NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1596946251|gb|TDW02134|]
View 

DNA-binding transcriptional LysR family regulator [Vibrio crassostreae]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

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

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

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-291 3.45e-47

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 158.49  E-value: 3.45e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251   1 MNLRQLEVFYAIMQTGTVSGAARSLHVSQPNVTRILAHTEQQLGFGLFERVKGRLVPTVEAKTLLPEAEKVYQQLGQFRS 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  81 LTNKVKQGHQ-HLRIGAPPILATKLLTPVIA-LMSREQELSFELLTANRDELCSGLLKHELDIAIAFGDEAPPAILAETL 158
Cdd:COG0583    81 ELRALRGGPRgTLRIGAPPSLARYLLPPLLArFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251 159 LTESLKVLAPSntverlpteltlddliNYPLPiigldsrdplglllhqslivrdehyHHPISVRGYSAAAELVKHQAGFA 238
Cdd:COG0583   161 GEERLVLVASP----------------DHPLA-------------------------RRAPLVNSLEALLAAVAAGLGIA 199

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1596946251 239 IVDPWTAEQYQNDDAVCVLPL-QPDIQFSVSILCAEHTPQSISVKQFIASLKSH 291
Cdd:COG0583   200 LLPRFLAADELAAGRLVALPLpDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREA 253
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-291 3.45e-47

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 158.49  E-value: 3.45e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251   1 MNLRQLEVFYAIMQTGTVSGAARSLHVSQPNVTRILAHTEQQLGFGLFERVKGRLVPTVEAKTLLPEAEKVYQQLGQFRS 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  81 LTNKVKQGHQ-HLRIGAPPILATKLLTPVIA-LMSREQELSFELLTANRDELCSGLLKHELDIAIAFGDEAPPAILAETL 158
Cdd:COG0583    81 ELRALRGGPRgTLRIGAPPSLARYLLPPLLArFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251 159 LTESLKVLAPSntverlpteltlddliNYPLPiigldsrdplglllhqslivrdehyHHPISVRGYSAAAELVKHQAGFA 238
Cdd:COG0583   161 GEERLVLVASP----------------DHPLA-------------------------RRAPLVNSLEALLAAVAAGLGIA 199

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1596946251 239 IVDPWTAEQYQNDDAVCVLPL-QPDIQFSVSILCAEHTPQSISVKQFIASLKSH 291
Cdd:COG0583   200 LLPRFLAADELAAGRLVALPLpDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREA 253
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 2-292 7.11e-38

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 135.89  E-value: 7.11e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251   2 NLRQLEVFYAIMQTGTVSGAARSLHVSQPNVTRILAHTEQQLGFGLFERVKGRLVPTVEAKTLLPEAEKVYQQLGQFRSL 81
Cdd:PRK11013    5 SLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSYYGLDRIVSA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  82 TNKVKQGHQ-HLRIGAPPILATKLLTPVIA-LMSREQELSF-----------ELLTANRDELcsGLLKHELdiaiafgde 148
Cdd:PRK11013   85 AESLREFRQgQLSIACLPVFSQSLLPGLCQpFLARYPDVSLnivpqesplleEWLSAQRHDL--GLTETLH--------- 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251 149 APPAILAETLLT-ESLKVLAPSNTVERLPTeLTLDDLINypLPIIGLDSRDPLGLLLHQslIVRDEHYHHPISVRGYSAA 227
Cdd:PRK11013  154 TPAGTERTELLTlDEVCVLPAGHPLAAKKV-LTPDDFAG--ENFISLSRTDSYRQLLDQ--LFAEHGVKRRMVVETHSAA 228

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1596946251 228 A--ELVKHQAGFAIVDPWTAEQYQNDDaVCVLPLQPDIQFSVSILCAEHTPQSISVKQFIASLKSHT 292
Cdd:PRK11013  229 SvcAMVRAGVGVSIVNPLTALDYAGSG-LVVRRFSISVPFTVSLIRPLHRPASALVDAFSEHLQQQA 294
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 92-288 1.37e-24

The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. LysR is the transcriptional activator of lysA gene encoding diaminopimelate decarboxylase, an enzyme that catalyses the decarboxylation of diaminopimelate to produce lysine. 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: 176107 [Multi-domain]  Cd Length: 196  Bit Score: 97.63  E-value: 1.37e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  92 LRIGAPPILATKLLTPVIA-LMSREQELSFELLTANRDELCSGLLKHELDIAIAFGDEAPPAILAETLLTESLKVLAPSN 170
Cdd:cd08415     2 LRIAALPALALSLLPRAIArFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLPPG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251 171 tvERLP--TELTLDDLINYPLpiIGLDSRDPLGLLLHQSLIVRDEHYHHPISVRGYSAAAELVKHQAGFAIVDPWTAEQY 248
Cdd:cd08415    82 --HPLArkDVVTPADLAGEPL--ISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIVDPLTAAGY 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1596946251 249 QnDDAVCVLPLQPDIQFSVSILCAEHTPQSISVKQFIASL 288
Cdd:cd08415   158 A-GAGLVVRPFRPAIPFEFALVRPAGRPLSRLAQAFIDLL 196
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-291 7.40e-23

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: 93.51  E-value: 7.40e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  91 HLRIGAPPILATKLLTPVIALMSREQ-ELSFELLTANRDELCSGLLKHELDIAIAFGDEAPPAILAETLLTESLKVLAPS 169
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYpDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAPP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251 170 NTVERLPTELTLDDLINYPLpiIGLDSRDPLGLLLHQSLIVRDEHYHHPISVRGYSAAAELVKHQAGFAIVDPWTAEQYQ 249
Cdd:pfam03466  83 DHPLARGEPVSLEDLADEPL--ILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1596946251 250 NDDAVCVLPLQ-PDIQFSVSILCAEHTPQSISVKQFIASLKSH 291
Cdd:pfam03466 161 ADGRLVALPLPePPLPRELYLVWRKGRPLSPAVRAFIEFLREA 203
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-189 2.93e-16

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: 77.27  E-value: 2.93e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251   1 MNLRQLEVFYAIMQTGTVSGAARSLHVSQPNVTRILAHTEQQLGFGLFERVKGRLVPT-------VEAKTLLPEAEKVYQ 73
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTedgkllyEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  74 QLGQFRsltnkvKQGHQHLRIGAPPILATKLLTPVIALMSREQ-ELSFELLTANRDELCSGLLKHELDIAIAfGDEAP-P 151
Cdd:NF040786   81 EFDRYG------KESKGVLRIGASTIPGQYLLPELLKKFKEKYpNVRFKLMISDSIKVIELLLEGEVDIGFT-GTKLEkK 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1596946251 152 AILAETLLTESLKVLAPSNT--VERLPTELTLDDLINYPL 189
Cdd:NF040786  154 RLVYTPFYKDRLVLITPNGTekYRMLKEEISISELQKEPF 193
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
1-82 7.90e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 35.26  E-value: 7.90e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251    1 MNLRQLEVFYAIMQTG--TVSGAARSLHVSQPNVTRILAHTEQQlgfGLFERVKG-------RLVPTVEAKTLLPEAEKV 71
Cdd:smart00347   8 LTPTQFLVLRILYEEGplSVSELAKRLGVSPSTVTRVLDRLEKK---GLVRREPSpedrrsvLVSLTEEGRELIEQLLEA 84

                           90
                   ....*....|...
gi 1596946251   72 YQQLGQ--FRSLT 82
Cdd:smart00347  85 RSETLAelLAGLT 97
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-291 3.45e-47

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 158.49  E-value: 3.45e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251   1 MNLRQLEVFYAIMQTGTVSGAARSLHVSQPNVTRILAHTEQQLGFGLFERVKGRLVPTVEAKTLLPEAEKVYQQLGQFRS 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  81 LTNKVKQGHQ-HLRIGAPPILATKLLTPVIA-LMSREQELSFELLTANRDELCSGLLKHELDIAIAFGDEAPPAILAETL 158
Cdd:COG0583    81 ELRALRGGPRgTLRIGAPPSLARYLLPPLLArFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251 159 LTESLKVLAPSntverlpteltlddliNYPLPiigldsrdplglllhqslivrdehyHHPISVRGYSAAAELVKHQAGFA 238
Cdd:COG0583   161 GEERLVLVASP----------------DHPLA-------------------------RRAPLVNSLEALLAAVAAGLGIA 199

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1596946251 239 IVDPWTAEQYQNDDAVCVLPL-QPDIQFSVSILCAEHTPQSISVKQFIASLKSH 291
Cdd:COG0583   200 LLPRFLAADELAAGRLVALPLpDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREA 253
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 2-292 7.11e-38

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 135.89  E-value: 7.11e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251   2 NLRQLEVFYAIMQTGTVSGAARSLHVSQPNVTRILAHTEQQLGFGLFERVKGRLVPTVEAKTLLPEAEKVYQQLGQFRSL 81
Cdd:PRK11013    5 SLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSYYGLDRIVSA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  82 TNKVKQGHQ-HLRIGAPPILATKLLTPVIA-LMSREQELSF-----------ELLTANRDELcsGLLKHELdiaiafgde 148
Cdd:PRK11013   85 AESLREFRQgQLSIACLPVFSQSLLPGLCQpFLARYPDVSLnivpqesplleEWLSAQRHDL--GLTETLH--------- 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251 149 APPAILAETLLT-ESLKVLAPSNTVERLPTeLTLDDLINypLPIIGLDSRDPLGLLLHQslIVRDEHYHHPISVRGYSAA 227
Cdd:PRK11013  154 TPAGTERTELLTlDEVCVLPAGHPLAAKKV-LTPDDFAG--ENFISLSRTDSYRQLLDQ--LFAEHGVKRRMVVETHSAA 228

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1596946251 228 A--ELVKHQAGFAIVDPWTAEQYQNDDaVCVLPLQPDIQFSVSILCAEHTPQSISVKQFIASLKSHT 292
Cdd:PRK11013  229 SvcAMVRAGVGVSIVNPLTALDYAGSG-LVVRRFSISVPFTVSLIRPLHRPASALVDAFSEHLQQQA 294
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 92-288 1.37e-24

The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. LysR is the transcriptional activator of lysA gene encoding diaminopimelate decarboxylase, an enzyme that catalyses the decarboxylation of diaminopimelate to produce lysine. 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: 176107 [Multi-domain]  Cd Length: 196  Bit Score: 97.63  E-value: 1.37e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  92 LRIGAPPILATKLLTPVIA-LMSREQELSFELLTANRDELCSGLLKHELDIAIAFGDEAPPAILAETLLTESLKVLAPSN 170
Cdd:cd08415     2 LRIAALPALALSLLPRAIArFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLPPG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251 171 tvERLP--TELTLDDLINYPLpiIGLDSRDPLGLLLHQSLIVRDEHYHHPISVRGYSAAAELVKHQAGFAIVDPWTAEQY 248
Cdd:cd08415    82 --HPLArkDVVTPADLAGEPL--ISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIVDPLTAAGY 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1596946251 249 QnDDAVCVLPLQPDIQFSVSILCAEHTPQSISVKQFIASL 288
Cdd:cd08415   158 A-GAGLVVRPFRPAIPFEFALVRPAGRPLSRLAQAFIDLL 196
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-291 7.40e-23

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: 93.51  E-value: 7.40e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  91 HLRIGAPPILATKLLTPVIALMSREQ-ELSFELLTANRDELCSGLLKHELDIAIAFGDEAPPAILAETLLTESLKVLAPS 169
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYpDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAPP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251 170 NTVERLPTELTLDDLINYPLpiIGLDSRDPLGLLLHQSLIVRDEHYHHPISVRGYSAAAELVKHQAGFAIVDPWTAEQYQ 249
Cdd:pfam03466  83 DHPLARGEPVSLEDLADEPL--ILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1596946251 250 NDDAVCVLPLQ-PDIQFSVSILCAEHTPQSISVKQFIASLKSH 291
Cdd:pfam03466 161 ADGRLVALPLPePPLPRELYLVWRKGRPLSPAVRAFIEFLREA 203
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 91-288 4.40e-21

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: 88.43  E-value: 4.40e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  91 HLRIGAPPILATKLLTPVIA-LMSREQELSFELLTANRDELCSGLLKHELDIAIAFGDEAPPAILAETLLTESLKVLAPS 169
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAaFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251 170 NTVERLPTELTLDDLINYPLpiIGLDSRDPLGLLLHQSLIVRDEHYHHPISVRGYSAAAELVKHQAGFAIVDPWTAEQYQ 249
Cdd:cd05466    81 DHPLAKRKSVTLADLADEPL--ILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELA 158

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1596946251 250 NDDAVCVLPLQPDIQFSVSILCAEHTPQSISVKQFIASL 288
Cdd:cd05466   159 DGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-188 1.29e-17

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 80.89  E-value: 1.29e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251   3 LRQLEVFYAIMQTGTVSGAARSLHVSQPNVTRILAHTEQQLGFGLFERVKGRLVPTVEAKTLLPEAEKVYQQLGQFRSLt 82
Cdd:PRK10837    5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIEQL- 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  83 nkVKQGHQHLRIGAPPILATKLLTPVIALMSRE-QELSFELLTANRDELCSGLLKHELDIAIAFGDEAPPAILAETLLTE 161
Cdd:PRK10837   84 --FREDNGALRIYASSTIGNYILPAMIARYRRDyPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPELISEPWLED 161

                         170       180
                  ....*....|....*....|....*...
gi 1596946251 162 SLKVL-APSNTVERLPteLTLDDLINYP 188
Cdd:PRK10837  162 ELVVFaAPDSPLARGP--VTLEQLAAAP 187
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 1.73e-16

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 72.03  E-value: 1.73e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251   3 LRQLEVFYAIMQTGTVSGAARSLHVSQPNVTRILAHTEQQLGFGLFERVKGRLVPTVEAK 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-189 2.93e-16

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: 77.27  E-value: 2.93e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251   1 MNLRQLEVFYAIMQTGTVSGAARSLHVSQPNVTRILAHTEQQLGFGLFERVKGRLVPT-------VEAKTLLPEAEKVYQ 73
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTedgkllyEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  74 QLGQFRsltnkvKQGHQHLRIGAPPILATKLLTPVIALMSREQ-ELSFELLTANRDELCSGLLKHELDIAIAfGDEAP-P 151
Cdd:NF040786   81 EFDRYG------KESKGVLRIGASTIPGQYLLPELLKKFKEKYpNVRFKLMISDSIKVIELLLEGEVDIGFT-GTKLEkK 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1596946251 152 AILAETLLTESLKVLAPSNT--VERLPTELTLDDLINYPL 189
Cdd:NF040786  154 RLVYTPFYKDRLVLITPNGTekYRMLKEEISISELQKEPF 193
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-189 7.74e-16

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 76.15  E-value: 7.74e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251   1 MNLRQLEVFYAIMQTGTVSGAARSLHVSQPNVTRILAHTEQQLGFGLFERvKGRLVPTVEAKTL-LPEAEKVYQQLGQFR 79
Cdd:PRK11242    1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDR-SGRTVRLTDAGEVyLRYARRALQDLEAGR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  80 SLTNKVKQ-GHQHLRIGAPPILATKLLTPVI-ALMSREQELSFELLTANRDELCSGLLKHELDIAIAFGDEAPPAILAET 157
Cdd:PRK11242   80 RAIHDVADlSRGSLRLAMTPTFTAYLIGPLIdAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQP 159

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1596946251 158 LLTESLK-VLAPSNTVERLPTELTLDDLINYPL 189
Cdd:PRK11242  160 LFTETLAlVVGRHHPLAARRKALTLDELADEPL 192
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-190 5.00e-15

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 73.65  E-value: 5.00e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251   1 MNLRQLEVFYAIMQTGTVSGAARSLHVSQPNVTRILAHTEQQLGFGLFERVKGRLVPTVEAKTLLPEAEKVYQQLGQFRS 80
Cdd:PRK09906    1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  81 LTNKVKQGHQHLRIGAPPILATKLLTPVIA-LMSREQELSFELLTANRDELCSGLLKHELDIAIAFGDEAPPAILAETLL 159
Cdd:PRK09906   81 RARKIVQEDRQLTIGFVPSAEVNLLPKVLPmFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLELL 160

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1596946251 160 TESLKVLAPSNTVERLPTELTLDDL--INYPLP 190
Cdd:PRK09906  161 DEPLVVVLPVDHPLAHEKEITAAQLdgVNFIST 193
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-288 1.61e-12

TThe 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: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 64.85  E-value: 1.61e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  91 HLRIGAPPILATKLLTPVIALMSREQ-ELSFELLTANRDELCSGLLKHELDIAIAFGDEAPPAILAETLLTESLKVLAPS 169
Cdd:cd08440     1 RVRVAALPSLAATLLPPVLAAFRRRHpGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251 170 NTVERLPTELTLDDLINYPLpiIGLDSRDPLGLLLHQSLIVRDEHYHHPISVRGYSAAAELVKHQAGFAIVdPWTAEQYQ 249
Cdd:cd08440    81 DHPLARRRSVTWAELAGYPL--IALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVL-PALALPLA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1596946251 250 NDDAVCVLPL-QPDIQFSVSILCAEHTPQSISVKQFIASL 288
Cdd:cd08440   158 DHPGLVARPLtEPVVTRTVGLIRRRGRSLSPAAQAFLDLL 197
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 21-198 3.07e-11

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 62.55  E-value: 3.07e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  21 AARSLHVSQPNVTRILAHTEQQLGFGLFERVKGRLVPTVEAKTLLPEAEKVYQQLgqfRSLTNKVKQG--HQHLRIGAPP 98
Cdd:PRK11139   26 AAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQL---AEATRKLRARsaKGALTVSLLP 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  99 ILATKLLTPVIALMS-REQELSFELLTANRDElcsGLLKHELDIAIAFGDEAPPAILAETLLTESL-KVLAPSNTVERLP 176
Cdd:PRK11139  103 SFAIQWLVPRLSSFNeAHPDIDVRLKAVDRLE---DFLRDDVDVAIRYGRGNWPGLRVEKLLDEYLlPVCSPALLNGGKP 179

                         170       180
                  ....*....|....*....|..
gi 1596946251 177 TElTLDDLINYPLpiIGLDSRD 198
Cdd:PRK11139  180 LK-TPEDLARHTL--LHDDSRE 198
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-189 7.79e-11

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 61.55  E-value: 7.79e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251   1 MNLRQLE-VFYAIMQTGTVSGAARSLHVSQPNVTRILAHTEQQLGFGLFERVKGRLVPTVE-AKTLLPEAEKVYQQLGQF 78
Cdd:PRK12682    1 MNLQQLRfVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKGLTEpGKAVLDVIERILREVGNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  79 RSLTNK-VKQGHQHLRIGAPPILATKLLTPVIA-LMSREQELSFELLTANRDELCSGLLKHELDIAIAfgdeappailAE 156
Cdd:PRK12682   81 KRIGDDfSNQDSGTLTIATTHTQARYVLPRVVAaFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIA----------TE 150

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1596946251 157 TLL-TESLK----------VLAPSNTVERLPTELTLDDLINYPL 189
Cdd:PRK12682  151 SLAdDPDLAtlpcydwqhaVIVPPDHPLAQEERITLEDLAEYPL 194
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 91-288 1.37e-10

The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 59.59  E-value: 1.37e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  91 HLRIGAPPILATKLLTPVIA-LMSREQELSFELLTANRDELCSGLLKHELDIAI--AFGDEAPPAILAETLLTESLKVLA 167
Cdd:cd08435     1 TVRVGAVPAAAPVLLPPAIArLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIgrLADDEQPPDLASEELADEPLVVVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251 168 -PSNTVERLPtELTLDDLINYP--LPIIGLDSRDPL-GLLLHQSLIVRdehyHHPISVRGYSAAAELVKHQAGFAIVDPW 243
Cdd:cd08435    81 rPGHPLARRA-RLTLADLADYPwvLPPPGTPLRQRLeQLFAAAGLPLP----RNVVETASISALLALLARSDMLAVLPRS 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1596946251 244 TAEQYQNDDAVCVLPL-QPDIQFSVSILCAEHTPQSISVKQFIASL 288
Cdd:cd08435   156 VAEDELRAGVLRELPLpLPTSRRPIGITTRRGGPLSPAARALLDAL 201
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-169 6.65e-10

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 58.93  E-value: 6.65e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251   1 MNLRQLEVFYAIMQTGTVSGAARSLHVSQPNVTRILAHTEQQLGFGLFERVKGRLVPTVEAKTLLPEAEKVYQQLGQFRS 80
Cdd:PRK11233    1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  81 LTNKVKQGHQ-HLRIG-APPILATKLLTPVIALMSREQELSFELLTANRDELCSGLL-KHELDIAIAFGDEAPPAILAET 157
Cdd:PRK11233   81 AVHNVGQALSgQVSIGlAPGTAASSLTMPLLQAVRAEFPGIVLYLHENSGATLNEKLmNGQLDMAVIYEHSPVAGLSSQP 160

                         170
                  ....*....|..
gi 1596946251 158 LLTESLKVLAPS 169
Cdd:PRK11233  161 LLKEDLFLVGTQ 172
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-151 3.12e-09

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 56.95  E-value: 3.12e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251   3 LRQLEVFYAIMQTGTVSGAARSLHVSQPNVTRILAHTEQQLGFGLFERVKGRLVPTVEAKTLLPEAEKV-------YQQL 75
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRIlalceetCRAL 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1596946251  76 GQFRSLtnkvKQGhqHLRIGAPPILATKLLTPVIALMSRE-QELSFELLTANRDELCSGLLKHELDIAIaFGDEAPP 151
Cdd:CHL00180   87 EDLKNL----QRG--TLIIGASQTTGTYLMPRLIGLFRQRyPQINVQLQVHSTRRIAWNVANGQIDIAI-VGGEVPT 156
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-189 1.31e-08

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 54.98  E-value: 1.31e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251   1 MNLRQLE-VFYAIMQTGTVSGAARSLHVSQPNVTRILAHTEQQLGFGLFERVKGRLVPTVEA-KTLLPEAEKVYQQLGQF 78
Cdd:PRK12684    1 MNLHQLRfVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRGLTEPgRIILASVERILQEVENL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  79 RSLTNKVKQGHQ-HLRIGAPPILATKLLTPVI-ALMSREQELSFELLTANRDELCSGLLKHELDIAIafgdeAPPAI-LA 155
Cdd:PRK12684   81 KRVGKEFAAQDQgNLTIATTHTQARYALPAAIkEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAI-----ATEAIaDY 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1596946251 156 ETLLteSLK-------VLAPSNTVERLPTELTLDDLINYPL 189
Cdd:PRK12684  156 KELV--SLPcyqwnhcVVVPPDHPLLERKPLTLEDLAQYPL 194
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 91-259 3.25e-08

The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 52.60  E-value: 3.25e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  91 HLRIGAPPILATKLLTPVIALMSRE-QELSFELLTANRDELCSGLLKHELDIAIAFGDEAPPAILAETLLTESLKVLAPS 169
Cdd:cd08417     1 TFRIAASDYLEALLLPPLLARLRQEaPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251 170 NTVeRLPTELTLDDLINYP--LPIIGLDSRDPLGLLLHQSLIVRDEhyhhPISVRGYSAAAELVKHQAGFAIVDPWTAEQ 247
Cdd:cd08417    81 DHP-LAGGPLTLEDYLAAPhvLVSPRGRGHGLVDDALAELGLSRRV----ALTVPHFLAAPALVAGTDLIATVPRRLAEA 155

                         170
                  ....*....|..
gi 1596946251 248 YQNDDAVCVLPL 259
Cdd:cd08417   156 LAERLGLRVLPL 167
PRK09986 PRK09986
LysR family transcriptional regulator;
1-189 3.86e-08

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 53.57  E-value: 3.86e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251   1 MNLRQLEVFYAIMQTGTVSGAARSLHVSQPNVTRILAHTEQQLGFGLFERVKGRLVPTVEAKTLLPEAEKVYQQLGQFRS 80
Cdd:PRK09986    7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  81 LTNKVKQG-HQHLRIGappILATKLLTPVIALMSReqelsFELLTANRD----ELCSG-----LLKHELDIAI--AFGDE 148
Cdd:PRK09986   87 RVEQIGRGeAGRIEIG---IVGTALWGRLRPAMRH-----FLKENPNVEwllrELSPSmqmaaLERRELDAGIwrMADLE 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1596946251 149 APPAILAETLLTESLKVLAPSNTVERLPTELTLDDLINYPL 189
Cdd:PRK09986  159 PNPGFTSRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYF 199
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-189 2.07e-07

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 51.20  E-value: 2.07e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251   1 MNLRQLE-VFYAIMQTGTVSGAARSLHVSQPNVTRILAHTEQQLGFGLFERVKGRLVPTVE-AKTLLPEAEKVYQQLGQF 78
Cdd:PRK12683    1 MNFQQLRiIREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTGLTEpGKELLQIVERMLLDAENL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  79 RSLTNKVKQGHQ-HLRIGAPPILATKLLTPVI-ALMSREQELSFELLTANRDELCSGLLKHELDIAIAfgdeappailae 156
Cdd:PRK12683   81 RRLAEQFADRDSgHLTVATTHTQARYALPKVVrQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIA------------ 148

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1596946251 157 tllTESLK-----------------VLAPSNTVERLPtELTLDDLINYPL 189
Cdd:PRK12683  149 ---TEALDrepdlvsfpyyswhhvvVVPKGHPLTGRE-NLTLEAIAEYPI 194
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 91-189 2.20e-07

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: 50.18  E-value: 2.20e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  91 HLRIGAPPILATKLLTPVIALMSRE-QELSFELLTANRDELCSGLLKHELDIAIAFGDEAPPAILAETLLTESLKVLAPS 169
Cdd:cd08420     1 TLRIGASTTIGEYLLPRLLARFRKRyPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPP 80

                          90       100
                  ....*....|....*....|
gi 1596946251 170 NTVERLPTELTLDDLINYPL 189
Cdd:cd08420    81 DHPLAGRKEVTAEELAAEPW 100
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 91-261 2.34e-07

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold; CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 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: 176116  Cd Length: 197  Bit Score: 50.02  E-value: 2.34e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  91 HLRIGAPPILATKLLTPVIA-LMSREQELSFELLTANRDELCSGLLKHELDIAIAFGDEAPPAILAETLLTESLK-VLAP 168
Cdd:cd08425     2 SLRLAMTPTFTAYLIGPLIDrFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDAQPLFDERLAlVVGA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251 169 SNTVERLPTELTLDDLINYPLpiigldsrdplgLLLHQSLIVRD-------EHYHHP---ISVRGYSAAAELVKHqAGFA 238
Cdd:cd08425    82 THPLAQRRTALTLDDLAAEPL------------ALLSPDFATRQhidryfqKQGIKPriaIEANSISAVLEVVRR-GRLA 148

                         170       180
                  ....*....|....*....|...
gi 1596946251 239 IVDPWTAEQYQNDdaVCVLPLQP 261
Cdd:cd08425   149 TILPDAIAREQPG--LCAVALEP 169
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 91-189 1.56e-06

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: 47.58  E-value: 1.56e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  91 HLRIGAPPILATKLLTPVIA-LMSREQELSFELLTANRDelcSGLLKHELDIAIAFGDEAPPAILAETLLTESLKVLAPS 169
Cdd:cd08432     1 VLTVSVTPSFAARWLIPRLArFQARHPDIDLRLSTSDRL---VDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSP 77

                          90       100
                  ....*....|....*....|
gi 1596946251 170 NTVERLPTeLTLDDLINYPL 189
Cdd:cd08432    78 ALLAGLPL-LSPADLARHTL 96
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 91-189 5.98e-06

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


Pssm-ID: 176106 [Multi-domain]  Cd Length: 197  Bit Score: 45.96  E-value: 5.98e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  91 HLRIGAPPILATKLLTPVIALMSREQ-ELSFELLTANRDELCSGLLKHELDIAIAFGDEAPPAILAETLLTESLKVLAPS 169
Cdd:cd08414     1 RLRIGFVGSALYGLLPRLLRRFRARYpDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALPA 80

                          90       100
                  ....*....|....*....|
gi 1596946251 170 NTVERLPTELTLDDLINYPL 189
Cdd:cd08414    81 DHPLAARESVSLADLADEPF 100
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-189 6.00e-06

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 47.11  E-value: 6.00e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251   1 MNLRQLEVFY-AIMQTGTVSGAARSLHVSQPNVTRILAHTEQQLGFGLFERVKGRLVPTVE-AKTLLPEAEKVYQQLGQF 78
Cdd:PRK12679    1 MNFQQLKIIReAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLGMTEpGKALLVIAERILNEASNV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  79 RSL----TNK------VKQGHQHLRIGAPPIL-ATKLLTPvialmsreqELSFELLTANRDELCSGLLKHELDIAIAFGD 147
Cdd:PRK12679   81 RRLadlfTNDtsgvltIATTHTQARYSLPEVIkAFRELFP---------EVRLELIQGTPQEIATLLQNGEADIGIASER 151

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1596946251 148 EAP-PAILAETLLTESLKVLAPSNTVERLPTELTLDDLINYPL 189
Cdd:PRK12679  152 LSNdPQLVAFPWFRWHHSLLVPHDHPLTQITPLTLESIAKWPL 194
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-109 6.30e-06

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 46.93  E-value: 6.30e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251   1 MNLRQLEVFYAIMQTGTVSGAARSLHVSQPNVTRILAHTEQQLGFGLFERVKGRLVPTVEAKTLLPEAEKVYQQLGQFRS 80
Cdd:PRK15421    2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                          90       100
                  ....*....|....*....|....*....
gi 1596946251  81 LTNKVKQghQHLRIGAPPILATKLLTPVI 109
Cdd:PRK15421   82 ACNEPQQ--TRLRIAIECHSCIQWLTPAL 108
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 91-189 1.43e-05

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: 44.89  E-value: 1.43e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  91 HLRIGAPPILATKLLTPVIALMSRE---------QELSFELLtanrdelcSGLLKHELDIAIAFGDEAPPAILAETLLTE 161
Cdd:cd08433     1 RVSVGLPPSAASVLAVPLLRAVRRRypgirlrivEGLSGHLL--------EWLLNGRLDLALLYGPPPIPGLSTEPLLEE 72

                          90       100
                  ....*....|....*....|....*...
gi 1596946251 162 SLKVLAPSNTVERLPTELTLDDLINYPL 189
Cdd:cd08433    73 DLFLVGPADAPLPRGAPVPLAELARLPL 100
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
21-150 1.52e-05

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 45.39  E-value: 1.52e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  21 AARSLHVSQPNVTRILAHTEQQLGFGLFERVKGRLVPTVEAKTLLPEAEKVYQQLGQFRSLTNKVKQgHQHLRIGAPPIL 100
Cdd:PRK03601   21 AAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKKEVAHTSQ-HNELSIGASASL 99

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1596946251 101 ATKLLTPVI-ALMSREQELSFELLTANRDELCSGLLKHELDIAIAfgDEAP 150
Cdd:PRK03601  100 WECMLTPWLgRLYQNQEALQFEARIAQRQSLVKQLHERQLDLLIT--TEAP 148
PRK09801 PRK09801
LysR family transcriptional regulator;
4-184 2.11e-05

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 45.41  E-value: 2.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251   4 RQLEVFYAIMQTGTVSGAARSLHVSQPNVTRILAHTEQQLGFGLFERvKGRLVPTVEAktllpeAEKVYQQ----LGQFR 79
Cdd:PRK09801    9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNR-SARGVALTES------GQRCYEHaleiLTQYQ 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  80 SLTNKVKQGHQH----LRIGAPPILATKLLTPVIALMSR---EQELSFELLTANRDelcsgLLKHELDIAIAFGDEAPPA 152
Cdd:PRK09801   82 RLVDDVTQIKTRpegmIRIGCSFGFGRSHIAPAITELMRnypELQVHFELFDRQID-----LVQDNIDLDIRINDEIPDY 156

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1596946251 153 ILAEtLLTESLKVL-APSNTVERLPTELTLDDL 184
Cdd:PRK09801  157 YIAH-LLTKNKRILcAAPEYLQKYPQPQSLQEL 188
PRK12680 PRK12680
LysR family transcriptional regulator;
1-189 2.35e-05

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 45.38  E-value: 2.35e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251   1 MNLRQLEVFYAIMQTG-TVSGAARSLHVSQPNVTRILAHTEQQLGFGLFERvKGRLVPTVE--AKTLLPEAEKVYQQLGQ 77
Cdd:PRK12680    1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVR-KGRSLESVTpaGVEVIERARAVLSEANN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  78 FRSLTNKVKQGHQ-HLRIGAPPILATKLLTPVIALM-SREQELSFELLTANRDELCSGLLKHELDIAI-AFGDEAPPAIL 154
Cdd:PRK12680   80 IRTYAANQRRESQgQLTLTTTHTQARFVLPPAVAQIkQAYPQVSVHLQQAAESAALDLLGQGDADIAIvSTAGGEPSAGI 159

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1596946251 155 AETLLTESLKVLAP-SNTVERLPTELTLDDLINYPL 189
Cdd:PRK12680  160 AVPLYRWRRLVVVPrGHALDTPRRAPDMAALAEHPL 195
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
4-87 2.60e-05

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 45.04  E-value: 2.60e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251   4 RQLEVFYAIMQTGTVSGAARSLHVSQPNVTRILAHTEQQLGFGLFERVKGRLVPTVEAKTLLPEAEKVY---QQLGQFRS 80
Cdd:PRK15243    7 KKLKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQTIYRKVKSHYiflHALEQEIG 86


                  ....*..
gi 1596946251  81 LTNKVKQ 87
Cdd:PRK15243   87 PTGKTKQ 93
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 92-288 3.03e-05

The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. 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: 176146 [Multi-domain]  Cd Length: 196  Bit Score: 44.02  E-value: 3.03e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  92 LRIGAPPILATKLLTPVIALMSREQ-ELSFELLTANRDELCSGLLKHELDIAIAFGDEA-PPAILAETLLTESLKVLAPS 169
Cdd:cd08457     2 LRIAAMPALANGFLPRFLAAFLRLRpNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEeRQGFLIETRSLPAVVAVPMG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251 170 NTVERLPtELTLDDLINYPlpIIGLDSRDPLGLLLHQSLIVRDEHYHHPISVRGYSAAAELVKHQAGFAIVDPWTAEQYQ 249
Cdd:cd08457    82 HPLAQLD-VVSPQDLAGER--IITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGIAIIDPATAIGLP 158

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1596946251 250 NdDAVCVLPLQPDIQFSVSILCAEHTPQSISVKQFIASL 288
Cdd:cd08457   159 L-DGIVIRPFDTFIDAGFLVVRAANGPPSTMVDRFIDEF 196
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-153 5.87e-05

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 43.86  E-value: 5.87e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251   1 MNLRQLEVFYAIMQTGTVSGAARSLHVSQPNVTRILAHTEQQLGFGLFERVKGRLVPT------VE-AKTLLPEAeKVYQ 73
Cdd:PRK11151    1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTqaglllVDqARTVLREV-KVLK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  74 QLGqfrSLTNKVKQGHQHlrIGAPPILATKLLtPVIALMSREQ--ELSFELLTANRDELCSGLLKHELDIAI-AFGDEAP 150
Cdd:PRK11151   80 EMA---SQQGETMSGPLH--IGLIPTVGPYLL-PHIIPMLHQTfpKLEMYLHEAQTHQLLAQLDSGKLDCAIlALVKESE 153


                  ...
gi 1596946251 151 PAI 153
Cdd:PRK11151  154 AFI 156
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-184 7.12e-05

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: 42.97  E-value: 7.12e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  91 HLRIGAPPILATKLLTPVIALMSREQ-ELSFELLTANRDELCSGLLKHELDIAIAFGDEAPPAILAET-----LLTESLK 164
Cdd:cd08423     1 TLRVGAFPTAAAALLPPALAALRARHpGLEVRLREAEPPESLDALRAGELDLAVVFDYPVTPPPDDPGltrvpLLDDPLD 80

                          90       100
                  ....*....|....*....|
gi 1596946251 165 VLAPSNTVERLPTELTLDDL 184
Cdd:cd08423    81 LVLPADHPLAGREEVALADL 100
PRK10341 PRK10341
transcriptional regulator TdcA;
4-84 2.30e-04

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 42.16  E-value: 2.30e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251   4 RQLEVFYAIMQTGTVSGAARSLHVSQPNVTRILAHTEQQLGFGLFERVKGRLVPTVEAKTLLPEAEKVYQQL----GQFR 79
Cdd:PRK10341   10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMknmvNEIN 89


                  ....*
gi 1596946251  80 SLTNK 84
Cdd:PRK10341   90 GMSSE 94
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 92-207 3.99e-04

The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of N2 fixing bacteria, and synthesis of virulence factors, to a name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 40.61  E-value: 3.99e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  92 LRIGAPPILATKLLTPVIALMSREQ-ELSFELLTANRDELCSGLLKHELDIAIAFGDEAPPAILAETLLTESLKVLAPSN 170
Cdd:cd08412     2 LRIGCFSTLAPYYLPGLLRRFREAYpGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARLPPYVWLPAD 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1596946251 171 tvERLP--TELTLDDLINYPLpiIGLD---SRDPLGLLLHQS 207
Cdd:cd08412    82 --HPLAgkDEVSLADLAAEPL--ILLDlphSREYFLSLFAAA 119
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 92-189 6.31e-04

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: 39.84  E-value: 6.31e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  92 LRIGAPPILATKLLTPVIALMSREQ-ELSFELLTANRdelCSGLLKHELDIAIAFGDEAPPAILAETLLTESLKVLAPSN 170
Cdd:cd08487     2 LTVGAVGTFAVGWLLPRLAEFRQLHpFIELRLRTNNN---VVDLATEGLDFAIRFGEGLWPATHNERLLDAPLSVLCSPE 78

                          90       100
                  ....*....|....*....|.
gi 1596946251 171 TVERL--PTeltldDLINYPL 189
Cdd:cd08487    79 IAKRLshPA-----DLINETL 94
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 92-288 8.87e-04

The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold; LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The 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: 176145 [Multi-domain]  Cd Length: 196  Bit Score: 39.71  E-value: 8.87e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  92 LRIGAPPILATKLLTPVI-ALMSREQELSFELLTANRDELCSGLLKHELDIAIAFGDEAPPAILAETLLTESLKVLAPSN 170
Cdd:cd08456     2 LRIAVLPALSQSFLPRAIkAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGIERERLLRIDGVCVLPPG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251 171 tvERLPTE--LTLDDLINYPLpiIGLDSRDplGLLLHQSLIVRDEHYHHPISVRGYSAAA--ELVKHQAGFAIVDPWTAE 246
Cdd:cd08456    82 --HRLAVKkvLTPSDLEGEPF--ISLARTD--GTRQRVDALFEQAGVKRRIVVETSYAATicALVAAGVGVSVVNPLTAL 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1596946251 247 QYQNDDAVcVLPLQPDIQFSVSILCAEHTPQSISVKQFIASL 288
Cdd:cd08456   156 DYAAAGLV-VRRFSPAVPFEVSLIRPKHRPSSALVAAFSACL 196
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-266 1.35e-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: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 39.09  E-value: 1.35e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  91 HLRIGAPPILATKLLTPVIA-LMSREQELSFELLTANRDELCSGLLKHELDIAI----AFGdeAPPAILAETLLTESLKV 165
Cdd:cd08427     1 RLRLGAIATVLTGLLPRALArLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIvvepPFP--LPKDLVWTPLVREPLVL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251 166 LAPSNTVERLPTELTLDdlinypLPIIGLDSRDPLG-----LLLHQSLIVRDEhyhhpISVRGYSAAAELVKHQAGFAIV 240
Cdd:cd08427    79 IAPAELAGDDPRELLAT------QPFIRYDRSAWGGrlvdrFLRRQGIRVREV-----MELDSLEAIAAMVAQGLGVAIV 147

                         170       180
                  ....*....|....*....|....*.
gi 1596946251 241 dPWTAEQYQNDDAVCVLPLqPDIQFS 266
Cdd:cd08427   148 -PDIAVPLPAGPRVRVLPL-GDPAFS 171
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 91-189 1.77e-03

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


Pssm-ID: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 38.67  E-value: 1.77e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  91 HLRIGAPPILATKLLTPVIALMSREQ-ELSFELLTANRDELCSGLLKHELDIAIAFGDEAPPAILAETLLTESLKVLAPS 169
Cdd:cd08434     1 TVRLGFLHSLGTSLVPDLIRAFRKEYpNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPK 80

                          90       100
                  ....*....|....*....|..
gi 1596946251 170 NtvERLP--TELTLDDLINYPL 189
Cdd:cd08434    81 D--HPLAgrDSVDLAELADEPF 100
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-230 2.48e-03

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 38.80  E-value: 2.48e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251   2 NLRQLEVFYAIMQTGTVSGAARSLHVSQPNVTRILAHTEQQLGFGLFerVKGRLV-PTveaktllPEAEKVYQQLGQFRS 80
Cdd:PRK13348    3 DYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLL--VRGRPCrPT-------PAGQRLLRHLRQVAL 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  81 LTNKVKQGHQHLRIGAPPI--------LATKLLTPVIALMSREQELsFELLTANRDELCSGLLKHELDIAIAFGDEAPPA 152
Cdd:PRK13348   74 LEADLLSTLPAERGSPPTLaiavnadsLATWFLPALAAVLAGERIL-LELIVDDQDHTFALLERGEVVGCVSTQPKPMRG 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251 153 ILAETLLTESLKVLAPSNTVER-LPTELTLDDLINypLPIIGLDSRDPL-GLLLHQSLIVRDEHY--HHPISVRGYSAAA 228
Cdd:PRK13348  153 CLAEPLGTMRYRCVASPAFAARyFAQGLTRHSALK--APAVAFNRKDTLqDSFLEQLFGLPVGAYprHYVPSTHAHLAAI 230


                  ..
gi 1596946251 229 EL 230
Cdd:PRK13348  231 RH 232
PRK09791 PRK09791
LysR family transcriptional regulator;
3-50 2.75e-03

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 38.59  E-value: 2.75e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1596946251   3 LRQLEVFYAIMQTGTVSGAARSLHVSQPNVTRILAHTEQQLGFGLFER 50
Cdd:PRK09791    7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFR 54
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 100-259 3.79e-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: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 37.67  E-value: 3.79e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251 100 LATKLLTPVIA-LMSREQELSFELLTANRDELCSGLLKHELDIAIAFGDEAPPAILAETLLTESLK-VLAPSNTVERLPT 177
Cdd:cd08426    10 LAAELLPSLIArFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGaVVPPGHPLARQPS 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251 178 eLTLDDLINYPL--PIIGLDSRDPLGLLLHQslivRDEHYHHPISVRGYSAAAELVKHQAGFAIVDPWTAEQYQNDDAVC 255
Cdd:cd08426    90 -VTLAQLAGYPLalPPPSFSLRQILDAAFAR----AGVQLEPVLISNSIETLKQLVAAGGGISLLTELAVRREIRRGQLV 164


                  ....
gi 1596946251 256 VLPL 259
Cdd:cd08426   165 AVPL 168
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
3-163 5.61e-03

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 37.67  E-value: 5.61e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251   3 LRQLEVFYAIMQTGTVSGAARSLHVSQPNVTRILAHTEQQLGFGLFERVKGRLvptveakTLLPEAEKVYQQLGQ-FRSL 81
Cdd:PRK10086   16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKV-------ELTEEGKRVFWALKSsLDTL 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  82 TNKV-KQGHQH----LRIGAPPILATKLLTPVIALMSREQ-ELSFELLTANRDelcSGLLKHELDIAIAFGDEAPPAILA 155
Cdd:PRK10086   89 NQEIlDIKNQElsgtLTVYSRPSIAQCWLVPRLADFTRRYpSISLTILTGNEN---VNFQRAGIDLAIYFDDAPSAQLTH 165


                  ....*...
gi 1596946251 156 ETLLTESL 163
Cdd:PRK10086  166 HFLMDEEI 173
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 91-285 5.72e-03

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: 37.03  E-value: 5.72e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  91 HLRIGAPPILATKLLTPVIA-LMSREQELSFELLTANR--DelcsgLLKHELDIAIAFGDEAPPAILAetllteslKVLA 167
Cdd:cd08422     2 RLRISAPVSFGRLHLAPLLAeFLARYPDVRLELVLSDRlvD-----LVEEGFDLAIRIGELPDSSLVA--------RRLG 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251 168 PSNTV--------ERLPTELTLDDLINypLPIIGLDSRDPLGLLlhqSLIVRDEHYHHPISVR----GYSAAAELVKHQA 235
Cdd:cd08422    69 PVRRVlvaspaylARHGTPQTPEDLAR--HRCLGYRLPGRPLRW---RFRRGGGEVEVRVRGRlvvnDGEALRAAALAGL 143

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1596946251 236 GFAIVDPWTAEQY-QNDDAVCVLPLQPDIQFSVSILCAEHTPQSISVKQFI 285
Cdd:cd08422   144 GIALLPDFLVAEDlASGRLVRVLPDWRPPPLPIYAVYPSRRHLPAKVRAFI 194
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
1-82 7.90e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 35.26  E-value: 7.90e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251    1 MNLRQLEVFYAIMQTG--TVSGAARSLHVSQPNVTRILAHTEQQlgfGLFERVKG-------RLVPTVEAKTLLPEAEKV 71
Cdd:smart00347   8 LTPTQFLVLRILYEEGplSVSELAKRLGVSPSTVTRVLDRLEKK---GLVRREPSpedrrsvLVSLTEEGRELIEQLLEA 84

                           90
                   ....*....|...
gi 1596946251   72 YQQLGQ--FRSLT 82
Cdd:smart00347  85 RSETLAelLAGLT 97
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 91-189 8.93e-03

The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. 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: 176129 [Multi-domain]  Cd Length: 197  Bit Score: 36.77  E-value: 8.93e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1596946251  91 HLRIGAPPILATKLLTPVIALMsREQ--ELSFELLTANRDELCSGLLKHELDIAIAFGDEAPPAILAETLLTESLKVLAP 168
Cdd:cd08438     1 HLRLGLPPLGGSLLFAPLLAAF-RQRypNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLP 79

                          90       100
                  ....*....|....*....|.
gi 1596946251 169 SNTVERLPTELTLDDLINYPL 189
Cdd:cd08438    80 RGHPLAGRKTVSLADLADEPF 100
 
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