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Conserved domains on  [gi|501383361|ref|WP_012414927|]
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LysR family transcriptional regulator [Elusimicrobium minutum]

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];
2-191 1.08e-30

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 115.73  E-value: 1.08e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361   2 INLLHLKYVLEVEKTSSISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGISPTPRGEEFLQYAKKIISQVEEVTA 81
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361  82 MYKSSKTEKQ-SFSISVPR---ASYISHAFTEFAK---NIDLSLTaefyykETNSMRAISNILQADYRLGIIRYQAAfee 154
Cdd:COG0583   81 ELRALRGGPRgTLRIGAPPslaRYLLPPLLARFRArhpGVRLELR------EGNSDRLVDALLEGELDLAIRLGPPP--- 151

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 501383361 155 yfkvmlyEKQLAFEPVRQFSYVLLMSKDNPLAKKTDI 191
Cdd:COG0583  152 -------DPGLVARPLGEERLVLVASPDHPLARRAPL 181
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
2-191 1.08e-30

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 115.73  E-value: 1.08e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361   2 INLLHLKYVLEVEKTSSISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGISPTPRGEEFLQYAKKIISQVEEVTA 81
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361  82 MYKSSKTEKQ-SFSISVPR---ASYISHAFTEFAK---NIDLSLTaefyykETNSMRAISNILQADYRLGIIRYQAAfee 154
Cdd:COG0583   81 ELRALRGGPRgTLRIGAPPslaRYLLPPLLARFRArhpGVRLELR------EGNSDRLVDALLEGELDLAIRLGPPP--- 151

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 501383361 155 yfkvmlyEKQLAFEPVRQFSYVLLMSKDNPLAKKTDI 191
Cdd:COG0583  152 -------DPGLVARPLGEERLVLVASPDHPLARRAPL 181
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
6-63 3.10e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 74.34  E-value: 3.10e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 501383361    6 HLKYVLEVEKTSSISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGISPTPRGE 63
Cdd:pfam00126   3 QLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 4-200 2.28e-15

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 74.81  E-value: 2.28e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361   4 LLHLKYVLEVEKTSSISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGISPTPRGEEFLQYAKKIISQVEEVTAMY 83
Cdd:PRK09906   3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361  84 KSSKTEKQSFSIS-VPRASYisHAFTEFAKNIDLS---LTAEFYykETNSMRAISNILQADYRLGIIRYQAAFEE-YFKV 158
Cdd:PRK09906  83 RKIVQEDRQLTIGfVPSAEV--NLLPKVLPMFRLRhpdTLIELV--SLITTQQEEKLRRGELDVGFMRHPVYSDEiDYLE 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 501383361 159 MLYekqlafEPVrqfsyVLLMSKDNPLAKKTDIKADDLK--NFI 200
Cdd:PRK09906 159 LLD------EPL-----VVVLPVDHPLAHEKEITAAQLDgvNFI 191
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 2-137 5.02e-11

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: 62.25  E-value: 5.02e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361   2 INLLHLKYVLEVEKTSSISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGISPTPRGEEFLQYAKKIISQVEE-VT 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKlEE 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 501383361  81 AMYKSSKTEKQSFSI---SVPrASYI--SH--AFTEFAKNIDlsltaeFYYKETNSMRAISNIL 137
Cdd:NF040786  81 EFDRYGKESKGVLRIgasTIP-GQYLlpELlkKFKEKYPNVR------FKLMISDSIKVIELLL 137
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 160-198 2.34e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mechanisms. In Escherichia coli and Salmonella enterica serovar Typhimurium, MetJ and MetR regulate the expression of methionine biosynthetic genes. The MetJ repressor negatively regulates the E. coli met genes, except for metH. Several of these genes are also under the positive control of MetR with homocysteine as a co-inducer. In Bacillus subtilis, the met genes are controlled by S-box termination-antitermination system. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176132  Cd Length: 198  Bit Score: 41.40  E-value: 2.34e-04
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 501383361 160 LYEKQLAFEPVRQFSYVLLMSKDNPLAKKTDIKADDLKN 198
Cdd:cd08441   59 LPLPGIAYEPLFDYEVVLVVAPDHPLAAKEFITPEDLAD 97
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
2-191 1.08e-30

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 115.73  E-value: 1.08e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361   2 INLLHLKYVLEVEKTSSISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGISPTPRGEEFLQYAKKIISQVEEVTA 81
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361  82 MYKSSKTEKQ-SFSISVPR---ASYISHAFTEFAK---NIDLSLTaefyykETNSMRAISNILQADYRLGIIRYQAAfee 154
Cdd:COG0583   81 ELRALRGGPRgTLRIGAPPslaRYLLPPLLARFRArhpGVRLELR------EGNSDRLVDALLEGELDLAIRLGPPP--- 151

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 501383361 155 yfkvmlyEKQLAFEPVRQFSYVLLMSKDNPLAKKTDI 191
Cdd:COG0583  152 -------DPGLVARPLGEERLVLVASPDHPLARRAPL 181
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
6-63 3.10e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 74.34  E-value: 3.10e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 501383361    6 HLKYVLEVEKTSSISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGISPTPRGE 63
Cdd:pfam00126   3 QLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 4-200 2.28e-15

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 74.81  E-value: 2.28e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361   4 LLHLKYVLEVEKTSSISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGISPTPRGEEFLQYAKKIISQVEEVTAMY 83
Cdd:PRK09906   3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361  84 KSSKTEKQSFSIS-VPRASYisHAFTEFAKNIDLS---LTAEFYykETNSMRAISNILQADYRLGIIRYQAAFEE-YFKV 158
Cdd:PRK09906  83 RKIVQEDRQLTIGfVPSAEV--NLLPKVLPMFRLRhpdTLIELV--SLITTQQEEKLRRGELDVGFMRHPVYSDEiDYLE 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 501383361 159 MLYekqlafEPVrqfsyVLLMSKDNPLAKKTDIKADDLK--NFI 200
Cdd:PRK09906 159 LLD------EPL-----VVVLPVDHPLAHEKEITAAQLDgvNFI 191
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-196 2.15e-12

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 66.58  E-value: 2.15e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361   1 MINLLHLKYVLEVEKTSSISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGISPTPRGEEFLQYAKKIISQVEevT 80
Cdd:PRK15421   1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQIS--Q 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361  81 AMYKSSKTEKQSFSISVPRAS---YISHAFTEFAKN-----IDLSLTAEFYYKETNSMRAISNILQADyrlgiiryqaaf 152
Cdd:PRK15421  79 ALQACNEPQQTRLRIAIECHSciqWLTPALENFHKNwpqveMDFKSGVTFDPQPALQQGELDLVMTSD------------ 146

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 501383361 153 eeyfkvMLYEKQLAFEPVRQFSYVLLMSKDNPLAKKTDIKADDL 196
Cdd:PRK15421 147 ------ILPRSGLHYSPMFDYEVRLVLAPDHPLAAKTRITPEDL 184
rbcR CHL00180
LysR transcriptional regulator; Provisional
 18-306 2.22e-11

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 63.50  E-value: 2.22e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361  18 SISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGISPTPRGEEFLQYAKKIISQVEEVTAMYKSSKTeKQSFSISV 97
Cdd:CHL00180  21 SFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALEDLKN-LQRGTLII 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361  98 -----------PRasyISHAFTEFAKNIDLSLtaefyykETNSMRAIS-NILQADYRLGIIRYQAAFEEYfkvmlyeKQL 165
Cdd:CHL00180 100 gasqttgtylmPR---LIGLFRQRYPQINVQL-------QVHSTRRIAwNVANGQIDIAIVGGEVPTELK-------KIL 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361 166 AFEPVRQFSYVLLMSKDNPLAKKTDIKADDLK--NFIEIahaDPYVPSLPVID---------VKKAELSTFVNKrIYVFE 234
Cdd:CHL00180 163 EITPYVEDELALIIPKSHPFAKLKKIQKEDLYrlNFITL---DSNSTIRKVIDniliqngidSKRFKIEMELNS-IEAIK 238

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 501383361 235 RASQFELlnkiKKTFMWVSPVPEE-QLKRYNLVQ-KKCSINKKIYkdILIYRKNYRFTPLdEKFIKELNKAKLL 306
Cdd:CHL00180 239 NAVQSGL----GAAFVSVSAIEKElELGLLHWIKiENITIKRMLS--IITNPNRYKSKAS-ETFYNEILTLFNT 305
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 2-196 3.68e-11

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 62.70  E-value: 3.68e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361   2 INLLHLKYVLE-VEKTSSISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGI-SPTPRGEEFLQYAKKIISQVEEV 79
Cdd:PRK12682   1 MNLQQLRFVREaVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLkGLTEPGKAVLDVIERILREVGNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361  80 TAMYKS-SKTEKQSFSISV--PRASY----ISHAFTEFAKNIDLSLTAefyyketNSMRAISNIL---QADyrLGIiryq 149
Cdd:PRK12682  81 KRIGDDfSNQDSGTLTIATthTQARYvlprVVAAFRKRYPKVNLSLHQ-------GSPDEIARMVisgEAD--IGI---- 147

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 501383361 150 aAFEeyfKVMLYEKQLAFePVRQFSYVLLMSKDNPLAKKTDIKADDL 196
Cdd:PRK12682 148 -ATE---SLADDPDLATL-PCYDWQHAVIVPPDHPLAQEERITLEDL 189
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 2-137 5.02e-11

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: 62.25  E-value: 5.02e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361   2 INLLHLKYVLEVEKTSSISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGISPTPRGEEFLQYAKKIISQVEE-VT 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKlEE 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 501383361  81 AMYKSSKTEKQSFSI---SVPrASYI--SH--AFTEFAKNIDlsltaeFYYKETNSMRAISNIL 137
Cdd:NF040786  81 EFDRYGKESKGVLRIgasTIP-GQYLlpELlkKFKEKYPNVR------FKLMISDSIKVIELLL 137
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
3-77 1.89e-10

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 60.76  E-value: 1.89e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 501383361   3 NLLHLKYVLEVEKTS-SISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGI-SPTPRGEEFLQYAKKIISQVE 77
Cdd:PRK12684   2 NLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLrGLTEPGRIILASVERILQEVE 78
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 4-78 9.67e-10

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 58.43  E-value: 9.67e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 501383361   4 LLHLKYVLEVEKTSSISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGISPTPRGEEFLQYAKKIISQVEE 78
Cdd:PRK11242   3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEA 77
PRK09986 PRK09986
LysR family transcriptional regulator;
2-81 2.04e-09

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 57.43  E-value: 2.04e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361   2 INLLHLKYVLEVEKTSSISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGISPTPRGEEFLQYAKKIISQVEEVTA 81
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86
PRK09791 PRK09791
LysR family transcriptional regulator;
2-76 2.82e-09

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 57.08  E-value: 2.82e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 501383361   2 INLLHLKYVLEVEKTSSISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGISPTPRGEEFLQYAKKIISQV 76
Cdd:PRK09791   5 VKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEEL 79
cysB PRK12681
HTH-type transcriptional regulator CysB;
4-77 4.15e-09

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 56.83  E-value: 4.15e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 501383361   4 LLHLKYVLEVEKTS-SISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGISP-TPRGEEFLQYAKKIISQVE 77
Cdd:PRK12681   3 LQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTQvTPAGEEIIRIAREILSKVE 78
PRK12680 PRK12680
LysR family transcriptional regulator;
2-91 1.10e-07

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 52.32  E-value: 1.10e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361   2 INLLHLKYVLEVEKTS-SISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGI-SPTPRGEEFLQYAKKIISQVEEV 79
Cdd:PRK12680   1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNI 80

                         90
                 ....*....|..
gi 501383361  80 TAMYKSSKTEKQ 91
Cdd:PRK12680  81 RTYAANQRRESQ 92
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
7-74 1.86e-07

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 51.56  E-value: 1.86e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 501383361   7 LKYVLEVEKTSSISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGISPTPRGEEFLQYAKKIIS 74
Cdd:PRK03601   6 LKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMN 73
PRK10341 PRK10341
transcriptional regulator TdcA;
6-98 1.90e-07

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 51.79  E-value: 1.90e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361   6 HLKYVLEVEKTSSISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGISPTPRGEEFLQYAKKIISQVEE-VTAMYK 84
Cdd:PRK10341  11 HLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNmVNEING 90

                         90
                 ....*....|....
gi 501383361  85 SSKTEKQSFSISVP 98
Cdd:PRK10341  91 MSSEAVVDVSFGFP 104
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
7-196 3.33e-07

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 50.96  E-value: 3.33e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361   7 LKYVLEVEKTSSISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGISPTPRGEEFLQYAKKIISQVE----EVTAM 82
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLEsmpsELQQV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361  83 ykSSKTEKQsFSISVPRASYISHAFTEFAKnidlSLTAEFYYKETNSMRAI-----SNILQADYRLGI-IRYQAAFEEYF 156
Cdd:PRK10094  87 --NDGVERQ-VNIVINNLLYNPQAVAQLLA----WLNERYPFTQFHISRQIymgvwDSLLYEGFSLAIgVTGTEALANTF 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 501383361 157 KVMlyekqlafePVRQFSYVLLMSKDNPLAKKTDIKADDL 196
Cdd:PRK10094 160 SLD---------PLGSVQWRFVMAADHPLANVEEPLTEAQ 190
nhaR PRK11062
transcriptional activator NhaR; Provisional
 2-74 4.29e-07

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 50.39  E-value: 4.29e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 501383361   2 INLLHLKYVLEVEKTSSISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGISPTPRGEEFLQYAKKIIS 74
Cdd:PRK11062   4 INYNHLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKMFT 76
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 18-120 2.73e-06

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 47.92  E-value: 2.73e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361  18 SISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGISPTPRGEEFLQYAKKIISQVEEVTAMYKSSKTEK------- 90
Cdd:PRK11139  22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRARSAKGaltvsll 101

                         90       100       110
                 ....*....|....*....|....*....|..
gi 501383361  91 QSFSIS--VPRASyishAFTEFAKNIDLSLTA 120
Cdd:PRK11139 102 PSFAIQwlVPRLS----SFNEAHPDIDVRLKA 129
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 2-79 4.43e-06

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 47.35  E-value: 4.43e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361   2 INLLHLKYVLE-VEKTSSISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSK---GIspTPRGEEFLQYAKKIISQVE 77
Cdd:PRK12683   1 MNFQQLRIIREaVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKrltGL--TEPGKELLQIVERMLLDAE 78


                 ..
gi 501383361  78 EV 79
Cdd:PRK12683  79 NL 80
PRK09801 PRK09801
LysR family transcriptional regulator;
7-113 6.45e-06

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 46.95  E-value: 6.45e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361   7 LKYVLEVEKTSSISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGISPTPRGEEFLQYAKKIISQ----VEEVTAM 82
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQyqrlVDDVTQI 90

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 501383361  83 ykssKTEKQSF-----SISVPRaSYISHAFTEFAKN 113
Cdd:PRK09801  91 ----KTRPEGMirigcSFGFGR-SHIAPAITELMRN 121
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
26-75 6.68e-06

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 46.74  E-value: 6.68e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 501383361  26 MYMGQPNLSRAIKELEKILGITIFKRTSKGISPTPRGEEFLQYAKKIISQ 75
Cdd:PRK11716   1 MHVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQ 50
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 2-78 1.03e-05

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 46.21  E-value: 1.03e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 501383361   2 INLLHLKYVLEVEKTSSISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGISPTPRGEEFLQYAKKIISQVEE 78
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQ 77
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 8-79 5.97e-05

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 43.78  E-value: 5.97e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 501383361   8 KYVLE----VEKTSSISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGISPTPRGEEFLQYAKKIISQVEEV 79
Cdd:PRK11074   4 EYSLEvvdaVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQET 79
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 21-82 1.23e-04

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 43.09  E-value: 1.23e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 501383361  21 KAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGISPTPRGEEFLQYAKKIISQVEEVTAM 82
Cdd:PRK11151  20 RAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEM 81
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
11-77 1.55e-04

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 42.73  E-value: 1.55e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 501383361  11 LEVEKTSSISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGISPTPRGEEFLQYAKKIISQVE 77
Cdd:PRK10082  20 LTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLE 86
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 160-198 2.34e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mechanisms. In Escherichia coli and Salmonella enterica serovar Typhimurium, MetJ and MetR regulate the expression of methionine biosynthetic genes. The MetJ repressor negatively regulates the E. coli met genes, except for metH. Several of these genes are also under the positive control of MetR with homocysteine as a co-inducer. In Bacillus subtilis, the met genes are controlled by S-box termination-antitermination system. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176132  Cd Length: 198  Bit Score: 41.40  E-value: 2.34e-04
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 501383361 160 LYEKQLAFEPVRQFSYVLLMSKDNPLAKKTDIKADDLKN 198
Cdd:cd08441   59 LPLPGIAYEPLFDYEVVLVVAPDHPLAAKEFITPEDLAD 97
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 1-62 3.28e-04

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 41.52  E-value: 3.28e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 501383361   1 MINLLHLKYVLEVEKTSSISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKGISPTPRG 62
Cdd:PRK11013   3 AVSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQG 64
cbl PRK12679
HTH-type transcriptional regulator Cbl;
2-199 8.50e-04

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 40.56  E-value: 8.50e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361   2 INLLHLKYVLEVEKTS-SISKAAANMYMGQPNLSRAIKELEKILGITIFKRTSKG-ISPTPRGEEFLQYAKKII---SQV 76
Cdd:PRK12679   1 MNFQQLKIIREAARQDyNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRlLGMTEPGKALLVIAERILneaSNV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361  77 EEVTAMYKSSKTEKQSFSISVPRASY----ISHAFTEFAKNIDLSLTaefyykeTNSMRAISNILQ---ADyrLGIIRYQ 149
Cdd:PRK12679  81 RRLADLFTNDTSGVLTIATTHTQARYslpeVIKAFRELFPEVRLELI-------QGTPQEIATLLQngeAD--IGIASER 151

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 501383361 150 aafeeyfkvMLYEKQLAFEPVRQFSYVLLMSKDNPLAKKTDIKADDLKNF 199
Cdd:PRK12679 152 ---------LSNDPQLVAFPWFRWHHSLLVPHDHPLTQITPLTLESIAKW 192
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 22-77 1.19e-03

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 39.97  E-value: 1.19e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 501383361  22 AAANMYMGQPN--LSRAIKELEKILGITIFKRTSKGISPTPRGEEFLQYAKKIISQVE 77
Cdd:PRK14997  20 AAAGRALDEPKskLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQ 77
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
1-72 5.31e-03

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 38.03  E-value: 5.31e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 501383361   1 MINLLHLKYVLEVEKTSSISKAAANMYMGQPNLSRAIKELEKILGITIFKRTsKGISPTPRGEEFLQYAKKI 72
Cdd:PRK13348   1 MLDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHLRQV 71
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
2-81 7.46e-03

DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 35.57  E-value: 7.46e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501383361   2 INLLHLkyvleVEKTSSISKAAANMymgqpNLS-----RAIKELEKILGITIFKRTSKGIS-----PTPRGEEFLQYAKK 71
Cdd:COG2005   24 IELLEA-----IDETGSISAAAKAM-----GMSykrawDLIDAMNNLLGEPLVERQTGGKGgggarLTPEGRRLLALYRR 93

                         90
                 ....*....|
gi 501383361  72 IISQVEEVTA 81
Cdd:COG2005   94 LEAEAQRALA 103
 
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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