NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|727186734|ref|WP_033648583|]
View 

MULTISPECIES: LysR family transcriptional regulator [Serratia]

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];
7-290 5.52e-45

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 152.71  E-value: 5.52e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734   7 LAHLTMFKDIVHCGSLHEAAKKLAISQPTLSRVLKELEMTIGARLLERSNRGVRLTAVGELFYRRIDAATNQLLNAFDEL 86
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  87 RGLSADGEKRLRVGMSVDPLLCYLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSSlnGAAGGADLAMQAL 166
Cdd:COG0583   83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRL--GPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734 167 KSERFSLYqggdltaagqppaeakwvvprsCSVGHAAIReiaerytpHGQIVetDSFLATWCLVRQQGYIALLSDRVVAH 246
Cdd:COG0583  161 GEERLVLV----------------------ASPDHPLAR--------RAPLV--NSLEALLAAVAAGLGIALLPRFLAAD 208

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 727186734 247 YAPQLHLQKIPTQAIDISARFYVFTRHEPATPPLSAAFIHLLQA 290
Cdd:COG0583  209 ELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLRE 252
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-290 5.52e-45

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 152.71  E-value: 5.52e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734   7 LAHLTMFKDIVHCGSLHEAAKKLAISQPTLSRVLKELEMTIGARLLERSNRGVRLTAVGELFYRRIDAATNQLLNAFDEL 86
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  87 RGLSADGEKRLRVGMSVDPLLCYLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSSlnGAAGGADLAMQAL 166
Cdd:COG0583   83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRL--GPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734 167 KSERFSLYqggdltaagqppaeakwvvprsCSVGHAAIReiaerytpHGQIVetDSFLATWCLVRQQGYIALLSDRVVAH 246
Cdd:COG0583  161 GEERLVLV----------------------ASPDHPLAR--------RAPLV--NSLEALLAAVAAGLGIALLPRFLAAD 208

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 727186734 247 YAPQLHLQKIPTQAIDISARFYVFTRHEPATPPLSAAFIHLLQA 290
Cdd:COG0583  209 ELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLRE 252
PRK10341 PRK10341
transcriptional regulator TdcA;
4-239 7.92e-30

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 114.57  E-value: 7.92e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734   4 MPKLAHLTMFKDIVHCGSLHEAAKKLAISQPTLSRVLKELEMTIGARLLERSNRGVRLTAVGELFYRRIDAATNQLLNAF 83
Cdd:PRK10341   6 LPKTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMV 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  84 DELRGLSADGEKRLRVGMSVDPLLCYLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSSLNGAAGGADLAM 163
Cdd:PRK10341  86 NEINGMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMKLQDLHV 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734 164 QALKSERFSLYQGGDLTAAG----QPPAEAKWVVPRSCSVGHAAIREIAERytpHG----QIVETDSFLATWCLVRQQGY 235
Cdd:PRK10341 166 EPLFESEFVLVASKSRTCTGtttlESLKNEQWVLPQTNMGYYSELLTTLQR---NGisieNIVKTDSVVTIYNLVLNADF 242


                 ....
gi 727186734 236 IALL 239
Cdd:PRK10341 243 LTVI 246
TF_pcaQ TIGR02424
pca operon transcription factor PcaQ; Members of this family are LysR-family transcription ...
 6-210 4.99e-29

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: 112.12  E-value: 4.99e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734    6 KLAHLTMFKDIVHCGSLHEAAKKLAISQPTLSRVLKELEMTIGARLLERSNRGVRLTAVGELFYRRIDAATNQLLNAFDE 85
Cdd:TIGR02424   4 KFRHLQCFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGTPLFERDRRGIRLTRYGELFLRHAGASLAALRQGVAS 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734   86 LRGLSADGEKRLRVGM--SVDPLLcyLPQVLEGFNRRYPHTRVTVVeDGPEG-LLARLRNCELDLAVSSLNGAAGGADLA 162
Cdd:TIGR02424  84 LSQLGEGEGPTVRIGAlpTVAARL--MPEVVKRFLARAPRLRVRIM-TGPNAyLLDQLRVGALDLVVGRLGAPETMQGLS 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 727186734  163 MQALKSER--FSLYQGGDLTAAGQPPAEAKWVVPRSCSVGHAAIREIAER 210
Cdd:TIGR02424 161 FEHLYNEPvvFVVRAGHPLLAAPSLPVASLADYPVLLPPEGSAIRPLAER 210
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 96-290 3.64e-19

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: 83.49  E-value: 3.64e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734   96 RLRVGMSVDPLLCYLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSSLNGAagGADLAMQALKSERFSLYQ 175
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPD--DPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  176 GGDLTAAGQPP------AEAKWVVPRSCSVGHAAIREIAERYTPHGQIV-ETDSFLATWCLVRQQGYIALLSDRVVAHYA 248
Cdd:pfam03466  81 PPDHPLARGEPvsledlADEPLILLPPGSGLRDLLDRALRAAGLRPRVVlEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 727186734  249 PQLHLQKIPTQAIDISARFYVFTRHEPATPPLSAAFIHLLQA 290
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLRE 202
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 96-288 2.63e-18

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: 81.11  E-value: 2.63e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  96 RLRVGMSVDPLLCYLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSSLNGAAggADLAMQALKSERFSLYQ 175
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDD--PGLESEPLFEEPLVLVV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734 176 GGDLTAAGQPP------AEAKWVVPRSCSVGHAAIREIAERYTPHGQIV-ETDSFLATWCLVRQQGYIALLSDRVVAHYA 248
Cdd:cd05466   79 PPDHPLAKRKSvtladlADEPLILFERGSGLRRLLDRAFAEAGFTPNIAlEVDSLEAIKALVAAGLGIALLPESAVEELA 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 727186734 249 PQlHLQKIPTQAIDISARFYVFTRHEPATPPLSAAFIHLL 288
Cdd:cd05466  159 DG-GLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
21-92 2.54e-04

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 39.50  E-value: 2.54e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 727186734    21 SLHEAAKKLAISQPTLSRVLKELEmtiGARLLERS-----NRGVR--LTAVGELFYRRIDAATNQLLNAFdeLRGLSAD 92
Cdd:smart00347  26 SVSELAKRLGVSPSTVTRVLDRLE---KKGLVRREpspedRRSVLvsLTEEGRELIEQLLEARSETLAEL--LAGLTAE 99
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-290 5.52e-45

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 152.71  E-value: 5.52e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734   7 LAHLTMFKDIVHCGSLHEAAKKLAISQPTLSRVLKELEMTIGARLLERSNRGVRLTAVGELFYRRIDAATNQLLNAFDEL 86
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  87 RGLSADGEKRLRVGMSVDPLLCYLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSSlnGAAGGADLAMQAL 166
Cdd:COG0583   83 RALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRL--GPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734 167 KSERFSLYqggdltaagqppaeakwvvprsCSVGHAAIReiaerytpHGQIVetDSFLATWCLVRQQGYIALLSDRVVAH 246
Cdd:COG0583  161 GEERLVLV----------------------ASPDHPLAR--------RAPLV--NSLEALLAAVAAGLGIALLPRFLAAD 208

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 727186734 247 YAPQLHLQKIPTQAIDISARFYVFTRHEPATPPLSAAFIHLLQA 290
Cdd:COG0583  209 ELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLRE 252
PRK10341 PRK10341
transcriptional regulator TdcA;
4-239 7.92e-30

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 114.57  E-value: 7.92e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734   4 MPKLAHLTMFKDIVHCGSLHEAAKKLAISQPTLSRVLKELEMTIGARLLERSNRGVRLTAVGELFYRRIDAATNQLLNAF 83
Cdd:PRK10341   6 LPKTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMV 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  84 DELRGLSADGEKRLRVGMSVDPLLCYLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSSLNGAAGGADLAM 163
Cdd:PRK10341  86 NEINGMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMKLQDLHV 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734 164 QALKSERFSLYQGGDLTAAG----QPPAEAKWVVPRSCSVGHAAIREIAERytpHG----QIVETDSFLATWCLVRQQGY 235
Cdd:PRK10341 166 EPLFESEFVLVASKSRTCTGtttlESLKNEQWVLPQTNMGYYSELLTTLQR---NGisieNIVKTDSVVTIYNLVLNADF 242


                 ....
gi 727186734 236 IALL 239
Cdd:PRK10341 243 LTVI 246
TF_pcaQ TIGR02424
pca operon transcription factor PcaQ; Members of this family are LysR-family transcription ...
 6-210 4.99e-29

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: 112.12  E-value: 4.99e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734    6 KLAHLTMFKDIVHCGSLHEAAKKLAISQPTLSRVLKELEMTIGARLLERSNRGVRLTAVGELFYRRIDAATNQLLNAFDE 85
Cdd:TIGR02424   4 KFRHLQCFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGTPLFERDRRGIRLTRYGELFLRHAGASLAALRQGVAS 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734   86 LRGLSADGEKRLRVGM--SVDPLLcyLPQVLEGFNRRYPHTRVTVVeDGPEG-LLARLRNCELDLAVSSLNGAAGGADLA 162
Cdd:TIGR02424  84 LSQLGEGEGPTVRIGAlpTVAARL--MPEVVKRFLARAPRLRVRIM-TGPNAyLLDQLRVGALDLVVGRLGAPETMQGLS 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 727186734  163 MQALKSER--FSLYQGGDLTAAGQPPAEAKWVVPRSCSVGHAAIREIAER 210
Cdd:TIGR02424 161 FEHLYNEPvvFVVRAGHPLLAAPSLPVASLADYPVLLPPEGSAIRPLAER 210
PRK09791 PRK09791
LysR family transcriptional regulator;
1-289 2.38e-23

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 97.14  E-value: 2.38e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734   1 MKTMPKLAHLTMFKDIVHCGSLHEAAKKLAISQPTLSRVLKELEMTIGARLLERSNRGVRLTAVGELFYRRIDAATNQLL 80
Cdd:PRK09791   1 MAFQVKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  81 NAFDELRGLSADGEKRLRVGMSVDPLLCYLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSSLNGAAGGAD 160
Cdd:PRK09791  81 AAQEDIRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYYQGPYDHE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734 161 LAMQALKSERFSLYqggdlTAAGQPPAEAK---------WVVPRSCSvghAAIREIAERYTPHGQI----VETDSFLATW 227
Cdd:PRK09791 161 FTFEKLLEKQFAVF-----CRPGHPAIGARslkqlldysWTMPTPHG---SYYKQLSELLDDQAQTpqvgVVCETFSACI 232

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 727186734 228 CLVRQQGYIALLSDRVVAHYAPQLHLQKIPTQAIDISARFYVFTRHEPATPPLSAAFIHLLQ 289
Cdd:PRK09791 233 SLVAKSDFLSILPEEMGCDPLHGQGLVMLPVSEILPKATYYLIQRRDTRQTPLTASLITLFR 294
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 96-290 3.64e-19

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: 83.49  E-value: 3.64e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734   96 RLRVGMSVDPLLCYLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSSLNGAagGADLAMQALKSERFSLYQ 175
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPD--DPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  176 GGDLTAAGQPP------AEAKWVVPRSCSVGHAAIREIAERYTPHGQIV-ETDSFLATWCLVRQQGYIALLSDRVVAHYA 248
Cdd:pfam03466  81 PPDHPLARGEPvsledlADEPLILLPPGSGLRDLLDRALRAAGLRPRVVlEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 727186734  249 PQLHLQKIPTQAIDISARFYVFTRHEPATPPLSAAFIHLLQA 290
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLRE 202
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 96-288 2.63e-18

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: 81.11  E-value: 2.63e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  96 RLRVGMSVDPLLCYLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSSLNGAAggADLAMQALKSERFSLYQ 175
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDD--PGLESEPLFEEPLVLVV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734 176 GGDLTAAGQPP------AEAKWVVPRSCSVGHAAIREIAERYTPHGQIV-ETDSFLATWCLVRQQGYIALLSDRVVAHYA 248
Cdd:cd05466   79 PPDHPLAKRKSvtladlADEPLILFERGSGLRRLLDRAFAEAGFTPNIAlEVDSLEAIKALVAAGLGIALLPESAVEELA 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 727186734 249 PQlHLQKIPTQAIDISARFYVFTRHEPATPPLSAAFIHLL 288
Cdd:cd05466  159 DG-GLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 96-288 4.34e-17

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: 77.70  E-value: 4.34e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  96 RLRVG--MSVDPLLcyLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSSLNGAAGGADLAMQALKSERFS- 172
Cdd:cd08435    1 TVRVGavPAAAPVL--LPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLADDEQPPDLASEELADEPLVv 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734 173 -------LYQGGDLTAAGQppAEAKWVVPRscsVGHAAIREIAERYTPHGQ-----IVETDSFLATWCLVRQQGYIALLS 240
Cdd:cd08435   79 varpghpLARRARLTLADL--ADYPWVLPP---PGTPLRQRLEQLFAAAGLplprnVVETASISALLALLARSDMLAVLP 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 727186734 241 DRVVAHYAPQLHLQKIPTQAIDISARFYVFTRHEPATPPLSAAFIHLL 288
Cdd:cd08435  154 RSVAEDELRAGVLRELPLPLPTSRRPIGITTRRGGPLSPAARALLDAL 201
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-66 3.03e-16

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 71.26  E-value: 3.03e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734    7 LAHLTMFKDIVHCGSLHEAAKKLAISQPTLSRVLKELEMTIGARLLERSNRGVRLTAVGE 66
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 7-187 1.34e-14

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 72.30  E-value: 1.34e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734   7 LAHLTMFKDIVHCGSLHEAAKKLAISQPTLSRVLKELEMTIGARLLERSNRGVRLTAVGELFYRRIDAATNQLLNAFDEL 86
Cdd:PRK11242   3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAI 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  87 RGLSADGEKRLRVGMSvdP-LLCYL--PqVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSSlnGAAGGADLAM 163
Cdd:PRK11242  83 HDVADLSRGSLRLAMT--PtFTAYLigP-LIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAF--APVHSPEIEA 157

                        170       180
                 ....*....|....*....|....
gi 727186734 164 QALKSERFSLYQGGDLTAAGQPPA 187
Cdd:PRK11242 158 QPLFTETLALVVGRHHPLAARRKA 181
rbcR CHL00180
LysR transcriptional regulator; Provisional
 7-149 3.86e-14

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 71.20  E-value: 3.86e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734   7 LAHLTMFKDIVHCGSLHEAAKKLAISQPTLSRVLKELEMTIGARLLERSNRGVRLTAVGELFYR---RIDAATNQLLNAF 83
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRygnRILALCEETCRAL 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 727186734  84 DELRGLSADgekRLRVGMSvDPLLCYL-PQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAV 149
Cdd:CHL00180  87 EDLKNLQRG---TLIIGAS-QTTGTYLmPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAI 149
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 6-148 7.64e-14

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 70.18  E-value: 7.64e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734   6 KLAHLTMFKDIVHCGSLHEAAKKLAISQPTLSRVLKELEMTIGARLLERSNRGVRLTAVGELFYRRIDAATNQLLNAFDE 85
Cdd:PRK09906   2 ELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLR 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 727186734  86 LRGLSADgEKRLRVGMSVDPLLCYLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLA 148
Cdd:PRK09906  82 ARKIVQE-DRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVG 143
phn_lysR TIGR03339
aminoethylphosphonate catabolism associated LysR family transcriptional regulator; This group ...
 10-151 4.59e-12

aminoethylphosphonate catabolism associated LysR family transcriptional regulator; This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466). [Regulatory functions, DNA interactions]


Pssm-ID: 132382 [Multi-domain]  Cd Length: 279  Bit Score: 65.14  E-value: 4.59e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734   10 LTMFKDIVHCGSLHEAAKKLAISQPTLSRVLKELEMTIGARLLERSNRGVRLTAVGELFYRRIDAATNQLLNAFDELRGL 89
Cdd:TIGR03339   2 LKAFHAVARCGSFTRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRLELTDAGHRLLPIVERLFQQEAEAEFLLRES 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 727186734   90 SADGEKRLRVGmsVDPLLCYLPQVlEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSS 151
Cdd:TIGR03339  82 GALREGSLRIA--ATAPYYVLDLV-ARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVSS 140
PRK09986 PRK09986
LysR family transcriptional regulator;
22-173 6.46e-11

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 61.66  E-value: 6.46e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  22 LH--EAAKKLAISQPTLSRVLKELEMTIGARLLERSNRGVRLTAVGELFY---RRIDAATNQLLNAFDELrglsADGEK- 95
Cdd:PRK09986  22 LHfgRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMeesRRLLDNAEQSLARVEQI----GRGEAg 97

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 727186734  96 RLRVGMSVDPLLCYLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSSLNGAAGGADLAMQALKSERFSL 173
Cdd:PRK09986  98 RIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNPGFTSRRLHESAFAV 175
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
4-151 1.48e-10

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 60.80  E-value: 1.48e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734   4 MPKLAHLTMFKDIVHCGSLHEAAKKLAISQPTLSRVLKELEMTIGARLLERSNRGVRLTAVGELFYRRIDAATNQLLNAf 83
Cdd:PRK15421   1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQA- 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 727186734  84 deLRGLSADGEKRLRVGMSVDPLLCYLPQVLEGFNRRYPHTRV---TVVEDGPEgllARLRNCELDLAVSS 151
Cdd:PRK15421  80 --LQACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMdfkSGVTFDPQ---PALQQGELDLVMTS 145
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
31-152 2.34e-10

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 59.83  E-value: 2.34e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  31 ISQPTLSRVLKELEMTIGARLLERSNRGVRLTAVGE---LFYRRIDAATNQLLNAF----DELRGlsadgekRLRVGMSV 103
Cdd:PRK11716   3 VSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEelrPFAQQTLLQWQQLRHTLdqqgPSLSG-------ELSLFCSV 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 727186734 104 DPLLCYLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSSL 152
Cdd:PRK11716  76 TAAYSHLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAK 124
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 96-290 4.24e-10

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: 58.13  E-value: 4.24e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  96 RLRVGMSVDPLLCYLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSSLNGAAGGADLAMQALKSERFSLYQ 175
Cdd:cd08418    1 KVSIGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLKELISEPLFESDFVVVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734 176 GGDLTAAG----QPPAEAKWVVPRSCSVGHAAIREIAER--YTPHGQIVeTDSFLATWCLVRQQGYIALLSDRVVAHYAP 249
Cdd:cd08418   81 RKDHPLQGarslEELLDASWVLPGTRMGYYNNLLEALRRlgYNPRVAVR-TDSIVSIINLVEKADFLTILSRDMGRGPLD 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 727186734 250 QLHLQKIPTQAIDISARFYVFTRHEPATPPLSAAFIHLLQA 290
Cdd:cd08418  160 SFRLITIPVEEPLPSADYYLIYRKKSRLTPLAEQLVELFRR 200
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 4-190 2.72e-09

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 56.92  E-value: 2.72e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734   4 MPKLAHLTMFKDIVHCGSLHEAAKKLAISQPTLSRVLKELEMTIGARLLERSNRGVRLTAVGELFYRRIDAATNQLLNAF 83
Cdd:PRK14997   1 KTDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  84 DELRGLSADGEKRLRVGMSVDPLLCYLPQVLEGFNRRYP---------HTRVTVVEDGpegllarlrnceLDLAVSSLNG 154
Cdd:PRK14997  81 DAIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPdvslqleatNRRVDVVGEG------------VDVAIRVRPR 148

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 727186734 155 AAGGADLAMQALKSERFSLYQGGDLTA-AGQPPAEAK 190
Cdd:PRK14997 149 PFEDSDLVMRVLADRGHRLFASPDLIArMGIPSAPAE 185
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
10-125 6.11e-09

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 55.97  E-value: 6.11e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  10 LTMFKDIVHCGSLHEAAKKLAISQPTLSRVLKELEMTIGARLLERSNRGVRLTAVGELFYRRIDAATNQLLNAFDELRGL 89
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQV 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 727186734  90 SaDGEKRlRVGMSVDPLLcYLPQ----VLEGFNRRYPHTR 125
Cdd:PRK10094  87 N-DGVER-QVNIVINNLL-YNPQavaqLLAWLNERYPFTQ 123
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 7-129 4.52e-08

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 53.46  E-value: 4.52e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734   7 LAHLTMFKDIVHCGSLHEAAKKLAISQPTLSRVLKELEMTIGARLLERSNrgvrltavGELFyrridaATNQLLNAFDEL 86
Cdd:PRK11013   6 LRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVR--------GRLH------PTVQGLRLFEEV 71

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 727186734  87 R----GL-----SADGEKRLRVG-MSVDPLLCY----LPQVLEGFNRRYPHTRVTVV 129
Cdd:PRK11013  72 QrsyyGLdrivsAAESLREFRQGqLSIACLPVFsqslLPGLCQPFLARYPDVSLNIV 128
PRK09801 PRK09801
LysR family transcriptional regulator;
1-126 6.41e-08

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 53.12  E-value: 6.41e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734   1 MKTMPKLAHLTMFKDIVHCGSLHEAAKKLAISQPTLSRVLKELEMTIGARLLERSNRGVRLTAVGELFYRRIDAATNQLL 80
Cdd:PRK09801   2 LNSWPLAKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQ 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 727186734  81 NAFDELRGLSADGEKRLRVGMSVDPLLCYLPQVLEGFNRRYPHTRV 126
Cdd:PRK09801  82 RLVDDVTQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQV 127
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
13-114 7.12e-08

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 52.75  E-value: 7.12e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  13 FKDIVHCGSLHEAAKKLAISQPTLSRVLKELEMTIGARLLERSNRGVRLTAVGELFYRRIDAATNQLLNAFDELRGLSAD 92
Cdd:PRK10082  19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGGSDY 98

                         90       100
                 ....*....|....*....|..
gi 727186734  93 GEKRLRVGMSVDPLLCYLPQVL 114
Cdd:PRK10082  99 AQRKIKIAAAHSLSLGLLPSII 120
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
4-84 9.03e-08

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 52.46  E-value: 9.03e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734   4 MPKLAHLTMFKDIVHCGSLHEAAKKLAISQPTLSRVLKELEMTIGARLLERSNRGVRLTAVGELFY---RRIDAATNQL- 79
Cdd:PRK10632   1 MERLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYqgcRRMLHEVQDVh 80


                 ....*..
gi 727186734  80 --LNAFD 84
Cdd:PRK10632  81 eqLYAFN 87
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 96-254 1.44e-07

The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. 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. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. 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: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 50.68  E-value: 1.44e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  96 RLRVGMSVDPLLCYLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSSLNGAagGADLAMQALKSERFSLYQ 175
Cdd:cd08417    1 TFRIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPEL--PPGLRSQPLFEDRFVCVA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734 176 GGDLTAAGQPP-----AEAKWVVPRSCSVGHAAIREIAERYTPHGQI-VETDSFLATWCLVRQQGYIALLSDRVVAHYAP 249
Cdd:cd08417   79 RKDHPLAGGPLtledyLAAPHVLVSPRGRGHGLVDDALAELGLSRRVaLTVPHFLAAPALVAGTDLIATVPRRLAEALAE 158


                 ....*
gi 727186734 250 QLHLQ 254
Cdd:cd08417  159 RLGLR 163
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 96-194 1.47e-07

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: 50.60  E-value: 1.47e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  96 RLRVGM--SVDPLLcyLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSSLngAAGGADLAMQALKSERFSL 173
Cdd:cd08411    2 PLRLGVipTIAPYL--LPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLAL--PVDEPGLEEEPLFDEPFLL 77

                         90       100
                 ....*....|....*....|.
gi 727186734 174 YqggdlTAAGQPPAEAKWVVP 194
Cdd:cd08411   78 A-----VPKDHPLAKRKSVTP 93
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 7-169 4.36e-07

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 50.45  E-value: 4.36e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734   7 LAHLTMFKDIVHCGSLHEAAKKLAISQPTLSRVLKELEMTIGARLLERSNRGVRLTAVGELFY-------RRIDAATNQL 79
Cdd:PRK11233   3 FRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYtharailRQCEQAQLAV 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  80 LNAFDELRGLSADGekrLRVGMSVDPLLcyLPqVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVssLNGAAGGA 159
Cdd:PRK11233  83 HNVGQALSGQVSIG---LAPGTAASSLT--MP-LLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAV--IYEHSPVA 154

                        170
                 ....*....|
gi 727186734 160 DLAMQALKSE 169
Cdd:PRK11233 155 GLSSQPLLKE 164
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 96-288 4.73e-07

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 49.14  E-value: 4.73e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  96 RLRVGMSVDPLLCYLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSSLnGAAGGADLAMQALKSERFSLyq 175
Cdd:cd08436    1 RLAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGL-PERRPPGLASRELAREPLVA-- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734 176 ggdLTAAGQPPAEAKWVVPRSCSV--------GHAAIREIAERYTPHG-------QIVETDSFLAtwcLVRQQGYIALLS 240
Cdd:cd08436   78 ---VVAPDHPLAGRRRVALADLADepfvdfppGTGARRQVDRAFAAAGvrrrvafEVSDVDLLLD---LVARGLGVALLP 151

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 727186734 241 DRVVAHyAPQLHLQKIPTQAidiSARFYVFTRhEPATPPLSAAFIHLL 288
Cdd:cd08436  152 ASVAAR-LPGLAALPLEPAP---RRRLYLAWS-APPPSPAARAFLELL 194
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
 107-257 1.13e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. 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. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate of the oxidative degradation of the aromatic ring in soil bacteria. LinR positively regulates expression of the genes (linD and linE) encoding enzymes for gamma-hexachlorocyclohexane (a haloorganic insecticide) degradation. Expression of linD and linE are induced by their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ) and chlorohydroquinone (CHQ). 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: 176148 [Multi-domain]  Cd Length: 201  Bit Score: 48.34  E-value: 1.13e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734 107 LCYLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSSLNGAagGADLAMQALKSERFSLyqggdLTAAGQPP 186
Cdd:cd08459   12 MYFLPRLLAALREVAPGVRIETVRLPVDELEEALESGEIDLAIGYLPDL--GAGFFQQRLFRERYVC-----LVRKDHPR 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734 187 A----------EAKWVVPRSCSVGHAAIREIAERYTPHGQIV-ETDSFLATWCLVRQQGYIALLSDRVVAHYAPQLHLQK 255
Cdd:cd08459   85 IgstltleqflAARHVVVSASGTGHGLVEQALREAGIRRRIAlRVPHFLALPLIVAQTDLVATVPERLARLFARAGGLRI 164


                 ..
gi 727186734 256 IP 257
Cdd:cd08459  165 VP 166
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 110-288 1.25e-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: 47.87  E-value: 1.25e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734 110 LPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVssLNGAAGGADLAMQALKSERFSLYQGGDLTAAGQPP--- 186
Cdd:cd08420   15 LPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGL--VEGPVDHPDLIVEPFAEDELVLVVPPDHPLAGRKEvta 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734 187 ---AEAKWVV--PRSCsvghaaIREIAERY-TPHGQ-------IVETDSFLAtwclVRQ---QGY-IALLSDRVVAHYAP 249
Cdd:cd08420   93 eelAAEPWILrePGSG------TREVFERAlAEAGLdgldlniVMELGSTEA----IKEaveAGLgISILSRLAVRKELE 162

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 727186734 250 QLHLQKIPTQAIDISARFYVFTRHEPATPPLSAAFIHLL 288
Cdd:cd08420  163 LGRLVALPVEGLRLTRPFSLIYHKDKYLSPAAEAFLEFL 201
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 110-288 1.32e-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: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 47.98  E-value: 1.32e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734 110 LPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVS---SLNGAAGGADLAMQALKSERFSLYQGGDLTAAGQPP 186
Cdd:cd08423   15 LPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVfdyPVTPPPDDPGLTRVPLLDDPLDLVLPADHPLAGREE 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734 187 ------AEAKWVVPRSCSVGHAAIREIAER--YTPhgQIV-ETDSFLATWCLVRQQGYIALLSDRVVAHYAPQLHLQKIP 257
Cdd:cd08423   95 valadlADEPWIAGCPGSPCHRWLVRACRAagFTP--RIAhEADDYATVLALVAAGLGVALVPRLALGARPPGVVVRPLR 172

                        170       180       190
                 ....*....|....*....|....*....|.
gi 727186734 258 TQaidISARFYVFTRHEPATPPLSAAFIHLL 288
Cdd:cd08423  173 PP---PTRRIYAAVRAGAARRPAVAAALEAL 200
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-173 1.43e-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: 47.91  E-value: 1.43e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 727186734  98 RVGMSVDPLLCY--LPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSSLNGAAggADLAMQALKSERFSL 173
Cdd:cd08440    1 RVRVAALPSLAAtlLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEAD--PDLEFEPLLRDPFVL 76
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 109-149 2.72e-06

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


Pssm-ID: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 47.15  E-value: 2.72e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 727186734 109 YLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAV 149
Cdd:cd08412   14 YLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLAL 54
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 22-151 3.53e-06

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 47.73  E-value: 3.53e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  22 LHEAAKKLAISQPTLSRVLKELEMTIGARLLERsnRGVRLTAVGELFYRRIDAATNQLLNAfDELRGLS---ADGEK-RL 97
Cdd:PRK12683  19 LTEVANALYTSQSGVSKQIKDLEDELGVEIFIR--RGKRLTGLTEPGKELLQIVERMLLDA-ENLRRLAeqfADRDSgHL 95

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 727186734  98 RVGMSVDPLLCYLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSS 151
Cdd:PRK12683  96 TVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIAT 149
PBP2_SyrM cd08467
The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates ...
 110-257 7.40e-06

The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold; Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. 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: 176156 [Multi-domain]  Cd Length: 200  Bit Score: 45.89  E-value: 7.40e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734 110 LPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSSLNGAAGGadLAMQALKSERFSLyqggdLTAAGQPPAEA 189
Cdd:cd08467   15 LPRLAPRLRERAPGLDLRLCPIGDDLAERGLEQGTIDLAVGRFAVPPDG--LVVRRLYDDGFAC-----LVRHGHPALAQ 87

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 727186734 190 KWVVPRSCSVGHAAIRE-------IAERYTPHG----QIVETDSFLATWCLVRQQGYIALLSDRVVAHYAPQLHLQKIP 257
Cdd:cd08467   88 EWTLDDFATLRHVAIAPpgrlfggIYKRLENLGlkrnVAIAVSSFLTAAATVAATDLIATVPRRVATQVAAMLPLRVVP 166
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 96-282 1.28e-05

The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut. Hence, NAC allows the coupling of sigma70-RNAP dependent operons to the sigma54-RNAP dependent NTR system. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176124  Cd Length: 198  Bit Score: 44.89  E-value: 1.28e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  96 RLRVGM--SVDPLLCylPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVssLNGAAGGADLAMQALKSERFSL 173
Cdd:cd08433    1 RVSVGLppSAASVLA--VPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLAL--LYGPPPIPGLSTEPLLEEDLFL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734 174 YQGGDLTAAGQPPAEAKWV------VPrscSVGHaAIREIAERY-TPHGQ----IVETDSFLATWCLVRQQ-GYiALLSD 241
Cdd:cd08433   77 VGPADAPLPRGAPVPLAELarlpliLP---SRGH-GLRRLVDEAaARAGLtlnvVVEIDSVATLKALVAAGlGY-TILPA 151

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 727186734 242 RVVAHYAPQ--LHLQKIPTQAIdISARFYVFTRHEPATPPLSA 282
Cdd:cd08433  152 SAVAAEVAAgrLVAAPIVDPAL-TRTLSLATPRDRPLSPAALA 193
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 25-149 1.88e-05

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 45.41  E-value: 1.88e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  25 AAKKLAISQPTLSRVLKELEMTIGARLLERSNRGVRLTAVGELFyrrIDAATNQLLNA--FDELRglSADGEKR---LRV 99
Cdd:PRK11151  21 AADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLL---VDQARTVLREVkvLKEMA--SQQGETMsgpLHI 95

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 727186734 100 GM--SVDPLLcyLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAV 149
Cdd:PRK11151  96 GLipTVGPYL--LPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAI 145
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 7-126 3.03e-05

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 44.68  E-value: 3.03e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734   7 LAHLTMFKDIVHCGSLHEAAKKLAISQPTLSRVLKELEMTIGARLLERSNRGVRLTAVGELFYRRIDAatnqLLNAFDEL 86
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALA----LLEQAVEI 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 727186734  87 RGLSADGEKRLRVGMSVDPLLCYLPQVLEGFNRRYPHTRV 126
Cdd:PRK10837  81 EQLFREDNGALRIYASSTIGNYILPAMIARYRRDYPQLPL 120
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 96-288 1.04e-04

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: 42.49  E-value: 1.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  96 RLRVGMSVDPLLCYLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVssLNGAAGGADLAMQALKSERFS--L 173
Cdd:cd08414    1 RLRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGF--VRPPPDPPGLASRPLLREPLVvaL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734 174 YQGGDLTAAGQPP----AEAKWVV--PRSCSVGHAAIREIAER--YTPHgqIV-ETDSFLATWCLVRQQGYIALLSDRVV 244
Cdd:cd08414   79 PADHPLAARESVSladlADEPFVLfpREPGPGLYDQILALCRRagFTPR--IVqEASDLQTLLALVAAGLGVALVPASVA 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 727186734 245 AHYAPQLHLqkIPTQAIDISARFYVFTRHEPATPPLsAAFIHLL 288
Cdd:cd08414  157 RLQRPGVVY--RPLADPPPRSELALAWRRDNASPAL-RAFLELA 197
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 110-288 1.82e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold; YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176133  Cd Length: 193  Bit Score: 41.44  E-value: 1.82e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734 110 LPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSSlnGAAGGADLAMQALKSERFSLyqggdLTAAGQPPAEA 189
Cdd:cd08442   15 LPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVA--GPVEHPRLEQEPVFQEELVL-----VSPKGHPPVSR 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734 190 KWVVPRS--------CSVGHAAIREIAERYTPHGQIVETDSFLATWCLVRQQGYIALLSDRVVAHYA--PQLHLQKIPTQ 259
Cdd:cd08442   88 AEDLAGStllafragCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSLQgrGSVSIHPLPEP 167

                        170       180
                 ....*....|....*....|....*....
gi 727186734 260 AIDISARFYvfTRHEPATPPLsAAFIHLL 288
Cdd:cd08442  168 FADVTTWLV--WRKDSFTAAL-QAFLDLL 193
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 6-151 1.94e-04

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 42.29  E-value: 1.94e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734   6 KLAHLTMFKDIVHCG-SLHEAAKKLAISQPTLSRVLKELEMTIGARLLERS-NRGVRLTAVGELFYRRIDAatnqLLNAF 83
Cdd:PRK12682   2 NLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHgKRLKGLTEPGKAVLDVIER----ILREV 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 727186734  84 DELRGLSADGEKR----LRVGMSVDPLLCYLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSS 151
Cdd:PRK12682  78 GNIKRIGDDFSNQdsgtLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIAT 149
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 109-151 2.17e-04

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


Pssm-ID: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 41.37  E-value: 2.17e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 727186734 109 YLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSS 151
Cdd:cd08434   14 LVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCS 56
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
21-92 2.54e-04

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 39.50  E-value: 2.54e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 727186734    21 SLHEAAKKLAISQPTLSRVLKELEmtiGARLLERS-----NRGVR--LTAVGELFYRRIDAATNQLLNAFdeLRGLSAD 92
Cdd:smart00347  26 SVSELAKRLGVSPSTVTRVLDRLE---KKGLVRREpspedRRSVLvsLTEEGRELIEQLLEARSETLAEL--LAGLTAE 99
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
21-149 3.47e-04

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 41.50  E-value: 3.47e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  21 SLHEAAKKLAISQPTLSRVLKELEMTIGARLLERsnRGVRLTAVGELfYRRIDAATNQLLNAFDELRGLSAD----GEKR 96
Cdd:PRK12684  18 NLTEAAKALYTSQPGVSKAIIELEDELGVEIFTR--HGKRLRGLTEP-GRIILASVERILQEVENLKRVGKEfaaqDQGN 94

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 727186734  97 LRVGMSVDPLLCYLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAV 149
Cdd:PRK12684  95 LTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAI 147
cbl PRK12679
HTH-type transcriptional regulator Cbl;
21-151 4.12e-04

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 41.33  E-value: 4.12e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  21 SLHEAAKKLAISQPTLSRVLKELEMTIGARLLERsnRGVRLTAVGE-------LFYRRIDAATN--QLLNAFdelrglSA 91
Cdd:PRK12679  18 NLTEVANMLFTSQSGVSRHIRELEDELGIEIFIR--RGKRLLGMTEpgkallvIAERILNEASNvrRLADLF------TN 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  92 DGEKRLRVGMSVDPLLCYLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSS 151
Cdd:PRK12679  90 DTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIAS 149
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
18-128 4.29e-04

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 41.14  E-value: 4.29e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  18 HCgSLHEAAKKLAISQPTLSRVLKELEMTIGARLLERSNRGVRLTAVGELFYRRIDAATNQLLNAFDELRGLSADGekrl 97
Cdd:PRK10086  28 HQ-SFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDIKNQELSG---- 102

                         90       100       110
                 ....*....|....*....|....*....|...
gi 727186734  98 RVGMSVDPLL--CYLPQVLEGFNRRYPHTRVTV 128
Cdd:PRK10086 103 TLTVYSRPSIaqCWLVPRLADFTRRYPSISLTI 135
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 96-152 4.30e-04

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: 40.62  E-value: 4.30e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 727186734  96 RLRVGMSvdPLLC--YLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSSL 152
Cdd:cd08438    1 HLRLGLP--PLGGslLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVL 57
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 96-288 6.54e-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: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 39.86  E-value: 6.54e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  96 RLRVGMSVDPLLCYLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSSLNGAAGGADLAMQALKSERFSLYQ 175
Cdd:cd08427    1 RLRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPPFPLPKDLVWTPLVREPLVLIA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734 176 GGDLtaAGQPPAEAKWVVP-----RSCSVGHAAIREI-AERYTPHgQIVETDSFLATWCLVRQQGYIALLSDRVVAHYAP 249
Cdd:cd08427   81 PAEL--AGDDPRELLATQPfirydRSAWGGRLVDRFLrRQGIRVR-EVMELDSLEAIAAMVAQGLGVAIVPDIAVPLPAG 157

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 727186734 250 qLHLQKIPTQAIDISARFYVFTRHEPATPPLSAAFIHLL 288
Cdd:cd08427  158 -PRVRVLPLGDPAFSRRVGLLWRRSSPRSRLIQALLEAL 195
PRK12680 PRK12680
LysR family transcriptional regulator;
25-186 7.54e-04

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 40.38  E-value: 7.54e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734  25 AAKKLAISQPTLSRVLKELEMTIGARLLERSNRGVR-LTAVGELFYRRIDAatnqLLNAFDELRGLSADGEK----RLRV 99
Cdd:PRK12680  22 AAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARA----VLSEANNIRTYAANQRResqgQLTL 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734 100 GMSVDPLLCYLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSSLNGAAGGADLAMQALKSERFSLY-QGGD 178
Cdd:PRK12680  98 TTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAGIAVPLYRWRRLVVVpRGHA 177


                 ....*...
gi 727186734 179 LTAAGQPP 186
Cdd:PRK12680 178 LDTPRRAP 185
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 96-152 1.29e-03

The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold; This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176130  Cd Length: 185  Bit Score: 38.85  E-value: 1.29e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 727186734  96 RLRVGMSVDPLLCYLPQVLEGFNRRYPHTRVTVVEDGPEGLLARLRNCELDLAVSSL 152
Cdd:cd08439    1 TLRIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALITH 57
Rfk COG1339
Archaeal CTP-dependent riboflavin kinase [Coenzyme transport and metabolism]; Archaeal ...
 21-88 1.57e-03

Archaeal CTP-dependent riboflavin kinase [Coenzyme transport and metabolism]; Archaeal CTP-dependent riboflavin kinase is part of the Pathway/BioSystem: Riboflavin/FAD biosynthesis


Pssm-ID: 440950 [Multi-domain]  Cd Length: 219  Bit Score: 39.06  E-value: 1.57e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 727186734  21 SLHEAAKKLAISQPTLSRVLKELEmtiGARLLER--SNRG--VRLTAVGELF-------YRRIDAATNQLlnafdELRG 88
Cdd:COG1339   24 SSSELAKRLGISQQTASRRLQELE---DAGLIERdlVGDGqwVKITEKGEELlrreyadYRRIFEIKDSL-----ELTG 94
COG4742 COG4742
Predicted transcriptional regulator, contains HTH domain [Transcription];
21-87 1.68e-03

Predicted transcriptional regulator, contains HTH domain [Transcription];


Pssm-ID: 443776 [Multi-domain]  Cd Length: 267  Bit Score: 39.11  E-value: 1.68e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 727186734  21 SLHEAAKKLAISQPTLSRVLKELEmtiGARLLERSNRGVRLTAVGELFYRRIDAATNqLLNAFDELR 87
Cdd:COG4742   31 TRSELAESLDVSRSTILRQLKELE---ERGLIERDDGEYELTTLGRLVVEEMEPLLD-TLEVLEENR 93
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
4-152 5.41e-03

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 37.83  E-value: 5.41e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727186734   4 MPKLAHLTMFKDIVHCGSLHEAAKKLAISQPTLSRVLKELEMTIGARLLERSnRGVRLTAVGEL---FYRRIdaatnQLL 80
Cdd:PRK03635   1 MLDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQRllrHARQV-----RLL 74

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 727186734  81 NAfdELRG-LSADGEKRLRVGMSV--DPLLCYLPQVLEGFNRRYPHTRVTVVEDGPEGlLARLRNCELDLAVSSL 152
Cdd:PRK03635  75 EA--ELLGeLPALDGTPLTLSIAVnaDSLATWFLPALAPVLARSGVLLDLVVEDQDHT-AELLRRGEVVGAVTTE 146
 
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