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Conserved domains on  [gi|829056759|ref|WP_047290525|]
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LysR family transcriptional regulator [Bifidobacterium bifidum]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426520)

LysR family transcriptional regulator negatively or positively regulates the transcription of specific genes; contains 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 proteins

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0006355|GO:0003677
PubMed:  8257110|19047729
SCOP:  3000083|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];
4-170 1.56e-28

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 109.19  E-value: 1.56e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759   4 LLDTLVAVYEIGQFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNAKSdVTPTEAGRLLYRAATGIDGTWRDACEQIA 83
Cdd:COG0583    5 QLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRG-LRLTEAGERLLERARRILAELEEAEAELR 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759  84 RMRESRE-PLSVAFSHTTAAVLLPVALPVMAEALSGFDCSIRVLNSDAILEQTGMKAVQLGVVEKPIVNDSVDRVTLRED 162
Cdd:COG0583   84 ALRGGPRgTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPLGEE 163


                 ....*...
gi 829056759 163 RLVLAGDP 170
Cdd:COG0583  164 RLVLVASP 171
Periplasmic_Binding_Protein_Type_2 super family cl21456
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
 92-251 9.77e-12

Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1 (PBP1), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The origin of PBP module can be traced across the distant phyla, including eukaryotes, archebacteria, and prokaryotes. The majority of PBP2 proteins are involved in the uptake of a variety of soluble substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. 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 family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. The substrate binding domain of the LysR transcriptional regulators and the oligopeptide-like transport systems also contain the type 2 periplasmic binding fold and thus they are significantly homologous to that of the PBP2; however, these two families are grouped into a separate hierarchy of the PBP2 superfamily due to the large number of protein sequences.


The actual alignment was detected with superfamily member cd08420:

Pssm-ID: 473866 [Multi-domain]  Cd Length: 201  Bit Score: 62.51  E-value: 9.77e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759  92 LSVAFSHTTAAVLLPVALPVMAEALSGFDCSIRVLNSDAILEQTGMKAVQLGVVEKPIVNDSVDRVTLREDRLVL---AG 168
Cdd:cd08420    2 LRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLvvpPD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759 169 DP-------------HGVWMVREHGSGVRYYTDLYFKTVGFMPSRM---IEVANNAAIGAALAAGFGCSLVSAAAVPAGV 232
Cdd:cd08420   82 HPlagrkevtaeelaAEPWILREPGSGTREVFERALAEAGLDGLDLnivMELGSTEAIKEAVEAGLGISILSRLAVRKEL 161

                        170       180
                 ....*....|....*....|....*
gi 829056759 233 PTREL------GDEFVRRFYALVPR 251
Cdd:cd08420  162 ELGRLvalpveGLRLTRPFSLIYHK 186
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
4-170 1.56e-28

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 109.19  E-value: 1.56e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759   4 LLDTLVAVYEIGQFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNAKSdVTPTEAGRLLYRAATGIDGTWRDACEQIA 83
Cdd:COG0583    5 QLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRG-LRLTEAGERLLERARRILAELEEAEAELR 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759  84 RMRESRE-PLSVAFSHTTAAVLLPVALPVMAEALSGFDCSIRVLNSDAILEQTGMKAVQLGVVEKPIVNDSVDRVTLRED 162
Cdd:COG0583   84 ALRGGPRgTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPLGEE 163


                 ....*...
gi 829056759 163 RLVLAGDP 170
Cdd:COG0583  164 RLVLVASP 171
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 4-184 2.99e-25

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: 101.54  E-value: 2.99e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759   4 LLDTLVAVYEIGQFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNAKSdVTPTEAGRLLYRAATGIDGTWRDACEQIA 83
Cdd:NF040786   5 QLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKE-VSLTEDGKLLYEYAKEMLDLWEKLEEEFD 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759  84 RMR-ESREPLSVAFSHTTAAVLLPVALPVMAEALSGFDCSIRVLNSDAILEQTGMKAVQLGVVEKPIVNDSVDRVTLRED 162
Cdd:NF040786  84 RYGkESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPFYKD 163

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 829056759 163 RLVLAGDPHGV------------------WMVREHGSGVR 184
Cdd:NF040786 164 RLVLITPNGTEkyrmlkeeisiselqkepFIMREEGSGTR 203
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
4-62 1.95e-16

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 71.65  E-value: 1.95e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 829056759    4 LLDTLVAVYEIGQFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNAKSdVTPTEAGR 62
Cdd:pfam00126   3 QLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRG-VRLTEAGE 60
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 92-251 9.77e-12

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: 62.51  E-value: 9.77e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759  92 LSVAFSHTTAAVLLPVALPVMAEALSGFDCSIRVLNSDAILEQTGMKAVQLGVVEKPIVNDSVDRVTLREDRLVL---AG 168
Cdd:cd08420    2 LRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLvvpPD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759 169 DP-------------HGVWMVREHGSGVRYYTDLYFKTVGFMPSRM---IEVANNAAIGAALAAGFGCSLVSAAAVPAGV 232
Cdd:cd08420   82 HPlagrkevtaeelaAEPWILREPGSGTREVFERALAEAGLDGLDLnivMELGSTEAIKEAVEAGLGISILSRLAVRKEL 161

                        170       180
                 ....*....|....*....|....*
gi 829056759 233 PTREL------GDEFVRRFYALVPR 251
Cdd:cd08420  162 ELGRLvalpveGLRLTRPFSLIYHK 186
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
3-118 1.89e-11

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 63.07  E-value: 1.89e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759   3 PLLDTLVAVYEIGQFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNakSDVTPTEAGRLLYRAATGIDGTWRDACEQI 82
Cdd:PRK13348   5 KQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG--RPCRPTPAGQRLLRHLRQVALLEADLLSTL 82

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 829056759  83 ARMRESREPLSVAFSHTTAAVLLpvaLPVMAEALSG 118
Cdd:PRK13348  83 PAERGSPPTLAIAVNADSLATWF---LPALAAVLAG 115
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 89-270 2.93e-06

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: 46.90  E-value: 2.93e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759   89 REPLSVAFSHTTAAVLLPVALPVMAEALSGFDCSIRVLNSDAILEQTGMKAVQLGVVEKPIVNDSVDRVTLREDRLVLAG 168
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759  169 DPHGV----------------WMVREHGSGVRYYTDLYFKTVGFMPSRMIEVANNAAIGAALAAGFGCSLVSAAAVPAGV 232
Cdd:pfam03466  81 PPDHPlargepvsledladepLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 829056759  233 PTREL------GDEFVRRFYALVPR-SGLTPGQRELAGRVIAALR 270
Cdd:pfam03466 161 ADGRLvalplpEPPLPRELYLVWRKgRPLSPAVRAFIEFLREALA 205
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
4-170 1.56e-28

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 109.19  E-value: 1.56e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759   4 LLDTLVAVYEIGQFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNAKSdVTPTEAGRLLYRAATGIDGTWRDACEQIA 83
Cdd:COG0583    5 QLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRG-LRLTEAGERLLERARRILAELEEAEAELR 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759  84 RMRESRE-PLSVAFSHTTAAVLLPVALPVMAEALSGFDCSIRVLNSDAILEQTGMKAVQLGVVEKPIVNDSVDRVTLRED 162
Cdd:COG0583   84 ALRGGPRgTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPLGEE 163


                 ....*...
gi 829056759 163 RLVLAGDP 170
Cdd:COG0583  164 RLVLVASP 171
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 4-184 2.99e-25

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: 101.54  E-value: 2.99e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759   4 LLDTLVAVYEIGQFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNAKSdVTPTEAGRLLYRAATGIDGTWRDACEQIA 83
Cdd:NF040786   5 QLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKE-VSLTEDGKLLYEYAKEMLDLWEKLEEEFD 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759  84 RMR-ESREPLSVAFSHTTAAVLLPVALPVMAEALSGFDCSIRVLNSDAILEQTGMKAVQLGVVEKPIVNDSVDRVTLRED 162
Cdd:NF040786  84 RYGkESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPFYKD 163

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 829056759 163 RLVLAGDPHGV------------------WMVREHGSGVR 184
Cdd:NF040786 164 RLVLITPNGTEkyrmlkeeisiselqkepFIMREEGSGTR 203
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
4-62 1.95e-16

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 71.65  E-value: 1.95e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 829056759    4 LLDTLVAVYEIGQFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNAKSdVTPTEAGR 62
Cdd:pfam00126   3 QLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRG-VRLTEAGE 60
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 92-251 9.77e-12

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: 62.51  E-value: 9.77e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759  92 LSVAFSHTTAAVLLPVALPVMAEALSGFDCSIRVLNSDAILEQTGMKAVQLGVVEKPIVNDSVDRVTLREDRLVL---AG 168
Cdd:cd08420    2 LRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLvvpPD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759 169 DP-------------HGVWMVREHGSGVRYYTDLYFKTVGFMPSRM---IEVANNAAIGAALAAGFGCSLVSAAAVPAGV 232
Cdd:cd08420   82 HPlagrkevtaeelaAEPWILREPGSGTREVFERALAEAGLDGLDLnivMELGSTEAIKEAVEAGLGISILSRLAVRKEL 161

                        170       180
                 ....*....|....*....|....*
gi 829056759 233 PTREL------GDEFVRRFYALVPR 251
Cdd:cd08420  162 ELGRLvalpveGLRLTRPFSLIYHK 186
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
3-118 1.89e-11

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 63.07  E-value: 1.89e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759   3 PLLDTLVAVYEIGQFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNakSDVTPTEAGRLLYRAATGIDGTWRDACEQI 82
Cdd:PRK13348   5 KQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG--RPCRPTPAGQRLLRHLRQVALLEADLLSTL 82

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 829056759  83 ARMRESREPLSVAFSHTTAAVLLpvaLPVMAEALSG 118
Cdd:PRK13348  83 PAERGSPPTLAIAVNADSLATWF---LPALAAVLAG 115
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
3-68 2.58e-11

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 62.48  E-value: 2.58e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 829056759   3 PLLDTLVAVYEIGQFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNAKsdVTPTEAGRLLYRAA 68
Cdd:PRK03635   5 KQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRTQP--CRPTEAGQRLLRHA 68
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 8-68 8.69e-11

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 61.13  E-value: 8.69e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 829056759   8 LVAVYEIGQFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNAKSdVTPTEAGRLLYRAA 68
Cdd:PRK11242   9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRT-VRLTDAGEVYLRYA 68
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 5-184 2.44e-10

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 59.70  E-value: 2.44e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759   5 LDTLVAVYEIGQFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNAKSDVTpTEAGRLLYRAATGIdgtwRDACEQIAR 84
Cdd:PRK10837   8 LEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVV-NEHGRLLYPRALAL----LEQAVEIEQ 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759  85 M-RESREPLSVAFSHTTAAVLLPVALPVMAEALSGFDCSIRVLNSDAILEQTGMKAVQLGVVEKPIVNDSVDRVTLREDR 163
Cdd:PRK10837  83 LfREDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPELISEPWLEDE 162

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 829056759 164 LV--------LAGDPHGV-------WMVREHGSGVR 184
Cdd:PRK10837 163 LVvfaapdspLARGPVTLeqlaaapWILRERGSGTR 198
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 5-114 8.34e-09

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 55.07  E-value: 8.34e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759   5 LDTLVAVYEIGQFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNaKSDVTPTEAGRLLYRAATGIdgtWRDaCEQ--- 81
Cdd:PRK11233   6 LKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRT-KRGVTPTEAGKILYTHARAI---LRQ-CEQaql 80

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 829056759  82 --IARMRESREPLSVAFSHTTAAVLLpvALPVMAE 114
Cdd:PRK11233  81 avHNVGQALSGQVSIGLAPGTAASSL--TMPLLQA 113
rbcR CHL00180
LysR transcriptional regulator; Provisional
 1-106 1.53e-08

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 54.64  E-value: 1.53e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759   1 MFPL-LDTLV---AVYEIGQFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRnAKSDVTPTEAGRLLYRAATGIDGTWR 76
Cdd:CHL00180   2 DLPFtLDQLRilkAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDR-SKNKASLTEAGELLLRYGNRILALCE 80

                         90       100       110
                 ....*....|....*....|....*....|.
gi 829056759  77 DACEQIARMRE-SREPLSVAFSHTTAAVLLP 106
Cdd:CHL00180  81 ETCRALEDLKNlQRGTLIIGASQTTGTYLMP 111
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 17-83 4.00e-08

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 53.31  E-value: 4.00e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 829056759  17 FTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNAKSdVTPTEAGRllyRAATGIdgtwRDACEQIA 83
Cdd:PRK11139  23 FTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRS-LLLTEEGQ---RYFLDI----REIFDQLA 81
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 9-166 1.99e-07

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 50.92  E-value: 1.99e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759   9 VAVYEIGQFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNaKSDVTPTEAGRLLYRAATGIDGTWRDACEQIARMRES 88
Cdd:PRK09906  10 VAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRD-KRKVALTAAGEVFLQDARAILEQAEKAKLRARKIVQE 88

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 829056759  89 REPLSVAFSHTTAAVLLPVALPVMAEALSGFDCSIRVLNSDAILEQTGMKAVQLGVVEKPIVNDSVD-RVTLREDRLVL 166
Cdd:PRK09906  89 DRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDyLELLDEPLVVV 167
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
4-94 2.55e-07

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 50.79  E-value: 2.55e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759   4 LLDTLVAVYEIGQFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNaKSDVTPTEAG-RLLYRAATGIDgTWRDACEQI 82
Cdd:PRK03601   5 LLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRH-RNNIRLTAAGeRLLPYAETLMN-TWQAAKKEV 82

                         90
                 ....*....|..
gi 829056759  83 ARMRESREpLSV 94
Cdd:PRK03601  83 AHTSQHNE-LSI 93
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
17-67 2.73e-07

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 50.77  E-value: 2.73e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 829056759  17 FTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNAKSdVTPTEAGRLLYRA 67
Cdd:PRK10086  31 FALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRK-VELTEEGKRVFWA 80
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
5-78 5.88e-07

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 49.80  E-value: 5.88e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 829056759   5 LDTLVAVYEIGQFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNAKSdVTPTEAGRLLYRAATGIDGtWRDA 78
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRS-VTLTAAGEHLLSQARDWLS-WLES 78
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
18-109 1.39e-06

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 48.43  E-value: 1.39e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759  18 TLAADELKVSQSTVSSRIAQLERMVGAPLFVRNAKSDVTPTEAGRLLYRAATGIdgtWRDAcEQIARM-----RESREPL 92
Cdd:PRK12684  20 TEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRGLTEPGRIILASVERI---LQEV-ENLKRVgkefaAQDQGNL 95

                         90
                 ....*....|....*..
gi 829056759  93 SVAFSHTTAAVLLPVAL 109
Cdd:PRK12684  96 TIATTHTQARYALPAAI 112
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 5-83 1.88e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 48.01  E-value: 1.88e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759   5 LDTLVAVYEIGQFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNAKsDVTPTEAGRLLYRAATGI----DGTWRDaCE 80
Cdd:PRK11074   7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHR-DVELTPAGEWFVKEARSVikkmQETRRQ-CQ 84


                 ...
gi 829056759  81 QIA 83
Cdd:PRK11074  85 QVA 87
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 89-270 2.93e-06

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: 46.90  E-value: 2.93e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759   89 REPLSVAFSHTTAAVLLPVALPVMAEALSGFDCSIRVLNSDAILEQTGMKAVQLGVVEKPIVNDSVDRVTLREDRLVLAG 168
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759  169 DPHGV----------------WMVREHGSGVRYYTDLYFKTVGFMPSRMIEVANNAAIGAALAAGFGCSLVSAAAVPAGV 232
Cdd:pfam03466  81 PPDHPlargepvsledladepLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 829056759  233 PTREL------GDEFVRRFYALVPR-SGLTPGQRELAGRVIAALR 270
Cdd:pfam03466 161 ADGRLvalplpEPPLPRELYLVWRKgRPLSPAVRAFIEFLREALA 205
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 4-160 3.75e-05

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 44.25  E-value: 3.75e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759   4 LLDTLVAVYEIGQFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNAKSDvTPTEAGRLLYRAATGIDGTWRDACEQIa 83
Cdd:PRK15092  15 LLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNK-LLTEHGIQLLGYARKILRFNDEACSSL- 92

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 829056759  84 rMRESRE-PLSVAFSHTTAAVLLPVALPVMAEALSGFDCSIRVLNSDAILEQTGMKAVQLGVVEKPIVNdsVDRVTLR 160
Cdd:PRK15092  93 -MYSNLQgVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTTHRPSS--FPALNLR 167
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-249 5.53e-05

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: 42.97  E-value: 5.53e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759  92 LSVAFSHTTAAVLLPVALPVMAEALSGFDCSIRVLNSDAILEQTGMKAVQLGVVEKPIVNDSVDRVTLREDRLV------ 165
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVlvvppd 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759 166 -------------LAGDPhgvWMVREHGSGVRYYTDLYFKTVGFMPSRMIEVANNAAIGAALAAGFGCSLVSAAAV---- 228
Cdd:cd05466   82 hplakrksvtladLADEP---LILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVeela 158

                        170       180
                 ....*....|....*....|.
gi 829056759 229 PAGVPTRELGDEFVRRFYALV 249
Cdd:cd05466  159 DGGLVVLPLEDPPLSRTIGLV 179
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 10-110 1.19e-04

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 42.67  E-value: 1.19e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759  10 AVYEIGQFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRnAKSDVTPTEAGRLLY----RAATGIDGTWRDAceqiARM 85
Cdd:PRK11013  14 AVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFER-VRGRLHPTVQGLRLFeevqRSYYGLDRIVSAA----ESL 88

                         90       100       110
                 ....*....|....*....|....*....|
gi 829056759  86 RESRE-PLSVA----FSHTtaavLLPVALP 110
Cdd:PRK11013  89 REFRQgQLSIAclpvFSQS----LLPGLCQ 114
PRK09986 PRK09986
LysR family transcriptional regulator;
4-64 1.29e-04

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 42.40  E-value: 1.29e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 829056759   4 LLDTLVAVYEIGQFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNAKSdVTPTEAGRLL 64
Cdd:PRK09986  11 LLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRS-VVLTHAGKIL 70
PRK12680 PRK12680
LysR family transcriptional regulator;
5-145 1.43e-04

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 42.69  E-value: 1.43e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759   5 LDTLVAVYEIG-QFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNAKSDVTPTEAGRLLYRAATGIDGTWRDACEQIA 83
Cdd:PRK12680   6 LRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLESVTPAGVEVIERARAVLSEANNIRTYAA 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 829056759  84 -RMRESREPLSVAFSHTTAAVLLPVALPVMAEALSGFDCSIRVLNSDAILEQTGMKAVQLGVV 145
Cdd:PRK12680  86 nQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIV 148
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 18-106 1.75e-04

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 42.34  E-value: 1.75e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759  18 TLAADELKVSQSTVSSRIAQLERMVGAPLFVRNAKSDVTPTEAGRLLYRAATGI---DGTWRDACEQIARMRESRepLSV 94
Cdd:PRK12683  20 TEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTGLTEPGKELLQIVERMlldAENLRRLAEQFADRDSGH--LTV 97

                         90
                 ....*....|..
gi 829056759  95 AFSHTTAAVLLP 106
Cdd:PRK12683  98 ATTHTQARYALP 109
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 5-115 2.15e-04

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 41.94  E-value: 2.15e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759   5 LDTLVAVYEIGQFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNAKSdVTPTEAGRLLYRAAtgidgtwRDACEQIAR 84
Cdd:PRK11151   6 LEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRK-VLFTQAGLLLVDQA-------RTVLREVKV 77

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 829056759  85 MRE--SRE------PLSVAFSHTTAAVLLPVALPVMAEA 115
Cdd:PRK11151  78 LKEmaSQQgetmsgPLHIGLIPTVGPYLLPHIIPMLHQT 116
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 18-110 4.20e-04

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 41.13  E-value: 4.20e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759  18 TLAADELKVSQSTVSSRIAQLERMVGAPLFVRNAKSDVTPTEAGRLLYRAATGIdgtWRDA--CEQIARMRESREP--LS 93
Cdd:PRK12682  20 TEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKGLTEPGKAVLDVIERI---LREVgnIKRIGDDFSNQDSgtLT 96

                         90
                 ....*....|....*..
gi 829056759  94 VAFSHTTAAVLLPVALP 110
Cdd:PRK12682  97 IATTHTQARYVLPRVVA 113
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
26-64 4.98e-04

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 40.57  E-value: 4.98e-04
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 829056759  26 VSQSTVSSRIAQLERMVGAPLFVRNAKSdVTPTEAGRLL 64
Cdd:PRK11716   3 VSPSTLSRQIQRLEEELGQPLFVRDNRS-VTLTEAGEEL 40
nhaR PRK11062
transcriptional activator NhaR; Provisional
 11-68 5.78e-04

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 40.38  E-value: 5.78e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 829056759  11 VYEIGQFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNAKSdVTPTEAGRLLYRAA 68
Cdd:PRK11062  15 VCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRG-LEPTELGELVFRYA 71
cbl PRK12679
HTH-type transcriptional regulator Cbl;
18-106 5.93e-04

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 40.56  E-value: 5.93e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 829056759  18 TLAADELKVSQSTVSSRIAQLERMVGAPLFVRNAKSDVTPTEAGRLLYRAATGIdgtwRDACEQIARM-----RESREPL 92
Cdd:PRK12679  20 TEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLGMTEPGKALLVIAERI----LNEASNVRRLadlftNDTSGVL 95

                         90
                 ....*....|....
gi 829056759  93 SVAFSHTTAAVLLP 106
Cdd:PRK12679  96 TIATTHTQARYSLP 109
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
11-66 7.05e-04

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 40.51  E-value: 7.05e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 829056759  11 VYEIGQFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNAKSdVTPTEAGRLLYR 66
Cdd:PRK10632  13 VVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRS-IGLTEAGRIYYQ 67
PRK09791 PRK09791
LysR family transcriptional regulator;
5-82 9.86e-04

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 39.75  E-value: 9.86e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 829056759   5 LDTLVAVYEIGQFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNAKSdVTPTEAGRLLYRAATGIDGTWRDACEQI 82
Cdd:PRK09791  10 IRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKG-VTLTDAGESFYQHASLILEELRAAQEDI 86
PRK10341 PRK10341
transcriptional regulator TdcA;
20-64 1.68e-03

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 39.08  E-value: 1.68e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 829056759  20 AADELKVSQSTVSSRIAQLERMVGAPLFVRNaKSDVTPTEAGRLL 64
Cdd:PRK10341  27 AAKELGLTQPAVSKIINDIEDYFGVELIVRK-NTGVTLTPAGQVL 70
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
5-66 4.38e-03

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 37.73  E-value: 4.38e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 829056759   5 LDTLVAVYEIGQFTLAADELKVSQSTVSSRIAQLERMVGAPLFVRNaKSDVTPTEAGRLLYR 66
Cdd:PRK15243   9 LKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRK-NGTLIPTEFAQTIYR 69
 
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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