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Conserved domains on  [gi|1278639286|gb|PJB46883|]
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LysR family transcriptional regulator [Comamonadaceae bacterium CG_4_9_14_3_um_filter_60_33]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 1001158)

LysR family HTH-containing transcriptional regulator

Gene Ontology:  GO:0003677|GO:0003700
PubMed:  19047729

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK11139 super family cl32646
DNA-binding transcriptional activator GcvA; Provisional
 1-316 1.13e-111

DNA-binding transcriptional activator GcvA; Provisional


The actual alignment was detected with superfamily member PRK11139:

Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 325.64  E-value: 1.13e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286   1 MSYRLPPLKALRAFEAAARHLSFKDAAQEMSVTPTAISHQIKLLEEYLDLQLFHRLTRALELTPQGEAMLPKVREGLDCF 80
Cdd:PRK11139    1 MSRRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  81 AAAVASAHERVTSGRLIVVLPPSFATRWLVPRLRRFAEAEPSLSLHvirsLSTIDGDqvanpasfdlADLRQEDSVVVIR 160
Cdd:PRK11139   81 AEATRKLRARSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVR----LKAVDRL----------EDFLRDDVDVAIR 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 161 FGTGVYPGFQVDHMFASDCIAVCSPKLLETGPPLRVPADMRHQVLLHDQgissgrSGPAWDEWFKLAGVTGVDSSAGPHF 240
Cdd:PRK11139  147 YGRGNWPGLRVEKLLDEYLLPVCSPALLNGGKPLKTPEDLARHTLLHDD------SREDWRAWFRAAGLDDLNVQQGPIF 220

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1278639286 241 SDSGLVYVAALDGLGVALASKPLVATAIAQGRLVAPFDIAVGQKFAYYLVVPQAVAERPAVQAFRKWLLEEAKAEE 316
Cdd:PRK11139  221 SHSSMALQAAIHGQGVALGNRVLAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQEQ 296
 
Name Accession Description Interval E-value
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 1-316 1.13e-111

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 325.64  E-value: 1.13e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286   1 MSYRLPPLKALRAFEAAARHLSFKDAAQEMSVTPTAISHQIKLLEEYLDLQLFHRLTRALELTPQGEAMLPKVREGLDCF 80
Cdd:PRK11139    1 MSRRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  81 AAAVASAHERVTSGRLIVVLPPSFATRWLVPRLRRFAEAEPSLSLHvirsLSTIDGDqvanpasfdlADLRQEDSVVVIR 160
Cdd:PRK11139   81 AEATRKLRARSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVR----LKAVDRL----------EDFLRDDVDVAIR 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 161 FGTGVYPGFQVDHMFASDCIAVCSPKLLETGPPLRVPADMRHQVLLHDQgissgrSGPAWDEWFKLAGVTGVDSSAGPHF 240
Cdd:PRK11139  147 YGRGNWPGLRVEKLLDEYLLPVCSPALLNGGKPLKTPEDLARHTLLHDD------SREDWRAWFRAAGLDDLNVQQGPIF 220

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1278639286 241 SDSGLVYVAALDGLGVALASKPLVATAIAQGRLVAPFDIAVGQKFAYYLVVPQAVAERPAVQAFRKWLLEEAKAEE 316
Cdd:PRK11139  221 SHSSMALQAAIHGQGVALGNRVLAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQEQ 296
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 95-308 8.51e-64

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: 200.11  E-value: 8.51e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  95 RLIVVLPPSFATRWLVPRLRRFAEAEPSLSLHVIrslstidgdqvanpASFDLADLRQEDSVVVIRFGTGVYPGFQVDHM 174
Cdd:cd08432     1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLS--------------TSDRLVDFAREGIDLAIRYGDGDWPGLEAERL 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 175 FASDCIAVCSPKLLETGPPLRvPADMRHQVLLHDqgissGRSGPAWDEWFKLAGVTGVDSSAGPHFSDSGLVYVAALDGL 254
Cdd:cd08432    67 MDEELVPVCSPALLAGLPLLS-PADLARHTLLHD-----ATRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGL 140

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1278639286 255 GVALASKPLVATAIAQGRLVAPFDIAVGQKFAYYLVVPQAVAERPAVQAFRKWL 308
Cdd:cd08432   141 GVALAPRALVADDLAAGRLVRPFDLPLPSGGAYYLVYPPGRAESPAVAAFRDWL 194
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-314 1.13e-43

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 150.40  E-value: 1.13e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286   7 PLKALRAFEAAARHLSFKDAAQEMSVTPTAISHQIKLLEEYLDLQLFHRLTRALELTPQGEAMLPKVREGLDCFAAAVAS 86
Cdd:COG0583     2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  87 AHE--RVTSGRLIVVLPPSFATRWLVPRLRRFAEAEPSLSLHvirsLSTIDGDQVanpasfdLADLRQEDSVVVIRFGTG 164
Cdd:COG0583    82 LRAlrGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLE----LREGNSDRL-------VDALLEGELDLAIRLGPP 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 165 VYPGFQVDHMFASDCIAVCSPKLletgpPLrvpadmrhqvllhdqgissgrsgpawdewfklagvtgvdSSAGPHFSDSG 244
Cdd:COG0583   151 PDPGLVARPLGEERLVLVASPDH-----PL---------------------------------------ARRAPLVNSLE 186

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 245 LVYVAALDGLGVALASKPLVATAIAQGRLVAPFDIAVGQKFAYYLVVPQAVAERPAVQAFRKWLLEEAKA 314
Cdd:COG0583   187 ALLAAVAAGLGIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-67 9.49e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 78.58  E-value: 9.49e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286   8 LKALRAFEAAARHLSFKDAAQEMSVTPTAISHQIKLLEEYLDLQLFHRLTRALELTPQGE 67
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 1-316 1.13e-111

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 325.64  E-value: 1.13e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286   1 MSYRLPPLKALRAFEAAARHLSFKDAAQEMSVTPTAISHQIKLLEEYLDLQLFHRLTRALELTPQGEAMLPKVREGLDCF 80
Cdd:PRK11139    1 MSRRLPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  81 AAAVASAHERVTSGRLIVVLPPSFATRWLVPRLRRFAEAEPSLSLHvirsLSTIDGDqvanpasfdlADLRQEDSVVVIR 160
Cdd:PRK11139   81 AEATRKLRARSAKGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVR----LKAVDRL----------EDFLRDDVDVAIR 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 161 FGTGVYPGFQVDHMFASDCIAVCSPKLLETGPPLRVPADMRHQVLLHDQgissgrSGPAWDEWFKLAGVTGVDSSAGPHF 240
Cdd:PRK11139  147 YGRGNWPGLRVEKLLDEYLLPVCSPALLNGGKPLKTPEDLARHTLLHDD------SREDWRAWFRAAGLDDLNVQQGPIF 220

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1278639286 241 SDSGLVYVAALDGLGVALASKPLVATAIAQGRLVAPFDIAVGQKFAYYLVVPQAVAERPAVQAFRKWLLEEAKAEE 316
Cdd:PRK11139  221 SHSSMALQAAIHGQGVALGNRVLAQPEIEAGRLVCPFDTVLPSPNAFYLVCPDSQAELPKVAAFRQWLLAEAAQEQ 296
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 95-308 8.51e-64

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: 200.11  E-value: 8.51e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  95 RLIVVLPPSFATRWLVPRLRRFAEAEPSLSLHVIrslstidgdqvanpASFDLADLRQEDSVVVIRFGTGVYPGFQVDHM 174
Cdd:cd08432     1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLS--------------TSDRLVDFAREGIDLAIRYGDGDWPGLEAERL 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 175 FASDCIAVCSPKLLETGPPLRvPADMRHQVLLHDqgissGRSGPAWDEWFKLAGVTGVDSSAGPHFSDSGLVYVAALDGL 254
Cdd:cd08432    67 MDEELVPVCSPALLAGLPLLS-PADLARHTLLHD-----ATRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAGL 140

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1278639286 255 GVALASKPLVATAIAQGRLVAPFDIAVGQKFAYYLVVPQAVAERPAVQAFRKWL 308
Cdd:cd08432   141 GVALAPRALVADDLAAGRLVRPFDLPLPSGGAYYLVYPPGRAESPAVAAFRDWL 194
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
8-313 1.13e-60

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 195.99  E-value: 1.13e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286   8 LKALRAFEAAARHLSFKDAAQEMSVTPTAISHQIKLLEEYLDLQLFHRLTRALELTPQGEAMLPKVREGLDCFAAAVASA 87
Cdd:PRK10086   16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDI 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  88 HERVTSGRLIVVLPPSFATRWLVPRLRRFAEAEPSLSLHVIrslstidgdqVANpasfDLADLRQEDSVVVIRFGTGVYP 167
Cdd:PRK10086   96 KNQELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTIL----------TGN----ENVNFQRAGIDLAIYFDDAPSA 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 168 GFQVDHMFASDCIAVCSPKLLETGPPLRVPADMRHQVLLHDqgissgrsGPAW------DEWFKLA---GVTGVDSSAGP 238
Cdd:PRK10086  162 QLTHHFLMDEEILPVCSPEYAERHALTGNPDNLRHCTLLHD--------RQAWsndsgtDEWHSWAqhfGVNLLPPSSGI 233

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1278639286 239 HFSDSGLVYVAALDGLGVALASKPLVATAIAQGRLVAPF-DIAVGQKFAYYLVVPQavaER--PAVQAFRKWLLEEAK 313
Cdd:PRK10086  234 GFDRSDLAVIAAMNHIGVAMGRKRLVQKRLASGELVAPFgDMEVKCHQHYYVTTLP---GRqwPKIEAFIDWLKEQVK 308
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 102-308 5.27e-45

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: 151.68  E-value: 5.27e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 102 PSFATRWLVPRLRRFAEAEPSLSLhvirslstidgDQVANPASFDLAdlrQEDSVVVIRFGTGVYPGFQVDHMFASDCIA 181
Cdd:cd08481     8 PTFGTRWLIPRLPDFLARHPDITV-----------NLVTRDEPFDFS---QGSFDAAIHFGDPVWPGAESEYLMDEEVVP 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 182 VCSPKLLEtGPPLRVPADMRHQVLLHdqgiSSGRSGpAWDEWFKLAGVTGVDSSAGPHFSDSGLVYVAALDGLGVALASK 261
Cdd:cd08481    74 VCSPALLA-GRALAAPADLAHLPLLQ----QTTRPE-AWRDWFEEVGLEVPTAYRGMRFEQFSMLAQAAVAGLGVALLPR 147

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1278639286 262 PLVATAIAQGRLVAPFDIAVGQKFAYYLVVPQAVAERPAVQAFRKWL 308
Cdd:cd08481   148 FLIEEELARGRLVVPFNLPLTSDKAYYLVYPEDKAESPPVQAFRDWL 194
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-314 1.13e-43

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 150.40  E-value: 1.13e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286   7 PLKALRAFEAAARHLSFKDAAQEMSVTPTAISHQIKLLEEYLDLQLFHRLTRALELTPQGEAMLPKVREGLDCFAAAVAS 86
Cdd:COG0583     2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  87 AHE--RVTSGRLIVVLPPSFATRWLVPRLRRFAEAEPSLSLHvirsLSTIDGDQVanpasfdLADLRQEDSVVVIRFGTG 164
Cdd:COG0583    82 LRAlrGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLE----LREGNSDRL-------VDALLEGELDLAIRLGPP 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 165 VYPGFQVDHMFASDCIAVCSPKLletgpPLrvpadmrhqvllhdqgissgrsgpawdewfklagvtgvdSSAGPHFSDSG 244
Cdd:COG0583   151 PDPGLVARPLGEERLVLVASPDH-----PL---------------------------------------ARRAPLVNSLE 186

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 245 LVYVAALDGLGVALASKPLVATAIAQGRLVAPFDIAVGQKFAYYLVVPQAVAERPAVQAFRKWLLEEAKA 314
Cdd:COG0583   187 ALLAAVAAGLGIALLPRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 103-308 4.81e-28

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: 107.46  E-value: 4.81e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 103 SFATRWLVPRLRRFAEAEPSLSLHvirsLSTidGDQVANPAS--FDLAdlrqedsvvvIRFGTGVYPGFQVDHMFASDCI 180
Cdd:cd08484     9 TFAVGWLLPRLAEFRQLHPFIDLR----LST--NNNRVDIAAegLDFA----------IRFGEGAWPGTDATRLFEAPLS 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 181 AVCSPKLLETgppLRVPADMRHQVLLHdqgisSGRSGpAWDEWFKLAGVtGVDSSAGPHFSDSGLVYVAALDGLGVALAS 260
Cdd:cd08484    73 PLCTPELARR---LSEPADLANETLLR-----SYRAD-EWPQWFEAAGV-PPPPINGPVFDSSLLMVEAALQGAGVALAP 142

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1278639286 261 KPLVATAIAQGRLVAPFDIAV--GQkfaYYLVVPQAVAERPAVQAFRKWL 308
Cdd:cd08484   143 PSMFSRELASGALVQPFKITVstGS---YWLTRLKSKPETPAMSAFSQWL 189
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 96-308 2.59e-25

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: 100.11  E-value: 2.59e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  96 LIVVLPPSFATRWLVPRLRRFAEAEPSLSLHVIrslstidgdqvanpASFDLADLRQEDSVVVIRFGTGVYPGFQVDHMF 175
Cdd:cd08483     2 LTVTLTPSFASNWLMPRLGSFWAKHPEIELSLL--------------PSADLVDLRPDGIDVAIRYGNGDWPGLESEPLT 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 176 ASDCIAVCSPKLLEtGPPLRVPADMRHQVLLHDQGISSGRSgpawdeWFKLAGVTGvDSSAGPHFSDSGLVYVAALDGLG 255
Cdd:cd08483    68 AAPFVVVAAPGLLG-DRKVDSLADLAGLPWLQERGTNEQRV------WLASMGVVP-DLERGVTFLPGQLVLEAARAGLG 139

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1278639286 256 VALASKPLVATAIAQGRLVAPFDiAVGQKFAYYLVVPQAVAeRPAVQAFRKWL 308
Cdd:cd08483   140 LSIQARALVEPDIAAGRLTVLFE-EEEEGLGYHIVTRPGVL-RPAAKAFVRWL 190
PBP2_AmpR cd08488
The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in ...
 103-308 1.84e-24

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: 97.99  E-value: 1.84e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 103 SFATRWLVPRLRRFAEAEPSLSLHvirsLSTiDGDQVanpasfdlaDLRQEDSVVVIRFGTGVYPGFQVDHMFASDCIAV 182
Cdd:cd08488     9 TFAVGWLLPRLADFQNRHPFIDLR----LST-NNNRV---------DIAAEGLDYAIRFGSGAWHGIDATRLFEAPLSPL 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 183 CSPKLLETgppLRVPADMRHQVLLhdqgissgRSGPA--WDEWFKLAGVTG-VDSSAGPHFSDSGLVYVAALDGLGVALA 259
Cdd:cd08488    75 CTPELARQ---LREPADLARHTLL--------RSYRAdeWPQWFEAAGVGHpCGLPNSIMFDSSLGMMEAALQGLGVALA 143

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1278639286 260 SKPLVATAIAQGRLVAPFDIAVGQKfAYYLVVPQAVAERPAVQAFRKWL 308
Cdd:cd08488   144 PPSMFSRQLASGALVQPFATTLSTG-SYWLTRLQSRPETPAMSAFSAWL 191
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 103-308 3.03e-24

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: 97.23  E-value: 3.03e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 103 SFATRWLVPRLRRFAEAEPSLSLHvirsLSTIDgdqvanpasfDLADLRQEDSVVVIRFGTGVYPGFQVDHMFASDCIAV 182
Cdd:cd08487     9 TFAVGWLLPRLAEFRQLHPFIELR----LRTNN----------NVVDLATEGLDFAIRFGEGLWPATHNERLLDAPLSVL 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 183 CSPkllETGPPLRVPADMRHQVLLHdqgisSGRSGpAWDEWFKLAGVTGVDSSaGPHFSDSGLVYVAALDGLGVALASKP 262
Cdd:cd08487    75 CSP---EIAKRLSHPADLINETLLR-----SYRTD-EWLQWFEAANMPPIKIR-GPVFDSSRLMVEAAMQGAGVALAPAK 144

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1278639286 263 LVATAIAQGRLVAPFDIAVgQKFAYYLVVPQAVAERPAVQAFRKWL 308
Cdd:cd08487   145 MFSREIENGQLVQPFKIEV-ETGSYWLTWLKSKPMTPAMELFRQWI 189
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 95-308 1.28e-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: 93.24  E-value: 1.28e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  95 RLIVVLPPSFATRWLVPRLRRFAEAEPSLSLHvirsLSTIDGDQVANPASFDladlrqedsvVVIRFGTGVYP-GFQVDH 173
Cdd:cd08482     1 PLVLSCSGSLLMRWLIPRLPAFQAALPDIDLQ----LSASDGPVDSLRDGID----------AAIRFNDAPWPaGMQVIE 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 174 MFASDCIAVCSPKLLETGPPLRVP-ADMRHQVLLHDqgissgRSGP-AWDEWFKLAGVTGVDSSAGPHFSDSGLVYVAAL 251
Cdd:cd08482    67 LFPERVGPVCSPSLAPTVPLRQAPaAALLGAPLLHT------RSRPqAWPDWAAAQGLAPEKLGTGQSFEHFYYLLEAAV 140

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1278639286 252 DGLGVALASKPLVATAIAQGRLVAPFDIAVGQKFaYYLVVPQAVAErPAVQAFRKWL 308
Cdd:cd08482   141 AGLGVAIAPWPLVRDDLASGRLVAPWGFIETGSH-YVLLRPARLRD-SRAGALADWL 195
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-67 9.49e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 78.58  E-value: 9.49e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286   8 LKALRAFEAAARHLSFKDAAQEMSVTPTAISHQIKLLEEYLDLQLFHRLTRALELTPQGE 67
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 93-313 4.15e-17

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: 78.48  E-value: 4.15e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  93 SGRLIVVLPPSFATRWLVPRLRRFAEAEPSLSLHVirslstidgdQVANPAsfDLADLRQEDSV-VVIRFGTGVYPGFQV 171
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELEL----------TEGNSE--ELLDLLLEGELdLAIRRGPPDDPGLEA 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 172 DHMFASDCIAVCSPKL-LETGPPLRvPADMRHQVLLHDQGISSGRSgpAWDEWFKLAGVTgvdSSAGPHFSDSGLVYVAA 250
Cdd:pfam03466  69 RPLGEEPLVLVAPPDHpLARGEPVS-LEDLADEPLILLPPGSGLRD--LLDRALRAAGLR---PRVVLEVNSLEALLQLV 142

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1278639286 251 LDGLGVALASKPLVATAIAQGRLVAPFDIAVGQKFAYYLVVPQAVAERPAVQAFRKWLLEEAK 313
Cdd:pfam03466 143 AAGLGIALLPRSAVARELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 94-308 7.02e-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: 77.48  E-value: 7.02e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  94 GRLIVVLPPSFATRWLVPRLRRFAEAEPSLSLHVirSLStidgDQVANPAS--FDLAdlrqedsvvvIRFGTGVYPGFQV 171
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLEL--VLS----DRLVDLVEegFDLA----------IRIGELPDSSLVA 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 172 DHMFASDCIAVCSPKLLETGPPLRVPADM-RHQVLLHdqgissgRSGPAWDEW-FKLAGVTGVDSSAGPHFSDSGLVYV- 248
Cdd:cd08422    65 RRLGPVRRVLVASPAYLARHGTPQTPEDLaRHRCLGY-------RLPGRPLRWrFRRGGGEVEVRVRGRLVVNDGEALRa 137

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 249 AALDGLGVALASKPLVATAIAQGRLVAPFDIAVGQKFAYYLVVPQAVAERPAVQAFRKWL 308
Cdd:cd08422   138 AALAGLGIALLPDFLVAEDLASGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
9-77 3.34e-12

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 65.98  E-value: 3.34e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1278639286   9 KALRAFEAAARHLSFKDAAQEMSVTPTAISHQIKLLEEYLDLQLFHRLTRALELTPQGEAMLPKVREGL 77
Cdd:PRK10094    5 ETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWL 73
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 8-127 9.88e-11

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 61.51  E-value: 9.88e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286   8 LKALRAFEAAARHLSFKDAAQEMSVTPTAISHQIKLLEEYLDLQLFHRLTRALELTPQGEAMLPKVREGLDCFAAAVASA 87
Cdd:PRK11242    3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAI 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1278639286  88 H--ERVTSGRLIVVLPPSFATRWLVPRLRRFAEAEPSLSLHV 127
Cdd:PRK11242   83 HdvADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTI 124
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 10-75 7.96e-10

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 58.80  E-value: 7.96e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1278639286  10 ALRAFEAAARHLSFKDAAQEMSVTPTAISHQIKLLEEYLDLQLFHRLTRALELTPQGEAMLPKVRE 75
Cdd:PRK11074    6 SLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARS 71
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
8-125 7.78e-09

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 56.18  E-value: 7.78e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286   8 LKALRAFEAAARHLSFKDAAQEMSVTPTAISHQIKLLEEYLDLQLFHRLTRALELTPQGEAMLPKVREGLDCFAAAVASA 87
Cdd:PRK15421    4 VKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQAC 83

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1278639286  88 HERVTSgRLIVVLPPSFATRWLVPRLRRFAEAEPSLSL 125
Cdd:PRK15421   84 NEPQQT-RLRIAIECHSCIQWLTPALENFHKNWPQVEM 120
PRK09986 PRK09986
LysR family transcriptional regulator;
8-121 1.22e-08

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 55.11  E-value: 1.22e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286   8 LKALRAFEAAARHLSFKDAAQEMSVTPTAISHQIKLLEEYLDLQLFHRLTRALELTPQGEAMLPKVREGLDCFAAAVASA 87
Cdd:PRK09986    9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARV 88

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1278639286  88 HE--RVTSGRLIVVLPPSFATRWLVPRLRRFAEAEP 121
Cdd:PRK09986   89 EQigRGEAGRIEIGIVGTALWGRLRPAMRHFLKENP 124
rbcR CHL00180
LysR transcriptional regulator; Provisional
 8-70 2.31e-08

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 54.64  E-value: 2.31e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1278639286   8 LKALRAFEAAARHLSFKDAAQEMSVTPTAISHQIKLLEEYLDLQLFHRLTRALELTPQGEAML 70
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLL 69
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 8-87 5.40e-08

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 53.23  E-value: 5.40e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286   8 LKALRAFEAAARHLSFKDAAQEMSVTPTAISHQIKLLEEYLDLQLFHRLTRALELTPQGEAMLPKVREGLDCFAAAVASA 87
Cdd:PRK09906    3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRA 82
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-275 7.93e-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: 51.85  E-value: 7.93e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  94 GRLIVVLPPSFATRWLVPRLRRFAEAEPSLSLHVirSLSTidgdqvanpasfDLADLRQEDSVVVIRFGTgvypgfqvdh 173
Cdd:cd08477     1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDL--VLSD------------RLVDLVEEGFDAAFRIGE---------- 56

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 174 MFASDCIA---------VC-SPKLLETGPPLRVPAD-MRHQVLlhdqGISSGRSGPAWdEWFKLAGVTGVDSSAGPHFSD 242
Cdd:cd08477    57 LADSSLVArplapyrmvLCaSPDYLARHGTPTTPEDlARHECL----GFSYWRARNRW-RLEGPGGEVKVPVSGRLTVNS 131

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1278639286 243 SGLVYVAALDGLGVALASKPLVATAIAQGRLVA 275
Cdd:cd08477   132 GQALRVAALAGLGIVLQPEALLAEDLASGRLVE 164
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-310 8.01e-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 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: 51.74  E-value: 8.01e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  94 GRLIVVLPPSFATRWLVPRLRRFAEAEPSLSLHvirsLSTIDGdqvanpasfdLADLRQEDSVVVIRFGtgvypgfqvdH 173
Cdd:cd08472     1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELD----LGVSDR----------PVDLIREGVDCVIRVG----------E 56

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 174 MFASDCIA---------VC-SPKLLET-GPPlRVPADMRHQVLLHDQGISSGRSGPaWD-------EWFKLAGVTGVDss 235
Cdd:cd08472    57 LADSSLVArrlgelrmvTCaSPAYLARhGTP-RHPEDLERHRAVGYFSARTGRVLP-WEfqrdgeeREVKLPSRVSVN-- 132

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 236 agphfsDSGLVYVAALDGLGVALASKPLVATAIAQGRLV------APFDIAVgqkfayYLVVPQAVAERPAVQAFRKWLL 309
Cdd:cd08472   133 ------DSEAYLAAALAGLGIIQVPRFMVRPHLASGRLVevlpdwRPPPLPV------SLLYPHRRHLSPRVRVFVDWVA 200


                  .
gi 1278639286 310 E 310
Cdd:cd08472   201 E 201
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
11-128 9.78e-08

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 52.67  E-value: 9.78e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  11 LRAFEAAARHLSFKDAAQEMSVTPTAISHQIKLLEEYLDLQLFHRlTRALELTPQGEAMLPKVREgLDCFAAAVASAHER 90
Cdd:PRK13348    7 LEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQ-VALLEADLLSTLPA 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1278639286  91 VTSGRL---IVVLPPSFATrWLVPRLRRFAeAEPSLSLHVI 128
Cdd:PRK13348   85 ERGSPPtlaIAVNADSLAT-WFLPALAAVL-AGERILLELI 123
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
7-127 6.35e-07

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 50.16  E-value: 6.35e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286   7 PLKALRAFEAAARHLSFKDAAQEMSVTPTAISHQIKLLEEYLDLQLFHRlTRALELTPQGEAMLPKVRE-GL---DCFAA 82
Cdd:PRK03635    3 DYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQvRLleaELLGE 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1278639286  83 AVASAHERVtsgRL-IVVLPPSFATrWLVPRLRRFAEAEP-SLSLHV 127
Cdd:PRK03635   82 LPALDGTPL---TLsIAVNADSLAT-WFLPALAPVLARSGvLLDLVV 124
PBP2_CrgA_like_9 cd08479
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-304 1.16e-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: 48.36  E-value: 1.16e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  94 GRLIVVLPPSFATRWLVPRLRRFAEAEPSLSLHvirsLSTIDgdqvanpasfDLADLRQEDSVVVIRFGTGVYPGFqVDH 173
Cdd:cd08479     1 GLLRVNASFGFGRRHIAPALSDFAKRYPELEVQ----LELTD----------RPVDLVEEGFDLDIRVGDLPDSSL-IAR 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 174 MFASDCIAVC-SPKLLETGPPLRVPADM-RHQVLLHDQGissgrsgpawDEWFKLAGVTGVDSSA-----GPHFSDSGLV 246
Cdd:cd08479    66 KLAPNRRILCaSPAYLERHGAPASPEDLaRHDCLVIREN----------DEDFGLWRLRNGDGEAtvrvrGALSSNDGEV 135

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1278639286 247 YVA-ALDGLGVALASKPLVATAIAQGRLVAPFDIAVGQKFAYYLVVPQAVAERPAVQAF 304
Cdd:cd08479   136 VLQwALDGHGIILRSEWDVAPYLRSGRLVRVLPDWQLPDADIWAVYPSRLSRSARVRVF 194
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 95-308 1.37e-06

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: 47.98  E-value: 1.37e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  95 RLIVVLPPSFATRWLVPRLRRFAEAEPSLSLHVIrslsTIDGDQVanpasfdLADLRQEDSVVVIRFGTGVYPGFQVDHM 174
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLV----EGGSSEL-------LEALLEGELDLAIVALPVDDPGLESEPL 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 175 FASDCIAVCSPKLLETGPPLRVPADMRHQ-VLLHDQGISSGRsgpAWDEWFKLAGVTgvdssagPH----FSDSGLVYVA 249
Cdd:cd05466    70 FEEPLVLVVPPDHPLAKRKSVTLADLADEpLILFERGSGLRR---LLDRAFAEAGFT-------PNialeVDSLEAIKAL 139

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 250 ALDGLGVALASKpLVATAIAQGRLVA-PFDiAVGQKFAYYLVVPQAVAERPAVQAFRKWL 308
Cdd:cd05466   140 VAAGLGIALLPE-SAVEELADGGLVVlPLE-DPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-274 7.22e-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: 45.92  E-value: 7.22e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  93 SGRLIVVLPPSFATRWLVPRLRRFAEAEPSLSLhvirSLSTIDG--DQVAnpASFDlADLRQEDSV----VVIRFGtgvy 166
Cdd:cd08474     2 AGTLRINAPRVAARLLLAPLLARFLARYPDIRL----ELVVDDGlvDIVA--EGFD-AGIRLGESVekdmVAVPLG---- 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 167 PGFQvdhmfasdCIAVCSPKLLETGPPLRVPADMR-HQVLLHDQGiSSGRSgPAW-----DEWFKLAgvtgVDssaGPH- 239
Cdd:cd08474    71 PPLR--------MAVVASPAYLARHGTPEHPRDLLnHRCIRYRFP-TSGAL-YRWefergGRELEVD----VE---GPLi 133

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1278639286 240 FSDSGLVYVAALDGLGVALASKPLVATAIAQGRLV 274
Cdd:cd08474   134 LNDSDLMLDAALDGLGIAYLFEDLVAEHLASGRLV 168
PRK09791 PRK09791
LysR family transcriptional regulator;
8-128 2.40e-05

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 45.14  E-value: 2.40e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286   8 LKALRAFEAAARHLSFKDAAQEMSVTPTAISHQIKLLEEYLDLQLFHRLTRALELTPQGEAMLPKVREGLDCFAAAVASA 87
Cdd:PRK09791    7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDI 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1278639286  88 HERV--TSGRLIVVLPPSFAtRWLVPR-LRRFAEAEPSLSLHVI 128
Cdd:PRK09791   87 RQRQgqLAGQINIGMGASIA-RSLMPAvISRFHQQHPQVKVRIM 129
cbl PRK12679
HTH-type transcriptional regulator Cbl;
8-258 3.12e-05

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 44.80  E-value: 3.12e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286   8 LKALRafEAAARHLSFKDAAQEMSVTPTAISHQIKLLEEYLDLQLF-HRLTRALELTPQGEAML----------PKVREG 76
Cdd:PRK12679    6 LKIIR--EAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFiRRGKRLLGMTEPGKALLviaerilneaSNVRRL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  77 LDCFAAAvasahervTSGRLIVVLPPSFATRWLVPRLRRFAEAEPSLSLHVIR-SLSTIDGDQVANPASFDLADLRQEDS 155
Cdd:PRK12679   84 ADLFTND--------TSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQgTPQEIATLLQNGEADIGIASERLSND 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 156 VVVIRFgtgvyPGFQVDHmfasdciAVCSPK--LLETGPPLRVPADMRHQVLLHDQGIsSGRSgpAWDEWFKLAGVTGvD 233
Cdd:PRK12679  156 PQLVAF-----PWFRWHH-------SLLVPHdhPLTQITPLTLESIAKWPLITYRQGI-TGRS--RIDDAFARKGLLA-D 219

                         250       260
                  ....*....|....*....|....*
gi 1278639286 234 SSAGPHFSDSGLVYVAAldGLGVAL 258
Cdd:PRK12679  220 IVLSAQDSDVIKTYVAL--GLGIGL 242
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-303 4.63e-05

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: 43.70  E-value: 4.63e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  94 GRLIVVLPPSFATRWLVPRLRRFAEAEPSLSLHVirSLStidgDQVANPAS--FDLAdlrqedsvvvIRFGTGVYPGFQV 171
Cdd:cd08475     1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELEL--SFS----DRFVDLIEegIDLA----------VRIGELADSTGLV 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 172 DHMFASDCIAVC-SPKLLETGPPLRVPADmrhqvLLHDQGISSGRSGPAwdEWFKLAGVTGVDSSAGPH----FSDSGLV 246
Cdd:cd08475    65 ARRLGTQRMVLCaSPAYLARHGTPRTLED-----LAEHQCIAYGRGGQP--LPWRLADEQGRLVRFRPAprlqFDDGEAI 137

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1278639286 247 YVAALDGLGVALASKPLVATAIAQGRLVAPFDIAVGQKFAYYLVVPQAVAERPAVQA 303
Cdd:cd08475   138 ADAALAGLGIAQLPTWLVADHLQRGELVEVLPELAPEGLPIHAVWPRTRHLPPKVRA 194
PRK09801 PRK09801
LysR family transcriptional regulator;
22-274 1.53e-04

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 42.71  E-value: 1.53e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  22 SFKDAAQEMSVTPTAISHQIKLLEEYLDLQLFHRLTRALELTPQGEAMLPKVREGLDCFAAAVASAHERVT--SGRLIVV 99
Cdd:PRK09801   22 SFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQIKTrpEGMIRIG 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 100 LPPSFATRWLVPRLRRFAEAEPSLSLHVIRSLSTIDGDQvanpASFDLaDLRQEDSVvvirfgtgvyPGFQVDHMFASDC 179
Cdd:PRK09801  102 CSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQ----DNIDL-DIRINDEI----------PDYYIAHLLTKNK 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 180 IAVC-SPKLLETGP-PLRVPADMRHQVLL-HDQGISSGrsgpAWD----EWFKLAGVTGVDSsagphfSDSG-LVYVAAL 251
Cdd:PRK09801  167 RILCaAPEYLQKYPqPQSLQELSRHDCLVtKERDMTHG----IWElgngQEKKSVKVSGHLS------SNSGeIVLQWAL 236

                         250       260
                  ....*....|....*....|...
gi 1278639286 252 DGLGVALASKPLVATAIAQGRLV 274
Cdd:PRK09801  237 EGKGIMLRSEWDVLPFLESGKLV 259
PRK12680 PRK12680
LysR family transcriptional regulator;
8-261 1.64e-04

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 42.69  E-value: 1.64e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286   8 LKALRAFEAAA-RHLSFKDAAQEMSVTPTAISHQIKLLEEYLDLQLFHRLTRALE-LTPQGEAMLPKVREGLDCF--AAA 83
Cdd:PRK12680    3 LTQLRYLVAIAdAELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEAnnIRT 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  84 VASAHERVTSGRLIVVLPPSFATRWLVPRLRRFAEAEPSLSLHVirslstidgDQVANPASFDLADLRQEDSVVVIRFGT 163
Cdd:PRK12680   83 YAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHL---------QQAAESAALDLLGQGDADIAIVSTAGG 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 164 GVYPGFQVDHMFASDCIAVCSPKLLETgpPLRVPaDM----RHQVLLHDqgiSSGRSGPAWDEWFklAGVtGVDSSAGPH 239
Cdd:PRK12680  154 EPSAGIAVPLYRWRRLVVVPRGHALDT--PRRAP-DMaalaEHPLISYE---SSTRPGSSLQRAF--AQL-GLEPSIALT 224

                         250       260
                  ....*....|....*....|..
gi 1278639286 240 FSDSGLVYVAALDGLGVALASK 261
Cdd:PRK12680  225 ALDADLIKTYVRAGLGVGLLAE 246
cysB PRK12681
HTH-type transcriptional regulator CysB;
28-127 1.71e-04

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 42.58  E-value: 1.71e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  28 QEMSVTPTA---------ISHQIKLLEEYLDLQLFHR----LTRaleLTPQGEAMLPKVREGLDCFAA--AVASAHERVT 92
Cdd:PRK12681   15 HNLNVSATAeglytsqpgISKQVRMLEDELGIQIFARsgkhLTQ---VTPAGEEIIRIAREILSKVESikSVAGEHTWPD 91

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1278639286  93 SGRLivvlppSFAT-----RWLVPR-LRRFAEAEPSLSLHV 127
Cdd:PRK12681   92 KGSL------YIATthtqaRYALPPvIKGFIERYPRVSLHM 126
nhaR PRK11062
transcriptional activator NhaR; Provisional
 26-67 2.08e-04

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 42.30  E-value: 2.08e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1278639286  26 AAQEMSVTPTAISHQIKLLEEYLDLQLFHRLTRALELTPQGE 67
Cdd:PRK11062   24 AAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGE 65
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
30-71 3.15e-04

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 41.73  E-value: 3.15e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1278639286  30 MSVTPTAISHQIKLLEEYLDLQLFHRLTRALELTPQGEAMLP 71
Cdd:PRK11716    1 MHVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRP 42
PBP2_CrgA_like_10 cd08480
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 94-275 5.43e-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: 40.40  E-value: 5.43e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  94 GRLIVVLPPSFATRWLVPRLRRFAEAEPSLSLhvirSLSTIDGdqvanpasfdLADLRQEDSVVVIRFGtgvypgfqvdH 173
Cdd:cd08480     1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILV----DLSLTDE----------VVDLLAERTDVAIRVG----------P 56

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 174 MFASDCIA----------VCSPKLLET-GPPLRvPADM-RHQVLlhdqGISSGRSGPAWDewFKLAGVTGVDSSAGPHFS 241
Cdd:cd08480    57 LPDSSLVArklgesrrviVASPSYLARhGTPLT-PQDLaRHNCL----GFNFRRALPDWP--FRDGGRIVALPVSGNILV 129

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1278639286 242 DSG-LVYVAALDGLGVALASKPLVATAIAQGRLVA 275
Cdd:cd08480   130 NDGeALRRLALAGAGLARLALFHVADDIAAGRLVP 164
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 92-277 5.67e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain; This CD represents the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA. 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: 176167 [Multi-domain]  Cd Length: 199  Bit Score: 40.40  E-value: 5.67e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  92 TSGRLIVVLPPSFATRWLVPRLRRFAEAEPSLSLhvirSLSTIDGdqvanpasfdLADLRQEDSVVVIRFGTGVYPGFQV 171
Cdd:cd08478     1 PSGLLRVDAATPFVLHLLAPLIAKFRERYPDIEL----ELVSNEG----------IIDLIERKTDVAIRIGELTDSTLHA 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 172 DHMFASDCIAVCSPKLLET-GPPlRVPADMRHQVLLhdqgissGRSGPAWDEWFKLAGVTGVDSSAGPHF-SDSGLVYVA 249
Cdd:cd08478    67 RPLGKSRLRILASPDYLARhGTP-QSIEDLAQHQLL-------GFTEPASLNTWPIKDADGNLLKIQPTItASSGETLRQ 138

                         170       180
                  ....*....|....*....|....*....
gi 1278639286 250 -ALDGLGVALASKPLVATAIAQGRLVAPF 277
Cdd:cd08478   139 lALSGCGIACLSDFMTDKDIAEGRLIPLF 167
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 15-230 6.70e-04

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 40.80  E-value: 6.70e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  15 EAAARHLSFKDAAQEMSVTPTAISHQIKLLEEYLDLQLFHRL-TRALELTPQGEAMLPKV-REGLDcfaAA----VASAH 88
Cdd:PRK12683   11 EAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRgKRLTGLTEPGKELLQIVeRMLLD---AEnlrrLAEQF 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  89 ERVTSGRLIVVLPPSFATRWLVPRLRRFAEAEPSLSL--------HVIRSLSTIDGD-QVANPAsfdladLRQEDSVVVI 159
Cdd:PRK12683   88 ADRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLalrqgspqEIAEMLLNGEADiGIATEA------LDREPDLVSF 161

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1278639286 160 rfgtgvyPGFQVDHmfasdCIAVCSPKLLETGPPLRVPADMRHQVLLHDQGIsSGRSGpaWDEWFKLAGVT 230
Cdd:PRK12683  162 -------PYYSWHH-----VVVVPKGHPLTGRENLTLEAIAEYPIITYDQGF-TGRSR--IDQAFAEAGLV 217
PRK10341 PRK10341
transcriptional regulator TdcA;
5-70 1.66e-03

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 39.46  E-value: 1.66e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1278639286   5 LPPLKALRAFEAAARHLSFKDAAQEMSVTPTAISHQIKLLEEYLDLQLFHRLTRALELTPQGEAML 70
Cdd:PRK10341    6 LPKTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLL 71
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 14-316 2.69e-03

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 38.82  E-value: 2.69e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  14 FEAAARHLSFKDAAQEMSVTPTAISHQIKLLEEYLDLQLFHRLTRALELTPQGE-------AMLPKVREGLDCFAAAVAS 86
Cdd:PRK14997   10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQtfyehckAMLVEAQAAQDAIAALQVE 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286  87 AHervtsGRLIVVLPPSFATRWLVPRLRRFAEAEPSLSLHVIRSLSTID----GDQVA---NPASFdladlrqEDSVVVI 159
Cdd:PRK14997   90 PR-----GIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDvvgeGVDVAirvRPRPF-------EDSDLVM 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 160 RFGTGvypgfQVDHMFAsdciavcSPKLLETGPPLRVPADMRHQvllhdQGISSGrSGPAWDEWfKLAGVTGvdSSAGPH 239
Cdd:PRK14997  158 RVLAD-----RGHRLFA-------SPDLIARMGIPSAPAELSHW-----PGLSLA-SGKHIHRW-ELYGPQG--ARAEVH 216

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639286 240 F------SDSGLVYVAALDGLGVALASKPLVATAIAQGRLVAPFDIAVGQKFAYYLVVPQAVAERPAVQAFRKWLLEE-A 312
Cdd:PRK14997  217 FtprmitTDMLALREAAMAGVGLVQLPVLMVKEQLAAGELVAVLEEWEPRREVIHAVFPSRRGLLPSVRALVDFLTEEyA 296


                  ....
gi 1278639286 313 KAEE 316
Cdd:PRK14997  297 RMVE 300
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 8-71 4.55e-03

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 38.43  E-value: 4.55e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1278639286   8 LKALRAFEAAARH-LSFKDAAQEMSVTPTAISHQIKLLEEYLDLQLFHRL-TRALELTPQGEAMLP 71
Cdd:PRK12682    3 LQQLRFVREAVRRnLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHgKRLKGLTEPGKAVLD 68
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
19-71 4.93e-03

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 38.07  E-value: 4.93e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1278639286  19 RHlsFKDAAQEMSVTPTAISHQIKLLEEYLDLQLFHRLTRALELTPQGEAMLP 71
Cdd:PRK03601   16 RH--FGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLP 66
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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