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Conserved domains on  [gi|504341693|ref|WP_014528795|]
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LysR family transcriptional regulator [Sinorhizobium meliloti]

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];
8-299 4.18e-47

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 158.88  E-value: 4.18e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693   8 TFDQLKVFLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRdSTRRPCLTEAGRIVLSETRSVANGVNRLRA 87
Cdd:COG0583    2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFER-TGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  88 KAQGLLQGLEPSLSIALDAMLPASRVLDALKGFRSEFPTIPLQIRTEGLGAVTDLVLNGAASIGVCGPPDVDiDGLDRMG 167
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPD-PGLVARP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693 168 IGSVELIPVAAPNHPLalasdkrigagrehiqivltdrsertkgidlgvvATHTWRVADLSTKHMLLLEGLGWGNMPVPM 247
Cdd:COG0583  160 LGEERLVLVASPDHPL----------------------------------ARRAPLVNSLEALLAAVAAGLGIALLPRFL 205

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|..
gi 504341693 248 IREDLLSGRLVRIELPDIKGGnYRFFAIHRSDAPPGPAGSFLIQKFAKQVPD 299
Cdd:COG0583  206 AADELAAGRLVALPLPDPPPP-RPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
8-299 4.18e-47

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 158.88  E-value: 4.18e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693   8 TFDQLKVFLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRdSTRRPCLTEAGRIVLSETRSVANGVNRLRA 87
Cdd:COG0583    2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFER-TGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  88 KAQGLLQGLEPSLSIALDAMLPASRVLDALKGFRSEFPTIPLQIRTEGLGAVTDLVLNGAASIGVCGPPDVDiDGLDRMG 167
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPD-PGLVARP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693 168 IGSVELIPVAAPNHPLalasdkrigagrehiqivltdrsertkgidlgvvATHTWRVADLSTKHMLLLEGLGWGNMPVPM 247
Cdd:COG0583  160 LGEERLVLVASPDHPL----------------------------------ARRAPLVNSLEALLAAVAAGLGIALLPRFL 205

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|..
gi 504341693 248 IREDLLSGRLVRIELPDIKGGnYRFFAIHRSDAPPGPAGSFLIQKFAKQVPD 299
Cdd:COG0583  206 AADELAAGRLVALPLPDPPPP-RPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 16-266 3.87e-28

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 110.42  E-value: 3.87e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  16 LTVVD----VGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRDStRRPCLTEAGRIVLSETRSVANGVNRLRAKAQG 91
Cdd:PRK11074   7 LEVVDavarTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRH-RDVELTPAGEWFVKEARSVIKKMQETRRQCQQ 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  92 LLQGLEPSLSIALDAMLPASRVLDALKGFRSEFPTIPLQIRTEglgavtdlVLNGAAsigvcgppDVDIDGLDRMGIGSV 171
Cdd:PRK11074  86 VANGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQE--------VFNGVW--------DALADGRVDIAIGAT 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693 172 ELIPVA-----------------APNHPLALA----SDKRIgagREHIQIVLTDRS----ERtkgidlgvvatHTW---- 222
Cdd:PRK11074 150 RAIPVGgrfafrdmgmlswacvvSSDHPLASMdgplSDDEL---RPYPSLCLEDTSrtlpKR-----------ITWlldn 215

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 504341693 223 --R--VADLSTKHMLLLEGLGWGNMPVPMIREDLLSGRLVRIELPDIK 266
Cdd:PRK11074 216 qrRlvVPDWESAINCLSAGLCVGMVPTHFAKPLINSGKLVELTLENPF 263
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 99-285 2.01e-20

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: 87.34  E-value: 2.01e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693   99 SLSIALDAMLPASRVLDALKGFRSEFPTIPLQIRTEGLGAVTDLVLNGAASIGVCGPPdVDIDGLDRMGIGSVELIPVAA 178
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGP-PDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  179 PNHPLALASDKRIGAGREHIQIVLTDRSERTKGID-----LGVVATHTWRVADLSTKHMLLLEGLGWGNMPVPMIREDLL 253
Cdd:pfam03466  82 PDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDralraAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA 161

                         170       180       190
                  ....*....|....*....|....*....|..
gi 504341693  254 SGRLVRIELPDIKGGnYRFFAIHRSDAPPGPA 285
Cdd:pfam03466 162 DGRLVALPLPEPPLP-RELYLVWRKGRPLSPA 192
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 9-154 1.43e-16

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 78.43  E-value: 1.43e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693   9 FDQLKVFLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRdSTRRPCLTEAGRIVLSETRSVANGVNRLRAK 88
Cdd:NF040786   3 LKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVR-NTKEVSLTEDGKLLYEYAKEMLDLWEKLEEE 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 504341693  89 AQGLLQGLEPSLSIALDA-----MLPasrvlDALKGFRSEFPTIPLQIRTEGLGAVTDLVLNGAASIGVCG 154
Cdd:NF040786  82 FDRYGKESKGVLRIGASTipgqyLLP-----ELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTG 147
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 100-262 1.11e-15

The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. 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: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 73.84  E-value: 1.11e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693 100 LSIALDAMLPASRVLDALKGFRSEFPTIPLQIRTEGLGAVTDLVLNGAASIGVCGPPDVDIDGLDRMGIGSVELIPVAAP 179
Cdd:cd08431    2 LRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPPGGVKTRPLGEVEFVFAVAP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693 180 NHPLA-----LASDKRigagREHIQIVLTDRSERTKGIDLGVVATH-TWRVADLSTKHMLLLEGLGWGNMPVPMIREDLL 253
Cdd:cd08431   82 NHPLAkldgpLDASAI----KQYPAIVVADTSRNLPPRSSGLLEGQdRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELA 157


                 ....*....
gi 504341693 254 SGRLVRIEL 262
Cdd:cd08431  158 SGELVEKAL 166
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 12-78 4.96e-08

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 53.20  E-value: 4.96e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 504341693  12 LKVFLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRDSTRRPcLTEAGRIVLSETRSV 78
Cdd:NF041036   6 LKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLE-PTAAGEMVLEKARRI 71
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
8-299 4.18e-47

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 158.88  E-value: 4.18e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693   8 TFDQLKVFLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRdSTRRPCLTEAGRIVLSETRSVANGVNRLRA 87
Cdd:COG0583    2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFER-TGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  88 KAQGLLQGLEPSLSIALDAMLPASRVLDALKGFRSEFPTIPLQIRTEGLGAVTDLVLNGAASIGVCGPPDVDiDGLDRMG 167
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPD-PGLVARP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693 168 IGSVELIPVAAPNHPLalasdkrigagrehiqivltdrsertkgidlgvvATHTWRVADLSTKHMLLLEGLGWGNMPVPM 247
Cdd:COG0583  160 LGEERLVLVASPDHPL----------------------------------ARRAPLVNSLEALLAAVAAGLGIALLPRFL 205

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|..
gi 504341693 248 IREDLLSGRLVRIELPDIKGGnYRFFAIHRSDAPPGPAGSFLIQKFAKQVPD 299
Cdd:COG0583  206 AADELAAGRLVALPLPDPPPP-RPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 16-266 3.87e-28

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 110.42  E-value: 3.87e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  16 LTVVD----VGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRDStRRPCLTEAGRIVLSETRSVANGVNRLRAKAQG 91
Cdd:PRK11074   7 LEVVDavarTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRH-RDVELTPAGEWFVKEARSVIKKMQETRRQCQQ 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  92 LLQGLEPSLSIALDAMLPASRVLDALKGFRSEFPTIPLQIRTEglgavtdlVLNGAAsigvcgppDVDIDGLDRMGIGSV 171
Cdd:PRK11074  86 VANGWRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQE--------VFNGVW--------DALADGRVDIAIGAT 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693 172 ELIPVA-----------------APNHPLALA----SDKRIgagREHIQIVLTDRS----ERtkgidlgvvatHTW---- 222
Cdd:PRK11074 150 RAIPVGgrfafrdmgmlswacvvSSDHPLASMdgplSDDEL---RPYPSLCLEDTSrtlpKR-----------ITWlldn 215

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 504341693 223 --R--VADLSTKHMLLLEGLGWGNMPVPMIREDLLSGRLVRIELPDIK 266
Cdd:PRK11074 216 qrRlvVPDWESAINCLSAGLCVGMVPTHFAKPLINSGKLVELTLENPF 263
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
9-298 4.88e-26

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 104.89  E-value: 4.88e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693   9 FDQ--LKVFLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRdSTRRPCLTEAGRIVLSETRSVANGVNRLR 86
Cdd:PRK10094   2 FDPetLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFR-TTRSVTLTAAGEHLLSQARDWLSWLESMP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  87 AKAQGLLQGLEPSLSIALDAML-PASRVLDALKGFRSEFPTIPLQIRTEGLGAVTDLVLNGAAS--IGVCGPPDVDiDGL 163
Cdd:PRK10094  81 SELQQVNDGVERQVNIVINNLLyNPQAVAQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSlaIGVTGTEALA-NTF 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693 164 DRMGIGSVELIPVAAPNHPLALASDKRIGAG-REHIQIVLTDRSER-TKGIDLGVVATHTWRVADLSTKHMLLLEGLGWG 241
Cdd:PRK10094 160 SLDPLGSVQWRFVMAADHPLANVEEPLTEAQlRRFPAVNIEDSARTlTKRVAWRLPGQKEIIVPDMETKIAAHLAGVGIG 239

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 504341693 242 NMPVPMIREDLLSGRLVRIELPDIKGGNYRFFAIHRSDAppGPAGSFLIQKFAKQVP 298
Cdd:PRK10094 240 FLPKSLCQSMIDNQQLVSRVIPTMRPPSPLSLAWRKFGS--GKAVEDIVTLFTQRRP 294
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 99-285 2.01e-20

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: 87.34  E-value: 2.01e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693   99 SLSIALDAMLPASRVLDALKGFRSEFPTIPLQIRTEGLGAVTDLVLNGAASIGVCGPPdVDIDGLDRMGIGSVELIPVAA 178
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGP-PDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  179 PNHPLALASDKRIGAGREHIQIVLTDRSERTKGID-----LGVVATHTWRVADLSTKHMLLLEGLGWGNMPVPMIREDLL 253
Cdd:pfam03466  82 PDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDralraAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA 161

                         170       180       190
                  ....*....|....*....|....*....|..
gi 504341693  254 SGRLVRIELPDIKGGnYRFFAIHRSDAPPGPA 285
Cdd:pfam03466 162 DGRLVALPLPEPPLP-RELYLVWRKGRPLSPA 192
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
9-69 3.72e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 76.65  E-value: 3.72e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 504341693    9 FDQLKVFLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRdSTRRPCLTEAGR 69
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFER-TTRGVRLTEAGE 60
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 9-154 1.43e-16

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 78.43  E-value: 1.43e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693   9 FDQLKVFLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRdSTRRPCLTEAGRIVLSETRSVANGVNRLRAK 88
Cdd:NF040786   3 LKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVR-NTKEVSLTEDGKLLYEYAKEMLDLWEKLEEE 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 504341693  89 AQGLLQGLEPSLSIALDA-----MLPasrvlDALKGFRSEFPTIPLQIRTEGLGAVTDLVLNGAASIGVCG 154
Cdd:NF040786  82 FDRYGKESKGVLRIGASTipgqyLLP-----ELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTG 147
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 100-262 1.11e-15

The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. 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: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 73.84  E-value: 1.11e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693 100 LSIALDAMLPASRVLDALKGFRSEFPTIPLQIRTEGLGAVTDLVLNGAASIGVCGPPDVDIDGLDRMGIGSVELIPVAAP 179
Cdd:cd08431    2 LRIAIDTVLPLQPLYPLIAEFYQLNKATRIRLSEEVLGGTWDALASGRADLVIGATGELPPGGVKTRPLGEVEFVFAVAP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693 180 NHPLA-----LASDKRigagREHIQIVLTDRSERTKGIDLGVVATH-TWRVADLSTKHMLLLEGLGWGNMPVPMIREDLL 253
Cdd:cd08431   82 NHPLAkldgpLDASAI----KQYPAIVVADTSRNLPPRSSGLLEGQdRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELA 157


                 ....*....
gi 504341693 254 SGRLVRIEL 262
Cdd:cd08431  158 SGELVEKAL 166
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
10-260 2.74e-12

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 65.95  E-value: 2.74e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  10 DQLKVFLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRDstrRPC-LTEAGRIVLSETRSVAngvnRLRAK 88
Cdd:PRK03635   5 KQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT---QPCrPTEAGQRLLRHARQVR----LLEAE 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  89 AQGLLQGLEP---SLSIALDAMLPASRVLDALKGFRSEFPtIPLQIRTEGLGAVTDLVLNGAASIGVCGPPDVdIDGLDR 165
Cdd:PRK03635  78 LLGELPALDGtplTLSIAVNADSLATWFLPALAPVLARSG-VLLDLVVEDQDHTAELLRRGEVVGAVTTEPQP-VQGCRV 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693 166 MGIGSVELIPVAAPnhplALA----SDkriGAGREHIQ---IVLTDRS--------ERTKGIDLGVVATHTwrvadLSTK 230
Cdd:PRK03635 156 DPLGAMRYLAVASP----AFAaryfPD---GVTAEALAkapAVVFNRKddlqdrflRQAFGLPPGSVPCHY-----VPSS 223

                        250       260       270
                 ....*....|....*....|....*....|...
gi 504341693 231 HM---LLLEGLGWGNMPVPMIREDLLSGRLVRI 260
Cdd:PRK03635 224 EAfvrAALAGLGWGMIPELQIEPELASGELVDL 256
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 99-285 8.04e-11

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: 60.31  E-value: 8.04e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  99 SLSIALDAMLPASRVLDALKGFRSEFPTIPLQIRTEGLGAVTDLVLNGAASIGVCGPPDVDiDGLDRMGIGSVELIPVAA 178
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDD-PGLESEPLFEEPLVLVVP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693 179 PNHPLALASDKRIGAGREHIQIVLTDRSERTKGID-----LGVVATHTWRVADLSTKHMLLLEGLGWGNMPVPMIREdLL 253
Cdd:cd05466   80 PDHPLAKRKSVTLADLADEPLILFERGSGLRRLLDrafaeAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEE-LA 158

                        170       180       190
                 ....*....|....*....|....*....|....
gi 504341693 254 SGRLVRIEL--PDIKggnYRFFAIHRSDAPPGPA 285
Cdd:cd05466  159 DGGLVVLPLedPPLS---RTIGLVWRKGRYLSPA 189
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
10-106 1.47e-10

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 60.76  E-value: 1.47e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  10 DQLKVFLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRDSTRRPclTEAGRIVLSETRSV----ANGVNRL 85
Cdd:PRK13348   5 KQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRPCRP--TPAGQRLLRHLRQValleADLLSTL 82

                         90       100
                 ....*....|....*....|.
gi 504341693  86 RAKAQGLlqglePSLSIALDA 106
Cdd:PRK13348  83 PAERGSP-----PTLAIAVNA 98
rbcR CHL00180
LysR transcriptional regulator; Provisional
 8-184 1.55e-10

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 60.80  E-value: 1.55e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693   8 TFDQLKVFLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRdSTRRPCLTEAGRIVLsetrSVANGVNRL-- 85
Cdd:CHL00180   6 TLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDR-SKNKASLTEAGELLL----RYGNRILALce 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  86 -RAKAQGLLQGLEP-SLSIALDAMLPA---SRVLdALkgFRSEFPTIPLQIRTEGLGAVTDLVLNGAASIGVCG---PPD 157
Cdd:CHL00180  81 eTCRALEDLKNLQRgTLIIGASQTTGTylmPRLI-GL--FRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGgevPTE 157

                        170       180
                 ....*....|....*....|....*..
gi 504341693 158 VdIDGLDRMGIGSVELIPVAAPNHPLA 184
Cdd:CHL00180 158 L-KKILEITPYVEDELALIIPKSHPFA 183
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
11-70 2.29e-10

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 60.54  E-value: 2.29e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  11 QLKVFLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRdSTRRPCLTEAGRI 70
Cdd:PRK10632   6 RMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNR-STRSIGLTEAGRI 64
PRK09986 PRK09986
LysR family transcriptional regulator;
12-132 3.75e-10

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 59.74  E-value: 3.75e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  12 LKVFLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRDStRRPCLTEAGRIVLSETR----SVANGVNRLRA 87
Cdd:PRK09986  12 LRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHS-RSVVLTHAGKILMEESRrlldNAEQSLARVEQ 90

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 504341693  88 KAQGLLQGLEpsLSIALDAMLpaSRVLDALKGFRSEFPTIPLQIR 132
Cdd:PRK09986  91 IGRGEAGRIE--IGIVGTALW--GRLRPAMRHFLKENPNVEWLLR 131
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 8-184 4.19e-10

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 59.32  E-value: 4.19e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693   8 TFDQLKVFLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRdSTRRPCLTEAGRIVLSETRSV---ANGVNR 84
Cdd:PRK10837   4 TLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDR-VGKRLVVNEHGRLLYPRALALleqAVEIEQ 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  85 LRAKAQGLLQgLEPSLSIAlDAMLPAsrvldALKGFRSEFPTIPLQIRTEGLGAVTDLVLNGAASIGV----CGPPDVDI 160
Cdd:PRK10837  83 LFREDNGALR-IYASSTIG-NYILPA-----MIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLiegpCHSPELIS 155

                        170       180
                 ....*....|....*....|....*.
gi 504341693 161 DG--LDrmgigsvELIPVAAPNHPLA 184
Cdd:PRK10837 156 EPwlED-------ELVVFAAPDSPLA 174
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 15-260 1.54e-09

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 58.08  E-value: 1.54e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  15 FLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRdSTRRPCLTEAG-------RIVLSETRSVANGVNRLRA 87
Cdd:PRK14997  10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQR-TTRQFNVTEVGqtfyehcKAMLVEAQAAQDAIAALQV 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  88 KAQGLLQGLEPS--LSIALDAMLPAsrvldalkgFRSEFPTIPLQIRT---------EGLGAV----------TDLVLNG 146
Cdd:PRK14997  89 EPRGIVKLTCPVtlLHVHIGPMLAK---------FMARYPDVSLQLEAtnrrvdvvgEGVDVAirvrprpfedSDLVMRV 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693 147 AASIGVC--GPPDVdidgLDRMGIGSVELIPVAAPNhpLALASDKRI------GAGREHIQIVLTDRSERTKGIDLGVVA 218
Cdd:PRK14997 160 LADRGHRlfASPDL----IARMGIPSAPAELSHWPG--LSLASGKHIhrwelyGPQGARAEVHFTPRMITTDMLALREAA 233

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 504341693 219 thtwrvadlstkhmllLEGLGWGNMPVPMIREDLLSGRLVRI 260
Cdd:PRK14997 234 ----------------MAGVGLVQLPVLMVKEQLAAGELVAV 259
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 12-78 4.96e-08

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 53.20  E-value: 4.96e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 504341693  12 LKVFLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRDSTRRPcLTEAGRIVLSETRSV 78
Cdd:NF041036   6 LKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLE-PTAAGEMVLEKARRI 71
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
9-133 7.55e-08

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 52.70  E-value: 7.55e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693   9 FDQLKVFLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRdSTRRPCLTEAGRIVLSETRSVANGVNrlrak 88
Cdd:PRK10086  16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVR-SHRKVELTEEGKRVFWALKSSLDTLN----- 89

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 504341693  89 aQGLL--QGLEPS--------LSIALDAMLPasrvldALKGFRSEFPTIPLQIRT 133
Cdd:PRK10086  90 -QEILdiKNQELSgtltvysrPSIAQCWLVP------RLADFTRRYPSISLTILT 137
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 9-146 2.35e-07

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 51.22  E-value: 2.35e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693   9 FDQLKVFLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRdsTRR---PclTEAGRIVLSETRSVangvnrL 85
Cdd:PRK11233   3 FRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIR--TKRgvtP--TEAGKILYTHARAI------L 72

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504341693  86 RAKAQGLL------QGLEPSLSIALDAMLPASRV-LDALKGFRSEFPTIPLQIRtEGLGAV-TDLVLNG 146
Cdd:PRK11233  73 RQCEQAQLavhnvgQALSGQVSIGLAPGTAASSLtMPLLQAVRAEFPGIVLYLH-ENSGATlNEKLMNG 140
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
11-184 2.49e-07

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 51.17  E-value: 2.49e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  11 QLKVFLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRDStrRPC-LTEAGRIVLSetrsVANGVnrLRAKA 89
Cdd:PRK15421   6 HLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKS--QPLrFTPQGEILLQ----LANQV--LPQIS 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  90 QGLLQGLEPS---LSIALDAMLPASRVLDALKGFRSEFPTIPLQIRTeglgAVT------------DLVLNGaasigvcg 154
Cdd:PRK15421  78 QALQACNEPQqtrLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKS----GVTfdpqpalqqgelDLVMTS-------- 145

                        170       180       190
                 ....*....|....*....|....*....|...
gi 504341693 155 ppdvDI---DGLDRMGIGSVELIPVAAPNHPLA 184
Cdd:PRK15421 146 ----DIlprSGLHYSPMFDYEVRLVLAPDHPLA 174
PRK10341 PRK10341
transcriptional regulator TdcA;
7-125 2.63e-07

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 51.40  E-value: 2.63e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693   7 PTFDQLKVFLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRDSTrRPCLTEAGRIVLSETRSVANGVNRLR 86
Cdd:PRK10341   7 PKTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNT-GVTLTPAGQVLLSRSESITREMKNMV 85

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 504341693  87 AKAQGLLQGLEPSLSIALDAMLPASRVLDALKGFRSEFP 125
Cdd:PRK10341  86 NEINGMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFP 124
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 23-293 7.99e-07

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 49.46  E-value: 7.99e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  23 SFAGAARKLNRATSVVSYTIANLEAQLGFALFDRDStRRPCLTEAGRIVLSETR----SVANGVNRLRAKaqgllqGLEP 98
Cdd:PRK11139  22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRN-RSLLLTEEGQRYFLDIReifdQLAEATRKLRAR------SAKG 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  99 SLSIALDAMLPASRVLDALKGFRSEFPTIPLQIRteglgAVTDLVlnGAASIGVcgppDVDIdgldRMGIGS-----VE- 172
Cdd:PRK11139  95 ALTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLK-----AVDRLE--DFLRDDV----DVAI----RYGRGNwpglrVEk 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693 173 -----LIPVAAP-----NHPLALASDKrigagREHiqiVLTDRSERTKgidlgvvathtWR-------VADLSTKH---- 231
Cdd:PRK11139 160 lldeyLLPVCSPallngGKPLKTPEDL-----ARH---TLLHDDSRED-----------WRawfraagLDDLNVQQgpif 220

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 504341693 232 ----MLL---LEGLGWGNMPVPMIREDLLSGRLVR---IELPDIKGgnyrFFAIhrsdAPPGPAGSFLIQKF 293
Cdd:PRK11139 221 shssMALqaaIHGQGVALGNRVLAQPEIEAGRLVCpfdTVLPSPNA----FYLV----CPDSQAELPKVAAF 284
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 8-131 1.98e-06

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 48.45  E-value: 1.98e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693   8 TFDQLKVFLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRDSTR-RPclTEAGRIVLSETRSVANGVNRLR 86
Cdd:PRK11013   5 SLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRlHP--TVQGLRLFEEVQRSYYGLDRIV 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 504341693  87 AKAQGLLQGLEPSLSIALDAMLPASRVLDALKGFRSEFPTIPLQI 131
Cdd:PRK11013  83 SAAESLREFRQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNI 127
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 27-188 2.74e-06

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 48.06  E-value: 2.74e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  27 AARKLNRATSVVSYTIANLEAQLGFALFDRDSTRRPCLTEAGRIVLSETRSVANGVNRLRAKAQGLLQGLEPSLSIALDA 106
Cdd:PRK12682  22 AAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKGLTEPGKAVLDVIERILREVGNIKRIGDDFSNQDSGTLTIATTH 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693 107 -----MLPAsrvldALKGFRSEFPTIPLQIRTEGLGAVTDLVLNGAASIGVCGPPDVDIDGLDRMGIGSVELIPVAAPNH 181
Cdd:PRK12682 102 tqaryVLPR-----VVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATESLADDPDLATLPCYDWQHAVIVPPDH 176


                 ....*..
gi 504341693 182 PLALASD 188
Cdd:PRK12682 177 PLAQEER 183
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
27-152 8.78e-06

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 46.51  E-value: 8.78e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  27 AARKLNRATSVVSYTIANLEAQLGFALFDRDSTRRPCLTEAGRIVLSETRSVANGVNRLR-------AKAQGllqglepS 99
Cdd:PRK12684  22 AAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRGLTEPGRIILASVERILQEVENLKrvgkefaAQDQG-------N 94

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 504341693 100 LSIALDA-----MLPAsrvldALKGFRSEFPTIPLQIRTEGLGAVTDLVLNGAASIGV 152
Cdd:PRK12684  95 LTIATTHtqaryALPA-----AIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAI 147
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
36-182 9.20e-06

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 46.35  E-value: 9.20e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  36 SVVSYTIANLEAQLGFALFDRDStRRPCLTEAGRIVLSETRSVANGVNRLRAKAQGLLQGLEPSLSI-----ALDAMLPa 110
Cdd:PRK11716   6 STLSRQIQRLEEELGQPLFVRDN-RSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLfcsvtAAYSHLP- 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 504341693 111 srvlDALKGFRSEFPTIPLQIRTeglG----AVtDLVLNGAASIGVCGPPDVDIDGLDRMGIGSVELIpVAAPNHP 182
Cdd:PRK11716  84 ----PILDRFRAEHPLVEIKLTT---GdaadAV-EKVQSGEADLAIAAKPETLPASVAFSPIDEIPLV-LIAPALP 150
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 117-285 1.32e-05

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: 45.18  E-value: 1.32e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693 117 LKGFRSEFPTIPLQIRTEGLGAVTDLVLNGAASIGVCGPPDVDiDGLDRMGIGSVELIPVAAPNHPLA---------LAS 187
Cdd:cd08420   19 LARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDH-PDLIVEPFAEDELVLVVPPDHPLAgrkevtaeeLAA 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693 188 DKRI----GAG-REHIQIVLTDRSERTKGIDLGVVATHTWRVadlstKHmLLLEGLGWGNMPVPMIREDLLSGRL--VRI 260
Cdd:cd08420   98 EPWIlrepGSGtREVFERALAEAGLDGLDLNIVMELGSTEAI-----KE-AVEAGLGISILSRLAVRKELELGRLvaLPV 171

                        170       180
                 ....*....|....*....|....*
gi 504341693 261 ELPDIKggnYRFFAIHRSDAPPGPA 285
Cdd:cd08420  172 EGLRLT---RPFSLIYHKDKYLSPA 193
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 27-152 1.42e-05

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 45.80  E-value: 1.42e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  27 AARKLNRATSVVSYTIANLEAQLGFALFDRDSTRRPCLTEAGRIVLSETRSVANGVNRLRAKAQGLLQGLEPSLSIAlDA 106
Cdd:PRK12683  22 VANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTGLTEPGKELLQIVERMLLDAENLRRLAEQFADRDSGHLTVA-TT 100

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 504341693 107 MLPASRVL-DALKGFRSEFPTIPLQIRTEGLGAVTDLVLNGAASIGV 152
Cdd:PRK12683 101 HTQARYALpKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGI 147
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 12-184 2.13e-05

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 45.15  E-value: 2.13e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  12 LKVFLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRDStRRPCLTEAGRIVLSETRSV----ANGVNRLRA 87
Cdd:PRK09906   6 LRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDK-RKVALTAAGEVFLQDARAIleqaEKAKLRARK 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  88 KAQGLLQ---GLEPSLSIALdamLPasrvlDALKGFRSEFP--TIPLQ--IRTEGLGAvtdlVLNGAASIGVCGPPdVDI 160
Cdd:PRK09906  85 IVQEDRQltiGFVPSAEVNL---LP-----KVLPMFRLRHPdtLIELVslITTQQEEK----LRRGELDVGFMRHP-VYS 151

                        170       180
                 ....*....|....*....|....
gi 504341693 161 DGLDRMGIGSVELIPVAAPNHPLA 184
Cdd:PRK09906 152 DEIDYLELLDEPLVVVLPVDHPLA 175
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 110-291 2.20e-05

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: 44.44  E-value: 2.20e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693 110 ASRVL-DALKGFRSEFPTIPLQIRTEGLGAVTDLVLNGAASIGVCGPPDVDiDGLDRMGIGSVELIPVAAPNHPLA---- 184
Cdd:cd08440   11 AATLLpPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEAD-PDLEFEPLLRDPFVLVCPKDHPLArrrs 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693 185 -----LASDKRIGAGREHIQIVLTDRSERTKGIDLGVVathtWRVADLSTKHMLLLEGLGWGNMP---VPMIREDLLsgR 256
Cdd:cd08440   90 vtwaeLAGYPLIALGRGSGVRALIDRALAAAGLTLRPA----YEVSHMSTALGMVAAGLGVAVLPalaLPLADHPGL--V 163

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 504341693 257 LVRIELPDIkggNYRFFAIHRSDAPPGPAGSFLIQ 291
Cdd:cd08440  164 ARPLTEPVV---TRTVGLIRRRGRSLSPAAQAFLD 195
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 15-184 3.30e-05

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 44.56  E-value: 3.30e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  15 FLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRdSTRRPCLTEAGRIVLSETRsvangvnrlRAkaqglLQ 94
Cdd:PRK11242   9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDR-SGRTVRLTDAGEVYLRYAR---------RA-----LQ 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  95 GLEP--------------SLSIALDAMLPASRVLDALKGFRSEFPTIPLQIRTEGLGAVTDLVLNGAASIGV--CGPPDV 158
Cdd:PRK11242  74 DLEAgrraihdvadlsrgSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIafAPVHSP 153

                        170       180
                 ....*....|....*....|....*..
gi 504341693 159 DIDGLDRMgigsVE-LIPVAAPNHPLA 184
Cdd:PRK11242 154 EIEAQPLF----TEtLALVVGRHHPLA 176
PRK12680 PRK12680
LysR family transcriptional regulator;
8-152 5.84e-05

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 44.23  E-value: 5.84e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693   8 TFDQLKVFLTVVDVG-SFAGAARKLNRATSVVSYTIANLEAQLGFALFDRDSTRRPCLTEAGRIVLSETRSVANGVNRLR 86
Cdd:PRK12680   2 TLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLESVTPAGVEVIERARAVLSEANNIR 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504341693  87 AKAQGllQGLEPSLSIALDAMLPASRVL--DALKGFRSEFPTIPLQIRTEGLGAVTDLVLNGAASIGV 152
Cdd:PRK12680  82 TYAAN--QRRESQGQLTLTTTHTQARFVlpPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAI 147
PRK09801 PRK09801
LysR family transcriptional regulator;
7-94 1.58e-04

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 42.71  E-value: 1.58e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693   7 PTFDQLKVFLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRdSTRRPCLTEAGRI-------VLSETRSVA 79
Cdd:PRK09801   6 PLAKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNR-SARGVALTESGQRcyehaleILTQYQRLV 84

                         90
                 ....*....|....*
gi 504341693  80 NGVNRLRAKAQGLLQ 94
Cdd:PRK09801  85 DDVTQIKTRPEGMIR 99
PRK09791 PRK09791
LysR family transcriptional regulator;
9-135 1.61e-04

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 42.83  E-value: 1.61e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693   9 FDQLKVFLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRDStRRPCLTEAG-------RIVLSETRsVANG 81
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRS-KGVTLTDAGesfyqhaSLILEELR-AAQE 84

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 504341693  82 VNRLRakaQGLLQGlepSLSIALDAMLPASRVLDALKGFRSEFPTIPLQIrTEG 135
Cdd:PRK09791  85 DIRQR---QGQLAG---QINIGMGASIARSLMPAVISRFHQQHPQVKVRI-MEG 131
cbl PRK12679
HTH-type transcriptional regulator Cbl;
9-152 3.11e-04

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 41.72  E-value: 3.11e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693   9 FDQLKVF---------LTVVdvgsfagaARKLNRATSVVSYTIANLEAQLGFALFDRDSTRRPCLTEAGRIVLSETRSVA 79
Cdd:PRK12679   3 FQQLKIIreaarqdynLTEV--------ANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLGMTEPGKALLVIAERIL 74

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 504341693  80 NGVNRLRAKAQGLLQGLEPSLSIALDAMLPASRVLDALKGFRSEFPTIPLQIRTEGLGAVTDLVLNGAASIGV 152
Cdd:PRK12679  75 NEASNVRRLADLFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGI 147
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 98-184 4.32e-04

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: 40.62  E-value: 4.32e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  98 PSLSIALdamLPAsrvldALKGFRSEFPTIPLQIRTEGLGAVTDLVLNGAASIGVCGPPdVDIDGLDRMGIGSVELIPVA 177
Cdd:cd08415    8 PALALSL---LPR-----AIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLP-LDHPGLESEPLASGRAVCVL 78


                 ....*..
gi 504341693 178 APNHPLA 184
Cdd:cd08415   79 PPGHPLA 85
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 10-68 4.42e-04

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 41.17  E-value: 4.42e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 504341693  10 DQLKVFLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFDRdSTRRPCLTEAG 68
Cdd:PRK15092  14 DLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFAR-HGRNKLLTEHG 71
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 99-285 6.34e-04

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: 39.89  E-value: 6.34e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693  99 SLSIALDAMLPASRVLDALKGFRSEFPTIPLQIRTEGLGAVTDLVLNGAASIGVCGPPDVDIDGLDRMGIGSVELIPVAA 178
Cdd:cd08436    1 RLAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRPPGLASRELAREPLVAVVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693 179 PNHPLALASDKRIGAGREHIQI---------VLTDRSERtkgiDLGVVATHTWRVADLSTKHMLLLEGLGWGNMPVPMIR 249
Cdd:cd08436   81 PDHPLAGRRRVALADLADEPFVdfppgtgarRQVDRAFA----AAGVRRRVAFEVSDVDLLLDLVARGLGVALLPASVAA 156

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 504341693 250 EDllsGRLVRIELPDikGGNYRFFAIHRSDaPPGPA 285
Cdd:cd08436  157 RL---PGLAALPLEP--APRRRLYLAWSAP-PPSPA 186
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
12-68 3.89e-03

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 38.07  E-value: 3.89e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 504341693  12 LKVFLTVVDVGSFAGAARKLNRATSVVSYTIANLEAQLGFALFD--RDSTRrpcLTEAG 68
Cdd:PRK03601   6 LKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTrhRNNIR---LTAAG 61
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 116-184 7.11e-03

The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176129 [Multi-domain]  Cd Length: 197  Bit Score: 37.15  E-value: 7.11e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504341693 116 ALKGFRSEFPTIPLQIRTEGLGAVTDLVLNGAASIGVCGPPdVDIDGLDRMGIGSVELIPVAAPNHPLA 184
Cdd:cd08438   18 LLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLP-VDEEEFDSQPLCNEPLVAVLPRGHPLA 85
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 117-184 7.73e-03

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


Pssm-ID: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 36.75  E-value: 7.73e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504341693 117 LKGFRSEFPTIPLQIRTEGLGAVTDLVLNGAASIGVCGPPDVDiDGLDRMGIGSVELIPVAAPNHPLA 184
Cdd:cd08434   19 IRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDE-PDIEWIPLFTEELVLVVPKDHPLA 85
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 158-278 7.93e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 36.65  E-value: 7.93e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504341693 158 VDI--DGLD---RMG-----------IGSVELIPVAAP---------NHPLALASDKRIG--AGREHIQIVLTDRSERTK 210
Cdd:cd08422   41 VDLveEGFDlaiRIGelpdsslvarrLGPVRRVLVASPaylarhgtpQTPEDLARHRCLGyrLPGRPLRWRFRRGGGEVE 120

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504341693 211 gidlgVVATHTWRVADLSTKHMLLLEGLGWGNMPVPMIREDLLSGRLVRIeLPDIKGGNYRFFAIHRS 278
Cdd:cd08422  121 -----VRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLASGRLVRV-LPDWRPPPLPIYAVYPS 182
 
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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