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Conserved domains on  [gi|2772088495|ref|WP_367278687|]
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LysR family transcriptional regulator [uncultured Sulfitobacter sp.]

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];
20-295 8.97e-40

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 140.00  E-value: 8.97e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  20 TLDQIKTFFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREGMRLMAYAEQMLFVQEEIRRR 99
Cdd:COG0583     2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 100 VSN-TAEMEGLFRIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAFLMGPVSDFTIGNVALP 178
Cdd:COG0583    82 LRAlRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPLG 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 179 QFPLtwykaagvgevdlgrVPVISfsantrpyRELMAALRRRLGPGVRMfssaslsaSLRMIAAGVAVGPYPRALAGPLI 258
Cdd:COG0583   162 EERL---------------VLVAS--------PDHPLARRAPLVNSLEA--------LLAAVAAGLGIALLPRFLAADEL 210

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 2772088495 259 AAGQIEAFDPGLTPNPLEFTASYLAEPY---------DALSEQAAQ 295
Cdd:COG0583   211 AAGRLVALPLPDPPPPRPLYLVWRRRRHlspavraflDFLREALAE 256
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
20-295 8.97e-40

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 140.00  E-value: 8.97e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  20 TLDQIKTFFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREGMRLMAYAEQMLFVQEEIRRR 99
Cdd:COG0583     2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 100 VSN-TAEMEGLFRIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAFLMGPVSDFTIGNVALP 178
Cdd:COG0583    82 LRAlRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPLG 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 179 QFPLtwykaagvgevdlgrVPVISfsantrpyRELMAALRRRLGPGVRMfssaslsaSLRMIAAGVAVGPYPRALAGPLI 258
Cdd:COG0583   162 EERL---------------VLVAS--------PDHPLARRAPLVNSLEA--------LLAAVAAGLGIALLPRFLAADEL 210

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 2772088495 259 AAGQIEAFDPGLTPNPLEFTASYLAEPY---------DALSEQAAQ 295
Cdd:COG0583   211 AAGRLVALPLPDPPPPRPLYLVWRRRRHlspavraflDFLREALAE 256
rbcR CHL00180
LysR transcriptional regulator; Provisional
 20-169 1.73e-23

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 97.78  E-value: 1.73e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  20 TLDQIKTFFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREGMRLMAYAEQMLFVQEEIRRR 99
Cdd:CHL00180    6 TLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRA 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2772088495 100 VSNTAEME-GLFRIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAFLMGPVSD 169
Cdd:CHL00180   86 LEDLKNLQrGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGEVPT 156
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
21-79 7.45e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 73.19  E-value: 7.45e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2772088495  21 LDQIKTFFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREG 79
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 111-261 2.58e-13

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: 67.24  E-value: 2.58e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 111 RIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAFLMGPVSD-----FTIGN----VALP-QF 180
Cdd:cd05466     3 RIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDpglesEPLFEeplvLVVPpDH 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 181 PLtwykaAGVGEV---DLGRVPVISFSANTRPYRELMAALRRRLGPGVRMFSSASLSASLRMIAAGVAVGPYPRALAGPL 257
Cdd:cd05466    83 PL-----AKRKSVtlaDLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEEL 157


                  ....
gi 2772088495 258 IAAG 261
Cdd:cd05466   158 ADGG 161
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 22-271 2.60e-10

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 59.93  E-value: 2.60e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  22 DQIKTFFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGdKALTLTREGMRLMAYAEQMLFVQEEIRRRVS 101
Cdd:TIGR03298   4 RQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVRT-QPCRATEAGQRLLRHARQVRLLEAELLAELP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 102 NTAE-MEGLFRIGA-SETVAQSWLPEFLRVfsAAYPRIDVDLTV---DISCD-LREGLVgrqldvaflMGPVSdfTIGN- 174
Cdd:TIGR03298  83 GLAPgAPTRLTIAVnADSLATWFLPALAPV--LAREGVLLDLVVedqDHTAElLRSGEV---------LGAVT--TEAKp 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 175 ----------------VALPQFPLTWYkAAGVGEVDLGRVPVISFSantrPYRELMAALRRRLG-----------PGVRM 227
Cdd:TIGR03298 150 vpgcrvvplgamrylaVASPAFAARYF-PDGVTAAALARAPVIVFN----RKDDLQDRFLRRLFglpvspprhyvPSSEG 224

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 2772088495 228 FssaslsasLRMIAAGVAVGPYPRALAGPLIAAGQIEAFDPGLT 271
Cdd:TIGR03298 225 F--------VDAARAGLGWGMVPELQAEPHLAAGRLVELAPGRA 260
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
20-295 8.97e-40

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 140.00  E-value: 8.97e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  20 TLDQIKTFFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREGMRLMAYAEQMLFVQEEIRRR 99
Cdd:COG0583     2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 100 VSN-TAEMEGLFRIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAFLMGPVSDFTIGNVALP 178
Cdd:COG0583    82 LRAlRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPLG 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 179 QFPLtwykaagvgevdlgrVPVISfsantrpyRELMAALRRRLGPGVRMfssaslsaSLRMIAAGVAVGPYPRALAGPLI 258
Cdd:COG0583   162 EERL---------------VLVAS--------PDHPLARRAPLVNSLEA--------LLAAVAAGLGIALLPRFLAADEL 210

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 2772088495 259 AAGQIEAFDPGLTPNPLEFTASYLAEPY---------DALSEQAAQ 295
Cdd:COG0583   211 AAGRLVALPLPDPPPPRPLYLVWRRRRHlspavraflDFLREALAE 256
rbcR CHL00180
LysR transcriptional regulator; Provisional
 20-169 1.73e-23

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 97.78  E-value: 1.73e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  20 TLDQIKTFFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREGMRLMAYAEQMLFVQEEIRRR 99
Cdd:CHL00180    6 TLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRA 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2772088495 100 VSNTAEME-GLFRIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAFLMGPVSD 169
Cdd:CHL00180   86 LEDLKNLQrGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGEVPT 156
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
21-79 7.45e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 73.19  E-value: 7.45e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2772088495  21 LDQIKTFFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREG 79
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 107-265 1.23e-16

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: 76.94  E-value: 1.23e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 107 EGLFRIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAFLMGPVSDFTIGNVALPQFPLTW-- 184
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLva 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 185 ---YKAAGVGEV---DLGRVPVISFSANTRPYRELMAALRRRLGPGVRMFSSASLSASLRMIAAGVAVGPYPRALAGPLI 258
Cdd:pfam03466  81 ppdHPLARGEPVsleDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160


                  ....*..
gi 2772088495 259 AAGQIEA 265
Cdd:pfam03466 161 ADGRLVA 167
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 21-214 3.21e-16

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 77.38  E-value: 3.21e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  21 LDQIKTFFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREGMRLMAYAEQMLFVQEE--IRR 98
Cdd:PRK15092   13 LDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEacSSL 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  99 RVSNtaeMEGLFRIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAFLMGPVSDFTigNVALP 178
Cdd:PRK15092   93 MYSN---LQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTTHRPSSFP--ALNLR 167

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2772088495 179 QFPLTWYKAAGVgEVDLGR-VPVISFSaNTRPYRELM 214
Cdd:PRK15092  168 TSPTLWYCAAEY-VLQKGEpIPLVLLD-EPSPFRDMA 202
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
26-161 4.16e-16

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 77.35  E-value: 4.16e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  26 TFFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREGMRLMAYAEQML-FVQEEIRRRvsNTA 104
Cdd:PRK10086   21 TFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLdTLNQEILDI--KNQ 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2772088495 105 EMEGLFRIGASETVAQSWLPEFLRVFSAAYPRIDVD-LTVDISCDLReglvGRQLDVA 161
Cdd:PRK10086   99 ELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTiLTGNENVNFQ----RAGIDLA 152
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 18-166 1.91e-15

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 75.11  E-value: 1.91e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  18 HVTLDQIKTFFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREGM----RLMAYAEQMLFVQ 93
Cdd:PRK10837    2 HITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRllypRALALLEQAVEIE 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2772088495  94 EEIRrrvsntaEMEGLFRIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAFLMGP 166
Cdd:PRK10837   82 QLFR-------EDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGP 147
PRK09791 PRK09791
LysR family transcriptional regulator;
15-152 1.27e-14

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 72.87  E-value: 1.27e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  15 MGCHVTLDQIKTFFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREGMRLMAYA----EQML 90
Cdd:PRK09791    1 MAFQVKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHAslilEELR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2772088495  91 FVQEEIRRRVsntAEMEGLFRIGASETVAQSWLPEFLRVFSAAYPRIDVDLT----VDISCDLREG 152
Cdd:PRK09791   81 AAQEDIRQRQ---GQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMegqlVSMINELRQG 143
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 21-167 1.65e-13

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 69.60  E-value: 1.65e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  21 LDQIKTFFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREGMRLMAYAEQMLFVQEEIRRRV 100
Cdd:PRK11242    3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAI 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2772088495 101 SNTAEME-GLFRIGASETVAQSWLPEFLRVFSAAYPRIDVDLTvDISCD-LREGLVGRQLDVAFLMGPV 167
Cdd:PRK11242   83 HDVADLSrGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIR-EMSQErIEALLADDELDVGIAFAPV 150
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 111-261 2.58e-13

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: 67.24  E-value: 2.58e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 111 RIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAFLMGPVSD-----FTIGN----VALP-QF 180
Cdd:cd05466     3 RIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDpglesEPLFEeplvLVVPpDH 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 181 PLtwykaAGVGEV---DLGRVPVISFSANTRPYRELMAALRRRLGPGVRMFSSASLSASLRMIAAGVAVGPYPRALAGPL 257
Cdd:cd05466    83 PL-----AKRKSVtlaDLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEEL 157


                  ....
gi 2772088495 258 IAAG 261
Cdd:cd05466   158 ADGG 161
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 36-166 1.02e-12

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 67.18  E-value: 1.02e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  36 FRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREGMRlmaYAEQM--LFVQ-----EEIRRRVSNTAemeg 108
Cdd:PRK11139   23 FTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQR---YFLDIreIFDQlaeatRKLRARSAKGA---- 95

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2772088495 109 lFRIGASETVAQSWLPEFLRVFSAAYPRIDVDLTvdiSCDLREGLVGRQLDVAFLMGP 166
Cdd:PRK11139   96 -LTVSLLPSFAIQWLVPRLSSFNEAHPDIDVRLK---AVDRLEDFLRDDVDVAIRYGR 149
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
22-270 1.42e-12

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 66.72  E-value: 1.42e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  22 DQIKTFFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGdKALTLTREGMRLMAYAEQMLFVQEEIRRRVS 101
Cdd:PRK03635    5 KQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQRLLRHARQVRLLEAELLGELP 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 102 NTAEMEGLFRIGaseTVAQS---WLPEFLRVFsAAYPRIDVDLTVDiscD-------LREGLVgrqldvaflMGPVSD-- 169
Cdd:PRK03635   84 ALDGTPLTLSIA---VNADSlatWFLPALAPV-LARSGVLLDLVVE---DqdhtaelLRRGEV---------VGAVTTep 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 170 --------FTIGN-----VALPQFPLTWYkAAGVGEVDLGRVPVISFSAN--------TRPYRELMAALRRRLGPGVRMF 228
Cdd:PRK03635  148 qpvqgcrvDPLGAmrylaVASPAFAARYF-PDGVTAEALAKAPAVVFNRKddlqdrflRQAFGLPPGSVPCHYVPSSEAF 226

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 2772088495 229 ssaslsasLRMIAAGVAVGPYPRALAGPLIAAGQIEAFDPGL 270
Cdd:PRK03635  227 --------VRAALAGLGWGMIPELQIEPELASGELVDLTPGR 260
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
20-269 4.67e-12

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 65.38  E-value: 4.67e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  20 TLD--QIKTFFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGdKALTLTREGMRLMAYAEQMLFVQEEIR 97
Cdd:PRK13348    1 MLDykQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHLRQVALLEADLL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  98 RRvsNTAEMEGLFRIGA---SETVAqSWLPEFLRVFsAAYPRIDVDLTVDiscD-------LREGLV------GRQLDVA 161
Cdd:PRK13348   80 ST--LPAERGSPPTLAIavnADSLA-TWFLPALAAV-LAGERILLELIVD---DqdhtfalLERGEVvgcvstQPKPMRG 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 162 FLMGPVSDFTIGNVALPQFPLTWYkAAGVGEVDLGRVPVISFSANTRpyreLMAA-LRRRLGPGVRMFSS---ASLSASL 237
Cdd:PRK13348  153 CLAEPLGTMRYRCVASPAFAARYF-AQGLTRHSALKAPAVAFNRKDT----LQDSfLEQLFGLPVGAYPRhyvPSTHAHL 227

                         250       260       270
                  ....*....|....*....|....*....|..
gi 2772088495 238 RMIAAGVAVGPYPRALAGPLIAAGQIEAFDPG 269
Cdd:PRK13348  228 AAIRHGLGYGMVPELLIGPLLAAGRLVDLAPG 259
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
24-159 6.65e-12

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 64.65  E-value: 6.65e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  24 IKTFFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREGMRLMAYAEQMLFVQEEIRRRVSNT 103
Cdd:PRK03601    6 LKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKKEVAHT 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 104 AEmEGLFRIGASETVAQSWLPEFLRVFSAAYPridvDLTVDISCDLREGLVG----RQLD 159
Cdd:PRK03601   86 SQ-HNELSIGASASLWECMLTPWLGRLYQNQE----ALQFEARIAQRQSLVKqlheRQLD 140
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
44-142 7.55e-11

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 61.37  E-value: 7.55e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  44 NLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREGMRLMAYAEQMLFVQEEIRRRVS-NTAEMEGLFRIGASETVAQSW 122
Cdd:PRK11716    2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDqQGPSLSGELSLFCSVTAAYSH 81

                          90       100
                  ....*....|....*....|
gi 2772088495 123 LPEFLRVFSAAYPRIDVDLT 142
Cdd:PRK11716   82 LPPILDRFRAEHPLVEIKLT 101
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
21-182 1.44e-10

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 60.93  E-value: 1.44e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  21 LDQIKTFFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREGMRLMAYAEQMLFVQEEIRRRV 100
Cdd:PRK10632    4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 101 ---SNTAemEGLFRIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCdlrEGLVGRQLDVAFLMGPVSDFTIGNVAL 177
Cdd:PRK10632   84 yafNNTP--IGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPA---PDLIADGLDVVIRVGALQDSSLFSRRL 158


                  ....*
gi 2772088495 178 PQFPL 182
Cdd:PRK10632  159 GAMPM 163
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 39-141 1.48e-10

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 60.83  E-value: 1.48e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  39 AAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALT-LTREGMRLMAYAEQMLFVQEEIRRRVSNTAEM-EGLFRIGASE 116
Cdd:PRK12683   22 VANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLLDAENLRRLAEQFADRdSGHLTVATTH 101

                          90       100
                  ....*....|....*....|....*
gi 2772088495 117 TVAQSWLPEFLRVFSAAYPRIDVDL 141
Cdd:PRK12683  102 TQARYALPKVVRQFKEVFPKVHLAL 126
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
39-137 1.70e-10

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 60.76  E-value: 1.70e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  39 AAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALT-LTREGMRLMAYAEQMLFVQEEIrRRVSN--TAEMEGLFRIGAS 115
Cdd:PRK12684   22 AAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENL-KRVGKefAAQDQGNLTIATT 100

                          90       100
                  ....*....|....*....|..
gi 2772088495 116 ETVAQSWLPEFLRVFSAAYPRI 137
Cdd:PRK12684  101 HTQARYALPAAIKEFKKRYPKV 122
PRK09986 PRK09986
LysR family transcriptional regulator;
19-162 2.09e-10

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 60.51  E-value: 2.09e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  19 VTLDQIKTFFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREGMRLMAYAEQMLFVQEEIRR 98
Cdd:PRK09986    7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2772088495  99 RVSNTAEME-GLFRIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAF 162
Cdd:PRK09986   87 RVEQIGRGEaGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGI 151
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 22-271 2.60e-10

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 59.93  E-value: 2.60e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  22 DQIKTFFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGdKALTLTREGMRLMAYAEQMLFVQEEIRRRVS 101
Cdd:TIGR03298   4 RQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVRT-QPCRATEAGQRLLRHARQVRLLEAELLAELP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 102 NTAE-MEGLFRIGA-SETVAQSWLPEFLRVfsAAYPRIDVDLTV---DISCD-LREGLVgrqldvaflMGPVSdfTIGN- 174
Cdd:TIGR03298  83 GLAPgAPTRLTIAVnADSLATWFLPALAPV--LAREGVLLDLVVedqDHTAElLRSGEV---------LGAVT--TEAKp 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 175 ----------------VALPQFPLTWYkAAGVGEVDLGRVPVISFSantrPYRELMAALRRRLG-----------PGVRM 227
Cdd:TIGR03298 150 vpgcrvvplgamrylaVASPAFAARYF-PDGVTAAALARAPVIVFN----RKDDLQDRFLRRLFglpvspprhyvPSSEG 224

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 2772088495 228 FssaslsasLRMIAAGVAVGPYPRALAGPLIAAGQIEAFDPGLT 271
Cdd:TIGR03298 225 F--------VDAARAGLGWGMVPELQAEPHLAAGRLVELAPGRA 260
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
21-90 4.00e-10

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 59.82  E-value: 4.00e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2772088495  21 LDQ--IKTFFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREGMRLMAYAEQML 90
Cdd:PRK10094    2 FDPetLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWL 73
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 19-159 5.21e-10

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 59.24  E-value: 5.21e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  19 VTLDQIKTFFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREGMRLMayaeqmlfvqEEIRR 98
Cdd:PRK11013    4 VSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLF----------EEVQR 73

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2772088495  99 ------RVSNTAEMEGLFR-----IGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLD 159
Cdd:PRK11013   74 syygldRIVSAAESLREFRqgqlsIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESPLLEEWLSAQRHD 145
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
17-152 1.41e-09

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 58.14  E-value: 1.41e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  17 CHVTLDQIKT-----FFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREGMRLMAYAEQMLF 91
Cdd:PRK10082    4 CGAGLHNIETkwlydFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQ 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2772088495  92 VQEeirrrvSNTAEMEG-------LFRIGASETVAQSWLPEFLR----VFSAAYPRIDVDLTVDIscdLREG 152
Cdd:PRK10082   84 QLE------SNLAELRGgsdyaqrKIKIAAAHSLSLGLLPSIISqmppLFTWAIEAIDVDEAVDK---LREG 146
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 21-167 1.65e-09

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 57.86  E-value: 1.65e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  21 LDQIKTFFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREGMRLMAYAEQMLFVQEEIRRRV 100
Cdd:PRK09906    3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRA 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2772088495 101 SNTAEMEGLFRIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAFLMGPV 167
Cdd:PRK09906   83 RKIVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPV 149
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 39-141 2.46e-09

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 57.31  E-value: 2.46e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  39 AAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALT-LTREGMRLMAYAEQMLFVQEEIrRRVSN--TAEMEGLFRIGAS 115
Cdd:PRK12682   22 AAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNI-KRIGDdfSNQDSGTLTIATT 100

                          90       100
                  ....*....|....*....|....*.
gi 2772088495 116 ETVAQSWLPEFLRVFSAAYPRIDVDL 141
Cdd:PRK12682  101 HTQARYVLPRVVAAFRKRYPKVNLSL 126
PRK10341 PRK10341
transcriptional regulator TdcA;
27-141 7.57e-09

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 56.02  E-value: 7.57e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  27 FFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREGMRLMAYAEQmlfVQEEIRRRVSntaEM 106
Cdd:PRK10341   15 FQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSES---ITREMKNMVN---EI 88

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2772088495 107 EGL-------FRIGASETVAQSWLPEFLRVFSAAYPRIDVDL 141
Cdd:PRK10341   89 NGMsseavvdVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSM 130
cysB PRK12681
HTH-type transcriptional regulator CysB;
39-137 8.30e-09

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 55.67  E-value: 8.30e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  39 AAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALT-LTREGMRLMAYAEQMLFVQEEIrRRVSN--TAEMEGLFRIGAS 115
Cdd:PRK12681   22 TAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSKVESI-KSVAGehTWPDKGSLYIATT 100

                          90       100
                  ....*....|....*....|..
gi 2772088495 116 ETVAQSWLPEFLRVFSAAYPRI 137
Cdd:PRK12681  101 HTQARYALPPVIKGFIERYPRV 122
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 36-141 1.02e-08

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 55.42  E-value: 1.02e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  36 FRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREGMRLMAYAEQMLFVQEEIRRRVSN-TAEMEGLFRIGA 114
Cdd:PRK11151   18 FRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEMASQqGETMSGPLHIGL 97

                          90       100
                  ....*....|....*....|....*..
gi 2772088495 115 SETVAQSWLPEFLRVFSAAYPRIDVDL 141
Cdd:PRK11151   98 IPTVGPYLLPHIIPMLHQTFPKLEMYL 124
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 110-220 1.22e-08

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


Pssm-ID: 176106 [Multi-domain]  Cd Length: 197  Bit Score: 54.05  E-value: 1.22e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 110 FRIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAFLMGPVSDFTIGN---------VALP-Q 179
Cdd:cd08414     2 LRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASrpllreplvVALPaD 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2772088495 180 FPLtwykaAGVGEV---DLGRVPVISFSANTRP--YRELMAALRRR 220
Cdd:cd08414    82 HPL-----AARESVslaDLADEPFVLFPREPGPglYDQILALCRRA 122
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 111-169 1.30e-08

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: 54.03  E-value: 1.30e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2772088495 111 RIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAFLMGPVSD 169
Cdd:cd08420     3 RIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDH 61
cbl PRK12679
HTH-type transcriptional regulator Cbl;
40-187 1.91e-08

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 54.82  E-value: 1.91e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  40 AGQLNLSQPAVSNRVATLEDTLRVSLF-ERGDKALTLTREGMRLMAYAEQMLFVQEEIRRRVSN-TAEMEGLFRIGASET 117
Cdd:PRK12679   23 ANMLFTSQSGVSRHIRELEDELGIEIFiRRGKRLLGMTEPGKALLVIAERILNEASNVRRLADLfTNDTSGVLTIATTHT 102

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2772088495 118 VAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVaflmGPVSDFTIGNVALPQFP-LTWYKA 187
Cdd:PRK12679  103 QARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADI----GIASERLSNDPQLVAFPwFRWHHS 169
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 21-165 2.59e-08

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 54.30  E-value: 2.59e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  21 LDQIKTFFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREGMRLMAYAEQMLFVQEEIRRRV 100
Cdd:PRK11233    3 FRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAV 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2772088495 101 SNTAE-MEGLFRIG-ASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAFLMG 165
Cdd:PRK11233   83 HNVGQaLSGQVSIGlAPGTAASSLTMPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYE 149
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
19-182 5.34e-08

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 53.48  E-value: 5.34e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  19 VTLDQIKTFFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREGMRLMAYAEQMLfvqEEIRR 98
Cdd:PRK15421    2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVL---PQISQ 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  99 RVSNTAE-MEGLFRIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAFL----------MGPV 167
Cdd:PRK15421   79 ALQACNEpQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTsdilprsglhYSPM 158

                         170
                  ....*....|....*
gi 2772088495 168 SDFTIGNVALPQFPL 182
Cdd:PRK15421  159 FDYEVRLVLAPDHPL 173
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 21-166 1.17e-07

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 52.30  E-value: 1.17e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  21 LDQIKTFFWVAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREGMRLMAYAEQMLFVQEEIRRRV 100
Cdd:PRK14997    4 LNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAI 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2772088495 101 SN-TAEMEGLFRIGASETVAQSWLPEFLRVFSAAYPRIDVDLTvdiSCDLREGLVGRQLDVAFLMGP 166
Cdd:PRK14997   84 AAlQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLE---ATNRRVDVVGEGVDVAIRVRP 147
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 111-274 1.47e-07

The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold; This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. 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: 176130  Cd Length: 185  Bit Score: 50.79  E-value: 1.47e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 111 RIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAFLMGPVSDFTigNVALPQFPLTWYKAAGV 190
Cdd:cd08439     3 RIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALITHPPPGAS--ATILRRSPTVWYCAAGY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 191 GEVDLGRVPVIsFSANTRPYRELMAALRRRLGPGVRMFSSASLSASLRMIA-AGVAVGPYPRALAGPLIaagQIEAFDPG 269
Cdd:cd08439    81 ILAPGEPLPLA-LLDEPTLDRRAALAALDAAGIPWRIAYAASSLSGLRAAVrAGLGITARTQEMVPPDL---RILGESEG 156


                  ....*
gi 2772088495 270 LTPNP 274
Cdd:cd08439   157 LPPLP 161
PRK12680 PRK12680
LysR family transcriptional regulator;
39-303 1.87e-07

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 51.93  E-value: 1.87e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  39 AAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKAL-TLTREGMRLMAYAEQMLFVQEEIRRRVSNT-AEMEGLFRIGASE 116
Cdd:PRK12680   22 AAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNIRTYAANQrRESQGQLTLTTTH 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 117 TVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAFLMGPVSDFTIGnVALPQFplTWYKAAGVGE---- 192
Cdd:PRK12680  102 TQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAG-IAVPLY--RWRRLVVVPRghal 178

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 193 ---------VDLGRVPVISFSANTRPYRELMAALRRR-LGPGVRMfSSASLSASLRMIAAGVAVGpypralagpLIAAGQ 262
Cdd:PRK12680  179 dtprrapdmAALAEHPLISYESSTRPGSSLQRAFAQLgLEPSIAL-TALDADLIKTYVRAGLGVG---------LLAEMA 248

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 2772088495 263 IEAFDPGL----TPNPLEFTASYLAEPYDalseqaaQMARDVALE 303
Cdd:PRK12680  249 VNANDEDLrawpAPAPIAECIAWAVLPRD-------RVLRDYALE 286
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 109-169 3.15e-07

The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold; YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. 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: 176133  Cd Length: 193  Bit Score: 49.91  E-value: 3.15e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2772088495 109 LFRIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAFLMGPVSD 169
Cdd:cd08442     1 PLRLGSMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEH 61
PRK09801 PRK09801
LysR family transcriptional regulator;
34-161 1.51e-06

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 48.88  E-value: 1.51e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495  34 GGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREGMRLMAYAEQMLfvqEEIRRRVSNTAEM----EGL 109
Cdd:PRK09801   21 GSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEIL---TQYQRLVDDVTQIktrpEGM 97

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2772088495 110 FRIGASETVAQSWLPEFLRVFSAAYPRIDVDLTvdiscdlregLVGRQLDVA 161
Cdd:PRK09801   98 IRIGCSFGFGRSHIAPAITELMRNYPELQVHFE----------LFDRQIDLV 139
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 111-220 1.77e-06

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: 47.56  E-value: 1.77e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 111 RIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAFLMGPV--SDFTI-------GNVALPQ-F 180
Cdd:cd08415     3 RIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLdhPGLESeplasgrAVCVLPPgH 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2772088495 181 PLtwykaAGVGEV---DLGRVPVISFSANTRPYRELMAALRRR 220
Cdd:cd08415    83 PL-----ARKDVVtpaDLAGEPLISLGRGDPLRQRVDAAFERA 120
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 111-165 2.43e-06

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


Pssm-ID: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 47.15  E-value: 2.43e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2772088495 111 RIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAFLMG 165
Cdd:cd08412     3 RIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYD 57
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 110-257 1.30e-05

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 45.28  E-value: 1.30e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 110 FRIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAFL------MGPVSDFTIGNVAL-----P 178
Cdd:cd08436     2 LAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVglperrPPGLASRELAREPLvavvaP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 179 QFPLtwykaAGVGEV---DLGRVPVISFSANTRPYRELMAALRRR-LGPGVRmFSSASLSASLRMIAAGVAVGPYPRALA 254
Cdd:cd08436    82 DHPL-----AGRRRValaDLADEPFVDFPPGTGARRQVDRAFAAAgVRRRVA-FEVSDVDLLLDLVARGLGVALLPASVA 155


                  ...
gi 2772088495 255 GPL 257
Cdd:cd08436   156 ARL 158
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 30-102 1.41e-05

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 45.70  E-value: 1.41e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2772088495  30 VAKLGGFRRAAGQLNLSQPAVSNRVATLEDTLRVSLFERGDKALTLTREGMRLMAYAEQMLFVQEEIRR---RVSN 102
Cdd:PRK11074   13 VARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRqcqQVAN 88
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 111-265 3.88e-05

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


Pssm-ID: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 43.80  E-value: 3.88e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 111 RIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVA-------FLMGPVSDFTIGN-----VALP 178
Cdd:cd08435     3 RVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAigrladdEQPPDLASEELADeplvvVARP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 179 QFPLTwyKAAGVGEVDLGRVPVISFSANTRPYRELMAALRRR-LGPGVRMFSSASLSASLRMIAAGVAVGPYPRALAGPL 257
Cdd:cd08435    83 GHPLA--RRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAgLPLPRNVVETASISALLALLARSDMLAVLPRSVAEDE 160


                  ....*...
gi 2772088495 258 IAAGQIEA 265
Cdd:cd08435   161 LRAGVLRE 168
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 110-172 5.98e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold; HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. 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: 176141 [Multi-domain]  Cd Length: 196  Bit Score: 43.13  E-value: 5.98e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2772088495 110 FRIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAFLMGPVSDFTI 172
Cdd:cd08450     2 LTIGFLPGAEVQWLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGI 64
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 111-222 1.24e-04

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176138 [Multi-domain]  Cd Length: 198  Bit Score: 42.25  E-value: 1.24e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 111 RIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAFLMGPVSDFTIGN---------VALPQ-F 180
Cdd:cd08447     3 RIGFTAASAYSFLPRLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFARPGLETrplvreplvAAVPAgH 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2772088495 181 PLTWykAAGVGEVDLGRVPVISFSAN-TRPYRELMAALRRRLG 222
Cdd:cd08447    83 PLAG--AERLTLEDLDGQPFIMYSPTeARYFHDLVVRLFASAG 123
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 111-170 1.42e-04

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: 42.14  E-value: 1.42e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 111 RIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAFLmGPVSDF 170
Cdd:cd08434     3 RLGFLHSLGTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALC-SPVPDE 61
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 108-169 1.38e-03

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


Pssm-ID: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 39.05  E-value: 1.38e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2772088495 108 GLFRIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAFLMGPVSD 169
Cdd:cd08411     1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDE 62
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 108-281 2.60e-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: 38.19  E-value: 2.60e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 108 GLFRIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDiscDLREGLVGRQLDVAFLMGPVSDFTIgnVALPQFPLTWY-- 185
Cdd:cd08422     1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLS---DRLVDLVEEGFDLAIRIGELPDSSL--VARRLGPVRRVlv 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 186 ------KAAGVGEV--DLGRVPVISFSANTRPYR--------ELMAALRRRL----GPGVRmfssaslsaslRMIAAGVA 245
Cdd:cd08422    76 aspaylARHGTPQTpeDLARHRCLGYRLPGRPLRwrfrrgggEVEVRVRGRLvvndGEALR-----------AAALAGLG 144

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2772088495 246 VGPYPRALAGPLIAAGQIEAFDPGLTPNPLEFTASY 281
Cdd:cd08422   145 IALLPDFLVAEDLASGRLVRVLPDWRPPPLPIYAVY 180
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 109-167 3.92e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 37.55  E-value: 3.92e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2772088495 109 LFRIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLDVAFLMGPV 167
Cdd:cd08427     1 RLRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPP 59
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 111-265 8.95e-03

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: 36.73  E-value: 8.95e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 111 RIGASETVAQSWLPEFLRVFSAAYPRIDVDLTVDISCDLREGLVGRQLD--VAFLMGPVSDFT--------IGNVALPQF 180
Cdd:cd08440     3 RVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDfgIGSEPEADPDLEfepllrdpFVLVCPKDH 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772088495 181 PLTwyKAAGVGEVDLGRVPVISFSANT--RPYRE-LMAALRRRLGPGVRMfssASLSASLRMIAAGVAVGPYPrALAGPL 257
Cdd:cd08440    83 PLA--RRRSVTWAELAGYPLIALGRGSgvRALIDrALAAAGLTLRPAYEV---SHMSTALGMVAAGLGVAVLP-ALALPL 156


                  ....*...
gi 2772088495 258 IAAGQIEA 265
Cdd:cd08440   157 ADHPGLVA 164
 
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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