NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|488192442|ref|WP_002263650|]
View 

LysR family transcriptional regulator [Streptococcus mutans]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

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

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

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-295 1.07e-38

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 136.92  E-value: 1.07e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442   1 MNFQQCRYVEAIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRILGEADLLK- 79
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEa 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442  80 --KRYQDNYKKSFTISSHHYdFLAIPLLEIAEKFKKDFQ--HFHLIETTTKKILESVLNFESDLGILYLNDDNRhilery 155
Cdd:COG0583   81 elRALRGGPRGTLRIGAPPS-LARYLLPPLLARFRARHPgvRLELREGNSDRLVDALLEGELDLAIRLGPPPDP------ 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442 156 fkqhDLAFTPLGDFPTRIFLRKDHPLAQQKVIekvqlkdykqvrfrqeisglnfdedtldipenqsvfySNDRGTIMNIL 235
Cdd:COG0583  154 ----GLVARPLGEERLVLVASPDHPLARRAPL-------------------------------------VNSLEALLAAV 192

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488192442 236 cgsdayASGLGI-------VNSFIKD-QIVLIPLKDSKMH-TLGFVSNKRKQETDITQQFITAVKNSLR 295
Cdd:COG0583  193 ------AAGLGIallprflAADELAAgRLVALPLPDPPPPrPLYLVWRRRRHLSPAVRAFLDFLREALA 255
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-295 1.07e-38

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 136.92  E-value: 1.07e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442   1 MNFQQCRYVEAIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRILGEADLLK- 79
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEa 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442  80 --KRYQDNYKKSFTISSHHYdFLAIPLLEIAEKFKKDFQ--HFHLIETTTKKILESVLNFESDLGILYLNDDNRhilery 155
Cdd:COG0583   81 elRALRGGPRGTLRIGAPPS-LARYLLPPLLARFRARHPgvRLELREGNSDRLVDALLEGELDLAIRLGPPPDP------ 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442 156 fkqhDLAFTPLGDFPTRIFLRKDHPLAQQKVIekvqlkdykqvrfrqeisglnfdedtldipenqsvfySNDRGTIMNIL 235
Cdd:COG0583  154 ----GLVARPLGEERLVLVASPDHPLARRAPL-------------------------------------VNSLEALLAAV 192

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488192442 236 cgsdayASGLGI-------VNSFIKD-QIVLIPLKDSKMH-TLGFVSNKRKQETDITQQFITAVKNSLR 295
Cdd:COG0583  193 ------AAGLGIallprflAADELAAgRLVALPLPDPPPPrPLYLVWRRRRHLSPAVRAFLDFLREALA 255
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-206 1.60e-25

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 103.15  E-value: 1.60e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442   1 MNFQQCRYVEAIANTG-SFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSntGARL---TDDGYDFLKYAKRILGEAD 76
Cdd:PRK12682   1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRH--GKRLkglTEPGKAVLDVIERILREVG 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442  77 LLKK---RYQDNYKKSFTISSHH----YdflAIPllEIAEKFKKDFQ--HFHLIETTTKKILESVLNFESDLGIlylndd 147
Cdd:PRK12682  79 NIKRigdDFSNQDSGTLTIATTHtqarY---VLP--RVVAAFRKRYPkvNLSLHQGSPDEIARMVISGEADIGI------ 147

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 488192442 148 nrhILERYFKQHDLAFTPLGDFPTRIFLRKDHPLAQQKVIEKVQLKDYKQVRFRQEISG 206
Cdd:PRK12682 148 ---ATESLADDPDLATLPCYDWQHAVIVPPDHPLAQEERITLEDLAEYPLITYHPGFTG 203
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-141 1.30e-24

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: 100.38  E-value: 1.30e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442   1 MNFQQcryVEA---IANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRILGEADL 77
Cdd:NF040786   1 MNLKQ---LEAfvnVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEK 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488192442  78 LK---KRYQDNYKKSFTISSHhydflAIP----LLEIAEKFKKDFQH--FHLIETTTKKILESVLNFESDLGI 141
Cdd:NF040786  78 LEeefDRYGKESKGVLRIGAS-----TIPgqylLPELLKKFKEKYPNvrFKLMISDSIKVIELLLEGEVDIGF 145
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 3.47e-21

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 84.74  E-value: 3.47e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 488192442    3 FQQCRYVEAIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 104-290 5.58e-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: 74.56  E-value: 5.58e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442 104 LLEIAEKFKKDFQ--HFHLIETTTKKILESVLNFESDLGILYLNDDnrhileryfkQHDLAFTPLGDFPTRIFLRKDHPL 181
Cdd:cd05466   15 LPPLLAAFRQRYPgvELSLVEGGSSELLEALLEGELDLAIVALPVD----------DPGLESEPLFEEPLVLVVPPDHPL 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442 182 AQQKVIEKVQLKDYKQVRFRQEISGLNFDEDTLD--IPENQSVFYSNDRGTIMnilcgsDAYASGLGI-------VNSFI 252
Cdd:cd05466   85 AKRKSVTLADLADEPLILFERGSGLRRLLDRAFAeaGFTPNIALEVDSLEAIK------ALVAAGLGIallpesaVEELA 158

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 488192442 253 KDQIVLIPLKDSKMH-TLGFVSNKRKQETDITQQFITAV 290
Cdd:cd05466  159 DGGLVVLPLEDPPLSrTIGLVWRKGRYLSPAARAFLELL 197
TF_pcaQ TIGR02424
pca operon transcription factor PcaQ; Members of this family are LysR-family transcription ...
 11-195 8.81e-13

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: 67.43  E-value: 8.81e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442   11 AIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRIL-----GEADLLKKRYQDn 85
Cdd:TIGR02424  13 EVARQGSVKRAAEALHITQPAVSKTLRELEEILGTPLFERDRRGIRLTRYGELFLRHAGASLaalrqGVASLSQLGEGE- 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442   86 yKKSFTISshhydflAIPLLE--IAEKFKKDFQH------FHLIETTTKKILESVLNFESDLGILYLNDDNRhileryfk 157
Cdd:TIGR02424  92 -GPTVRIG-------ALPTVAarLMPEVVKRFLAraprlrVRIMTGPNAYLLDQLRVGALDLVVGRLGAPET-------- 155

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 488192442  158 QHDLAFTPLGDFPTRIFLRKDHPLAQQKVIEKVQLKDY 195
Cdd:TIGR02424 156 MQGLSFEHLYNEPVVFVVRAGHPLLAAPSLPVASLADY 193
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 1-178 8.50e-10

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


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 58.59  E-value: 8.50e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442   1 MNFQQCRYVEAIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRILGEADLLKK 80
Cdd:NF041036   1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442  81 RYqdnykKSFTISSHHY-----DFLAIPLLEIAEKFKKDFQHFH---LIETTTKKILESVLNFESDLGIL-YLNDDNRHI 151
Cdd:NF041036  81 EL-----KSFKGRQRLSicctpTFGMAHLPGVLNRFMLRNADVVdlkFLFHSPAQALEGIQNKEFDLAIIeHCADLDLGR 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 488192442 152 LERY-FKQHDLAF--TPLGDFPT-----------RIFLRKD 178
Cdd:NF041036 156 FHTYpLPQDELVFvsAPSLGLPTpnvtlerllelCLITRRD 196
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-295 1.07e-38

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 136.92  E-value: 1.07e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442   1 MNFQQCRYVEAIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRILGEADLLK- 79
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEa 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442  80 --KRYQDNYKKSFTISSHHYdFLAIPLLEIAEKFKKDFQ--HFHLIETTTKKILESVLNFESDLGILYLNDDNRhilery 155
Cdd:COG0583   81 elRALRGGPRGTLRIGAPPS-LARYLLPPLLARFRARHPgvRLELREGNSDRLVDALLEGELDLAIRLGPPPDP------ 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442 156 fkqhDLAFTPLGDFPTRIFLRKDHPLAQQKVIekvqlkdykqvrfrqeisglnfdedtldipenqsvfySNDRGTIMNIL 235
Cdd:COG0583  154 ----GLVARPLGEERLVLVASPDHPLARRAPL-------------------------------------VNSLEALLAAV 192

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488192442 236 cgsdayASGLGI-------VNSFIKD-QIVLIPLKDSKMH-TLGFVSNKRKQETDITQQFITAVKNSLR 295
Cdd:COG0583  193 ------AAGLGIallprflAADELAAgRLVALPLPDPPPPrPLYLVWRRRRHLSPAVRAFLDFLREALA 255
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-206 1.60e-25

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 103.15  E-value: 1.60e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442   1 MNFQQCRYVEAIANTG-SFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSntGARL---TDDGYDFLKYAKRILGEAD 76
Cdd:PRK12682   1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRH--GKRLkglTEPGKAVLDVIERILREVG 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442  77 LLKK---RYQDNYKKSFTISSHH----YdflAIPllEIAEKFKKDFQ--HFHLIETTTKKILESVLNFESDLGIlylndd 147
Cdd:PRK12682  79 NIKRigdDFSNQDSGTLTIATTHtqarY---VLP--RVVAAFRKRYPkvNLSLHQGSPDEIARMVISGEADIGI------ 147

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 488192442 148 nrhILERYFKQHDLAFTPLGDFPTRIFLRKDHPLAQQKVIEKVQLKDYKQVRFRQEISG 206
Cdd:PRK12682 148 ---ATESLADDPDLATLPCYDWQHAVIVPPDHPLAQEERITLEDLAEYPLITYHPGFTG 203
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-141 1.30e-24

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: 100.38  E-value: 1.30e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442   1 MNFQQcryVEA---IANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRILGEADL 77
Cdd:NF040786   1 MNLKQ---LEAfvnVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEK 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488192442  78 LK---KRYQDNYKKSFTISSHhydflAIP----LLEIAEKFKKDFQH--FHLIETTTKKILESVLNFESDLGI 141
Cdd:NF040786  78 LEeefDRYGKESKGVLRIGAS-----TIPgqylLPELLKKFKEKYPNvrFKLMISDSIKVIELLLEGEVDIGF 145
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-141 1.14e-22

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 95.50  E-value: 1.14e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442   1 MNFQQCRYV-EAIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSntGARL---TDDGYDFLKYAKRILGEAD 76
Cdd:PRK12683   1 MNFQQLRIIrEAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRR--GKRLtglTEPGKELLQIVERMLLDAE 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488192442  77 LLKK---RYQDNYKKSFTISSHH----YdflAIPllEIAEKFKKDFQHFHLI--ETTTKKILESVLNFESDLGI 141
Cdd:PRK12683  79 NLRRlaeQFADRDSGHLTVATTHtqarY---ALP--KVVRQFKEVFPKVHLAlrQGSPQEIAEMLLNGEADIGI 147
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-141 5.25e-22

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 93.50  E-value: 5.25e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442   1 MNFQQCRYVEAIANTG-SFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSntGAR---LTDDGYDFLKYAKRILGEAD 76
Cdd:PRK12684   1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRH--GKRlrgLTEPGRIILASVERILQEVE 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488192442  77 LLK---KRYQDNYKKSFTISSHH----YdflAIPLLeIAEkFKKDFQHFHL--IETTTKKILESVLNFESDLGI 141
Cdd:PRK12684  79 NLKrvgKEFAAQDQGNLTIATTHtqarY---ALPAA-IKE-FKKRYPKVRLsiLQGSPTQIAEMVLHGQADLAI 147
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 3.47e-21

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 84.74  E-value: 3.47e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 488192442    3 FQQCRYVEAIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-292 9.69e-19

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 84.44  E-value: 9.69e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442   1 MNFQQCRYVEAIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRILGEADLLKK 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442  81 --RYQDNYKKSFTISshhydFLAIPLLEIAEKFKKDFQHFH------LIETTTKKILESVLNFESDLGILylnddnRHIL 152
Cdd:PRK09906  81 raRKIVQEDRQLTIG-----FVPSAEVNLLPKVLPMFRLRHpdtlieLVSLITTQQEEKLRRGELDVGFM------RHPV 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442 153 ERYFKQHDLAFTPlgdfPTRIFLRKDHPLAQQKVIEKVQLK-------DYKQVRFRQEISgLNFdedtldIPENQSVFys 225
Cdd:PRK09906 150 YSDEIDYLELLDE----PLVVVLPVDHPLAHEKEITAAQLDgvnfistDPAYSGSLAPII-KAW------FAQHNSQP-- 216

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488192442 226 NDRGTIMNILCGSDAYASGLGI------VNSFIKDQIVLIPLKDSKMHTLGFVSNKRKQETDITQQFITAVKN 292
Cdd:PRK09906 217 NIVQVATNILVTMNLVGMGLGCtiipgyMNNFNTGQVVFRPLAGNVPSIALLMAWKKGEMKPALRDFIAIVQE 289
rbcR CHL00180
LysR transcriptional regulator; Provisional
 4-192 9.66e-18

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 81.60  E-value: 9.66e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442   4 QQCRYVEAIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRILG---EADLLKK 80
Cdd:CHL00180   8 DQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILAlceETCRALE 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442  81 RYQDNYKKSFTISSHHY--DFLAIPLLEIaekFKKDFQHFH--LIETTTKKILESVLNFESDLGIL--YLNDDNRHILER 154
Cdd:CHL00180  88 DLKNLQRGTLIIGASQTtgTYLMPRLIGL---FRQRYPQINvqLQVHSTRRIAWNVANGQIDIAIVggEVPTELKKILEI 164

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 488192442 155 yfkqhdlafTPLGDFPTRIFLRKDHPLAQQKVIEKVQL 192
Cdd:CHL00180 165 ---------TPYVEDELALIIPKSHPFAKLKKIQKEDL 193
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-206 3.63e-17

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 80.24  E-value: 3.63e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442   1 MNFQQCRYV-EAIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSntGARL---TDDGYDFLKYAKRILGEAD 76
Cdd:PRK12679   1 MNFQQLKIIrEAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRR--GKRLlgmTEPGKALLVIAERILNEAS 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442  77 LLkKRYQDNYKKS----FTISSHHYDF-LAIPllEIAEKFKKDFQH--FHLIETTTKKILESVLNFESDLGIL--YLNDD 147
Cdd:PRK12679  79 NV-RRLADLFTNDtsgvLTIATTHTQArYSLP--EVIKAFRELFPEvrLELIQGTPQEIATLLQNGEADIGIAseRLSND 155

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 488192442 148 NRHILERYFKQHDLAFTPlgdfptriflrKDHPLAQQKVIEKVQLKDYKQVRFRQEISG 206
Cdd:PRK12679 156 PQLVAFPWFRWHHSLLVP-----------HDHPLTQITPLTLESIAKWPLITYRQGITG 203
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 7-76 3.55e-16

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 76.92  E-value: 3.55e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442   7 RYVEAIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRILGEAD 76
Cdd:PRK11242   7 RYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLE 76
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 104-290 5.58e-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: 74.56  E-value: 5.58e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442 104 LLEIAEKFKKDFQ--HFHLIETTTKKILESVLNFESDLGILYLNDDnrhileryfkQHDLAFTPLGDFPTRIFLRKDHPL 181
Cdd:cd05466   15 LPPLLAAFRQRYPgvELSLVEGGSSELLEALLEGELDLAIVALPVD----------DPGLESEPLFEEPLVLVVPPDHPL 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442 182 AQQKVIEKVQLKDYKQVRFRQEISGLNFDEDTLD--IPENQSVFYSNDRGTIMnilcgsDAYASGLGI-------VNSFI 252
Cdd:cd05466   85 AKRKSVTLADLADEPLILFERGSGLRRLLDRAFAeaGFTPNIALEVDSLEAIK------ALVAAGLGIallpesaVEELA 158

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 488192442 253 KDQIVLIPLKDSKMH-TLGFVSNKRKQETDITQQFITAV 290
Cdd:cd05466  159 DGGLVVLPLEDPPLSrTIGLVWRKGRYLSPAARAFLELL 197
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-187 3.45e-14

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 71.85  E-value: 3.45e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442   1 MNFQQCRYVEAIANTG-SFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSntG---ARLTDDGYDFLKYAKRILGEAD 76
Cdd:PRK12681   1 MKLQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARS--GkhlTQVTPAGEEIIRIAREILSKVE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442  77 LLKK---RYQDNYKKSFTISSHH----YdflAIPllEIAEKFKKDFQ----HFHliETTTKKILESVLNFESDLGI---- 141
Cdd:PRK12681  79 SIKSvagEHTWPDKGSLYIATTHtqarY---ALP--PVIKGFIERYPrvslHMH--QGSPTQIAEAAAKGNADFAIatea 151

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 488192442 142 LYLNDD---------NRHILeryfkqhdlaftplgdfptrifLRKDHPLAQQKVI 187
Cdd:PRK12681 152 LHLYDDlimlpcyhwNRSVV----------------------VPPDHPLAKKKKL 184
PRK09791 PRK09791
LysR family transcriptional regulator;
3-74 8.66e-13

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 67.48  E-value: 8.66e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488192442   3 FQQCRYVEAIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRILGE 74
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEE 78
TF_pcaQ TIGR02424
pca operon transcription factor PcaQ; Members of this family are LysR-family transcription ...
 11-195 8.81e-13

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: 67.43  E-value: 8.81e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442   11 AIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRIL-----GEADLLKKRYQDn 85
Cdd:TIGR02424  13 EVARQGSVKRAAEALHITQPAVSKTLRELEEILGTPLFERDRRGIRLTRYGELFLRHAGASLaalrqGVASLSQLGEGE- 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442   86 yKKSFTISshhydflAIPLLE--IAEKFKKDFQH------FHLIETTTKKILESVLNFESDLGILYLNDDNRhileryfk 157
Cdd:TIGR02424  92 -GPTVRIG-------ALPTVAarLMPEVVKRFLAraprlrVRIMTGPNAYLLDQLRVGALDLVVGRLGAPET-------- 155

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 488192442  158 QHDLAFTPLGDFPTRIFLRKDHPLAQQKVIEKVQLKDY 195
Cdd:TIGR02424 156 MQGLSFEHLYNEPVVFVVRAGHPLLAAPSLPVASLADY 193
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 104-295 1.66e-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: 65.00  E-value: 1.66e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442  104 LLEIAEKFKKDF--QHFHLIETTTKKILESVLNFESDLGILYLNDDNrhileryfkqHDLAFTPLGDFPTRIFLRKDHPL 181
Cdd:pfam03466  17 LPPLLARFRERYpdVELELTEGNSEELLDLLLEGELDLAIRRGPPDD----------PGLEARPLGEEPLVLVAPPDHPL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442  182 AQQKVIEKVQLKDYKQVRFRQEISGLNFDEDTLD--IPENQSVFYSNDRGTIMNILcgsdayASGLGI-------VNSFI 252
Cdd:pfam03466  87 ARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRaaGLRPRVVLEVNSLEALLQLV------AAGLGIallprsaVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 488192442  253 KD-QIVLIPLKDSKMH-TLGFVSNKRKQETDITQQFITAVKNSLR 295
Cdd:pfam03466 161 ADgRLVALPLPEPPLPrELYLVWRKGRPLSPAVRAFIEFLREALA 205
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-196 5.32e-12

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 65.05  E-value: 5.32e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442   1 MNFQQCRYVEAIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRILGEADLLKK 80
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442  81 RYQdNYKKSFTiSSHHYDFlaIP------LLEIAEKFKKDFQ--HFHLIETTTKKILESVLNFESDLGILYLNDDNRHIL 152
Cdd:PRK11151  81 MAS-QQGETMS-GPLHIGL--IPtvgpylLPHIIPMLHQTFPklEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFI 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 488192442 153 EryfkqhdlafTPLGDFPTRIFLRKDHPLAQQKVIEKVQLKDYK 196
Cdd:PRK11151 157 E----------VPLFDEPMLLAVYEDHPWANRDRVPMSDLAGEK 190
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-78 1.76e-11

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 63.45  E-value: 1.76e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488192442   2 NFQQCRYVEAIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTgARLTDDGYDFLKYAKRI-LGEADLL 78
Cdd:PRK13348   3 DYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRP-CRPTPAGQRLLRHLRQVaLLEADLL 79
PRK10341 PRK10341
transcriptional regulator TdcA;
12-115 3.76e-10

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 59.88  E-value: 3.76e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442  12 IANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRILGE-----ADLLKKRYQDNY 86
Cdd:PRK10341  18 VIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREmknmvNEINGMSSEAVV 97

                         90       100       110
                 ....*....|....*....|....*....|
gi 488192442  87 KKSFTISSH-HYDFLAipllEIAEKFKKDF 115
Cdd:PRK10341  98 DVSFGFPSLiGFTFMS----DMINKFKEVF 123
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
11-198 3.79e-10

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 59.82  E-value: 3.79e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442  11 AIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRILGEADLLKKRYQ---DNYK 87
Cdd:PRK10094  12 AVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQqvnDGVE 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442  88 KSFTISSHH--YDFLAIP--LLEIAEKFKkdFQHFHLIETTTKKILESVLN--FESDLGIlylndDNRHILERYFkqhdl 161
Cdd:PRK10094  92 RQVNIVINNllYNPQAVAqlLAWLNERYP--FTQFHISRQIYMGVWDSLLYegFSLAIGV-----TGTEALANTF----- 159

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 488192442 162 AFTPLGDFPTRIFLRKDHPLAQ-QKVIEKVQLKDYKQV 198
Cdd:PRK10094 160 SLDPLGSVQWRFVMAADHPLANvEEPLTEAQLRRFPAV 197
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
7-187 4.75e-10

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 59.65  E-value: 4.75e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442   7 RYVEAIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRILGEadlLKKRYQD-- 84
Cdd:PRK15421   8 KTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQ---ISQALQAcn 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442  85 ---NYKKSFTISSHHYDFLAIPLLeiaEKFKKDFQHFHLiETTTKKILESVLNFESDLGILYLNDDnrhILERyfkqHDL 161
Cdd:PRK15421  85 epqQTRLRIAIECHSCIQWLTPAL---ENFHKNWPQVEM-DFKSGVTFDPQPALQQGELDLVMTSD---ILPR----SGL 153

                        170       180
                 ....*....|....*....|....*.
gi 488192442 162 AFTPLGDFPTRIFLRKDHPLAQQKVI 187
Cdd:PRK15421 154 HYSPMFDYEVRLVLAPDHPLAAKTRI 179
PRK09986 PRK09986
LysR family transcriptional regulator;
7-75 7.03e-10

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 58.97  E-value: 7.03e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488192442   7 RYVEAIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRILGEA 75
Cdd:PRK09986  13 RYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNA 81
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 1-178 8.50e-10

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


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 58.59  E-value: 8.50e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442   1 MNFQQCRYVEAIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRILGEADLLKK 80
Cdd:NF041036   1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442  81 RYqdnykKSFTISSHHY-----DFLAIPLLEIAEKFKKDFQHFH---LIETTTKKILESVLNFESDLGIL-YLNDDNRHI 151
Cdd:NF041036  81 EL-----KSFKGRQRLSicctpTFGMAHLPGVLNRFMLRNADVVdlkFLFHSPAQALEGIQNKEFDLAIIeHCADLDLGR 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 488192442 152 LERY-FKQHDLAF--TPLGDFPT-----------RIFLRKD 178
Cdd:NF041036 156 FHTYpLPQDELVFvsAPSLGLPTpnvtlerllelCLITRRD 196
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 10-72 9.62e-10

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 58.32  E-value: 9.62e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488192442  10 EAIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRIL 72
Cdd:PRK11139  15 EAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIF 77
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 102-290 1.39e-09

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: 56.78  E-value: 1.39e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442 102 IPLLeIAEkFKKDFQH--FHLIETTTKKILESVLNFESDLGILYLNDDNRHIleryfkqhdlAFTPLGDFPTRIFLRKDH 179
Cdd:cd08434   15 VPDL-IRA-FRKEYPNvtFELHQGSTDELLDDLKNGELDLALCSPVPDEPDI----------EWIPLFTEELVLVVPKDH 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442 180 PLAQQKVIEKVQLKDYKQVRFRQEiSGLN--FDEDTLDI---PenQSVFYSNDRGTIMNILcgsdayASGLGI-----VN 249
Cdd:cd08434   83 PLAGRDSVDLAELADEPFVLLSPG-FGLRpiVDELCAAAgftP--KIAFEGEEDSTIAGLV------AAGLGVailpeMT 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 488192442 250 SFIKDQIVLIPLKDSKMH-TLGFVSNKRKQETDITQQFITAV 290
Cdd:cd08434  154 LLNPPGVKKIPIKDPDAErTIGLAWLKDRYLSPAARRFKDFV 195
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
26-170 2.60e-09

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 56.75  E-value: 2.60e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442  26 YVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRILGEADLLKKRYQDNYKK---------SFTIS-SH 95
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSlsgelslfcSVTAAySH 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488192442  96 hydflaipLLEIAEKFKKdfQHFHL-IETTT---KKILESVLNFESDLGILYLNDDnrhileryfKQHDLAFTPLGDFP 170
Cdd:PRK11716  82 --------LPPILDRFRA--EHPLVeIKLTTgdaADAVEKVQSGEADLAIAAKPET---------LPASVAFSPIDEIP 141
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-166 6.23e-09

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 55.84  E-value: 6.23e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442   1 MNFQQCRYVEAIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRIL---GEADL 77
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILrqcEQAQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442  78 LKKRYQDNYKKSFTI--------SShhydfLAIPLL-EIAEKFKKDFQHFHliETTTKKILESVLNFESDLGILYlndDN 148
Cdd:PRK11233  81 AVHNVGQALSGQVSIglapgtaaSS-----LTMPLLqAVRAEFPGIVLYLH--ENSGATLNEKLMNGQLDMAVIY---EH 150

                        170
                 ....*....|....*...
gi 488192442 149 RHIleryfkqHDLAFTPL 166
Cdd:PRK11233 151 SPV-------AGLSSQPL 161
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 9-83 8.82e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 55.33  E-value: 8.82e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488192442   9 VEAIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRILGEADLLKKRYQ 83
Cdd:PRK11074  10 VDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQ 84
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-78 2.27e-08

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 54.39  E-value: 2.27e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488192442   1 MNFQQCRYVEAIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTgARLTDDGYDFLKYAKRI-LGEADLL 78
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRTQP-CRPTEAGQRLLRHARQVrLLEAELL 79
PRK12680 PRK12680
LysR family transcriptional regulator;
1-96 5.54e-08

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 53.47  E-value: 5.54e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442   1 MNFQQCRYVEAIANTG-SFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGAR-LTDDGYDFLKYAKRILGEADLL 78
Cdd:PRK12680   1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNI 80

                         90       100
                 ....*....|....*....|..
gi 488192442  79 KKrYQDNYKK----SFTISSHH 96
Cdd:PRK12680  81 RT-YAANQRResqgQLTLTTTH 101
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
15-80 1.08e-07

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 51.94  E-value: 1.08e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488192442  15 TGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRILGEADLLKK 80
Cdd:PRK03601  15 TRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKK 80
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
10-61 1.16e-07

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 52.31  E-value: 1.16e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 488192442  10 EAIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDG 61
Cdd:PRK10086  23 EVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEG 74
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 89-288 2.42e-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: 2.42e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442  89 SFTISSHhydflAIPLLeIAEkFKKDFQH--FHLIETTTKKILESVLNFESDLGilylnddnrhILERYFKQHDLAFTPL 166
Cdd:cd08420    7 STTIGEY-----LLPRL-LAR-FRKRYPEvrVSLTIGNTEEIAERVLDGEIDLG----------LVEGPVDHPDLIVEPF 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442 167 GDFPTRIFLRKDHPLAQQKVIEKVQLKDYKQV-R---------FRQEISGLNFDEDTLDI----PENQSvfysndrgtIM 232
Cdd:cd08420   70 AEDELVLVVPPDHPLAGRKEVTAEELAAEPWIlRepgsgtrevFERALAEAGLDGLDLNIvmelGSTEA---------IK 140

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488192442 233 NilcgsdAYASGLGIvnSF-----IKDQI-----VLIPLKDSKMH-TLGFVSNKRKQETDITQQFIT 288
Cdd:cd08420  141 E------AVEAGLGI--SIlsrlaVRKELelgrlVALPVEGLRLTrPFSLIYHKDKYLSPAAEAFLE 199
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 117-187 2.84e-06

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: 47.13  E-value: 2.84e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488192442 117 HFHLIETTTKKILESVLNFESDLGILYLNDDnrhileryfkQHDLAFTPLGDFPTRIFLRKDHPLAQQKVI 187
Cdd:cd08440   30 RVRLRDVSAEQVIEAVRSGEVDFGIGSEPEA----------DPDLEFEPLLRDPFVLVCPKDHPLARRRSV 90
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 117-205 4.54e-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: 4.54e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442 117 HFHLIETTTKKILESVLNFESDLGILYLNDDnrhileryfkQHDLAFTPLGDFPTRIFLRKDHPLAQQKVIEKVQLKDYK 196
Cdd:cd08438   30 ELELVEYGGKKVEQAVLNGELDVGITVLPVD----------EEEFDSQPLCNEPLVAVLPRGHPLAGRKTVSLADLADEP 99


                 ....*....
gi 488192442 197 QVRFRQEIS 205
Cdd:cd08438  100 FILFNEDFA 108
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 11-72 1.25e-05

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 46.17  E-value: 1.25e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488192442  11 AIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRIL 72
Cdd:PRK15092  21 AVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKIL 82
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 11-186 1.46e-05

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 45.83  E-value: 1.46e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442  11 AIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRsnTGARLTDDGYDFLKY--AKRILGEADLLKKRYQD---- 84
Cdd:PRK10837  13 EVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDR--VGKRLVVNEHGRLLYprALALLEQAVEIEQLFREdnga 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442  85 ----------NYKKSFTISSHHYDFLAIPL-LEIAekfkkdfqhfhlietTTKKILESVLNFESDLGILYLNDDNRHILE 153
Cdd:PRK10837  91 lriyasstigNYILPAMIARYRRDYPQLPLeLSVG---------------NSQDVINAVLDFRVDIGLIEGPCHSPELIS 155

                        170       180       190
                 ....*....|....*....|....*....|...
gi 488192442 154 RYFKQHDLAftplgdfptrIFLRKDHPLAQQKV 186
Cdd:PRK10837 156 EPWLEDELV----------VFAAPDSPLARGPV 178
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
1-96 6.83e-05

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 43.89  E-value: 6.83e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442   1 MNFQQCRyveaiantgSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRILG--EADLL 78
Cdd:PRK10082  20 LTLEKCR---------NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQqlESNLA 90

                         90
                 ....*....|....*....
gi 488192442  79 KKRYQDNY-KKSFTISSHH 96
Cdd:PRK10082  91 ELRGGSDYaQRKIKIAAAH 109
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
10-83 8.60e-05

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


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 41.35  E-value: 8.60e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442  10 EAIANTGSFSEAAKKLyvtqpNLS-----SSIKELENDLGVQLFIRS-----NTGARLTDdgydflkYAKRILGEADLLK 79
Cdd:COG2005   28 EAIDETGSISAAAKAM-----GMSykrawDLIDAMNNLLGEPLVERQtggkgGGGARLTP-------EGRRLLALYRRLE 95


                 ....
gi 488192442  80 KRYQ 83
Cdd:COG2005   96 AEAQ 99
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 117-194 5.64e-04

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: 40.20  E-value: 5.64e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488192442 117 HFHLIETTTKKILESVLNFESDLGILYLNDDNrhileryfkqHDLAFTPLGDFPTRIFLRKDHPLAQQKVIEKVQLKD 194
Cdd:cd08411   31 RLYLREDQTERLLEKLRSGELDAALLALPVDE----------PGLEEEPLFDEPFLLAVPKDHPLAKRKSVTPEDLAG 98
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
16-75 8.15e-04

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 40.51  E-value: 8.15e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442  16 GSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRILGEA 75
Cdd:PRK10632  17 GSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEV 76
PRK09801 PRK09801
LysR family transcriptional regulator;
12-72 1.05e-03

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 40.02  E-value: 1.05e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488192442  12 IANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRIL 72
Cdd:PRK09801  17 IVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEIL 77
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 120-194 1.23e-03

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: 39.06  E-value: 1.23e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488192442 120 LIETTTKKILESVLNFESDLGILYLNDDnrhileryfkQHDLAFTPLGDFPTRIFLRKDHPLAQQKViekVQLKD 194
Cdd:cd08412   33 VVEGNQEELEEGLRSGELDLALTYDLDL----------PEDIAFEPLARLPPYVWLPADHPLAGKDE---VSLAD 94
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
 104-206 3.80e-03

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: 37.87  E-value: 3.80e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442 104 LLEIAEKFKKDFQHFHLI--ETTTKKILESVLNFESDLGIL---YLNDDNRHILeRYFKQHDLAFTPlgdfptriflrKD 178
Cdd:cd08444   15 LPWVVQAFKEQFPNVHLVlhQGSPEEIASMLANGQADIGIAteaLENHPELVSF-PYYDWHHHIIVP-----------VG 82

                         90       100
                 ....*....|....*....|....*...
gi 488192442 179 HPLAQQKVIEKVQLKDYKQVRFRQEISG 206
Cdd:cd08444   83 HPLESITPLTIETIAKWPIITYHGGFTG 110
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 12-76 4.25e-03

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 38.05  E-value: 4.25e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488192442  12 IANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSNTGARLTDDGYDFLKYAKRILGEAD 76
Cdd:PRK14997  13 VVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQ 77
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 7-57 4.80e-03

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 38.05  E-value: 4.80e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 488192442   7 RYVE---AIANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRsnTGARL 57
Cdd:PRK11013   7 RHIEifhAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFER--VRGRL 58
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 129-291 5.00e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold; TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176110 [Multi-domain]  Cd Length: 201  Bit Score: 37.33  E-value: 5.00e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442 129 LESVLNFESDLGILYLNDDnrhileryFKQHDLAFTPLGDFPTRIFLRKDHPLAQQKVIEkvQLKDYKQVRFRQEISGLN 208
Cdd:cd08418   42 LPELRDGRLDFAIGTLPDE--------MYLKELISEPLFESDFVVVARKDHPLQGARSLE--ELLDASWVLPGTRMGYYN 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442 209 FDEDTLD----IPENQSVfySNDRGTIMNILCGSD-------AYASGLGIVNSFikdqIVLIPLKDSKMHTLGFVSNKRK 277
Cdd:cd08418  112 NLLEALRrlgyNPRVAVR--TDSIVSIINLVEKADfltilsrDMGRGPLDSFRL----ITIPVEEPLPSADYYLIYRKKS 185

                        170
                 ....*....|....
gi 488192442 278 QETDITQQFITAVK 291
Cdd:cd08418  186 RLTPLAEQLVELFR 199
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
12-52 5.13e-03

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 38.11  E-value: 5.13e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 488192442  12 IANTGSFSEAAKKLYVTQPNLSSSIKELENDLGVQLFIRSN 52
Cdd:PRK15243  15 LMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKN 55
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 103-210 8.73e-03

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: 36.48  E-value: 8.73e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488192442 103 PLLEIAEKFKKDFQ--HFHLIETTTKKILESVLNFESDLGILYLNDDnrhileryfkQHDLAFTPLGDFPTRIFLRKDHP 180
Cdd:cd08448   14 GLPRILRAFRAEYPgiEVALHEMSSAEQIEALLRGELDLGFVHSRRL----------PAGLSARLLHREPFVCCLPAGHP 83

                         90       100       110
                 ....*....|....*....|....*....|
gi 488192442 181 LAQQKVIEKVQLKDYKQVRFRQEISGLNFD 210
Cdd:cd08448   84 LAARRRIDLRELAGEPFVLFSREVSPDYYD 113
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH