDGeIDLGLVEGPVDHPDLIVEPFAEDELVLVVPP----DHPLA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 190 K----NPHNLSHCTLLhDRQAwsnDSGT----DEWLSWAQHFAINMPPSSGIGfdrSDLAIIAAI-NDVGVAMGRKRLVQ 260
Cdd:cd08420   86 GrkevTAEELAAEPWI-LREP---GSGTrevfERALAEAGLDGLDLNIVMELG---STEAIKEAVeAGLGISILSRLAVR 158


                 ....*...
gi 504694821 261 KRLEKGEL 268
Cdd:cd08420  159 KELELGRL 166
PRK12680 PRK12680
LysR family transcriptional regulator;
21-134 3.29e-04

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 41.92  E-value: 3.29e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  21 YTFEVAARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVE-LTQEGKRVYWTLKSSLDTLNQEILDIKNQ 99
Cdd:PRK12680   8 YLVAIADAELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNIRTYAANQ 87

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 504694821 100 --ALSGTLTVYSRPSIAQCWLVPMLGDFTRRYPSISL 134
Cdd:PRK12680  88 rrESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSV 124
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-136 3.62e-04

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 41.55  E-value: 3.62e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821   1 MTDANEArnrLLNgWQLSKMYTFEVAARHESFALAAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGkrvyw 80
Cdd:PRK15092   1 MINANRP---IIN-LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHG----- 71

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 504694821  81 tlkssLDTLN--QEILDIKNQA--------LSGTLTVYSRPSIAQCWLVPMLGDFTRRYPSISLTV 136
Cdd:PRK15092  72 -----IQLLGyaRKILRFNDEAcsslmysnLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDV 132
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 103-216 6.62e-04

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 10. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176169  Cd Length: 198  Bit Score: 40.01  E-value: 6.62e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 103 GTLTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGNDYVNMQRTGIDLALYFDDTPANHLSHHFLMDEEILPVCSPAY 182
Cdd:cd08480    1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGESRRVIVASPSY 80

                         90       100       110
                 ....*....|....*....|....*....|....
gi 504694821 183 AREHQLVKNPHNLSHctllHDRQAWSNDSGTDEW 216
Cdd:cd08480   81 LARHGTPLTPQDLAR----HNCLGFNFRRALPDW 110
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 111-181 7.09e-04

The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut. Hence, NAC allows the coupling of sigma70-RNAP dependent operons to the sigma54-RNAP dependent NTR system. This substrate-binding domain has 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: 176124  Cd Length: 198  Bit Score: 39.89  E-value: 7.09e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 504694821 111 PSIAQCWLVPMLGDFTRRYPSISLTVLTG-----NDYVNMQRtgIDLALYFDDTPANHLSHHFLMDEEILPVCSPA 181
Cdd:cd08433    8 PSAASVLAVPLLRAVRRRYPGIRLRIVEGlsghlLEWLLNGR--LDLALLYGPPPIPGLSTEPLLEEDLFLVGPAD 81
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 117-201 1.85e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mechanisms. In Escherichia coli and Salmonella enterica serovar Typhimurium, MetJ and MetR regulate the expression of methionine biosynthetic genes. The MetJ repressor negatively regulates the E. coli met genes, except for metH. Several of these genes are also under the positive control of MetR with homocysteine as a co-inducer. In Bacillus subtilis, the met genes are controlled by S-box termination-antitermination system. 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: 176132  Cd Length: 198  Bit Score: 38.70  E-value: 1.85e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 117 WLVPMLGDFTRRYPSISLTVLTGNDY--VNMQRTG-IDLALYFDDTPANHLSHHFLMDEEILPVCSPayarEHQLVK--- 190
Cdd:cd08441   14 WLMPVLDQFRERWPDVELDLSSGFHFdpLPALLRGeLDLVITSDPLPLPGIAYEPLFDYEVVLVVAP----DHPLAAkef 89

                         90
                 ....*....|..
gi 504694821 191 -NPHNLSHCTLL 201
Cdd:cd08441   90 iTPEDLADETLI 101
HTH_ARSR cd00090
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ...
 36-98 3.51e-03

Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.


Pssm-ID: 238042 [Multi-domain]  Cd Length: 78  Bit Score: 35.74  E-value: 3.51e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 504694821  36 AEELSLSPSAVSHRINLLEEElGIqlfvrshrkVELTQEGKRVYWTLkSSLDTLNQEILDIKN 98
Cdd:cd00090   27 AERLGLSQSTVSRHLKKLEEA-GL---------VESRREGRRVYYSL-TDAERLLALLESLLE 78
HTH_ARSR smart00418
helix_turn_helix, Arsenical Resistance Operon Repressor;
36-85 3.97e-03

helix_turn_helix, Arsenical Resistance Operon Repressor;


Pssm-ID: 197713 [Multi-domain]  Cd Length: 66  Bit Score: 35.26  E-value: 3.97e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 504694821    36 AEELSLSPSAVSHRINLLEEElGIqlfvrshrkVELTQEGKRVYWTLKSS 85
Cdd:smart00418  17 AEILGLSQSTVSHHLKKLREA-GL---------VESRREGKRVYYSLTDE 56
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 35-138 7.13e-03

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 37.66  E-value: 7.13e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821  35 AAEELSLSPSAVSHRINLLEEELGIQLFVRSHRKVELTQEGKRVYWTLKSS---LDTLNQEILDIKnQALSGTLTVYSRP 111
Cdd:PRK11013  24 AARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSyygLDRIVSAAESLR-EFRQGQLSIACLP 102

                         90       100
                 ....*....|....*....|....*..
gi 504694821 112 SIAQCWLVPMLGDFTRRYPSISLTVLT 138
Cdd:PRK11013 103 VFSQSLLPGLCQPFLARYPDVSLNIVP 129
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 104-185 7.67e-03

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: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 36.81  E-value: 7.67e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504694821 104 TLTVYSRPSIAQCWLVPMLGDFTRRYPSISLTVLTGN--DYVNMQRTG-IDLAL---YFDDTPANH--LSHHFLMDEE-- 173
Cdd:cd08423    1 TLRVGAFPTAAAALLPPALAALRARHPGLEVRLREAEppESLDALRAGeLDLAVvfdYPVTPPPDDpgLTRVPLLDDPld 80

                         90
                 ....*....|...
gi 504694821 174 -ILPVCSPAYARE 185
Cdd:cd08423   81 lVLPADHPLAGRE 93
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH