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Conserved domains on  [gi|488294061|ref|WP_002365269|]
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MULTISPECIES: LysR family transcriptional regulator [Enterococcus]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-292 1.81e-52

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 172.36  E-value: 1.81e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   1 MELRVIHYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDILSLANKTVT 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  81 NLSQ-NEFINGEITIGGGETKAMSFLANALQQITSQHSaDIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQKYSYLT 159
Cdd:COG0583   81 ELRAlRGGPRGTLRIGAPPSLARYLLPPLLARFRARHP-GVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 160 LpIVDTWGLITVKDHPLATKNvitaadlkeeplfisrqaqvpsqlsdwleasldqfRIVGTYNLLYNaslMVEAGLG--- 236
Cdd:COG0583  160 L-GEERLVLVASPDHPLARRA-----------------------------------PLVNSLEALLA---AVAAGLGial 200

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 488294061 237 -SALSIDGILETKQtnLRFIPL-YPALTAKISLIWRKNTVLSTAAALFLEQIKKSIQR 292
Cdd:COG0583  201 lPRFLAADELAAGR--LVALPLpDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-292 1.81e-52

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 172.36  E-value: 1.81e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   1 MELRVIHYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDILSLANKTVT 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  81 NLSQ-NEFINGEITIGGGETKAMSFLANALQQITSQHSaDIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQKYSYLT 159
Cdd:COG0583   81 ELRAlRGGPRGTLRIGAPPSLARYLLPPLLARFRARHP-GVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 160 LpIVDTWGLITVKDHPLATKNvitaadlkeeplfisrqaqvpsqlsdwleasldqfRIVGTYNLLYNaslMVEAGLG--- 236
Cdd:COG0583  160 L-GEERLVLVASPDHPLARRA-----------------------------------PLVNSLEALLA---AVAAGLGial 200

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 488294061 237 -SALSIDGILETKQtnLRFIPL-YPALTAKISLIWRKNTVLSTAAALFLEQIKKSIQR 292
Cdd:COG0583  201 lPRFLAADELAAGR--LVALPLpDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-288 7.62e-32

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: 119.64  E-value: 7.62e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   1 MELRVIHYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDILSLANKTVT 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  81 NLSQN-EFINGEITIGGGETKAMSFLANALQQITSQHsADIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQKYSYLT 159
Cdd:NF040786  81 EFDRYgKESKGVLRIGASTIPGQYLLPELLKKFKEKY-PNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 160 LpIVDTWGLITVKDHPL--ATKNVITAADLKEEPlFISRQ------AQVPSQLSDWlEASLDQFRIVGTYNLLYNASLMV 231
Cdd:NF040786 160 F-YKDRLVLITPNGTEKyrMLKEEISISELQKEP-FIMREegsgtrKEAEKALKSL-GISLEDLNVVASLGSTEAIKQSV 236

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488294061 232 EAGLG----SALSIDGilETKQTNLRFIPLYPA-LTAKISLIWRKNTVLSTAAALFLEQIKK 288
Cdd:NF040786 237 EAGLGisviSELAAEK--EVERGRVLIFPIPGLpKNRDFYLVYNKNRQLSPTAEAFLQFVKE 296
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 91-286 6.41e-27

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: 103.83  E-value: 6.41e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  91 EITIGGGETKAMSFLANALQQITSQHSaDIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQKYSYLTL---PIVdtwg 167
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYP-GVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLfeePLV---- 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 168 LITVKDHPLATKNVITAADLKEEPLFISRQAQVPSQLSD-WLEASLDQFRIVGTYNLLYNASLMVEAGLGSAL---SIdg 243
Cdd:cd05466   76 LVVPPDHPLAKRKSVTLADLADEPLILFERGSGLRRLLDrAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALlpeSA-- 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 488294061 244 ILETKQTNLRFIPL-YPALTAKISLIWRKNTVLSTAAALFLEQI 286
Cdd:cd05466  154 VEELADGGLVVLPLeDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-288 1.19e-26

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 105.62  E-value: 1.19e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   1 MELRVIHYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDILSLANKTVT 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  81 NLSQNEFINGEITIGGGETKAMSFLANALQQITSQHsADIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQKYSY--- 157
Cdd:PRK09906  81 RARKIVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRH-PDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYlel 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 158 LTLPIVdtwgLITVKDHPLATKNVITAADLKEEPLFI--SRQAQVPSQ-LSDWLEASLDQFRIVGTY-NLLYNASlMVEA 233
Cdd:PRK09906 160 LDEPLV----VVLPVDHPLAHEKEITAAQLDGVNFIStdPAYSGSLAPiIKAWFAQHNSQPNIVQVAtNILVTMN-LVGM 234

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 488294061 234 GLGSALSIDGILETKQTNLRFIPLYPAL-TAKISLIWRKNTvLSTAAALFLEQIKK 288
Cdd:PRK09906 235 GLGCTIIPGYMNNFNTGQVVFRPLAGNVpSIALLMAWKKGE-MKPALRDFIAIVQE 289
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 1.59e-24

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 93.22  E-value: 1.59e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061    3 LRVIHYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGE 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
TF_pcaQ TIGR02424
pca operon transcription factor PcaQ; Members of this family are LysR-family transcription ...
 1-287 7.73e-23

pca operon transcription factor PcaQ; Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria. [Energy metabolism, Other, Regulatory functions, DNA interactions]


Pssm-ID: 274127 [Multi-domain]  Cd Length: 300  Bit Score: 95.55  E-value: 7.73e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061    1 MELRVIHYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDILSLANKTVT 80
Cdd:TIGR02424   3 IKFRHLQCFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGTPLFERDRRGIRLTRYGELFLRHAGASLAALRQGVA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   81 NLSQNEFINGE-ITIGGGETKAMSFLANALQQITSQHsADIHLHLYSGNADDVIERLDKGLLDF--GLIIEPAPKQKYSY 157
Cdd:TIGR02424  83 SLSQLGEGEGPtVRIGALPTVAARLMPEVVKRFLARA-PRLRVRIMTGPNAYLLDQLRVGALDLvvGRLGAPETMQGLSF 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  158 LTL---PIVdtwgLITVKDHPLATKNVITAADLKEEPLFISRQAQVPSQLSD-WLEA---SLDQFRI------VG-TYNL 223
Cdd:TIGR02424 162 EHLynePVV----FVVRAGHPLLAAPSLPVASLADYPVLLPPEGSAIRPLAErLFIAcgiPPPPQRIetvsgsFGrRYVQ 237

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488294061  224 LYNASLMVEAGLGSALSIDGILETKQTNLRfIPLYPaltakISLIWRKNTVLSTAAALFLEQIK 287
Cdd:TIGR02424 238 ESDAIWIISRGVVALDLADGTLVELPFDTR-ETGGP-----VGLCTRPDTQLSRAAQLFVDALR 295
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-292 1.81e-52

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 172.36  E-value: 1.81e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   1 MELRVIHYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDILSLANKTVT 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  81 NLSQ-NEFINGEITIGGGETKAMSFLANALQQITSQHSaDIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQKYSYLT 159
Cdd:COG0583   81 ELRAlRGGPRGTLRIGAPPSLARYLLPPLLARFRARHP-GVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 160 LpIVDTWGLITVKDHPLATKNvitaadlkeeplfisrqaqvpsqlsdwleasldqfRIVGTYNLLYNaslMVEAGLG--- 236
Cdd:COG0583  160 L-GEERLVLVASPDHPLARRA-----------------------------------PLVNSLEALLA---AVAAGLGial 200

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 488294061 237 -SALSIDGILETKQtnLRFIPL-YPALTAKISLIWRKNTVLSTAAALFLEQIKKSIQR 292
Cdd:COG0583  201 lPRFLAADELAAGR--LVALPLpDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-288 7.62e-32

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: 119.64  E-value: 7.62e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   1 MELRVIHYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDILSLANKTVT 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  81 NLSQN-EFINGEITIGGGETKAMSFLANALQQITSQHsADIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQKYSYLT 159
Cdd:NF040786  81 EFDRYgKESKGVLRIGASTIPGQYLLPELLKKFKEKY-PNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 160 LpIVDTWGLITVKDHPL--ATKNVITAADLKEEPlFISRQ------AQVPSQLSDWlEASLDQFRIVGTYNLLYNASLMV 231
Cdd:NF040786 160 F-YKDRLVLITPNGTEKyrMLKEEISISELQKEP-FIMREegsgtrKEAEKALKSL-GISLEDLNVVASLGSTEAIKQSV 236

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488294061 232 EAGLG----SALSIDGilETKQTNLRFIPLYPA-LTAKISLIWRKNTVLSTAAALFLEQIKK 288
Cdd:NF040786 237 EAGLGisviSELAAEK--EVERGRVLIFPIPGLpKNRDFYLVYNKNRQLSPTAEAFLQFVKE 296
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 91-286 6.41e-27

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: 103.83  E-value: 6.41e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  91 EITIGGGETKAMSFLANALQQITSQHSaDIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQKYSYLTL---PIVdtwg 167
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYP-GVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLfeePLV---- 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 168 LITVKDHPLATKNVITAADLKEEPLFISRQAQVPSQLSD-WLEASLDQFRIVGTYNLLYNASLMVEAGLGSAL---SIdg 243
Cdd:cd05466   76 LVVPPDHPLAKRKSVTLADLADEPLILFERGSGLRRLLDrAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALlpeSA-- 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 488294061 244 ILETKQTNLRFIPL-YPALTAKISLIWRKNTVLSTAAALFLEQI 286
Cdd:cd05466  154 VEELADGGLVVLPLeDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-288 1.19e-26

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 105.62  E-value: 1.19e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   1 MELRVIHYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDILSLANKTVT 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  81 NLSQNEFINGEITIGGGETKAMSFLANALQQITSQHsADIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQKYSY--- 157
Cdd:PRK09906  81 RARKIVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRH-PDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYlel 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 158 LTLPIVdtwgLITVKDHPLATKNVITAADLKEEPLFI--SRQAQVPSQ-LSDWLEASLDQFRIVGTY-NLLYNASlMVEA 233
Cdd:PRK09906 160 LDEPLV----VVLPVDHPLAHEKEITAAQLDGVNFIStdPAYSGSLAPiIKAWFAQHNSQPNIVQVAtNILVTMN-LVGM 234

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 488294061 234 GLGSALSIDGILETKQTNLRFIPLYPAL-TAKISLIWRKNTvLSTAAALFLEQIKK 288
Cdd:PRK09906 235 GLGCTIIPGYMNNFNTGQVVFRPLAGNVpSIALLMAWKKGE-MKPALRDFIAIVQE 289
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-284 4.64e-25

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 101.57  E-value: 4.64e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   1 MELRVIHYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGE-YL-----AKQGQDILSL 74
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEvYLryarrALQDLEAGRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  75 ANKTVTNLSQnefinGEITIGGGETKAMSFLANALQQITSQHsADIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQK 154
Cdd:PRK11242  81 AIHDVADLSR-----GSLRLAMTPTFTAYLIGPLIDAFHARY-PGITLTIREMSQERIEALLADDELDVGIAFAPVHSPE 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 155 YSYLTLpIVDTWGLITVKDHPLATK-NVITAADLKEEPL------FISRQaqvpsQLSDWLEASLDQFRIVGTYNLLYNA 227
Cdd:PRK11242 155 IEAQPL-FTETLALVVGRHHPLAARrKALTLDELADEPLvllsaeFATRE-----QIDRYFRRHGVTPRVAIEANSISAV 228

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 488294061 228 SLMVEAGLGSALSIDGIlETKQTNLRFIPLYPAL-TAKISLIWRKNTVLSTAAALFLE 284
Cdd:PRK11242 229 LEIVRRGRLATLLPAAI-AREHDGLCAIPLDPPLpQRTAALLRRKGAYRSAAARAFIE 285
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 1.59e-24

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 93.22  E-value: 1.59e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061    3 LRVIHYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGE 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 11-198 4.25e-24

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 99.30  E-value: 4.25e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  11 AVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIR-GNRQIQLTPEGEYLAKQGQDILSLANkTVTNLSqNEFIN 89
Cdd:PRK12682  12 AVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRhGKRLKGLTEPGKAVLDVIERILREVG-NIKRIG-DDFSN 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  90 ---GEITIGGGETKAMSFLANALQQITSQHSaDIHLHLYSGNADDVIERLDKGLLDFGLIIEPApkQKYSYL-TLPIVDt 165
Cdd:PRK12682  90 qdsGTLTIATTHTQARYVLPRVVAAFRKRYP-KVNLSLHQGSPDEIARMVISGEADIGIATESL--ADDPDLaTLPCYD- 165

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 488294061 166 W--GLITVKDHPLATKNVITAADLKEEPLFISRQA 198
Cdd:PRK12682 166 WqhAVIVPPDHPLAQEERITLEDLAEYPLITYHPG 200
PRK09986 PRK09986
LysR family transcriptional regulator;
3-269 1.05e-23

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 97.87  E-value: 1.05e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   3 LRVIHYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDILSLANKTvtnL 82
Cdd:PRK09986   9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQS---L 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  83 SQNEFIN----GEITIGGGETKAMSFLANALQQITSQHsADIHLHLYSGNADDVIERLDKGLLDFG----LIIEPAPKQK 154
Cdd:PRK09986  86 ARVEQIGrgeaGRIEIGIVGTALWGRLRPAMRHFLKEN-PNVEWLLRELSPSMQMAALERRELDAGiwrmADLEPNPGFT 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 155 YSYLTlpiVDTWGLITVKDHPLATKNVITAADLKEEPlFISrqaqVPSQLSDW---LEASLDQ--FR--IVGTYNLLYNA 227
Cdd:PRK09986 165 SRRLH---ESAFAVAVPEEHPLASRSSVPLKALRNEY-FIT----LPFVHSDWgkfLQRVCQQagFSpqIIRQVNEPQTV 236

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 488294061 228 SLMVEAGLGSALSIDGILETKQTNLRFIPLYPALTAKISLIW 269
Cdd:PRK09986 237 LAMVSMGIGITLLPDSYAQIPWPGVVFRPLKERIPADLYAVY 278
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-288 4.07e-23

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: 94.28  E-value: 4.07e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   90 GEITIGGGETKAMSFLANALQQITSQHSaDIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQKYSYLTL---PIVdtw 166
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYP-DVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLgeePLV--- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  167 gLITVKDHPLATKNVITAADLKEEPL-FISRQAQVPSQLSDWLEASLDQFRIVGTYNLLYNASLMVEAGLGSALSIDGIL 245
Cdd:pfam03466  78 -LVAPPDHPLARGEPVSLEDLADEPLiLLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAV 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 488294061  246 --ETKQTNLRFIPLY-PALTAKISLIWRKNTVLSTAAALFLEQIKK 288
Cdd:pfam03466 157 arELADGRLVALPLPePPLPRELYLVWRKGRPLSPAVRAFIEFLRE 202
TF_pcaQ TIGR02424
pca operon transcription factor PcaQ; Members of this family are LysR-family transcription ...
 1-287 7.73e-23

pca operon transcription factor PcaQ; Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria. [Energy metabolism, Other, Regulatory functions, DNA interactions]


Pssm-ID: 274127 [Multi-domain]  Cd Length: 300  Bit Score: 95.55  E-value: 7.73e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061    1 MELRVIHYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDILSLANKTVT 80
Cdd:TIGR02424   3 IKFRHLQCFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGTPLFERDRRGIRLTRYGELFLRHAGASLAALRQGVA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   81 NLSQNEFINGE-ITIGGGETKAMSFLANALQQITSQHsADIHLHLYSGNADDVIERLDKGLLDF--GLIIEPAPKQKYSY 157
Cdd:TIGR02424  83 SLSQLGEGEGPtVRIGALPTVAARLMPEVVKRFLARA-PRLRVRIMTGPNAYLLDQLRVGALDLvvGRLGAPETMQGLSF 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  158 LTL---PIVdtwgLITVKDHPLATKNVITAADLKEEPLFISRQAQVPSQLSD-WLEA---SLDQFRI------VG-TYNL 223
Cdd:TIGR02424 162 EHLynePVV----FVVRAGHPLLAAPSLPVASLADYPVLLPPEGSAIRPLAErLFIAcgiPPPPQRIetvsgsFGrRYVQ 237

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488294061  224 LYNASLMVEAGLGSALSIDGILETKQTNLRfIPLYPaltakISLIWRKNTVLSTAAALFLEQIK 287
Cdd:TIGR02424 238 ESDAIWIISRGVVALDLADGTLVELPFDTR-ETGGP-----VGLCTRPDTQLSRAAQLFVDALR 295
PRK12680 PRK12680
LysR family transcriptional regulator;
1-260 4.26e-20

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 88.53  E-value: 4.26e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   1 MELRVIHYFLAVVQ-EKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQ-LTPEGEYLAKQGQDILSLANKT 78
Cdd:PRK12680   1 MTLTQLRYLVAIADaELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  79 VT-NLSQNEFINGEITIGGGETKAMSFLANALQQItSQHSADIHLHLYSGNADDVIERLDKGLLDFGlIIEPAPKQKYSY 157
Cdd:PRK12680  81 RTyAANQRRESQGQLTLTTTHTQARFVLPPAVAQI-KQAYPQVSVHLQQAAESAALDLLGQGDADIA-IVSTAGGEPSAG 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 158 LTLPIVDTWGLITV-KDHPLATKNVI-TAADLKEEPLfISRQAQVPSQLSdwLEASLDQFRIVGTYNLL-YNASLM---V 231
Cdd:PRK12680 159 IAVPLYRWRRLVVVpRGHALDTPRRApDMAALAEHPL-ISYESSTRPGSS--LQRAFAQLGLEPSIALTaLDADLIktyV 235

                        250       260
                 ....*....|....*....|....*....
gi 488294061 232 EAGLGSALSIDGILETKQTNLRFIPLyPA 260
Cdd:PRK12680 236 RAGLGVGLLAEMAVNANDEDLRAWPA-PA 263
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-192 6.21e-19

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 85.03  E-value: 6.21e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   1 MELRVIHYFLAVV-QEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIR-GNRQIQLTPEGEYLAKQGQDILslanKT 78
Cdd:PRK12684   1 MNLHQLRFVREAVrQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRhGKRLRGLTEPGRIILASVERIL----QE 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  79 VTNLSQ--NEFIN---GEITIGGGETKAMSFLANALQQITSQHsADIHLHLYSGNADDVIERLDKGLLDFGLIIEpAPKQ 153
Cdd:PRK12684  77 VENLKRvgKEFAAqdqGNLTIATTHTQARYALPAAIKEFKKRY-PKVRLSILQGSPTQIAEMVLHGQADLAIATE-AIAD 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 488294061 154 KYSYLTLPIVDtWG--LITVKDHPLATKNVITAADLKEEPL 192
Cdd:PRK12684 155 YKELVSLPCYQ-WNhcVVVPPDHPLLERKPLTLEDLAQYPL 194
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-286 7.28e-19

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: 82.57  E-value: 7.28e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  92 ITIGGGETKAMSFLANALQQITSQHsADIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQKYSYLTLpIVDTWGLITV 171
Cdd:cd08440    2 VRVAALPSLAATLLPPVLAAFRRRH-PGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPL-LRDPFVLVCP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 172 KDHPLATKNVITAADLKEEPlFISRQAqvPSQLSDWLEASLDQFRIvgTYNLLYNASL------MVEAGLG-SALSIDGI 244
Cdd:cd08440   80 KDHPLARRRSVTWAELAGYP-LIALGR--GSGVRALIDRALAAAGL--TLRPAYEVSHmstalgMVAAGLGvAVLPALAL 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 488294061 245 LETKQTNLRFIPLY-PALTAKISLIWRKNTVLSTAAALFLEQI 286
Cdd:cd08440  155 PLADHPGLVARPLTePVVTRTVGLIRRRGRSLSPAAQAFLDLL 197
rbcR CHL00180
LysR transcriptional regulator; Provisional
 2-187 9.17e-18

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 81.60  E-value: 9.17e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   2 ELRVIHyflAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDILSLANKTVTN 81
Cdd:CHL00180   9 QLRILK---AIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  82 LSQNEFIN-GEITIGGGETKAmSFLANALQQITSQHSADIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQKYSYLTL 160
Cdd:CHL00180  86 LEDLKNLQrGTLIIGASQTTG-TYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGEVPTELKKILEI 164

                        170       180
                 ....*....|....*....|....*....
gi 488294061 161 -PIV-DTWGLITVKDHPLATKNVITAADL 187
Cdd:CHL00180 165 tPYVeDELALIIPKSHPFAKLKKIQKEDL 193
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 2-192 4.69e-17

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 79.70  E-value: 4.69e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   2 ELRVIHYflAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIR-GNRQIQLTPEGEYLAKQGQDILSLANktvt 80
Cdd:PRK12683   5 QLRIIRE--AVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRrGKRLTGLTEPGKELLQIVERMLLDAE---- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  81 NLSQ--NEFIN---GEITIGGGETKAMSFLANALQQITSQHsADIHLHLYSGNADDVIERLDKGLLDFGLIIEpAPKQKY 155
Cdd:PRK12683  79 NLRRlaEQFADrdsGHLTVATTHTQARYALPKVVRQFKEVF-PKVHLALRQGSPQEIAEMLLNGEADIGIATE-ALDREP 156

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 488294061 156 SYLTLPiVDTW--GLITVKDHPLATKNVITAADLKEEPL 192
Cdd:PRK12683 157 DLVSFP-YYSWhhVVVVPKGHPLTGRENLTLEAIAEYPI 194
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 91-286 5.39e-17

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: 77.16  E-value: 5.39e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  91 EITIGGGETKAMSFLANALQQITSQHsADIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQKYSYLTLpivDTWGLIT 170
Cdd:cd08414    1 RLRIGFVGSALYGLLPRLLRRFRARY-PDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPL---LREPLVV 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 171 V--KDHPLATKNVITAADLKEEPLFISRQAQVPS---QLSDWLEASLDQFRIVGTYNLLYNASLMVEAGLGSALSIDGIL 245
Cdd:cd08414   77 AlpADHPLAARESVSLADLADEPFVLFPREPGPGlydQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPASVA 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 488294061 246 ETKQTNLRFIPLY-PALTAKISLIWRKNTVlSTAAALFLEQI 286
Cdd:cd08414  157 RLQRPGVVYRPLAdPPPRSELALAWRRDNA-SPALRAFLELA 197
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-194 6.05e-17

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 79.29  E-value: 6.05e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   1 MELRVIHYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLakqgqdiLSLANKTVT 80
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEIL-------LQLANQVLP 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  81 NLSQ-----NEFINGEITIGGGETKAMSFLANALQQItSQHSADIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQKY 155
Cdd:PRK15421  75 QISQalqacNEPQQTRLRIAIECHSCIQWLTPALENF-HKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGL 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 488294061 156 SYltLPIVD-TWGLITVKDHPLATKNVITAADLKEEPLFI 194
Cdd:PRK15421 154 HY--SPMFDyEVRLVLAPDHPLAAKTRITPEDLASETLLI 191
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-192 7.04e-17

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 78.92  E-value: 7.04e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   1 MELRVIHYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDILSLAnKTVT 80
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREV-KVLK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  81 NLS--QNEFINGEITIGGGETKAMSFLANALQQITSQHSaDIHLHLYSGNADDVIERLDKGLLD---FGLIIEPAPkqky 155
Cdd:PRK11151  80 EMAsqQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFP-KLEMYLHEAQTHQLLAQLDSGKLDcaiLALVKESEA---- 154

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 488294061 156 sYLTLPIVDTWGLITV-KDHPLATKNVITAADLKEEPL 192
Cdd:PRK11151 155 -FIEVPLFDEPMLLAVyEDHPWANRDRVPMSDLAGEKL 191
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-192 5.23e-16

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 76.86  E-value: 5.23e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   1 MELRVIHYFLAVV-QEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQI-QLTPEGEYLAKQGQDILSlankT 78
Cdd:PRK12681   1 MKLQQLRYIVEVVnHNLNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLtQVTPAGEEIIRIAREILS----K 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  79 VTNLSQ--NEFIN---GEITIGGGETKAMSFLANALQQITSQHSaDIHLHLYSGNADDVIERLDKGLLDFGLIIEpaPKQ 153
Cdd:PRK12681  77 VESIKSvaGEHTWpdkGSLYIATTHTQARYALPPVIKGFIERYP-RVSLHMHQGSPTQIAEAAAKGNADFAIATE--ALH 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 488294061 154 KYSYLTLPIVDTWG--LITVKDHPLATKNVITAADLKEEPL 192
Cdd:PRK12681 154 LYDDLIMLPCYHWNrsVVVPPDHPLAKKKKLTIEELAQYPL 194
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
26-149 2.47e-15

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 74.08  E-value: 2.47e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  26 HVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDILSLANKTVTNLSQN-EFINGEITIGGGETKAMSF 104
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQgPSLSGELSLFCSVTAAYSH 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 488294061 105 LANALQQITSQHSaDIHLHLYSGNADDVIERLDKGLLDFGLIIEP 149
Cdd:PRK11716  82 LPPILDRFRAEHP-LVEIKLTTGDAADAVEKVQSGEADLAIAAKP 125
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 119-284 6.15e-15

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: 71.75  E-value: 6.15e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 119 DIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQKYsyltlpIVDTWG-----LITVKDHPLATKNVITAADLKEEPlF 193
Cdd:cd08420   28 EVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDL------IVEPFAedelvLVVPPDHPLAGRKEVTAEELAAEP-W 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 194 ISRQAQvpS----QLSDWLEA---SLDQFRIV----GTYNLLyNAslmVEAGLG----SALSIDGILETKqtNLRFIPL- 257
Cdd:cd08420  101 ILREPG--SgtreVFERALAEaglDGLDLNIVmelgSTEAIK-EA---VEAGLGisilSRLAVRKELELG--RLVALPVe 172

                        170       180
                 ....*....|....*....|....*..
gi 488294061 258 YPALTAKISLIWRKNTVLSTAAALFLE 284
Cdd:cd08420  173 GLRLTRPFSLIYHKDKYLSPAAEAFLE 199
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 101-285 1.25e-14

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: 70.67  E-value: 1.25e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 101 AMSFLANALQQITSQHsADIHLHLYSGNADDVIERLDKGLLDFGLIIEPapkqkysyLTLPIVDTWGLITV-------KD 173
Cdd:cd08415   11 ALSLLPRAIARFRARH-PDVRISLHTLSSSTVVEAVLSGQADLGLASLP--------LDHPGLESEPLASGravcvlpPG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 174 HPLATKNVITAADLKEEPlFISRQAQVPS--QLSDWLEASLDQFRIVGTYNLLYNASLMVEAGLGSALsIDGIL--ETKQ 249
Cdd:cd08415   82 HPLARKDVVTPADLAGEP-LISLGRGDPLrqRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAI-VDPLTaaGYAG 159

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 488294061 250 TNLRFIPLYPALTAKISLIWRKNTVLSTAAALFLEQ 285
Cdd:cd08415  160 AGLVVRPFRPAIPFEFALVRPAGRPLSRLAQAFIDL 195
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 104-284 1.02e-13

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: 68.35  E-value: 1.02e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 104 FLANALQQITSQHSaDIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQKYSYLTL---PIVdtwgLITVKDHPLATKN 180
Cdd:cd08438   14 LFAPLLAAFRQRYP-NIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLcnePLV----AVLPRGHPLAGRK 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 181 VITAADLKEEPLFISRQAqvpSQLSDWLeasLDQFRIVGTY-NLLYNASL------MVEAGLGSALSIDGIL-ETKQTNL 252
Cdd:cd08438   89 TVSLADLADEPFILFNED---FALHDRI---IDACQQAGFTpNIAARSSQwdfiaeLVAAGLGVALLPRSIAqRLDNAGV 162

                        170       180       190
                 ....*....|....*....|....*....|...
gi 488294061 253 RFIPL-YPALTAKISLIWRKNTVLSTAAALFLE 284
Cdd:cd08438  163 KVIPLtDPDLRWQLALIWRKGRYLSHAARAWLA 195
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
7-128 4.40e-13

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 68.10  E-value: 4.40e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   7 HYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDILSLANKTVTNLSQNE 86
Cdd:PRK10086  20 HTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDIKNQE 99

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 488294061  87 fINGEITIGGGETKAMSFLANALQQITSQHSAdIHLHLYSGN 128
Cdd:PRK10086 100 -LSGTLTVYSRPSIAQCWLVPRLADFTRRYPS-ISLTILTGN 139
PRK09791 PRK09791
LysR family transcriptional regulator;
1-143 1.87e-12

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 66.32  E-value: 1.87e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   1 MELRVIHYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDILSLANKTVT 80
Cdd:PRK09791   5 VKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQE 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488294061  81 NLSQNE-FINGEITIGGGETKAMSFLANALQQITSQHsADIHLHLYSGNADDVIERLDKGLLDF 143
Cdd:PRK09791  85 DIRQRQgQLAGQINIGMGASIARSLMPAVISRFHQQH-PQVKVRIMEGQLVSMINELRQGELDF 147
PRK10341 PRK10341
transcriptional regulator TdcA;
9-287 2.64e-12

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 66.04  E-value: 2.64e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   9 FLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDILSLANKTVTNLSQNEF- 87
Cdd:PRK10341  15 FQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGMSSe 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  88 INGEITIGGGETKAMSFLANALQQITSQHSaDIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQKYSYLTLPIVDT-W 166
Cdd:PRK10341  95 AVVDVSFGFPSLIGFTFMSDMINKFKEVFP-KAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMKLQDLHVEPLFESeF 173

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 167 GLITVKDHPLAtkNVITAADLKEEplfisrQAQVP-------SQLSDWLE-ASLDQFRIVGT------YNLLYNASLMve 232
Cdd:PRK10341 174 VLVASKSRTCT--GTTTLESLKNE------QWVLPqtnmgyySELLTTLQrNGISIENIVKTdsvvtiYNLVLNADFL-- 243

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 488294061 233 aglgSALSIDGILETKQTNLRFIPLYPAL-TAKISLIWRKNTVLSTAAALFLEQIK 287
Cdd:PRK10341 244 ----TVIPCDMTSPFGSNQFITIPIEETLpVAQYAAVWSKNYRIKKAASVLVELAK 295
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-196 4.66e-12

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 65.09  E-value: 4.66e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   1 MELRVIHYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDIL---SLANK 77
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILrqcEQAQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  78 TVTNLSQNefINGEITIGGGETKAMSFLANALQQITSQHSADIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQKYSY 157
Cdd:PRK11233  81 AVHNVGQA--LSGQVSIGLAPGTAASSLTMPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYEHSPVAGLSS 158

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 488294061 158 LTLPIVDTWgLITVKDHPlatKNVITAADLKEEPLFISR 196
Cdd:PRK11233 159 QPLLKEDLF-LVGTQDCP---GQSVDLAAVAQMNLFLPR 193
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 3-239 4.68e-12

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 65.40  E-value: 4.68e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   3 LRVIHYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQ-------DILSLA 75
Cdd:PRK11013   6 LRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQrsyygldRIVSAA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  76 NktvtnlSQNEFINGEITIGGGETKAMSFLANALQQITSQHsADIHLHLYSGNADDVIERLDKGLLDFGL---IIEPAPK 152
Cdd:PRK11013  86 E------SLREFRQGQLSIACLPVFSQSLLPGLCQPFLARY-PDVSLNIVPQESPLLEEWLSAQRHDLGLtetLHTPAGT 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 153 QKYSYLTLPIVdtwgLITVKDHPLATKNVITAADLKEEPlFIS-------RQaqvpsQLSDWL-EASLDQFRIVGTYNLl 224
Cdd:PRK11013 159 ERTELLTLDEV----CVLPAGHPLAAKKVLTPDDFAGEN-FISlsrtdsyRQ-----LLDQLFaEHGVKRRMVVETHSA- 227

                        250
                 ....*....|....*..
gi 488294061 225 ynASL--MVEAGLGSAL 239
Cdd:PRK11013 228 --ASVcaMVRAGVGVSI 242
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 21-131 1.21e-11

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 63.71  E-value: 1.21e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  21 AAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDIL-SLANKTVTNLSQNEfiNGEITIGGGET 99
Cdd:PRK11139  26 AAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFdQLAEATRKLRARSA--KGALTVSLLPS 103

                         90       100       110
                 ....*....|....*....|....*....|..
gi 488294061 100 KAMSFLANALQQITSQHSaDIHLHLYSGNADD 131
Cdd:PRK11139 104 FAIQWLVPRLSSFNEAHP-DIDVRLKAVDRLE 134
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 115-286 3.19e-11

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: 61.39  E-value: 3.19e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 115 QHSADIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQKYSYLTL---PIVdtwgLITVKDHPLATKNVITAADLKEEP 191
Cdd:cd08411   25 QAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLfdePFL----LAVPKDHPLAKRKSVTPEDLAGER 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 192 LFI-------SRQA-----QVPSQLSDWLEA-SLDQFRivgtynllynasLMVEAGLGS----ALSIDGiLETKQTNLRF 254
Cdd:cd08411  101 LLLleeghclRDQAlelcrLAGAREQTDFEAtSLETLR------------QMVAAGLGItllpELAVPS-EELRGDRLVV 167

                        170       180       190
                 ....*....|....*....|....*....|...
gi 488294061 255 IPL-YPALTAKISLIWRKNTVLSTAAALFLEQI 286
Cdd:cd08411  168 RPFaEPAPSRTIGLVWRRSSPRAAAFEALAELI 200
cbl PRK12679
HTH-type transcriptional regulator Cbl;
11-197 7.93e-11

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 61.75  E-value: 7.93e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  11 AVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIR-GNRQIQLTPEGEYLAKQGQDILSLANKtVTNLSQNeFIN 89
Cdd:PRK12679  12 AARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRrGKRLLGMTEPGKALLVIAERILNEASN-VRRLADL-FTN 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  90 ---GEITIGGGETKAMSFLANALQQITSQHSaDIHLHLYSGNADDVIERLDKGLLDFGLiiepAPKQKYSYLTLPIVD-- 164
Cdd:PRK12679  90 dtsGVLTIATTHTQARYSLPEVIKAFRELFP-EVRLELIQGTPQEIATLLQNGEADIGI----ASERLSNDPQLVAFPwf 164

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 488294061 165 TW--GLITVKDHPLATKNVITAADLKEEPLFISRQ 197
Cdd:PRK12679 165 RWhhSLLVPHDHPLTQITPLTLESIAKWPLITYRQ 199
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 115-284 1.01e-10

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: 59.86  E-value: 1.01e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 115 QHSADIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQKYSYLTL---PIVdtwgLITVKDHPLATKNVITAADLKEEP 191
Cdd:cd08434   24 KEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLfteELV----LVVPKDHPLAGRDSVDLAELADEP 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 192 L------FISRQaqvpsQLSDWLEASLDQFRIVGTYNLLYNASLMVEAGLG-SALSIDGILETKQTnlRFIPL-YPALTA 263
Cdd:cd08434  100 FvllspgFGLRP-----IVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGvAILPEMTLLNPPGV--KKIPIkDPDAER 172

                        170       180
                 ....*....|....*....|.
gi 488294061 264 KISLIWRKNTVLSTAAALFLE 284
Cdd:cd08434  173 TIGLAWLKDRYLSPAARRFKD 193
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-73 2.35e-10

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 60.21  E-value: 2.35e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488294061   6 IHYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDILS 73
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLS 74
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 11-72 2.64e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 56.87  E-value: 2.64e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488294061  11 AVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDIL 72
Cdd:PRK11074  12 AVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVI 73
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 91-284 1.08e-08

The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176105 [Multi-domain]  Cd Length: 198  Bit Score: 54.17  E-value: 1.08e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  91 EITIGGGETKAMSFLANALQQITSQHSAdIHLHLYSGNADDVIERLDKGLLDFGLIIEpAPKQKYSYLTLPiVDTW--GL 168
Cdd:cd08413    1 QLTIATTHTQARYVLPPVIAAFRKRYPK-VKLSLHQGTPSQIAEMVLKGEADIAIATE-ALDDHPDLVTLP-CYRWnhCV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 169 ITVKDHPLATKNVITAADLKEEPLFISRQAQVP-SQLSDWLEASLDQFRIV---------GTYnllynaslmVEAGLG-- 236
Cdd:cd08413   78 IVPPGHPLADLGPLTLEDLAQYPLITYDFGFTGrSSIDRAFARAGLEPNIVltaldadviKTY---------VRLGLGvg 148

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 488294061 237 --SALSIDGIletKQTNLRFIP---LYPALTAKISLiwRKNTVLSTAAALFLE 284
Cdd:cd08413  149 iiAEMAYDPQ---RDADLVALDaghLFGPNTTRIAL--RRGTYLRSYAYDFIE 196
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-286 1.30e-08

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: 53.76  E-value: 1.30e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 105 LANALQQITSQHsADIHLHLYSGNADDVIERLDKGLLDFGLIiePAPKQKYSYLTLPIVDTWGLITV--KDHPLATKNVI 182
Cdd:cd08436   15 LPELLARFHRRH-PGVDIRLRQAGSDDLLAAVREGRLDLAFV--GLPERRPPGLASRELAREPLVAVvaPDHPLAGRRRV 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 183 TAADLKEEPL--FIS------------RQAQVPSQLSdwLEASldqfrivgtynllyNASLM---VEAGLGSAL---SID 242
Cdd:cd08436   92 ALADLADEPFvdFPPgtgarrqvdrafAAAGVRRRVA--FEVS--------------DVDLLldlVARGLGVALlpaSVA 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 488294061 243 GILEtkqtNLRFIPLYPALTAKISLIWRkNTVLSTAAALFLEQI 286
Cdd:cd08436  156 ARLP----GLAALPLEPAPRRRLYLAWS-APPPSPAARAFLELL 194
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-286 1.33e-08

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: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 53.76  E-value: 1.33e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  91 EITIGGGETKAMSFLANALQQITSQHSaDIHLHLYSGNADDVIERLDKGLLDFGLIIE----PAPKQKYSYLTLPIVDTW 166
Cdd:cd08423    1 TLRVGAFPTAAAALLPPALAALRARHP-GLEVRLREAEPPESLDALRAGELDLAVVFDypvtPPPDDPGLTRVPLLDDPL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 167 GLITVKDHPLATKNVITAADLKEEPlFISRQAQVPSQlsDWLEASLDQ--------FRIVGtynllYNASL-MVEAGLGS 237
Cdd:cd08423   80 DLVLPADHPLAGREEVALADLADEP-WIAGCPGSPCH--RWLVRACRAagftpriaHEADD-----YATVLaLVAAGLGV 151

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 488294061 238 ALSIDGILETKQTNLRFIPLYPALTAKISLIWRKNTVLSTAAALFLEQI 286
Cdd:cd08423  152 ALVPRLALGARPPGVVVRPLRPPPTRRIYAAVRAGAARRPAVAAALEAL 200
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 172-286 1.89e-08

The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold; In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176140 [Multi-domain]  Cd Length: 197  Bit Score: 53.43  E-value: 1.89e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 172 KDHPLATKNVITAADLKEEPLFISRQAQvpSQLSDWLEASLDQ--FRIVGTYNLLYNASLM--VEAGLGSALSIDGILET 247
Cdd:cd08449   82 EEHPLAGRKSLTLADLRDEPFVFLRLAN--SRFADFLINCCLQagFTPQITQEVVEPQTLMalVAAGFGVALVPESYARL 159

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 488294061 248 KQTNLRFIPLYPALTAKISLIWRKNTVLStAAALFLEQI 286
Cdd:cd08449  160 PWPGVRFIPLKQAISADLYAVYHPDSATP-VIQAFLALL 197
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-284 2.05e-08

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 54.31  E-value: 2.05e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   3 LRVIHYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDILSLANKtVTNL 82
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVE-IEQL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  83 SQNEfiNGEITIGGGETKAMSFLANALQQItSQHSADIHLHLYSGNADDVIERLDKGLLDFGLIiePAPKQKYSYLTLP- 161
Cdd:PRK10837  84 FRED--NGALRIYASSTIGNYILPAMIARY-RRDYPQLPLELSVGNSQDVINAVLDFRVDIGLI--EGPCHSPELISEPw 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 162 IVDTWGLITVKDHPLATKNViTAADLKEEPLFISRQAQVPSQLSDW-LEASLDQFRIV---GTYNLLYNAslmVEAGLG- 236
Cdd:PRK10837 159 LEDELVVFAAPDSPLARGPV-TLEQLAAAPWILRERGSGTREIVDYlLLSHLPRFELAmelGNSEAIKHA---VRHGLGi 234

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 488294061 237 SALS---IDGILETKQTNLRFIPLyPALTAKISLIWRKNTVLSTAAALFLE 284
Cdd:PRK10837 235 SCLSrrvIADQLQAGTLVEVAVPL-PRLMRTLYRIHHRQKHLSNALQRFLS 284
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
9-66 4.49e-08

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 53.44  E-value: 4.49e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 488294061   9 FLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGnRQIQLTPEGEYLAK 66
Cdd:PRK13348  10 LAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLR 66
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 109-278 4.91e-08

The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold; MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176128  Cd Length: 198  Bit Score: 52.33  E-value: 4.91e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 109 LQQITSQHSADIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQKySYLTLPIVDT--WGLITVKDHPLATKNVITAAD 186
Cdd:cd08437   18 LAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIALLGSLTPLEN-SALHSKIIKTqhFMIIVSKDHPLAKAKKVNFAD 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 187 LKEEPLFISRQAQVPSQLSDWLEaSLDQFR--IVGTYNLLYNASLMVEAGLGSALSIDgILETKQTNLRFIPL--YPALT 262
Cdd:cd08437   97 LKKENFILLNEHFVHPKAFDSLC-QQANFQpnIVYRTNDIHILKSMVRENVGIGFLTD-IAVKPDDHLVAIPLldNEQPT 174

                        170
                 ....*....|....*.
gi 488294061 263 AKISLIWRKNTVLSTA 278
Cdd:cd08437  175 FYISLAHRKDQLLTPA 190
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
1-143 5.16e-08

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 53.13  E-value: 5.16e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   1 MELRVIHYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDILSLANKTVT 80
Cdd:PRK10082  11 IETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLA 90

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488294061  81 NL-SQNEFINGEITIGGGETKAMSFLANALQQITSQHSADIHlhlySGNADDVIERLDKGLLDF 143
Cdd:PRK10082  91 ELrGGSDYAQRKIKIAAAHSLSLGLLPSIISQMPPLFTWAIE----AIDVDEAVDKLREGQSDC 150
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 91-284 8.96e-08

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


Pssm-ID: 176145 [Multi-domain]  Cd Length: 196  Bit Score: 51.27  E-value: 8.96e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  91 EITIGGGETKAMSFLANALQQITSQHSaDIHLHLYSGNADDVIERLDKGLLDFGL---IIEPAPKQKYSYLTLPIVdtwg 167
Cdd:cd08456    1 ELRIAVLPALSQSFLPRAIKAFLQRHP-DVTISIHTRDSPTVEQWLSAQQCDLGLvstLHEPPGIERERLLRIDGV---- 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 168 LITVKDHPLATKNVITAADLKEEPlFISrqaqvpSQLSDWLEASLDQ-FRIVGTYNLL-----YNASL--MVEAGLG-SA 238
Cdd:cd08456   76 CVLPPGHRLAVKKVLTPSDLEGEP-FIS------LARTDGTRQRVDAlFEQAGVKRRIvvetsYAATIcaLVAAGVGvSV 148

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 488294061 239 LSIDGILETKQTNLRFIPLYPALTAKISLIWRKNTVLSTAAALFLE 284
Cdd:cd08456  149 VNPLTALDYAAAGLVVRRFSPAVPFEVSLIRPKHRPSSALVAAFSA 194
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-286 4.57e-07

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 49.23  E-value: 4.57e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  91 EITIGGGETKAMSFLANALQQITSQHSaDIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQK---YSYLTLPIvdtwG 167
Cdd:cd08426    1 RVRVATGEGLAAELLPSLIARFRQRYP-GVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGirvHSRQPAPI----G 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 168 LITVKDHPLATKNVITAADLKEEPLFISRQAQVPSQLSDWLEASLD-QFRIVGTYNLLYNASLMVEAGLGSALS--IDGI 244
Cdd:cd08426   76 AVVPPGHPLARQPSVTLAQLAGYPLALPPPSFSLRQILDAAFARAGvQLEPVLISNSIETLKQLVAAGGGISLLteLAVR 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 488294061 245 LETKQTNLRFIPL-YPALTAK-ISLIWRKNTVLSTAAALFLEQI 286
Cdd:cd08426  156 REIRRGQLVAVPLaDPHMNHRqLELQTRAGRQLPAAASAFLQLL 199
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-114 7.21e-07

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 49.64  E-value: 7.21e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   1 MELRVIHYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDILSLANKTVT 80
Cdd:PRK15092  11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACS 90

                         90       100       110
                 ....*....|....*....|....*....|....
gi 488294061  81 NLSQNEfINGEITIGGGETKAMSFLANALQQITS 114
Cdd:PRK15092  91 SLMYSN-LQGVLTIGASDDTADTILPFLLNRVSS 123
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 92-286 2.15e-06

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: 47.27  E-value: 2.15e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  92 ITIGGGETKAMSFLANALQQITSQHSaDIHLHLYSGNADDVIERLDKGLLDF--GLIIEPAPKQKYSYLTL---PIVdtw 166
Cdd:cd08435    2 VRVGAVPAAAPVLLPPAIARLLARHP-RLTVRVVEGTSDELLEGLRAGELDLaiGRLADDEQPPDLASEELadePLV--- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 167 gLITVKDHPLATKNVITAADLKEEPLFISRqaqVPSQLSDWLEASldqFR---------IVGTYNLLYNASLMVEAGLGS 237
Cdd:cd08435   78 -VVARPGHPLARRARLTLADLADYPWVLPP---PGTPLRQRLEQL---FAaaglplprnVVETASISALLALLARSDMLA 150

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 488294061 238 ALSIDGI-LETKQTNLRFIPLyPALTAK--ISLIWRKNTVLSTAAALFLEQI 286
Cdd:cd08435  151 VLPRSVAeDELRAGVLRELPL-PLPTSRrpIGITTRRGGPLSPAARALLDAL 201
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
9-64 2.21e-06

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 48.23  E-value: 2.21e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 488294061   9 FLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGnRQIQLTPEGEYL 64
Cdd:PRK03635  10 LAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQRL 64
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
9-118 2.31e-06

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 48.09  E-value: 2.31e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   9 FLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDILS---LANKTVTNLSQN 85
Cdd:PRK03601   9 FLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNtwqAAKKEVAHTSQH 88

                         90       100       110
                 ....*....|....*....|....*....|...
gi 488294061  86 EfingEITIGGGETKAMSFLANALQQITSQHSA 118
Cdd:PRK03601  89 N----ELSIGASASLWECMLTPWLGRLYQNQEA 117
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-284 3.03e-06

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: 46.80  E-value: 3.03e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  91 EITIGGGETKAMSFLANALQQITSQHSaDIHLHLYSGNADDVIERLDKGLLDFGLIIEP---APKQkYSYLTL---PIVd 164
Cdd:cd08427    1 RLRLGAIATVLTGLLPRALARLRRRHP-DLEVHIVPGLSAELLARVDAGELDAAIVVEPpfpLPKD-LVWTPLvrePLV- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 165 twgLITVKDHPLATknviTAADLKEEPlFI--SRQAQVPSQLSDWLEASLDQFRIVGTYNLLYNASLMVEAGLGSAL--S 240
Cdd:cd08427   78 ---LIAPAELAGDD----PRELLATQP-FIryDRSAWGGRLVDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAIvpD 149

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 488294061 241 IDGILETKQtNLRFIPL-YPALTAKISLIWRKNTVLSTAAALFLE 284
Cdd:cd08427  150 IAVPLPAGP-RVRVLPLgDPAFSRRVGLLWRRSSPRSRLIQALLE 193
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 119-279 9.08e-06

The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut. Hence, NAC allows the coupling of sigma70-RNAP dependent operons to the sigma54-RNAP dependent NTR system. 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: 176124  Cd Length: 198  Bit Score: 45.66  E-value: 9.08e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 119 DIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQKYSYLTLPIVDTWgLITVKDHPLATKNVITAADLKEEPLFISRQA 198
Cdd:cd08433   28 GIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLF-LVGPADAPLPRGAPVPLAELARLPLILPSRG 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 199 QVPSQLsdwLEASLDQFRI-------VGTYNLLynaSLMVEAGLGSAL----SIDGilETKQTNLRFIPL-YPALTAKIS 266
Cdd:cd08433  107 HGLRRL---VDEAAARAGLtlnvvveIDSVATL---KALVAAGLGYTIlpasAVAA--EVAAGRLVAAPIvDPALTRTLS 178

                        170
                 ....*....|...
gi 488294061 267 LIWRKNTVLSTAA 279
Cdd:cd08433  179 LATPRDRPLSPAA 191
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 92-192 1.20e-05

The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176134  Cd Length: 198  Bit Score: 45.25  E-value: 1.20e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  92 ITIGGGETKAMSFLANALQQITSQHSAdIHLHLYSGNADDVIERLDKGLLDFGLIIEpAPKQKYSYLTLPIVdTWG--LI 169
Cdd:cd08443    2 LYVATTHTQARYVLPPVIKGFIERYPR-VSLQMHQGSPTQIAEMVSKGLVDFAIATE-ALHDYDDLITLPCY-HWNrcVV 78

                         90       100
                 ....*....|....*....|...
gi 488294061 170 TVKDHPLATKNVITAADLKEEPL 192
Cdd:cd08443   79 VKRDHPLADKQSISIEELATYPI 101
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 163-284 2.06e-05

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold; CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176116  Cd Length: 197  Bit Score: 44.63  E-value: 2.06e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 163 VDTWGLITVKDHPLATK-NVITAADLKEEPL------FISRQaqvpsQLSDWLEASLDQFRIVgtynllynaslmVEAGL 235
Cdd:cd08425   72 DERLALVVGATHPLAQRrTALTLDDLAAEPLallspdFATRQ-----HIDRYFQKQGIKPRIA------------IEANS 134

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488294061 236 GSAL-------SIDGIL----ETKQTNLRFIPLYPALTAK-ISLIWRKNTVLSTAAALFLE 284
Cdd:cd08425  135 ISAVlevvrrgRLATILpdaiAREQPGLCAVALEPPLPGRtAALLRRKGAYRSAAARAFAA 195
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-273 3.57e-05

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: 43.79  E-value: 3.57e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  92 ITIGGGETKAMSFLANALQQItSQHSADIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQKYSYLTL---PIVdtwgL 168
Cdd:cd08447    2 LRIGFTAASAYSFLPRLLAAA-RAALPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFARPGLETRPLvrePLV----A 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 169 ITVKDHPLATKNVITAADLKEEPlFIsrqAQVPSQ-------LSDWLEASLDQFRIVGTYNLLYNASLMVEAGLG----- 236
Cdd:cd08447   77 AVPAGHPLAGAERLTLEDLDGQP-FI---MYSPTEaryfhdlVVRLFASAGVQPRYVQYLSQIHTMLALVRAGLGvalvp 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 488294061 237 ---SALSIDGIletkqtnlRFIPLY--PALTAKISLIWRKNT 273
Cdd:cd08447  153 asaSRLRFEGV--------VFRPLDlpRDVPVELHLAWRRDN 186
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-62 1.29e-04

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 42.67  E-value: 1.29e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488294061   1 MELRVIHYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGE 62
Cdd:PRK14997   2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQ 63
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-107 1.29e-04

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 42.83  E-value: 1.29e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   1 ME-LRVIHYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDILSLANKTV 79
Cdd:PRK10632   1 MErLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVH 80

                         90       100
                 ....*....|....*....|....*....
gi 488294061  80 TNL-SQNEFINGEITIGGGETKAMSFLAN 107
Cdd:PRK10632  81 EQLyAFNNTPIGTLRIGCSSTMAQNVLAG 109
nhaR PRK11062
transcriptional activator NhaR; Provisional
 6-142 1.45e-04

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 42.69  E-value: 1.45e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   6 IHYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDILSLANKT--VTNLS 83
Cdd:PRK11062   9 LYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKMFTLSQEMldIVNYR 88

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 488294061  84 QNEFINGEITIGGGETKAMSflANALQQITSQHSAdIHLHLYSGNADDVIERLDKGLLD 142
Cdd:PRK11062  89 KESNLLFDVGVADALSKRLV--SRVLLTAVPEDES-IHLRCFESTHEMLLEQLSQHKLD 144
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 91-284 2.26e-04

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: 41.38  E-value: 2.26e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  91 EITIGGGETKAMSFLANALQQITSQHsADIHLHLYSGNADDVIERLDKGLLDFGLIiepapkqkYSYLTLPIVDTWGLIT 170
Cdd:cd08412    1 TLRIGCFSTLAPYYLPGLLRRFREAY-PGVEVRVVEGNQEELEEGLRSGELDLALT--------YDLDLPEDIAFEPLAR 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 171 VK-------DHPLATKNVITAADLKEEPLFI-----SRQaqvpSQLSDWLEASLdQFRIVGTYnllynASL-----MVEA 233
Cdd:cd08412   72 LPpyvwlpaDHPLAGKDEVSLADLAAEPLILldlphSRE----YFLSLFAAAGL-TPRIAYRT-----SSFeavrsLVAN 141

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 488294061 234 GLGSALSIDGI-----LETKQtnLRFIPLYPAL-TAKISLIWRKNTVLSTAAALFLE 284
Cdd:cd08412  142 GLGYSLLNDRPyrpwsYDGKR--LVRRPLADPVpPLRLGLAWRRGARLTRAARAFVD 196
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 104-196 2.30e-04

The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). 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: 176111  Cd Length: 197  Bit Score: 41.34  E-value: 2.30e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 104 FLANALQQITSQHsADIHLHLYSGNADDVIERLDKGLLDF---GLIIEPAPKQKYSYLTLPIVdtwgLITVKDHPLATKN 180
Cdd:cd08419   13 FAPRLLGAFCRRH-PGVEVSLRVGNREQVLERLADNEDDLaimGRPPEDLDLVAEPFLDNPLV----VIAPPDHPLAGQK 87

                         90
                 ....*....|....*.
gi 488294061 181 VITAADLKEEPlFISR 196
Cdd:cd08419   88 RIPLERLAREP-FLLR 102
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 91-287 6.29e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold; TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. 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: 176110 [Multi-domain]  Cd Length: 201  Bit Score: 40.03  E-value: 6.29e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061  91 EITIGGGETKAMSFLANALQQITSQHSaDIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQKYSYLTLPIVDT-WGLI 169
Cdd:cd08418    1 KVSIGVSSLIAHTLMPAVINRFKEQFP-DVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLKELISEPLFESdFVVV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 170 TVKDHPLATknvitAADLKEEPLFisrQAQVPSQLSDWLEASLDQFR--------------IVGTYNLLYNASLMveagl 235
Cdd:cd08418   80 ARKDHPLQG-----ARSLEELLDA---SWVLPGTRMGYYNNLLEALRrlgynprvavrtdsIVSIINLVEKADFL----- 146

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 488294061 236 gSALSIDgILETKQTNLRFIPLYPALT---AKISLIWRKNTVLSTAAALFLEQIK 287
Cdd:cd08418  147 -TILSRD-MGRGPLDSFRLITIPVEEPlpsADYYLIYRKKSRLTPLAEQLVELFR 199
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 131-272 7.34e-04

The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold; AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176143 [Multi-domain]  Cd Length: 197  Bit Score: 39.79  E-value: 7.34e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 131 DVIERLDKGLLDFGLIIEPAPKQKY---SYLTLPIVdtwgLITVKDHPLATKNVITAADLKEEPL-FISRQAQvPSQLSD 206
Cdd:cd08452   40 DQVEELLKGRIDIGFLHPPIQHTALhieTVQSSPCV----LALPKQHPLASKEEITIEDLRDEPIiTVAREAW-PTLYDE 114

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 207 WL---EASLDQFRIVGTYNLLYNASLMVEAGLGSALSIDGILETKQTNLRFIPLY-PALTAKISLIWRKN 272
Cdd:cd08452  115 IIqlcEQAGFRPKIVQEATEYQTVIGLVSAGIGVTFVPSSAKKLFNLEVAYRKIDqINLNAEWSIAYRKD 184
PRK09801 PRK09801
LysR family transcriptional regulator;
6-137 8.23e-04

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 40.40  E-value: 8.23e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061   6 IHYFLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLTPEGEYLAKQGQDILSLANKTVTNLSQ- 84
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQi 90

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 488294061  85 NEFINGEITIGGGETKAMSFLANALQQITSQH-SADIHLHLYSGNADDVIERLD 137
Cdd:PRK09801  91 KTRPEGMIRIGCSFGFGRSHIAPAITELMRNYpELQVHFELFDRQIDLVQDNID 144
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 119-193 1.09e-03

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


Pssm-ID: 176132  Cd Length: 198  Bit Score: 39.47  E-value: 1.09e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488294061 119 DIHLHLYSGNADDVIERLDKGLLDFGLIIEPAPKQKYSYLTL---PIVdtwgLITVKDHPLATKNVITAADLKEEPLF 193
Cdd:cd08441   28 DVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGIAYEPLfdyEVV----LVVAPDHPLAAKEFITPEDLADETLI 101
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 119-286 1.44e-03

The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176142 [Multi-domain]  Cd Length: 199  Bit Score: 39.08  E-value: 1.44e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 119 DIHLHLYSGNADDVIERLDKGLLDFGlIIEPAPKQKYSYLTLPIVDTWGLITV-KDHPLATKNVITAADLKEEPLFISRQ 197
Cdd:cd08451   29 DVELTLEEANTAELLEALREGRLDAA-FVRPPVARSDGLVLELLLEEPMLVALpAGHPLARERSIPLAALADEPFILFPR 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488294061 198 AQVPSqLSDWLEASLDQ--F---------RIVGTYNLlynaslmVEAGLGSALSIDGILETKQTNLRFIPLY-PALTAKI 265
Cdd:cd08451  108 PVGPG-LYDAIIAACRRagFtprigqeapQMASAINL-------VAAGLGVSIVPASMRQLQAPGVVYRPLAgAPLTAPL 179

                        170       180
                 ....*....|....*....|.
gi 488294061 266 SLIWRKNtVLSTAAALFLEQI 286
Cdd:cd08451  180 ALAYRRG-ERSPAVRNFIALV 199
MntR COG1321
Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];
22-67 1.91e-03

Mn-dependent transcriptional regulator MntR, DtxR family [Transcription];


Pssm-ID: 440932 [Multi-domain]  Cd Length: 135  Bit Score: 37.88  E-value: 1.91e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 488294061  22 AKQLHVSQPTLSKQLKELEEElGvtlFIR--GNRQIQLTPEGEYLAKQ 67
Cdd:COG1321   31 AERLGVSPPSVTEMLKKLEEK-G---LVEyePYGGITLTEEGRELALR 74
PRK11050 PRK11050
manganese-binding transcriptional regulator MntR;
22-67 2.26e-03

manganese-binding transcriptional regulator MntR;


Pssm-ID: 182927 [Multi-domain]  Cd Length: 152  Bit Score: 37.68  E-value: 2.26e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 488294061  22 AKQLHVSQPTLSKQLKELEEELGVTLfiRGNRQIQLTPEGEYLAKQ 67
Cdd:PRK11050  58 AARLGVSQPTVAKMLKRLARDGLVEM--RPYRGVFLTPEGEKLAQE 101
leuO PRK09508
leucine transcriptional activator; Reviewed
 9-58 7.52e-03

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 37.31  E-value: 7.52e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 488294061   9 FLAVVQEKTISGAAKQLHVSQPTLSKQLKELEEELGVTLFIRGNRQIQLT 58
Cdd:PRK09508  30 FDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPT 79
 
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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