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Conserved domains on  [gi|516290100|ref|WP_017693407|]
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MULTISPECIES: LysR substrate-binding domain-containing protein [Enterobacter]

Protein Classification

type 2 periplasmic-binding domain-containing protein( domain architecture ID 229383)

type 2 periplasmic-binding protein (PBP2) is typically comprised of two globular subdomains connected by a flexible hinge; it binds its ligand in the cleft between these domains in a manner resembling a Venus flytrap; similar to the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Periplasmic_Binding_Protein_Type_2 super family cl21456
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
 3-288 5.03e-58

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


The actual alignment was detected with superfamily member PRK09986:

Pssm-ID: 473866 [Multi-domain]  Cd Length: 294  Bit Score: 187.62  E-value: 5.03e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   3 LRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLMLEQMEHTRLAV 82
Cdd:PRK09986   9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARV 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  83 QRAIRGETGRVRVGFAGNAIFsGKMITDVRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTPDNSTTADPQIRVQK 162
Cdd:PRK09986  89 EQIGRGEAGRIEIGIVGTALW-GRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNPGFTSRR 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 163 TGNWEMIIAMCDDHPLAIHPHLSVEMLAGHPLVLYDAHDANENLTVL-LAQQLGDGFCVAHRSNSTLSVLAFAAAGLGLA 241
Cdd:PRK09986 168 LHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHSDWGKFLQrVCQQAGFSPQIIRQVNEPQTVLAMVSMGIGIT 247

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 516290100 242 LVPAPLQQVQIPGLIYRNLNaQALTANLVMISRMQEPGNAVTAFLAM 288
Cdd:PRK09986 248 LLPDSYAQIPWPGVVFRPLK-ERIPADLYAVYHPDQVTPALNKLLAA 293
 
Name Accession Description Interval E-value
PRK09986 PRK09986
LysR family transcriptional regulator;
3-288 5.03e-58

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 187.62  E-value: 5.03e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   3 LRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLMLEQMEHTRLAV 82
Cdd:PRK09986   9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARV 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  83 QRAIRGETGRVRVGFAGNAIFsGKMITDVRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTPDNSTTADPQIRVQK 162
Cdd:PRK09986  89 EQIGRGEAGRIEIGIVGTALW-GRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNPGFTSRR 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 163 TGNWEMIIAMCDDHPLAIHPHLSVEMLAGHPLVLYDAHDANENLTVL-LAQQLGDGFCVAHRSNSTLSVLAFAAAGLGLA 241
Cdd:PRK09986 168 LHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHSDWGKFLQrVCQQAGFSPQIIRQVNEPQTVLAMVSMGIGIT 247

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 516290100 242 LVPAPLQQVQIPGLIYRNLNaQALTANLVMISRMQEPGNAVTAFLAM 288
Cdd:PRK09986 248 LLPDSYAQIPWPGVVFRPLK-ERIPADLYAVYHPDQVTPALNKLLAA 293
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-196 2.04e-50

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 166.97  E-value: 2.04e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   1 MELRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLMLEQMEHTRL 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  81 AVQRAIRGETGRVRVGFagNAIFSGKMITDV-RRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTPDNSttADPQIR 159
Cdd:COG0583   81 ELRALRGGPRGTLRIGA--PPSLARYLLPPLlARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPP--PDPGLV 156

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 516290100 160 VQKTGNWEMIIAMCDDHPLAIHPHLSVEMLAGHPLVL 196
Cdd:COG0583  157 ARPLGEERLVLVASPDHPLARRAPLVNSLEALLAAVA 193
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 3.99e-26

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 97.46  E-value: 3.99e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 516290100    3 LRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-147 1.46e-25

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 102.70  E-value: 1.46e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   1 MELRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLMLEQMEHTRL 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 516290100  81 AVQRaiRGETGRVRVGFAGNAIFSGKMITDV-RRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYT 147
Cdd:NF040786  81 EFDR--YGKESKGVLRIGASTIPGQYLLPELlKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFT 146
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 92-289 1.82e-24

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: 97.58  E-value: 1.82e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  92 RVRVGFAGNAIFSGkMITDVRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTPdnSTTADPQIRVQKTGNWEMIIA 171
Cdd:cd08414    1 RLRIGFVGSALYGL-LPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVR--PPPDPPGLASRPLLREPLVVA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 172 MCDDHPLAIHPHLSVEMLAGHPLVLYDAHDA---NENLTVLLAQQlgdGFC--VAHRSNSTLSVLAFAAAGLGLALVPAP 246
Cdd:cd08414   78 LPADHPLAARESVSLADLADEPFVLFPREPGpglYDQILALCRRA---GFTprIVQEASDLQTLLALVAAGLGVALVPAS 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 516290100 247 LQQVQIPGLIYRNLNAQALTANLVMISRMQEPGNAVTAFLAMA 289
Cdd:cd08414  155 VARLQRPGVVYRPLADPPPRSELALAWRRDNASPALRAFLELA 197
TF_pcaQ TIGR02424
pca operon transcription factor PcaQ; Members of this family are LysR-family transcription ...
 1-196 6.48e-19

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: 84.77  E-value: 6.48e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100    1 MELRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLMLEQMEHTRL 80
Cdd:TIGR02424   3 IKFRHLQCFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGTPLFERDRRGIRLTRYGELFLRHAGASLAALRQGVA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   81 AVQRAIRGETGRVRVGfAGNAIFSGKMITDVRRFRKTHPDAEVTIQEIAPQKQVAAILAGHID--VGYTPDNSTTADpqI 158
Cdd:TIGR02424  83 SLSQLGEGEGPTVRIG-ALPTVAARLMPEVVKRFLARAPRLRVRIMTGPNAYLLDQLRVGALDlvVGRLGAPETMQG--L 159

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 516290100  159 RVQKTGNWEMIIAMCDDHPLAIHPHLSVEMLAGHPLVL 196
Cdd:TIGR02424 160 SFEHLYNEPVVFVVRAGHPLLAAPSLPVASLADYPVLL 197
 
Name Accession Description Interval E-value
PRK09986 PRK09986
LysR family transcriptional regulator;
3-288 5.03e-58

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 187.62  E-value: 5.03e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   3 LRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLMLEQMEHTRLAV 82
Cdd:PRK09986   9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARV 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  83 QRAIRGETGRVRVGFAGNAIFsGKMITDVRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTPDNSTTADPQIRVQK 162
Cdd:PRK09986  89 EQIGRGEAGRIEIGIVGTALW-GRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNPGFTSRR 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 163 TGNWEMIIAMCDDHPLAIHPHLSVEMLAGHPLVLYDAHDANENLTVL-LAQQLGDGFCVAHRSNSTLSVLAFAAAGLGLA 241
Cdd:PRK09986 168 LHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHSDWGKFLQrVCQQAGFSPQIIRQVNEPQTVLAMVSMGIGIT 247

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 516290100 242 LVPAPLQQVQIPGLIYRNLNaQALTANLVMISRMQEPGNAVTAFLAM 288
Cdd:PRK09986 248 LLPDSYAQIPWPGVVFRPLK-ERIPADLYAVYHPDQVTPALNKLLAA 293
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-196 2.04e-50

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 166.97  E-value: 2.04e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   1 MELRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLMLEQMEHTRL 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  81 AVQRAIRGETGRVRVGFagNAIFSGKMITDV-RRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTPDNSttADPQIR 159
Cdd:COG0583   81 ELRALRGGPRGTLRIGA--PPSLARYLLPPLlARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPP--PDPGLV 156

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 516290100 160 VQKTGNWEMIIAMCDDHPLAIHPHLSVEMLAGHPLVL 196
Cdd:COG0583  157 ARPLGEERLVLVASPDHPLARRAPLVNSLEALLAAVA 193
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-290 8.93e-40

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 140.68  E-value: 8.93e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   1 MELRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLMLEQMEHTRL 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  81 AVQRAIRgETGRVRVGFAGNAifSGKMITDV-RRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTPDNstTADPQIR 159
Cdd:PRK09906  81 RARKIVQ-EDRQLTIGFVPSA--EVNLLPKVlPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHP--VYSDEID 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 160 VQKTGNWEMIIAMCDDHPLAIHPHLSVEMLAGHPLVLYDAHDAN--ENLTVLLAQQLGDGFCVAHRSNSTLSVLAFAAAG 237
Cdd:PRK09906 156 YLELLDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYSGslAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMG 235

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 516290100 238 LGLALVPAPLQQVQIPGLIYRNLNAQALTANLVMISRMQEPGNAVTAFLAMAN 290
Cdd:PRK09906 236 LGCTIIPGYMNNFNTGQVVFRPLAGNVPSIALLMAWKKGEMKPALRDFIAIVQ 288
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-196 8.58e-34

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 124.68  E-value: 8.58e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   1 MELRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLMLEQMEhtrl 80
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLE---- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  81 AVQRAIR--GETGRVRVGFAGNAIFSGKMITD-VRRFRKTHPDAEVTIQEIaPQKQVAAILA-GHIDVGYTPDNSTTADp 156
Cdd:PRK11242  77 AGRRAIHdvADLSRGSLRLAMTPTFTAYLIGPlIDAFHARYPGITLTIREM-SQERIEALLAdDELDVGIAFAPVHSPE- 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 516290100 157 qIRVQKTGNWEMIIAMCDDHPLAIHPH-LSVEMLAGHPLVL 196
Cdd:PRK11242 155 -IEAQPLFTETLALVVGRHHPLAARRKaLTLDELADEPLVL 194
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 3.99e-26

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 97.46  E-value: 3.99e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 516290100    3 LRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-147 1.46e-25

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 102.70  E-value: 1.46e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   1 MELRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLMLEQMEHTRL 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 516290100  81 AVQRaiRGETGRVRVGFAGNAIFSGKMITDV-RRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYT 147
Cdd:NF040786  81 EFDR--YGKESKGVLRIGASTIPGQYLLPELlKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFT 146
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 92-289 1.82e-24

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: 97.58  E-value: 1.82e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  92 RVRVGFAGNAIFSGkMITDVRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTPdnSTTADPQIRVQKTGNWEMIIA 171
Cdd:cd08414    1 RLRIGFVGSALYGL-LPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVR--PPPDPPGLASRPLLREPLVVA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 172 MCDDHPLAIHPHLSVEMLAGHPLVLYDAHDA---NENLTVLLAQQlgdGFC--VAHRSNSTLSVLAFAAAGLGLALVPAP 246
Cdd:cd08414   78 LPADHPLAARESVSLADLADEPFVLFPREPGpglYDQILALCRRA---GFTprIVQEASDLQTLLALVAAGLGVALVPAS 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 516290100 247 LQQVQIPGLIYRNLNAQALTANLVMISRMQEPGNAVTAFLAMA 289
Cdd:cd08414  155 VARLQRPGVVYRPLADPPPRSELALAWRRDNASPALRAFLELA 197
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-221 1.59e-22

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 94.71  E-value: 1.59e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   1 MELRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLMLEQMEHTR- 79
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKe 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  80 LAVQraiRGE--TGRVRVGF---AGNAIFSgkMItdVRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTPDNSTTA 154
Cdd:PRK11151  81 MASQ---QGEtmSGPLHIGLiptVGPYLLP--HI--IPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESE 153

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 516290100 155 dPQIRVQkTGNWEMIIAMCDDHPLAIHPHLSVEMLAGHP-LVLYDAHdanenltVLLAQQLgdGFCVA 221
Cdd:PRK11151 154 -AFIEVP-LFDEPMLLAVYEDHPWANRDRVPMSDLAGEKlLMLEDGH-------CLRDQAM--GFCFE 210
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-127 1.58e-21

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 92.05  E-value: 1.58e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   1 MELRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLMLEQMEHTRL 80
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 516290100  81 AVQRAIRGETGRVRVGFAGNAIFSGKMITDVRRFRKTHPDAEVTIQE 127
Cdd:PRK11233  81 AVHNVGQALSGQVSIGLAPGTAASSLTMPLLQAVRAEFPGIVLYLHE 127
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-289 1.55e-20

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: 176139 [Multi-domain]  Cd Length: 197  Bit Score: 86.94  E-value: 1.55e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  92 RVRVGFAGNAIFSGkMITDVRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTpdNSTTADPQIRVQKTGNWEMIIA 171
Cdd:cd08448    1 RLRIGFVGSMLYRG-LPRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFV--HSRRLPAGLSARLLHREPFVCC 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 172 MCDDHPLAIHPHLSVEMLAGHPLVLYDAHDANENLTVLLAQQLGDGFC--VAHRSNSTLSVLAFAAAGLGLALVPAPLQQ 249
Cdd:cd08448   78 LPAGHPLAARRRIDLRELAGEPFVLFSREVSPDYYDQIIALCMDAGFHpkIRHEVRHWLTVVALVAAGMGVALVPRSLAR 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 516290100 250 VQIPGLIYRNLNAQALTANLVMISRMQEPGNAVTAFLAMA 289
Cdd:cd08448  158 AGLAGVRFLPLKGATQRSELYAAWKASAPNPALQAFLAAL 197
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-198 1.61e-19

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 86.58  E-value: 1.61e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   1 MELRHLRYFLAVAEEE-HFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVE-LTEAGSLLLSEARLMLEQMEHT 78
Cdd:PRK12682   1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  79 -RLAVQRAIRgETGRVRVGFA-GNAIFSGKMItdVRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTPDnSTTADP 156
Cdd:PRK12682  81 kRIGDDFSNQ-DSGTLTIATThTQARYVLPRV--VAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATE-SLADDP 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 516290100 157 QIRVQKTGNWEMIIAMCDDHPLAIHPHLSVEMLAGHPLVLYD 198
Cdd:PRK12682 157 DLATLPCYDWQHAVIVPPDHPLAQEERITLEDLAEYPLITYH 198
TF_pcaQ TIGR02424
pca operon transcription factor PcaQ; Members of this family are LysR-family transcription ...
 1-196 6.48e-19

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: 84.77  E-value: 6.48e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100    1 MELRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLMLEQMEHTRL 80
Cdd:TIGR02424   3 IKFRHLQCFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGTPLFERDRRGIRLTRYGELFLRHAGASLAALRQGVA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   81 AVQRAIRGETGRVRVGfAGNAIFSGKMITDVRRFRKTHPDAEVTIQEIAPQKQVAAILAGHID--VGYTPDNSTTADpqI 158
Cdd:TIGR02424  83 SLSQLGEGEGPTVRIG-ALPTVAARLMPEVVKRFLARAPRLRVRIMTGPNAYLLDQLRVGALDlvVGRLGAPETMQG--L 159

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 516290100  159 RVQKTGNWEMIIAMCDDHPLAIHPHLSVEMLAGHPLVL 196
Cdd:TIGR02424 160 SFEHLYNEPVVFVVRAGHPLLAAPSLPVASLADYPVLL 197
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-145 6.95e-19

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 84.69  E-value: 6.95e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   3 LRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLMLEQMEHTRLAV 82
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 516290100  83 QRAIRGETGRVRVGfAGNAIFSGKMITDVRRFRKTHPDAEVTIQeIAPQKQVA-AILAGHIDVG 145
Cdd:CHL00180  87 EDLKNLQRGTLIIG-ASQTTGTYLMPRLIGLFRQRYPQINVQLQ-VHSTRRIAwNVANGQIDIA 148
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 11-213 7.16e-19

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 84.61  E-value: 7.16e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  11 AVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLMLEQMEHTRLAVQRAIRGET 90
Cdd:PRK11074  12 AVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQVANGWR 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  91 GRVRVGFaGNAIFSGKMITDVRRFRKTHPDAEVTI-QEiapqkqV-----AAILAGHIDVGYtpdNSTTADP-----QIR 159
Cdd:PRK11074  92 GQLSIAV-DNIVRPDRTRQLIVDFYRHFDDVELIIrQE------VfngvwDALADGRVDIAI---GATRAIPvggrfAFR 161

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 516290100 160 VQKTGNWEMIIAmcDDHPLAIHPH-LSVEMLAGHP-LVLYD-AHDANENLTVLLAQQ 213
Cdd:PRK11074 162 DMGMLSWACVVS--SDHPLASMDGpLSDDELRPYPsLCLEDtSRTLPKRITWLLDNQ 216
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-199 1.17e-18

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 83.94  E-value: 1.17e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   1 MELRHLRYFL-AVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVE-LTEAGSLLLSEARLMLEQMEHT 78
Cdd:PRK12683   1 MNFQQLRIIReAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLLDAENL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  79 RLAVQRAIRGETGRVRVG-------FAGNAIfsgkmitdVRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTPDnS 151
Cdd:PRK12683  81 RRLAEQFADRDSGHLTVAtthtqarYALPKV--------VRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATE-A 151

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 516290100 152 TTADPQIRVQKTGNWEMIIAMCDDHPLAIHPHLSVEMLAGHPLVLYDA 199
Cdd:PRK12683 152 LDREPDLVSFPYYSWHHVVVVPKGHPLTGRENLTLEAIAEYPIITYDQ 199
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 6-194 7.45e-18

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 81.81  E-value: 7.45e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   6 LRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLMLEQM-EHTRlAVQR 84
Cdd:PRK11139  11 LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLaEATR-KLRA 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  85 aiRGETGRVRVgfagNAI--FSGKMITD-VRRFRKTHPDAEVtiqEIAPQKQVAAILAGHIDVG--YTPDNsttaDPQIR 159
Cdd:PRK11139  90 --RSAKGALTV----SLLpsFAIQWLVPrLSSFNEAHPDIDV---RLKAVDRLEDFLRDDVDVAirYGRGN----WPGLR 156

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 516290100 160 VQKTGNWEMIIAMCDDHPLAIHPHLSVEMLAGHPL 194
Cdd:PRK11139 157 VEKLLDEYLLPVCSPALLNGGKPLKTPEDLARHTL 191
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 92-289 1.24e-17

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: 79.24  E-value: 1.24e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  92 RVRVGFAGnAIFSGKMITDVRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGY--TPDnsTTADPQIRVQKTGNWEMI 169
Cdd:cd08449    1 HLNIGMVG-SVLWGGLGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFvrFAD--TLNDPPLASELLWREPMV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 170 IAMCDDHPLAIHPHLSVEMLAGHPLVLYD-AHDANENLTVLLAQQLGDGFCVAHRSNSTLSVLAFAAAGLGLALVPAPLQ 248
Cdd:cd08449   78 VALPEEHPLAGRKSLTLADLRDEPFVFLRlANSRFADFLINCCLQAGFTPQITQEVVEPQTLMALVAAGFGVALVPESYA 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 516290100 249 QVQIPGLIYRNLnAQALTANLVMISRMQEPGNAVTAFLAMA 289
Cdd:cd08449  158 RLPWPGVRFIPL-KQAISADLYAVYHPDSATPVIQAFLALL 197
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-77 4.41e-17

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 79.85  E-value: 4.41e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 516290100   6 LRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLMLEQMEH 77
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLES 78
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 111-289 3.37e-16

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: 75.33  E-value: 3.37e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 111 VRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTPDNSTtaDPQIRVQKTGNWEMIIAMCDDHPLAIHPHLSVEMLA 190
Cdd:cd05466   19 LAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVD--DPGLESEPLFEEPLVLVVPPDHPLAKRKSVTLADLA 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 191 GHPLVLYDAHDANENLTVLLAQQLGDGFCVAHRSNSTLSVLAFAAAGLGLALVPAP-LQQVQIPGLIYRNLNAQALTANL 269
Cdd:cd05466   97 DEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESaVEELADGGLVVLPLEDPPLSRTI 176

                        170       180
                 ....*....|....*....|.
gi 516290100 270 VMISRMQEPGN-AVTAFLAMA 289
Cdd:cd05466  177 GLVWRKGRYLSpAARAFLELL 197
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-200 9.39e-16

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 75.78  E-value: 9.39e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   1 MELRHLRYFLAVAEEE-HFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRR-VELTEAGSLLLSEARLMLEQMEHT 78
Cdd:PRK12684   1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRlRGLTEPGRIILASVERILQEVENL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  79 RlavqrairgetgrvRVGFAGNAIFSGKMITD-------------VRRFRKTHPDAEVTIQEIAPqKQVAA-ILAGHIDV 144
Cdd:PRK12684  81 K--------------RVGKEFAAQDQGNLTIAtthtqaryalpaaIKEFKKRYPKVRLSILQGSP-TQIAEmVLHGQADL 145

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 516290100 145 GYTPDnSTTADPQIRVQKTGNWEMIIAMCDDHPLAIHPHLSVEMLAGHPLVLYDAH 200
Cdd:PRK12684 146 AIATE-AIADYKELVSLPCYQWNHCVVVPPDHPLLERKPLTLEDLAQYPLITYDFA 200
PRK09791 PRK09791
LysR family transcriptional regulator;
1-127 4.26e-15

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 74.03  E-value: 4.26e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   1 MELRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLMLEQMEHTRL 80
Cdd:PRK09791   5 VKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQE 84

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 516290100  81 AVQRAIRGETGRVRVGFAGnAIFSGKMITDVRRFRKTHPDAEVTIQE 127
Cdd:PRK09791  85 DIRQRQGQLAGQINIGMGA-SIARSLMPAVISRFHQQHPQVKVRIME 130
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 92-289 7.99e-15

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: 71.44  E-value: 7.99e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  92 RVRVGFAGNAIFSGKMITDVRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGY--TPDNSttaDPQIRVQKTGNWEMI 169
Cdd:cd08451    1 RLRVGFTSSAAFHPLVPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFvrPPVAR---SDGLVLELLLEEPML 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 170 IAMCDDHPLAIHPHLSVEMLAGHPLVLYDAHDANENLTVLLAQQLGDGFC--VAHRSNSTLSVLAFAAAGLGLALVPAPL 247
Cdd:cd08451   78 VALPAGHPLARERSIPLAALADEPFILFPRPVGPGLYDAIIAACRRAGFTprIGQEAPQMASAINLVAAGLGVSIVPASM 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 516290100 248 QQVQIPGLIYRNLNAQALTANLVMISRMQEPGNAVTAFLAMA 289
Cdd:cd08451  158 RQLQAPGVVYRPLAGAPLTAPLALAYRRGERSPAVRNFIALV 199
PRK12680 PRK12680
LysR family transcriptional regulator;
1-199 4.08e-14

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 71.58  E-value: 4.08e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   1 MELRHLRYFLAVAEEE-HFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVE-LTEAGSLLLSEARLMLEQMEHT 78
Cdd:PRK12680   1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  79 RLAVQRAIRGETGRVRVGFA-GNAIFSgkMITDVRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGY--TPDNSTTAD 155
Cdd:PRK12680  81 RTYAANQRRESQGQLTLTTThTQARFV--LPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIvsTAGGEPSAG 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 516290100 156 PQIRVQKtgnWEMIIAMCDDHPLAiHPHLSVEM--LAGHPLVLYDA 199
Cdd:PRK12680 159 IAVPLYR---WRRLVVVPRGHALD-TPRRAPDMaaLAEHPLISYES 200
PBP2_BenM_CatM_CatR cd08445
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 92-287 6.15e-14

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold; This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes of the ortho-pathway required for benzoate catabolism: muconate lactonizing enzyme I, muconolactone isomerase, and catechol 1,2-dioxygenase. CatR normally responds to benzoate and cis,cis-muconate, an inducer molecule, to activate transcription of the catBCA operon, whose gene products convert benzoate to catechol. 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: 176136  Cd Length: 203  Bit Score: 69.18  E-value: 6.15e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  92 RVRVGFAGNAIFsGKMITDVRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYtpDNSTTADPQIRVQKTGNWEMIIA 171
Cdd:cd08445    2 TFSIGFVPSTLY-GLLPELIRRFRQAAPDVEIELIEMTTVQQIEALKEGRIDVGF--GRLRIEDPAIRRIVLREEPLVVA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 172 MCDDHPLAIHPH-LSVEMLAGHPLVLYDA------------------------HDANENLTVLLAQQLGDGFCVahrsns 226
Cdd:cd08445   79 LPAGHPLAQEKApLTLAQLADEPLILYPAsprpsfadqvlslfrdhglrprviQEVRELQTALGLVAAGEGVTL------ 152

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 516290100 227 tlsvlafaaaglglalVPAPLQQVQIPGLIYRNLNAQALTANLVMISRMQEPGNAVTAFLA 287
Cdd:cd08445  153 ----------------VPASVQRLRRDDVVYRPLLDPDATSPIIMSVRAGDESPYIALILQ 197
PRK10341 PRK10341
transcriptional regulator TdcA;
4-143 3.39e-13

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 68.74  E-value: 3.39e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   4 RHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLMLEQMEHtrlaVQ 83
Cdd:PRK10341  10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKN----MV 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 516290100  84 RAIRGETGR--VRVGFAGNAIFSGKMITDV-RRFRKTHPDAEVTIQEIAPQKQVAAILAGHID 143
Cdd:PRK10341  86 NEINGMSSEavVDVSFGFPSLIGFTFMSDMiNKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLD 148
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-101 6.21e-13

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 67.49  E-value: 6.21e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   1 MELRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTsRRVELTEAGSLLLSEARlMLEQMEHTRL 80
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQRLLRHAR-QVRLLEAELL 79

                         90       100
                 ....*....|....*....|.
gi 516290100  81 AVQRAIRGETGRVRVgfAGNA 101
Cdd:PRK03635  80 GELPALDGTPLTLSI--AVNA 98
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-289 1.01e-12

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: 65.77  E-value: 1.01e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   90 TGRVRVGfAGNAIFSGKMITDVRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTPDNstTADPQIRVQKTGNWEMI 169
Cdd:pfam03466   1 SGRLRIG-APPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGP--PDDPGLEARPLGEEPLV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  170 IAMCDDHPLAIHPHLSVEMLAGHPLVLYDAHDANENLTVLLAQQLGDGFCVAHRSNSTLSVLAFAAAGLGLALVPAPLQQ 249
Cdd:pfam03466  78 LVAPPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 516290100  250 VQI--PGLIYRNLNAQALTANLVMISR-MQEPGNAVTAFLAMA 289
Cdd:pfam03466 158 RELadGRLVALPLPEPPLPRELYLVWRkGRPLSPAVRAFIEFL 200
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-196 1.10e-12

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 67.02  E-value: 1.10e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   3 LRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLMLEQMehtrLAV 82
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQA----VEI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  83 QRAIRGETGRVRVGFA---GNAIFSGkMITdvrRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYT--PDNSttadPQ 157
Cdd:PRK10837  81 EQLFREDNGALRIYASstiGNYILPA-MIA---RYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIegPCHS----PE 152

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 516290100 158 IRVQKTGNWEMIIAMCDDHPLAIHPhLSVEMLAGHPLVL 196
Cdd:PRK10837 153 LISEPWLEDELVVFAAPDSPLARGP-VTLEQLAAAPWIL 190
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
4-101 1.45e-12

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 66.53  E-value: 1.45e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   4 RHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTsRRVELTEAGSLLLSEARlMLEQMEHTRLAVQ 83
Cdd:PRK13348   5 KQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHLR-QVALLEADLLSTL 82

                         90
                 ....*....|....*...
gi 516290100  84 RAirGETGRVRVGFAGNA 101
Cdd:PRK13348  83 PA--ERGSPPTLAIAVNA 98
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 91-287 2.92e-12

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tfdA and tfdB gene expression. These genes encode enzymes for the conversion of 2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenol. 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: 176137 [Multi-domain]  Cd Length: 198  Bit Score: 64.22  E-value: 2.92e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  91 GRVRVGFAGNAIFsGKMITDVRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYtpDNSTTADPQIRVQKTGNWEMII 170
Cdd:cd08446    1 GELDVGYFGSAIL-DTVPRLLRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGF--GRFYPVEPDIAVENVAQERLYL 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 171 AMCDDHPLAIHPHLSVEMLAGHPLVLYDAHD------------ANENLTVLLAQQLGDGF-CVAHRSNStlsvlafaaag 237
Cdd:cd08446   78 AVPKSHPLAARPAVSLADLRNEPLILFPRGGrpsfadevlglfRRAGVEPRVAQEVEDVVaALALVAAG----------- 146

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 516290100 238 LGLALVPAPLQQVQIPGLIYRNLNAQALTANLVMISRMQEPGNAVTAFLA 287
Cdd:cd08446  147 FGVCIVPESVAALRWPGVVFRPLADAEAKVPLSCIYRKDDRSPILRAFLD 196
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
31-145 2.37e-11

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 62.53  E-value: 2.37e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  31 ALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLMLEQMEHTRLAV---QRAIRGEtgrVRVGFAGNAIFS--G 105
Cdd:PRK11716   7 TLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLdqqGPSLSGE---LSLFCSVTAAYShlP 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 516290100 106 KMItdvRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVG 145
Cdd:PRK11716  84 PIL---DRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLA 120
cbl PRK12679
HTH-type transcriptional regulator Cbl;
22-197 3.02e-11

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 62.90  E-value: 3.02e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  22 AERLNIVQPALSMQIKALETELGGPLFIRTSRR-VELTEAGSLLLSEARLMLEQMEHTRLAVQRAIRGETGRVRVGFA-G 99
Cdd:PRK12679  23 ANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRlLGMTEPGKALLVIAERILNEASNVRRLADLFTNDTSGVLTIATThT 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 100 NAIFSGKMItdVRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTPDNsTTADPQIRVQKTGNWEMIIAMCDDHPLA 179
Cdd:PRK12679 103 QARYSLPEV--IKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASER-LSNDPQLVAFPWFRWHHSLLVPHDHPLT 179

                        170
                 ....*....|....*...
gi 516290100 180 IHPHLSVEMLAGHPLVLY 197
Cdd:PRK12679 180 QITPLTLESIAKWPLITY 197
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-197 3.46e-11

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 62.73  E-value: 3.46e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   1 MELRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLMLEQMEHtrl 80
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQ--- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  81 AVQRAIRGETGRVRVGFAGNAIFSGkMITDVRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTPDnsTTADPQIRV 160
Cdd:PRK15421  79 ALQACNEPQQTRLRIAIECHSCIQW-LTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSD--ILPRSGLHY 155

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 516290100 161 QKTGNWEMIIAMCDDHPLAIHPHLSVEMLAGHPLVLY 197
Cdd:PRK15421 156 SPMFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIY 192
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
3-61 6.41e-11

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 61.94  E-value: 6.41e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 516290100   3 LRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAG 61
Cdd:PRK10086  16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEG 74
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-71 1.26e-10

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 60.80  E-value: 1.26e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 516290100   1 MELRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEAR-LM 71
Cdd:PRK03601   1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAEtLM 72
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 111-201 1.06e-09

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: 56.80  E-value: 1.06e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 111 VRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTPDNSTTadPQIRVQKTGNWEMIIAMCDDHPLAIHPHLSVEMLA 190
Cdd:cd08415   19 IARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDH--PGLESEPLASGRAVCVLPPGHPLARKDVVTPADLA 96

                         90
                 ....*....|.
gi 516290100 191 GHPLVLYDAHD 201
Cdd:cd08415   97 GEPLISLGRGD 107
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
1-76 9.86e-09

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 55.45  E-value: 9.86e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 516290100   1 MELRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLMLEQME 76
Cdd:PRK10082  11 IETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLE 86
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-197 2.06e-08

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 54.52  E-value: 2.06e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   1 MELRHLRYFLAVAEEE-HFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRV-ELTEAGSLLLSEARLMLEQMEHT 78
Cdd:PRK12681   1 MKLQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLtQVTPAGEEIIRIAREILSKVESI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  79 RLAVQRAIRGETGRVRVgfAGNAIFSGKMITDV-RRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTpdnsTTA--- 154
Cdd:PRK12681  81 KSVAGEHTWPDKGSLYI--ATTHTQARYALPPViKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAIA----TEAlhl 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 516290100 155 --D----PQIRvqktgnWEMIIAMCDDHPLAIHPHLSVEMLAGHPLVLY 197
Cdd:PRK12681 155 ydDlimlPCYH------WNRSVVVPPDHPLAKKKKLTIEELAQYPLVTY 197
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-72 2.18e-08

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 54.26  E-value: 2.18e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 516290100   1 MELRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLML 72
Cdd:PRK15092  11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKIL 82
nhaR PRK11062
transcriptional activator NhaR; Provisional
 5-71 7.34e-08

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 52.70  E-value: 7.34e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 516290100   5 HLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLM 71
Cdd:PRK11062   8 HLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKM 74
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
 111-289 9.90e-08

The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold; The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. 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: 176144 [Multi-domain]  Cd Length: 200  Bit Score: 51.21  E-value: 9.90e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 111 VRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYT-PDNSTTADPQIRVQKTGNWEMIIAMCDDHPLAIHPHLSVEML 189
Cdd:cd08453   19 VRRFREAYPDVELQLREATSDVQLEALLAGEIDAGIViPPPGASAPPALAYRPLLSEPLVLAVPAAWAAEGGAPLALAAV 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 190 AGHPLVLYDAHDANENLTVLLA--QQLGDGFCVAHRSNSTLSVLAFAAAGLGLALVPAPLQQVQIPGLIYRNLNAQALTA 267
Cdd:cd08453   99 AAEPLVIFPRRIAPAFHDAVTGyyRAAGQTPRIAQEAIQMQTIISLVSAGMGVALVPASLRNLARPGVVYRELADPAPVL 178

                        170       180
                 ....*....|....*....|..
gi 516290100 268 NLVMISRMQEPGNAVTAFLAMA 289
Cdd:cd08453  179 ETGLVWRRDDASPVLARFLDLV 200
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 92-289 1.87e-07

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: 50.58  E-value: 1.87e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  92 RVRVGFAGNAIFSgKMITDVRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYT-PDNSTTADPQIRVQKTgnwEMII 170
Cdd:cd08452    1 LLVIGFVGAAIYE-FLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLhPPIQHTALHIETVQSS---PCVL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 171 AMCDDHPLAIHPHLSVEMLAGHPLVLYdAHDANENL---TVLLAQQLGDGFCVAHRSNSTLSVLAFAAAGLGLALVPAPL 247
Cdd:cd08452   77 ALPKQHPLASKEEITIEDLRDEPIITV-AREAWPTLydeIIQLCEQAGFRPKIVQEATEYQTVIGLVSAGIGVTFVPSSA 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 516290100 248 QQVQIPGLIYRNLNAQALTANLVMISRMQEPGNAVTAFLAMA 289
Cdd:cd08452  156 KKLFNLEVAYRKIDQINLNAEWSIAYRKDNHNPLLKHFIHIS 197
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 111-196 1.97e-07

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: 50.22  E-value: 1.97e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 111 VRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTPDnsTTADPQIRVQKTGNWEMIIAMCDDHPLAIHPHLSVEMLA 190
Cdd:cd08440   19 LAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSE--PEADPDLEFEPLLRDPFVLVCPKDHPLARRRSVTWAELA 96


                 ....*.
gi 516290100 191 GHPLVL 196
Cdd:cd08440   97 GYPLIA 102
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 113-196 2.37e-06

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: 47.10  E-value: 2.37e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 113 RFRKTHPDAEVTIQeIAPQKQVA-AILAGHIDVGYTpdNSTTADPQIRVQKTGNWEMIIAMCDDHPLAIHPHLSVEMLAG 191
Cdd:cd08420   21 RFRKRYPEVRVSLT-IGNTEEIAeRVLDGEIDLGLV--EGPVDHPDLIVEPFAEDELVLVVPPDHPLAGRKEVTAEELAA 97


                 ....*
gi 516290100 192 HPLVL 196
Cdd:cd08420   98 EPWIL 102
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 111-197 5.03e-06

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: 46.40  E-value: 5.03e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 111 VRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYT--PDNSTTADpqirVQKTGNWEMIIAMCDDHPLAIHPHLSVEM 188
Cdd:cd08438   19 LAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITvlPVDEEEFD----SQPLCNEPLVAVLPRGHPLAGRKTVSLAD 94


                 ....*....
gi 516290100 189 LAGHPLVLY 197
Cdd:cd08438   95 LADEPFILF 103
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 111-203 5.97e-06

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: 46.08  E-value: 5.97e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 111 VRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYtpdNSTTAD--PQIRVQKTGNWEMIIAMCDDHPLAIHPHLSVEM 188
Cdd:cd08413   19 IAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAI---ATEALDdhPDLVTLPCYRWNHCVIVPPGHPLADLGPLTLED 95

                         90
                 ....*....|....*
gi 516290100 189 LAGHPLVLYDAHDAN 203
Cdd:cd08413   96 LAQYPLITYDFGFTG 110
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-289 7.49e-06

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: 45.72  E-value: 7.49e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  92 RVRVGFAGNAIFS--GKMITDVRRfrkTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTpdNSTTADPQI---RVQKTGnw 166
Cdd:cd08447    1 SLRIGFTAASAYSflPRLLAAARA---ALPDVDLVLREMVTTDQIEALESGRIDLGLL--RPPFARPGLetrPLVREP-- 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 167 eMIIAMCDDHPLAIHPHLSVEMLAGHPLVLYDAHDA---NENLTVLLAQQlGDGFCVAHRSNSTLSVLAFAAAGLGLALV 243
Cdd:cd08447   74 -LVAAVPAGHPLAGAERLTLEDLDGQPFIMYSPTEAryfHDLVVRLFASA-GVQPRYVQYLSQIHTMLALVRAGLGVALV 151

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 516290100 244 PAPLQQVQIPGLIYRNLNAQALT-ANLVMISRMQEPGNAVTAFLAMA 289
Cdd:cd08447  152 PASASRLRFEGVVFRPLDLPRDVpVELHLAWRRDNDNPALRALLDLI 198
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-196 9.01e-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: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 45.38  E-value: 9.01e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  92 RVRVgfAGNAIFSGKMITDV-RRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTpdNSTTADPQIRVQKTGNWEMII 170
Cdd:cd08426    1 RVRV--ATGEGLAAELLPSLiARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLA--FSPPPEPGIRVHSRQPAPIGA 76

                         90       100
                 ....*....|....*....|....*.
gi 516290100 171 AMCDDHPLAIHPHLSVEMLAGHPLVL 196
Cdd:cd08426   77 VVPPGHPLARQPSVTLAQLAGYPLAL 102
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 111-227 1.08e-05

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: 45.23  E-value: 1.08e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 111 VRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTPDNSTTADPQIRVQKTGNWEMIIAmcDDHPLAIHPHLSVEMLA 190
Cdd:cd08412   19 LRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARLPPYVWLP--ADHPLAGKDEVSLADLA 96

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 516290100 191 GHPLVLYDAhDANENLTVLLAQQLGDGFCVAHRSNST 227
Cdd:cd08412   97 AEPLILLDL-PHSREYFLSLFAAAGLTPRIAYRTSSF 132
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-144 2.27e-05

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 44.98  E-value: 2.27e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   1 MELRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLMLEQMEHTRL 80
Cdd:PRK14997   2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQD 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 516290100  81 AVQrAIRGET-GRVRVGFAGNA--IFSGKMITdvrRFRKTHPDaeVTIQEIAPQKQVAAILAGhIDV 144
Cdd:PRK14997  82 AIA-ALQVEPrGIVKLTCPVTLlhVHIGPMLA---KFMARYPD--VSLQLEATNRRVDVVGEG-VDV 141
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 3-195 2.67e-05

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 44.98  E-value: 2.67e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100   3 LRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLMLEQMEHTRLAV 82
Cdd:PRK11013   6 LRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSYYGLDRIVSAA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  83 QRAIRGETGRVRVgfAGNAIFSGKMITDV-RRFRKTHPDAEVTiqeIAPQKQV---AAILAGHIDVGYTPDNSTTADPQI 158
Cdd:PRK11013  86 ESLREFRQGQLSI--ACLPVFSQSLLPGLcQPFLARYPDVSLN---IVPQESPlleEWLSAQRHDLGLTETLHTPAGTER 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 516290100 159 RVQKTGNweMIIAMCDDHPLAIHPHLSVEMLAGHPLV 195
Cdd:PRK11013 161 TELLTLD--EVCVLPAGHPLAAKKVLTPDDFAGENFI 195
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 111-196 3.97e-05

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: 43.67  E-value: 3.97e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 111 VRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGY--TPdnstTADPQIRVQKTGNWEMIIAMCDDHPLAIHPHLSVEM 188
Cdd:cd08411   20 LPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALlaLP----VDEPGLEEEPLFDEPFLLAVPKDHPLAKRKSVTPED 95


                 ....*...
gi 516290100 189 LAGHPLVL 196
Cdd:cd08411   96 LAGERLLL 103
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-74 8.21e-05

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 43.60  E-value: 8.21e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 516290100   1 ME-LRHLRYFLAVAEEEHFGRAAERLNIVQPALSMQIKALETELGGPLFIRTSRRVELTEAGSLLLSEARLMLEQ 74
Cdd:PRK10632   1 MErLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHE 75
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-215 2.08e-04

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


Pssm-ID: 176113  Cd Length: 198  Bit Score: 41.35  E-value: 2.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  92 RVRVgFAGNAIFSGKMITDVRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTPDNSTTADPQIRVQKTGnwEMIIA 171
Cdd:cd08421    1 HVRL-LANTSAIVEFLPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLETRPYRTD--RLVVV 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 516290100 172 MCDDHPLAIHPHLSVEMLAGHPLVLYDAHDANENLTVLLAQQLG 215
Cdd:cd08421   78 VPRDHPLAGRASVAFADTLDHDFVGLPAGSALHTFLREAAARLG 121
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 113-195 2.58e-04

The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors 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. In Agrobacterium tumefaciens, 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, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. 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: 176146 [Multi-domain]  Cd Length: 196  Bit Score: 41.32  E-value: 2.58e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 113 RFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTpdNSTTADPQIRVQKTGNWEMIIAMCDDHPLAIHPHLSVEMLAGH 192
Cdd:cd08457   21 AFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIA--DGPLEERQGFLIETRSLPAVVAVPMGHPLAQLDVVSPQDLAGE 98


                 ...
gi 516290100 193 PLV 195
Cdd:cd08457   99 RII 101
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
 111-197 4.79e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold; Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonation enzyme. Both Cbl and CysB require expression of the tau and ssu genes. Like many other members of the LTTR family, the Cbl 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: 176135  Cd Length: 198  Bit Score: 40.57  E-value: 4.79e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 111 VRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTPDnSTTADPQIRVQKTGNWEMIIAMCDDHPL-AIHPhLSVEML 189
Cdd:cd08444   19 VQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIGIATE-ALENHPELVSFPYYDWHHHIIVPVGHPLeSITP-LTIETI 96


                 ....*...
gi 516290100 190 AGHPLVLY 197
Cdd:cd08444   97 AKWPIITY 104
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 112-195 5.56e-04

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 40.28  E-value: 5.56e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 112 RRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTpdnSTTAD--PQIRVQKTGNWEMIIAMCDDHPLAIHPHLSVEML 189
Cdd:cd08436   20 ARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFV---GLPERrpPGLASRELAREPLVAVVAPDHPLAGRRRVALADL 96


                 ....*.
gi 516290100 190 AGHPLV 195
Cdd:cd08436   97 ADEPFV 102
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 111-289 9.08e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold; HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176141 [Multi-domain]  Cd Length: 196  Bit Score: 39.67  E-value: 9.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 111 VRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYTPDNSTTADpqIRVQKTGNWEMIIAMCDDHPLAIHPHLSVEMLA 190
Cdd:cd08450   19 LPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDG--IDYQLLLKEPLIVVLPADHRLAGREKIPPQDLA 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 191 GHPLVLYDAHDANENLTVL-LAQQLGDGFCVAHRSNSTLSVLAFAAAGLGLALVPAPLQQVQIPGLIYRNLNAQALTANL 269
Cdd:cd08450   97 GENFISPAPTAPVLQQVIEnYAAQHNIQPNIIQEADNLLSAMSLVASTLGCALLPLYANNLLPPSVVARPLSGETPTIDL 176

                        170       180
                 ....*....|....*....|
gi 516290100 270 VMISRMQEPGNAVTAFLAMA 289
Cdd:cd08450  177 VMGYNKANTSPLLKRFLSRA 196
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 111-245 1.92e-03

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


Pssm-ID: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 38.73  E-value: 1.92e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100 111 VRRFRKTHPDAEVTIQEIAPQKQVAAILAGHID---VGYTPDNSTTADPQIRVQKTGNWEMIIAMCDDHPLAIHPHLSVE 187
Cdd:cd08423   19 LAALRARHPGLEVRLREAEPPESLDALRAGELDlavVFDYPVTPPPDDPGLTRVPLLDDPLDLVLPADHPLAGREEVALA 98

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 516290100 188 MLAGHPLVL-YDAHDANENLTVLLAQQlgdGFC--VAHRSNSTLSVLAFAAAGLGLALVPA 245
Cdd:cd08423   99 DLADEPWIAgCPGSPCHRWLVRACRAA---GFTprIAHEADDYATVLALVAAGLGVALVPR 156
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 92-197 2.42e-03

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: 38.41  E-value: 2.42e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  92 RVRVGFAGnAIFSGKMITDVRRFRKTHPDAEVTIQEIAPQKQVAAILAGHID--VGYTPDnsTTADPQIRVQKTGNWEMI 169
Cdd:cd08435    1 TVRVGAVP-AAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDlaIGRLAD--DEQPPDLASEELADEPLV 77

                         90       100
                 ....*....|....*....|....*...
gi 516290100 170 IAMCDDHPLAIHPHLSVEMLAGHPLVLY 197
Cdd:cd08435   78 VVARPGHPLARRARLTLADLADYPWVLP 105
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 93-198 2.54e-03

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


Pssm-ID: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 38.29  E-value: 2.54e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516290100  93 VRVGFAgnAIFSGKMITD-VRRFRKTHPDAEVTIQEIAPQKQVAAILAGHIDVGYT---PDNSTTADPQIRVQktgnwEM 168
Cdd:cd08434    2 VRLGFL--HSLGTSLVPDlIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCspvPDEPDIEWIPLFTE-----EL 74

                         90       100       110
                 ....*....|....*....|....*....|
gi 516290100 169 IIAMCDDHPLAIHPHLSVEMLAGHPLVLYD 198
Cdd:cd08434   75 VLVVPKDHPLAGRDSVDLAELADEPFVLLS 104
 
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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