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Conserved domains on  [gi|488308860|ref|WP_002378358|]
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MULTISPECIES: LysR family transcriptional regulator [Enterococcus]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-295 1.27e-43

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 149.25  E-value: 1.27e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   1 MNIQLLKYFIEIVNTRSLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFQLTDTGVYLYEHGQEVVFQFDQLVT 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  81 DIREMNQKPvKKQLRLGLTTLFAVQFMKE-ISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLISFPNTLPEiIHIE 159
Cdd:COG0583   81 ELRALRGGP-RGTLRIGAPPSLARYLLPPlLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPG-LVAR 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 160 PLETttkgYHVYVVVPESNPLSQYEKLTfkdlkdqrfsslsdnfmigrllldrtrsfgyepniilhnDDLQVLLYSLQKN 239
Cdd:COG0583  159 PLGE----ERLVLVASPDHPLARRAPLV---------------------------------------NSLEALLAAVAAG 195

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 488308860 240 NSICLLPIEYYEVGKSQG-LKWIPLKDKFDYFPIGIALRRDFSMTEDVRDFIRIIKE 295
Cdd:COG0583  196 LGIALLPRFLAADELAAGrLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLRE 252
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-295 1.27e-43

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 149.25  E-value: 1.27e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   1 MNIQLLKYFIEIVNTRSLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFQLTDTGVYLYEHGQEVVFQFDQLVT 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  81 DIREMNQKPvKKQLRLGLTTLFAVQFMKE-ISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLISFPNTLPEiIHIE 159
Cdd:COG0583   81 ELRALRGGP-RGTLRIGAPPSLARYLLPPlLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPG-LVAR 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 160 PLETttkgYHVYVVVPESNPLSQYEKLTfkdlkdqrfsslsdnfmigrllldrtrsfgyepniilhnDDLQVLLYSLQKN 239
Cdd:COG0583  159 PLGE----ERLVLVASPDHPLARRAPLV---------------------------------------NSLEALLAAVAAG 195

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 488308860 240 NSICLLPIEYYEVGKSQG-LKWIPLKDKFDYFPIGIALRRDFSMTEDVRDFIRIIKE 295
Cdd:COG0583  196 LGIALLPRFLAADELAAGrLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLRE 252
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 94-293 3.73e-30

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: 112.69  E-value: 3.73e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  94 LRLGLTTLFAVQFMKE-ISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLISFPNTLPEiIHIEPLETttkgYHVYV 172
Cdd:cd05466    2 LRIGASPSIAAYLLPPlLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPG-LESEPLFE----EPLVL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 173 VVPESNPLSQYEKLTFKDLKDQRFSSLSDNFMIGRLLLDRTRSFGYEPNIILHNDDLQVLLYSLQKNNSICLLPIEYYEV 252
Cdd:cd05466   77 VVPPDHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEE 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 488308860 253 GKSQGLKWIPLKDKFDYFPIGIALRRDFSMTEDVRDFIRII 293
Cdd:cd05466  157 LADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-196 1.84e-23

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: 97.30  E-value: 1.84e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   1 MNIQLLKYFIEIVNTRSLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFQLTDTGVYLYEHGQEVVFQFDQLVT 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  81 DIREmNQKPVKKQLRLGLTTLFAVQFMKEI-SRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGlisFPNTLPEIIHI- 158
Cdd:NF040786  81 EFDR-YGKESKGVLRIGASTIPGQYLLPELlKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIG---FTGTKLEKKRLv 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 488308860 159 -EPLETTtkgyHVYVVVPesNPLSQYEKLTF----KDLKDQRF 196
Cdd:NF040786 157 yTPFYKD----RLVLITP--NGTEKYRMLKEeisiSELQKEPF 193
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 93-295 1.02e-22

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: 93.12  E-value: 1.02e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   93 QLRLGLTTLFAVQFMKE-ISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLISFPNTLPEiIHIEPLETttkgYHVY 171
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPlLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPG-LEARPLGE----EPLV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  172 VVVPESNPLSQYEKLTFKDLKDQRFSSLSDNFMIGRLLLDRTRSFGYEPNIILHNDDLQVLLYSLQKNNSICLLP----I 247
Cdd:pfam03466  78 LVAPPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPrsavA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 488308860  248 EYYEVGksqGLKWIPLKDKFDYFPIGIALRRDFSMTEDVRDFIRIIKE 295
Cdd:pfam03466 158 RELADG---RLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLRE 202
PRK09986 PRK09986
LysR family transcriptional regulator;
1-265 6.61e-22

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 92.86  E-value: 6.61e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   1 MNIQLLKYFIEIVNTRSLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFQLTDTGVYLYEHGQEVVFQFDQLVT 80
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  81 DIREMNQKPvKKQLRLGL--TTLFAvQFMKEISRFLTTHPHVNLILQQDgSPKLQ-TMLANKEIDMGL--ISFPNTLPEI 155
Cdd:PRK09986  87 RVEQIGRGE-AGRIEIGIvgTALWG-RLRPAMRHFLKENPNVEWLLREL-SPSMQmAALERRELDAGIwrMADLEPNPGF 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 156 IHIEPLETTtkgyhVYVVVPESNPLSQYEKLTFKDLKDQRFSSLSDNFM-IGRLLLDRTRSFGYEPNIILHNDDLQVLLY 234
Cdd:PRK09986 164 TSRRLHESA-----FAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHSdWGKFLQRVCQQAGFSPQIIRQVNEPQTVLA 238

                        250       260       270
                 ....*....|....*....|....*....|.
gi 488308860 235 SLQKNNSICLLPIEYYEVgKSQGLKWIPLKD 265
Cdd:PRK09986 239 MVSMGIGITLLPDSYAQI-PWPGVVFRPLKE 268
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-295 1.27e-43

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 149.25  E-value: 1.27e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   1 MNIQLLKYFIEIVNTRSLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFQLTDTGVYLYEHGQEVVFQFDQLVT 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  81 DIREMNQKPvKKQLRLGLTTLFAVQFMKE-ISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLISFPNTLPEiIHIE 159
Cdd:COG0583   81 ELRALRGGP-RGTLRIGAPPSLARYLLPPlLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPG-LVAR 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 160 PLETttkgYHVYVVVPESNPLSQYEKLTfkdlkdqrfsslsdnfmigrllldrtrsfgyepniilhnDDLQVLLYSLQKN 239
Cdd:COG0583  159 PLGE----ERLVLVASPDHPLARRAPLV---------------------------------------NSLEALLAAVAAG 195

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 488308860 240 NSICLLPIEYYEVGKSQG-LKWIPLKDKFDYFPIGIALRRDFSMTEDVRDFIRIIKE 295
Cdd:COG0583  196 LGIALLPRFLAADELAAGrLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLRE 252
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 94-293 3.73e-30

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: 112.69  E-value: 3.73e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  94 LRLGLTTLFAVQFMKE-ISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLISFPNTLPEiIHIEPLETttkgYHVYV 172
Cdd:cd05466    2 LRIGASPSIAAYLLPPlLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPG-LESEPLFE----EPLVL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 173 VVPESNPLSQYEKLTFKDLKDQRFSSLSDNFMIGRLLLDRTRSFGYEPNIILHNDDLQVLLYSLQKNNSICLLPIEYYEV 252
Cdd:cd05466   77 VVPPDHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEE 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 488308860 253 GKSQGLKWIPLKDKFDYFPIGIALRRDFSMTEDVRDFIRII 293
Cdd:cd05466  157 LADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-196 1.84e-23

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: 97.30  E-value: 1.84e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   1 MNIQLLKYFIEIVNTRSLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFQLTDTGVYLYEHGQEVVFQFDQLVT 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  81 DIREmNQKPVKKQLRLGLTTLFAVQFMKEI-SRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGlisFPNTLPEIIHI- 158
Cdd:NF040786  81 EFDR-YGKESKGVLRIGASTIPGQYLLPELlKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIG---FTGTKLEKKRLv 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 488308860 159 -EPLETTtkgyHVYVVVPesNPLSQYEKLTF----KDLKDQRF 196
Cdd:NF040786 157 yTPFYKD----RLVLITP--NGTEKYRMLKEeisiSELQKEPF 193
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 93-293 7.57e-23

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: 93.39  E-value: 7.57e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  93 QLRLGLTTLFAVQFMKE-ISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLISFPnTLPEIIHIEPLETttkgYHVY 171
Cdd:cd08438    1 HLRLGLPPLGGSLLFAPlLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLP-VDEEEFDSQPLCN----EPLV 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 172 VVVPESNPLSQYEKLTFKDLKDQRFSSLSDNFMIGRLLLDRTRSFGYEPNIILHNDDLQVLLYSLQKNNSICLLPIEYYE 251
Cdd:cd08438   76 AVLPRGHPLAGRKTVSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQ 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 488308860 252 VGKSQGLKWIPLKDKFDYFPIGIALRRDFSMTEDVRDFIRII 293
Cdd:cd08438  156 RLDNAGVKVIPLTDPDLRWQLALIWRKGRYLSHAARAWLALL 197
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 93-290 9.70e-23

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: 92.98  E-value: 9.70e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  93 QLRLGLTTLFAVQFMKE-ISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLISFPNTLPEIIHI----EPLetttkg 167
Cdd:cd08434    1 TVRLGFLHSLGTSLVPDlIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIplftEEL------ 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 168 yhvYVVVPESNPLSQYEKLTFKDLKDQRFSSLSDNFMIGRLLLDRTRSFGYEPNIILHNDDLQVL--LYSlqKNNSICLL 245
Cdd:cd08434   75 ---VLVVPKDHPLAGRDSVDLAELADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAFEGEEDSTIagLVA--AGLGVAIL 149

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 488308860 246 P---IEYYEvgksqGLKWIPLKDKFDYFPIGIALRRDFSMTEDVRDFI 290
Cdd:cd08434  150 PemtLLNPP-----GVKKIPIKDPDAERTIGLAWLKDRYLSPAARRFK 192
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 93-295 1.02e-22

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: 93.12  E-value: 1.02e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   93 QLRLGLTTLFAVQFMKE-ISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLISFPNTLPEiIHIEPLETttkgYHVY 171
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPlLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPG-LEARPLGE----EPLV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  172 VVVPESNPLSQYEKLTFKDLKDQRFSSLSDNFMIGRLLLDRTRSFGYEPNIILHNDDLQVLLYSLQKNNSICLLP----I 247
Cdd:pfam03466  78 LVAPPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPrsavA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 488308860  248 EYYEVGksqGLKWIPLKDKFDYFPIGIALRRDFSMTEDVRDFIRIIKE 295
Cdd:pfam03466 158 RELADG---RLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLRE 202
PRK09986 PRK09986
LysR family transcriptional regulator;
1-265 6.61e-22

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 92.86  E-value: 6.61e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   1 MNIQLLKYFIEIVNTRSLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFQLTDTGVYLYEHGQEVVFQFDQLVT 80
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  81 DIREMNQKPvKKQLRLGL--TTLFAvQFMKEISRFLTTHPHVNLILQQDgSPKLQ-TMLANKEIDMGL--ISFPNTLPEI 155
Cdd:PRK09986  87 RVEQIGRGE-AGRIEIGIvgTALWG-RLRPAMRHFLKENPNVEWLLREL-SPSMQmAALERRELDAGIwrMADLEPNPGF 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 156 IHIEPLETTtkgyhVYVVVPESNPLSQYEKLTFKDLKDQRFSSLSDNFM-IGRLLLDRTRSFGYEPNIILHNDDLQVLLY 234
Cdd:PRK09986 164 TSRRLHESA-----FAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHSdWGKFLQRVCQQAGFSPQIIRQVNEPQTVLA 238

                        250       260       270
                 ....*....|....*....|....*....|.
gi 488308860 235 SLQKNNSICLLPIEYYEVgKSQGLKWIPLKD 265
Cdd:PRK09986 239 MVSMGIGITLLPDSYAQI-PWPGVVFRPLKE 268
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 6-233 4.59e-20

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 87.70  E-value: 4.59e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   6 LKYFIEIVNTRSLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFQLTDTG-VYLyEHGQEVVFQFD---QLVTD 81
Cdd:PRK11242   6 IRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGeVYL-RYARRALQDLEagrRAIHD 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  82 IREMNqkpvKKQLRLGLTTLFAVQFMKE-ISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGlISF-PNTLPEIIHiE 159
Cdd:PRK11242  85 VADLS----RGSLRLAMTPTFTAYLIGPlIDAFHARYPGITLTIREMSQERIEALLADDELDVG-IAFaPVHSPEIEA-Q 158

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488308860 160 PLETTTKGyhvyVVVPESNPLSQYEK-LTFKDLKDQRFSSLSDNFmIGRLLLDR-TRSFGYEPNIILHNDDLQVLL 233
Cdd:PRK11242 159 PLFTETLA----LVVGRHHPLAARRKaLTLDELADEPLVLLSAEF-ATREQIDRyFRRHGVTPRVAIEANSISAVL 229
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 2.94e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 79.35  E-value: 2.94e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 488308860    3 IQLLKYFIEIVNTRSLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFQLTDTG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 93-293 3.10e-19

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: 83.33  E-value: 3.10e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  93 QLRLGLTTLFAVQFMKE-ISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLISFPNTLPEI----IHIEPLetttkg 167
Cdd:cd08414    1 RLRIGFVGSALYGLLPRlLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLasrpLLREPL------ 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 168 yhvYVVVPESNPLSQYEKLTFKDLKDQRF--------SSLSDNFMigRLLLDRtrsfGYEPNIILHNDDLQVLLySL-QK 238
Cdd:cd08414   75 ---VVALPADHPLAARESVSLADLADEPFvlfprepgPGLYDQIL--ALCRRA----GFTPRIVQEASDLQTLL-ALvAA 144

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 488308860 239 NNSICLLPiEYYEVGKSQGLKWIPLKDKFDYFPIGIALRRDfSMTEDVRDFIRII 293
Cdd:cd08414  145 GLGVALVP-ASVARLQRPGVVYRPLADPPPRSELALAWRRD-NASPALRAFLELA 197
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-295 6.76e-17

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 79.04  E-value: 6.76e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   1 MNIQLLKYFIEIVNTRSLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFQLTDTGVYLYEHGQEVVFQFDQLVT 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  81 DIREMNQKpvKKQLRLGLTTLFAVQ-FMKEISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLISFPNTLPEI---- 155
Cdd:PRK09906  81 RARKIVQE--DRQLTIGFVPSAEVNlLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIdyle 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 156 IHIEPLetttkgyhvYVVVPESNPLSQYEKLTFKDLKDQRFSSLSDNF--MIGRLLLDRTRSFGYEPNIILHNDDLQVLL 233
Cdd:PRK09906 159 LLDEPL---------VVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYsgSLAPIIKAWFAQHNSQPNIVQVATNILVTM 229

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488308860 234 YSLQKNNSICLLPIEYYEVGKSQGLkWIPLKDKFDYFPIGIALRRDfSMTEDVRDFIRIIKE 295
Cdd:PRK09906 230 NLVGMGLGCTIIPGYMNNFNTGQVV-FRPLAGNVPSIALLMAWKKG-EMKPALRDFIAIVQE 289
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-179 2.44e-14

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 72.02  E-value: 2.44e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   1 MNIQLLKYFIEIVNTRSLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFQLTDTGVYLYEHGQEVVFQFDQLVT 80
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  81 DIREMNQKpVKKQLRLGL-----TTLFAVQFMKEISRfltTHPHVNLILQQDGSPKLQTMLANKEIDMGLIsFPNTLPEI 155
Cdd:PRK11233  81 AVHNVGQA-LSGQVSIGLapgtaASSLTMPLLQAVRA---EFPGIVLYLHENSGATLNEKLMNGQLDMAVI-YEHSPVAG 155

                        170       180
                 ....*....|....*....|....*.
gi 488308860 156 IHIEPL--EtttkgyHVYVVVPESNP 179
Cdd:PRK11233 156 LSSQPLlkE------DLFLVGTQDCP 175
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 93-264 2.63e-14

The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold; In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. 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: 176140 [Multi-domain]  Cd Length: 197  Bit Score: 69.99  E-value: 2.63e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  93 QLRLGLT-TLFAVQFMKEISRFLTTHPHVNLILQqDGSPKLQ-TMLANKEIDMGLISFPNTLpeiiHIEPLETTTkGYH- 169
Cdd:cd08449    1 HLNIGMVgSVLWGGLGPALRRFKRQYPNVTVRFH-ELSPEAQkAALLSKRIDLGFVRFADTL----NDPPLASEL-LWRe 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 170 -VYVVVPESNPLSQYEKLTFKDLKDQRFSSLS-DNFMIGRLLLDRTRSFGYEPNIILHNDDLQVLLYSLQKNNSICLLPi 247
Cdd:cd08449   75 pMVVALPEEHPLAGRKSLTLADLRDEPFVFLRlANSRFADFLINCCLQAGFTPQITQEVVEPQTLMALVAAGFGVALVP- 153

                        170
                 ....*....|....*..
gi 488308860 248 EYYEVGKSQGLKWIPLK 264
Cdd:cd08449  154 ESYARLPWPGVRFIPLK 170
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 10-211 2.67e-14

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 71.95  E-value: 2.67e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  10 IEI----VNTRSLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFQLTDTGVYLYEHGQEVVFQFDQLVT---DI 82
Cdd:PRK11013   9 IEIfhavMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSYYGLDRIVSaaeSL 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  83 REMNQkpvkKQLRLGLTTLFAVQFM-KEISRFLTTHPHVNL-ILQQDgSPKLQTMLANKEIDMGLIsfpntlpEIIHIEP 160
Cdd:PRK11013  89 REFRQ----GQLSIACLPVFSQSLLpGLCQPFLARYPDVSLnIVPQE-SPLLEEWLSAQRHDLGLT-------ETLHTPA 156

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 488308860 161 ---LETTTKGYHVyVVVPESNPLSQYEKLTFKDLKDQRFSSLS--DNFmigRLLLD 211
Cdd:PRK11013 157 gteRTELLTLDEV-CVLPAGHPLAAKKVLTPDDFAGENFISLSrtDSY---RQLLD 208
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-221 4.45e-14

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 71.20  E-value: 4.45e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   3 IQLLKYFIEIVNTRSLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFQLTDTGVYLYEHGQEVVF---QFDQLV 79
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILAlceETCRAL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  80 TDIREMNqkpvKKQLRLGLTTLFAVQFM-KEISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLI--SFPNTLPEII 156
Cdd:CHL00180  87 EDLKNLQ----RGTLIIGASQTTGTYLMpRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVggEVPTELKKIL 162

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488308860 157 HIEPletttkgyhvYV------VVPESNPLSQYEKLTFKDLKDQRFSSLSDNFMIGRLLLDRTRSFGYEPN 221
Cdd:CHL00180 163 EITP----------YVedelalIIPKSHPFAKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGIDSK 223
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-290 2.01e-13

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 69.25  E-value: 2.01e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   1 MNIQLLKYFIEIVNTR-SLSAAARNLFVTQPTLSLALKKMESELGTALFD-HSDQPFQLTdtgvylyEHGQEVVFQFDQL 78
Cdd:PRK12682   1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIrHGKRLKGLT-------EPGKAVLDVIERI 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  79 VTDIREMNQ------KPVKKQLRLGLTTLFAVQFMKE-ISRFLTTHPHVNLILQQdGSP-KLQTMLANKEIDMGLISfpn 150
Cdd:PRK12682  74 LREVGNIKRigddfsNQDSGTLTIATTHTQARYVLPRvVAAFRKRYPKVNLSLHQ-GSPdEIARMVISGEADIGIAT--- 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 151 tlPEIIHIEPLETttkgYHVY-----VVVPESNPLSQYEKLTFKDLKDQRFSSLSDNFMiGRLLLDRTrsF---GYEPNI 222
Cdd:PRK12682 150 --ESLADDPDLAT----LPCYdwqhaVIVPPDHPLAQEERITLEDLAEYPLITYHPGFT-GRSRIDRA--FaaaGLQPDI 220

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488308860 223 ILHNDDLQVLLYSLQKNNSICLLPIEYYEVGKSQGLKWIPLKDKFDYFPIGIALRRDFSMTEDVRDFI 290
Cdd:PRK12682 221 VLEAIDSDVIKTYVRLGLGVGIVAEMAYRPDRDGDLVALPAGHLFGPNTAWVALKRGAYLRNYVYKFI 288
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-224 2.32e-13

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 68.92  E-value: 2.32e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   1 MNIQLLKYFIEIVNTR-SLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFqltdTGvyLYEHGQEVVFQFDQLV 79
Cdd:PRK12683   1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRL----TG--LTEPGKELLQIVERML 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  80 TDIRemNQKPVKKQL------RLGL-TTLFAVQFM--KEISRFLTTHPHVNLILQQdGSPK-LQTMLANKEIDMG----- 144
Cdd:PRK12683  75 LDAE--NLRRLAEQFadrdsgHLTVaTTHTQARYAlpKVVRQFKEVFPKVHLALRQ-GSPQeIAEMLLNGEADIGiatea 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 145 ------LISFPntlpeiihieplettTKGYHVYVVVPESNPLSQYEKLTFKDLKDQRFSSLSDNFMiGRLLLDRTrsF-- 216
Cdd:PRK12683 152 ldrepdLVSFP---------------YYSWHHVVVVPKGHPLTGRENLTLEAIAEYPIITYDQGFT-GRSRIDQA--Fae 213


                 ....*....
gi 488308860 217 -GYEPNIIL 224
Cdd:PRK12683 214 aGLVPDIVL 222
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 94-224 2.36e-12

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: 64.51  E-value: 2.36e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  94 LRLGLTTLFAVQFMKE-ISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLISFPNTLPEiIHIEPLETTtkgyHVYV 172
Cdd:cd08415    2 LRIAALPALALSLLPRaIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPG-LESEPLASG----RAVC 76

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 488308860 173 VVPESNPLSQYEKLTFKDLKDQRFSSLSDNFMIgRLLLDRT-RSFGYEPNIIL 224
Cdd:cd08415   77 VLPPGHPLARKDVVTPADLAGEPLISLGRGDPL-RQRVDAAfERAGVEPRIVI 128
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-258 7.32e-12

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 64.65  E-value: 7.32e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   1 MNIQLLKYFIEIVNTRSLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFQLTDTGVYLYEHGQEVVFQFDQLVT 80
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  81 DIREmnqkPVKKQLRLGLTTLFAVQFMK-EISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLISfpNTLPEI-IHI 158
Cdd:PRK15421  82 ACNE----PQQTRLRIAIECHSCIQWLTpALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTS--DILPRSgLHY 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 159 EPLETttkgYHVYVVVPESNPLSQYEKLTFKDLKDQRFSSlsdnFMIGRLLLDRTRSF----GYEPNiILHNDDLQVLLY 234
Cdd:PRK15421 156 SPMFD----YEVRLVLAPDHPLAAKTRITPEDLASETLLI----YPVQRSRLDVWRHFlqpaGVSPS-LKSVDNTLLLIQ 226

                        250       260
                 ....*....|....*....|....
gi 488308860 235 SLQKNNSICLLPIEYYEVGKSQGL 258
Cdd:PRK15421 227 MVAARMGIAALPHWVVESFERQGL 250
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-290 1.06e-11

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 64.23  E-value: 1.06e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   1 MNIQLLKYFIEIVNTR-SLSAAARNLFVTQPTLSLALKKMESELGTALFD-HSDQPFQLTdtgvylyEHGQEVVFQFDQL 78
Cdd:PRK12684   1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTrHGKRLRGLT-------EPGRIILASVERI 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  79 VTDIRemNQKPVKK-----------------QLRLGLTtlfavqfmKEISRFLTTHPHVNLILQQdGSPK-LQTMLANKE 140
Cdd:PRK12684  74 LQEVE--NLKRVGKefaaqdqgnltiatthtQARYALP--------AAIKEFKKRYPKVRLSILQ-GSPTqIAEMVLHGQ 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 141 IDMG-----------LISFPntlpeiihiepletttkGY--HVYVVVPESNPLSQYEKLTFKDLKDQRFSSLSDNFMiGR 207
Cdd:PRK12684 143 ADLAiateaiadykeLVSLP-----------------CYqwNHCVVVPPDHPLLERKPLTLEDLAQYPLITYDFAFA-GR 204

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 208 LLLDRT-RSFGYEPNIILHNDDLQVLLYSLQKNNSICLLPIEYYEVGKSQGLKWIPLKDKFDYFPIGIALRRDFSMTEDV 286
Cdd:PRK12684 205 SKINKAfALRGLKPDIVLEAIDADVIKTYVELGLGVGIVADMAFDPERDRNLRAIDAGHLFGSSTTRLGLRRGAYLRGYV 284


                 ....
gi 488308860 287 RDFI 290
Cdd:PRK12684 285 YTFI 288
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 93-291 2.17e-11

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: 61.79  E-value: 2.17e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  93 QLRLGLTTLFAVQFMKE-ISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGlISFPNTLPEIIHIEPLETTtkgyHVY 171
Cdd:cd08412    1 TLRIGCFSTLAPYYLPGlLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLA-LTYDLDLPEDIAFEPLARL----PPY 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 172 VVVPESNPLSQYEKLTFKDLKDQRFSSLsDNFMIGRLLLDRTRSFGYEPNIILHNDDLQVLLySLQKN-NSICLLPIEYY 250
Cdd:cd08412   76 VWLPADHPLAGKDEVSLADLAAEPLILL-DLPHSREYFLSLFAAAGLTPRIAYRTSSFEAVR-SLVANgLGYSLLNDRPY 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 488308860 251 EVGKSQGLKWI--PLKDKFDYFPIGIALRRDFSMTEDVRDFIR 291
Cdd:cd08412  154 RPWSYDGKRLVrrPLADPVPPLRLGLAWRRGARLTRAARAFVD 196
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 106-293 3.26e-11

The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold; MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. 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: 176128  Cd Length: 198  Bit Score: 61.19  E-value: 3.26e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 106 FMKEISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLISFPNTLPE-IIHIEPLETttkgYHVYVVVPESNPLSQYE 184
Cdd:cd08437   15 FPKLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIALLGSLTPLENsALHSKIIKT----QHFMIIVSKDHPLAKAK 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 185 KLTFKDLKDQRFSSLSDNFMIGRLLLDRTRSFGYEPNIILHNDDLQVLLYSLQKNNSICLLpIEyYEVGKSQGLKWIPLK 264
Cdd:cd08437   91 KVNFADLKKENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSMVRENVGIGFL-TD-IAVKPDDHLVAIPLL 168

                        170       180       190
                 ....*....|....*....|....*....|
gi 488308860 265 DKFDY-FPIGIALRRDFSMTEDVRDFIRII 293
Cdd:cd08437  169 DNEQPtFYISLAHRKDQLLTPAQKKLLDLL 198
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-191 1.52e-10

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 60.68  E-value: 1.52e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   1 MNIQLLKYFIEIVNTR-SLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPF-QLTDTGVYLYEHGQEVVFQfdql 78
Cdd:PRK12681   1 MKLQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLtQVTPAGEEIIRIAREILSK---- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  79 VTDIREMNQ---KPVKKQLRLGlTTLFAVQFM--KEISRFLTTHPHVNLILQQdGSP-KLQTMLANKEIDMGLisfpntl 152
Cdd:PRK12681  77 VESIKSVAGehtWPDKGSLYIA-TTHTQARYAlpPVIKGFIERYPRVSLHMHQ-GSPtQIAEAAAKGNADFAI------- 147

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 488308860 153 peiihiepletTTKGYHVY--------------VVVPESNPLSQYEKLTFKDL 191
Cdd:PRK12681 148 -----------ATEALHLYddlimlpcyhwnrsVVVPPDHPLAKKKKLTIEEL 189
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-265 2.33e-10

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: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 58.77  E-value: 2.33e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  93 QLRLG-LTTLFAVQFMKEISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLISFPNTLPE-----IIHIEPLEtttk 166
Cdd:cd08436    1 RLAIGtITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRPPglasrELAREPLV---- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 167 gyhvyVVVPESNPLSQYEKLTFKDLKDQRFSSLSDNFMIgRLLLDRT-RSFGYEPNIILHNDDLQVLLYSLQKNNSICLL 245
Cdd:cd08436   77 -----AVVAPDHPLAGRRRVALADLADEPFVDFPPGTGA-RRQVDRAfAAAGVRRRVAFEVSDVDLLLDLVARGLGVALL 150

                        170       180
                 ....*....|....*....|
gi 488308860 246 PIEYyeVGKSQGLKWIPLKD 265
Cdd:cd08436  151 PASV--AARLPGLAALPLEP 168
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 93-291 4.17e-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: 58.05  E-value: 4.17e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  93 QLRLGLTTLFAVQFMKE-ISRFLTTHPHVNLILQQDGSPKLQTMLANKEID--MGLISfPNTLPEIIHIEPLETTTkgyh 169
Cdd:cd08435    1 TVRVGAVPAAAPVLLPPaIARLLARHPRLTVRVVEGTSDELLEGLRAGELDlaIGRLA-DDEQPPDLASEELADEP---- 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 170 VYVVVPESNPLSQYEKLTFKDLKD-----QRFSSLSdnfmigRLLLDRT-RSFGYE-PNIILHNDDLQVLLYSLQKNNSI 242
Cdd:cd08435   76 LVVVARPGHPLARRARLTLADLADypwvlPPPGTPL------RQRLEQLfAAAGLPlPRNVVETASISALLALLARSDML 149

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 488308860 243 CLLPIEYYEVGKSQG-LKWIPLKDKFDYFPIGIALRRDFSMTEDVRDFIR 291
Cdd:cd08435  150 AVLPRSVAEDELRAGvLRELPLPLPTSRRPIGITTRRGGPLSPAARALLD 199
PRK09801 PRK09801
LysR family transcriptional regulator;
6-122 4.44e-10

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 59.28  E-value: 4.44e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   6 LKYFIEIVNTRSLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFQLTDTGVYLYEHGQEVVFQFDQLVTDIREM 85
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 488308860  86 NQKPvKKQLRLGLTTLFAVQFMK-EISRFLTTHPHVNL 122
Cdd:PRK09801  91 KTRP-EGMIRIGCSFGFGRSHIApAITELMRNYPELQV 127
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-218 8.07e-10

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 58.50  E-value: 8.07e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   1 MNIQLLKYFIEIVNTRSLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFQLTDTGVYLYEHGQEVVFQfdqlVT 80
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLRE----VK 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  81 DIREM--NQ-KPVKKQLRLGLT-TLFAVQFMKEISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMG-LISFPNTLPEI 155
Cdd:PRK11151  77 VLKEMasQQgETMSGPLHIGLIpTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAiLALVKESEAFI 156

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488308860 156 ---IHIEPLetttkgyhvYVVVPESNPLSQYEKLTFKDLKDQRFSSLSDnfmiGRLLldRTRSFGY 218
Cdd:PRK11151 157 evpLFDEPM---------LLAVYEDHPWANRDRVPMSDLAGEKLLMLED----GHCL--RDQAMGF 207
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 93-200 3.32e-09

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: 55.50  E-value: 3.32e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  93 QLRLGLTTLFAVQFM-KEISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLISFPNTLPEIihieplETTTKGYHVY 171
Cdd:cd08456    1 ELRIAVLPALSQSFLpRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGI------ERERLLRIDG 74

                         90       100       110
                 ....*....|....*....|....*....|
gi 488308860 172 V-VVPESNPLSQYEKLTFKDLKDQRFSSLS 200
Cdd:cd08456   75 VcVLPPGHRLAVKKVLTPSDLEGEPFISLA 104
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
4-86 7.61e-09

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 55.58  E-value: 7.61e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   4 QLLKYFIEIVNTRSLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFQLTDTGVYLYEHGQEVVFQFDQLVTDIR 83
Cdd:PRK10094   5 ETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQ 84


                 ...
gi 488308860  84 EMN 86
Cdd:PRK10094  85 QVN 87
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-212 1.77e-08

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: 53.30  E-value: 1.77e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  93 QLRLGLTTLFAVQFMKE-ISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLISFPNTLPEiIHIEPLETTtkgyHVY 171
Cdd:cd08440    1 RVRVAALPSLAATLLPPvLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPD-LEFEPLLRD----PFV 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 488308860 172 VVVPESNPLSQYEKLTFKDLKDQRFSSLSDNFMIgRLLLDR 212
Cdd:cd08440   76 LVCPKDHPLARRRSVTWAELAGYPLIALGRGSGV-RALIDR 115
PRK09791 PRK09791
LysR family transcriptional regulator;
2-122 1.85e-08

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 54.38  E-value: 1.85e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   2 NIQL--LKYFIEIVNTRSLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFQLTDTGVYLYEHGQEVVFQFDQLV 79
Cdd:PRK09791   4 QVKIhqIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQ 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 488308860  80 TDIREmNQKPVKKQLRLGLTTLFAVQFMKE-ISRFLTTHPHVNL 122
Cdd:PRK09791  84 EDIRQ-RQGQLAGQINIGMGASIARSLMPAvISRFHQQHPQVKV 126
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 93-223 2.08e-08

The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). 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: 176142 [Multi-domain]  Cd Length: 199  Bit Score: 53.34  E-value: 2.08e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  93 QLRLGLT--TLFAVQFMKEISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLISFPNTLPEIIHIEPL--ETTTkgy 168
Cdd:cd08451    1 RLRVGFTssAAFHPLVPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARSDGLVLELLleEPML--- 77

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488308860 169 hvyVVVPESNPLSQYEKLTFKDLKDQRF--------SSLSDNfmigrlLLDRTRSFGYEPNII 223
Cdd:cd08451   78 ---VALPAGHPLARERSIPLAALADEPFilfprpvgPGLYDA------IIAACRRAGFTPRIG 131
PRK10341 PRK10341
transcriptional regulator TdcA;
4-161 2.09e-08

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 54.48  E-value: 2.09e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   4 QLLKYFIEIVNTRSLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFQLTDTGVYLYEHGQEVVFQFDQLVTDIR 83
Cdd:PRK10341  10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  84 EMNQKPVKKqLRLGLTTLFAVQFMKE-ISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLISFPN-TLPEIIHIEPL 161
Cdd:PRK10341  90 GMSSEAVVD-VSFGFPSLIGFTFMSDmINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNeMKLQDLHVEPL 168
PRK12680 PRK12680
LysR family transcriptional regulator;
1-224 2.81e-08

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 54.24  E-value: 2.81e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   1 MNIQLLKYFIEIVNTR-SLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFQ-LTDTGVYLYEHGQEVVFQfdql 78
Cdd:PRK12680   1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSE---- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  79 VTDIR--EMNQKPvKKQLRLGLTTLFA-VQFM--KEISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLISFPNTLP 153
Cdd:PRK12680  77 ANNIRtyAANQRR-ESQGQLTLTTTHTqARFVlpPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEP 155

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488308860 154 EIIHIEPLETttkgYHVYVVVPESNPLSQYEK-LTFKDLKDQRFSSLSDNFMIGRLLLDRTRSFGYEPNIIL 224
Cdd:PRK12680 156 SAGIAVPLYR----WRRLVVVPRGHALDTPRRaPDMAALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIAL 223
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 93-224 3.06e-08

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: 52.72  E-value: 3.06e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  93 QLRLGLTTLFAVQFMKE-ISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGlISF-PNTLPEIIHiEPLETTTKGyhv 170
Cdd:cd08425    2 SLRLAMTPTFTAYLIGPlIDRFHARYPGIALSLREMPQERIEAALADDRLDLG-IAFaPVRSPDIDA-QPLFDERLA--- 76

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 488308860 171 yVVVPESNPLSQYEK-LTFKDLKDQRFSSLSDNFmIGRLLLDR-TRSFGYEPNIIL 224
Cdd:cd08425   77 -LVVGATHPLAQRRTaLTLDDLAAEPLALLSPDF-ATRQHIDRyFQKQGIKPRIAI 130
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
4-91 1.97e-07

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 51.51  E-value: 1.97e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   4 QLLKYFIEIVNTRSLSAAARNLFVTQPTLSLALKKMESELGTALFDHsDQPFQLTDTGVYLYEHGQEVVFQFDQLVTDIR 83
Cdd:PRK13348   5 KQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQVALLEADLLSTLP 83


                 ....*...
gi 488308860  84 EMNQKPVK 91
Cdd:PRK13348  84 AERGSPPT 91
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
26-164 2.02e-07

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 50.97  E-value: 2.02e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  26 FVTQPTLSLALKKMESELGTALFDHSDQPFQLTDTGVYLYEHGQEVVFQFDQLVTDIREmNQKPVKKQLRLGLTTLFAVQ 105
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQ-QGPSLSGELSLFCSVTAAYS 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488308860 106 FMKEI-SRFLTTHPHVNLilqqdgspKLQT--------MLANKEIDMGLISFPNTLPEIIHIEPLETT 164
Cdd:PRK11716  81 HLPPIlDRFRAEHPLVEI--------KLTTgdaadaveKVQSGEADLAIAAKPETLPASVAFSPIDEI 140
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 93-196 2.02e-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: 50.57  E-value: 2.02e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  93 QLRLGLTTLFAVQFMKE-ISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLISFPNTLPEIIHIEPLETttkgyHVY 171
Cdd:cd08420    1 TLRIGASTTIGEYLLPRlLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAED-----ELV 75

                         90       100
                 ....*....|....*....|....*
gi 488308860 172 VVVPESNPLSQYEKLTFKDLKDQRF 196
Cdd:cd08420   76 LVVPPDHPLAGRKEVTAEELAAEPW 100
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 94-224 2.81e-07

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: 49.80  E-value: 2.81e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  94 LRLGLTTLFAVQFMKE-ISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLISFPNTLPEIIHIEplettTKGYHVYV 172
Cdd:cd08457    2 LRIAAMPALANGFLPRfLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIE-----TRSLPAVV 76

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 488308860 173 VVPESNPLSQYEKLTFKDLKDQRFSSLSDNFMIGRLLLDRTRSFGYEPNIIL 224
Cdd:cd08457   77 AVPMGHPLAQLDVVSPQDLAGERIITLENGYLFRMRVEVALGKIGVKRRPII 128
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-212 3.15e-07

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: 176113  Cd Length: 198  Bit Score: 49.83  E-value: 3.15e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  93 QLRLGLTTLFAVQFM-KEISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLISfpntlpEIIHIEPLETTTkgYHV- 170
Cdd:cd08421    1 HVRLLANTSAIVEFLpEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVA------GNVDAAGLETRP--YRTd 72

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 488308860 171 --YVVVPESNPLSQYEKLTFKDLKDQRFSSLSDNFMIGRLLLDR 212
Cdd:cd08421   73 rlVVVVPRDHPLAGRASVAFADTLDHDFVGLPAGSALHTFLREA 116
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 110-224 1.72e-06

The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The 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: 176105 [Multi-domain]  Cd Length: 198  Bit Score: 47.62  E-value: 1.72e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 110 ISRFLTTHPHVNLILQQdGSPK-LQTMLANKEIDMGLISfpntlpEIIHIEPLETTTKGYHVY--VVVPESNPLSQYEKL 186
Cdd:cd08413   19 IAAFRKRYPKVKLSLHQ-GTPSqIAEMVLKGEADIAIAT------EALDDHPDLVTLPCYRWNhcVIVPPGHPLADLGPL 91

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 488308860 187 TFKDLK-------DQRFSslsdnfmiGRLLLDRTRS-FGYEPNIIL 224
Cdd:cd08413   92 TLEDLAqyplityDFGFT--------GRSSIDRAFArAGLEPNIVL 129
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
 110-292 2.47e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold; Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonation enzyme. Both Cbl and CysB require expression of the tau and ssu genes. Like many other members of the LTTR family, the Cbl is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The 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: 176135  Cd Length: 198  Bit Score: 47.11  E-value: 2.47e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 110 ISRFLTTHPHVNLILQQdGSPK-LQTMLANKEIDMGlisfpntlpeiIHIEPLETTTK-------GYHVYVVVPESNPLS 181
Cdd:cd08444   19 VQAFKEQFPNVHLVLHQ-GSPEeIASMLANGQADIG-----------IATEALENHPElvsfpyyDWHHHIIVPVGHPLE 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 182 QYEKLTFKDLKDQRFSSLSDNFMiGRLLLDRTRS-FGYEPNIILHNDDLQVLLYSLQKNNSICLLPIEYYEVGKSQGLKW 260
Cdd:cd08444   87 SITPLTIETIAKWPIITYHGGFT-GRSRIDRAFSrAELTPNIVLSALDADVIKTYVGLGMGIGIVAEMAFEGQRDTNLIK 165

                        170       180       190
                 ....*....|....*....|....*....|..
gi 488308860 261 IPLKDKFDYFPIGIALRRDFSMTEDVRDFIRI 292
Cdd:cd08444  166 LDTSHLFGKNTTWIALRRGGDLRNFAYRFIEL 197
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-125 3.44e-06

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 47.68  E-value: 3.44e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   1 MNIQLLKYFIEIVNTRSLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFQLTDTGVYLYEHGQEVVFQFDQLVT 80
Cdd:PRK14997   2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQD 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 488308860  81 DIREMNQKPvKKQLRLGL-TTLFAVQFMKEISRFLTTHPHVNLILQ 125
Cdd:PRK14997  82 AIAALQVEP-RGIVKLTCpVTLLHVHIGPMLAKFMARYPDVSLQLE 126
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 17-125 7.00e-06

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 46.76  E-value: 7.00e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  17 SLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFQLTDTGVYLYEHGQEVvfqFDQLVTDIREMNQKPVKKQLRL 96
Cdd:PRK11139  22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREI---FDQLAEATRKLRARSAKGALTV 98

                         90       100       110
                 ....*....|....*....|....*....|
gi 488308860  97 GLTTLFAVQF-MKEISRFLTTHPHVNLILQ 125
Cdd:PRK11139  99 SLLPSFAIQWlVPRLSSFNEAHPDIDVRLK 128
PBP2_MdcR cd08416
The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which ...
 131-268 8.44e-06

The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold; This family includes the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and 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. 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: 176108  Cd Length: 199  Bit Score: 45.80  E-value: 8.44e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 131 KLQTMLANKEIDMGLISFPNTL--PEIIHIEPLETttkgyHVYVVVPESNPLSQYEKLTFKDLKDQRFSSLSDNFMIGRL 208
Cdd:cd08416   40 DLLKKLKDGELDAILVATPEGLndPDFEVVPLFED-----DIFLAVPATSPLAASSEIDLRDLKDEKFVTLSEGFATYRG 114

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 209 LLDRTRSFGYEPNIILHNDDLQVLLYSLQKNNSICLLPIEYYEVgKSQGLKWIPLKDKFD 268
Cdd:cd08416  115 FDEAFEIAGFEPNVVMRVNDIFSLMSMVSGGVGYALLPGRIADV-YEDKVQLIPLAEPYQ 173
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-61 2.32e-05

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 45.01  E-value: 2.32e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488308860   1 MNIQLLKYFIEIVNTRSLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFQLTDTG 61
Cdd:PRK03601   1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAG 61
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 110-201 9.36e-05

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The C-terminal domain also contains the redox-active cysteines that mediate the redox-dependent conformational switch. Thus, the interaction between the OxyR-tetramer and DNA is notably different between the oxidized and reduced forms. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 42.51  E-value: 9.36e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 110 ISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLISFPNTLPEiIHIEPLetttkgYH--VYVVVPESNPLSQYEKLT 187
Cdd:cd08411   20 LPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPG-LEEEPL------FDepFLLAVPKDHPLAKRKSVT 92

                         90
                 ....*....|....
gi 488308860 188 FKDLKDQRFSSLSD 201
Cdd:cd08411   93 PEDLAGERLLLLEE 106
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
9-98 1.58e-04

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 42.73  E-value: 1.58e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   9 FIEIVNTRSLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFQLTDTGVYLYEHGQEVVFQFDQLVTDIR---EM 85
Cdd:PRK10082  19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRggsDY 98

                         90
                 ....*....|....*..
gi 488308860  86 NQKPVK----KQLRLGL 98
Cdd:PRK10082  99 AQRKIKiaaaHSLSLGL 115
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 1-193 3.60e-04

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 41.21  E-value: 3.60e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   1 MNIQL--LKYFIEIVNTRSLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFQLTDTGVYLY-------EHGQEV 71
Cdd:PRK10837   1 MHITLrqLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYpralallEQAVEI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  72 vfqfDQLvtdIREMNqkpvkKQLRLGLTTLFAVQFMKE-ISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLISFPN 150
Cdd:PRK10837  81 ----EQL---FREDN-----GALRIYASSTIGNYILPAmIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPC 148

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 488308860 151 TLPEIIHIEPLETttkgyHVYVVVPESNPLSQyEKLTFKDLKD 193
Cdd:PRK10837 149 HSPELISEPWLED-----ELVVFAAPDSPLAR-GPVTLEQLAA 185
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 110-223 1.05e-03

The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold; AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. 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: 176143 [Multi-domain]  Cd Length: 197  Bit Score: 39.41  E-value: 1.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 110 ISRFLTTHPHVNLILQQDGSPKLQTMLANKEIDMGLISfPNTLPEIIHIEPLETTTkgyhVYVVVPESNPLSQYEKLTFK 189
Cdd:cd08452   19 VREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLH-PPIQHTALHIETVQSSP----CVLALPKQHPLASKEEITIE 93

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 488308860 190 DLKDQRFSSLSD--NFMIGRLLLDRTRSFGYEPNII 223
Cdd:cd08452   94 DLRDEPIITVAReaWPTLYDEIIQLCEQAGFRPKIV 129
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 110-197 1.65e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tfdA and tfdB gene expression. These genes encode enzymes for the conversion of 2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenol. 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: 176137 [Multi-domain]  Cd Length: 198  Bit Score: 38.80  E-value: 1.65e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 110 ISRFLTTHPHVNLILQQ-DGSPKLQTMLANKeIDMGLISFPNTLPEI----IHIEPLetttkgyhvYVVVPESNPLSQYE 184
Cdd:cd08446   20 LRAFLTARPDVTVSLHNmTKDEQIEALRAGR-IHIGFGRFYPVEPDIavenVAQERL---------YLAVPKSHPLAARP 89

                         90
                 ....*....|...
gi 488308860 185 KLTFKDLKDQRFS 197
Cdd:cd08446   90 AVSLADLRNEPLI 102
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-232 1.97e-03

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 39.41  E-value: 1.97e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   1 MNIQLLKYFIEIVNTR-SLSAAARNLFVTQPTLSLALKKMESELGTALF-DHSDQPFQLTDTGVYLYEHGQEVVFQFDQl 78
Cdd:PRK12679   1 MNFQQLKIIREAARQDyNLTEVANMLFTSQSGVSRHIRELEDELGIEIFiRRGKRLLGMTEPGKALLVIAERILNEASN- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  79 VTDIREMNQKPVKKQLRLGLT-TLFAVQFMKEISRFLTTHPHVNLILQQdGSPK-LQTMLANKEIDMGLISfpntlpEII 156
Cdd:PRK12679  80 VRRLADLFTNDTSGVLTIATThTQARYSLPEVIKAFRELFPEVRLELIQ-GTPQeIATLLQNGEADIGIAS------ERL 152

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488308860 157 HIEPLETTTKGY--HVYVVVPESNPLSQYEKLTFKDLKDQRFSSLSDNfMIGRLLLDRT-RSFGYEPNIILHNDDLQVL 232
Cdd:PRK12679 153 SNDPQLVAFPWFrwHHSLLVPHDHPLTQITPLTLESIAKWPLITYRQG-ITGRSRIDDAfARKGLLADIVLSAQDSDVI 230
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 93-191 2.13e-03

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


Pssm-ID: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 38.35  E-value: 2.13e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  93 QLRLGLTTLFAVQFMKEISRFLTTH-PHVNLILQQDGSPKLQTMLANKEIDMGLISFPNtLPEIIHIEPLETTTkgyhvY 171
Cdd:cd08417    1 TFRIAASDYLEALLLPPLLARLRQEaPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPE-LPPGLRSQPLFEDR-----F 74

                         90       100
                 ....*....|....*....|.
gi 488308860 172 V-VVPESNPLSQyEKLTFKDL 191
Cdd:cd08417   75 VcVARKDHPLAG-GPLTLEDY 94
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 93-225 2.52e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. 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. 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: 176138 [Multi-domain]  Cd Length: 198  Bit Score: 38.40  E-value: 2.52e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860  93 QLRLGLTTLFAVQFMKE-ISRFLTTHPHVNLILQQdgspkLQTM-----LANKEIDMGLISFPNTLPEI----IHIEPLe 162
Cdd:cd08447    1 SLRIGFTAASAYSFLPRlLAAARAALPDVDLVLRE-----MVTTdqieaLESGRIDLGLLRPPFARPGLetrpLVREPL- 74

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488308860 163 tttkgyhvYVVVPESNPLSQYEKLTFKDLKDQRFSSLSDN----F--MIGRLLldrtRSFGYEPNIILH 225
Cdd:cd08447   75 --------VAAVPAGHPLAGAERLTLEDLDGQPFIMYSPTearyFhdLVVRLF----ASAGVQPRYVQY 131
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 110-292 2.55e-03

The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The 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: 176134  Cd Length: 198  Bit Score: 38.31  E-value: 2.55e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 110 ISRFLTTHPHVNLILQQdGSP-KLQTMLANKEIDMGLISfpntlpEIIHIEPLETTTKGYH--VYVVVPESNPLSQYEKL 186
Cdd:cd08443   19 IKGFIERYPRVSLQMHQ-GSPtQIAEMVSKGLVDFAIAT------EALHDYDDLITLPCYHwnRCVVVKRDHPLADKQSI 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860 187 TFKDLKDQRFSSLSDNFMiGRLLLDRTRS-FGYEPNIILHNDDLQVLLYSLQKNNSICLLPIEYYEVGKSQGLKWIPLKD 265
Cdd:cd08443   92 SIEELATYPIVTYTFGFT-GRSELDTAFNrAGLTPNIVLTATDADVIKTYVRLGLGVGVIASMAYDPVDDPDLVIRDARD 170

                        170       180
                 ....*....|....*....|....*..
gi 488308860 266 KFDYFPIGIALRRDFSMTEDVRDFIRI 292
Cdd:cd08443  171 LFPWSVTKIAFRRGTFLRSYMYDFIQR 197
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
9-123 3.53e-03

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 38.59  E-value: 3.53e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488308860   9 FIEIVNTRSLSAAARNLFVTQPTLSLALKKMESELGTALFDHSDQPFQLTDTGVYLYEHGQEVVFQFDQLVTDIREMNQK 88
Cdd:PRK10632  10 FAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAFNNT 89

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 488308860  89 PVkKQLRLGLTTLFAVQFMKEIS-RFLTTHP--HVNLI 123
Cdd:PRK10632  90 PI-GTLRIGCSSTMAQNVLAGLTaKMLKEYPglSVNLV 126
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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