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Conserved domains on  [gi|1417874314|gb|RAV72211|]
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LysR family transcriptional regulator [Aerococcus mictus]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
4-204 8.60e-37

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 131.53  E-value: 8.60e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314   4 RKLEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAGHSFYQDSLALIDQSQKAIHRAK 83
Cdd:COG0583     4 RQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELR 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314  84 QIAQKSPYLIRLGrSFLNPAQDFFP-LWHRFNQHYPQFKLEVVpfEDNQQSILETIkhLGQGFDLMVGAcDSLKWLEYVQ 162
Cdd:COG0583    84 ALRGGPRGTLRIG-APPSLARYLLPpLLARFRARHPGVRLELR--EGNSDRLVDAL--LEGELDLAIRL-GPPPDPGLVA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1417874314 163 lLPLKEAKLTCAMAKNHPLKGKACIqledLNDQDLI--MVKEGH 204
Cdd:COG0583   158 -RPLGEERLVLVASPDHPLARRAPL----VNSLEALlaAVAAGL 196
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
4-204 8.60e-37

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 131.53  E-value: 8.60e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314   4 RKLEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAGHSFYQDSLALIDQSQKAIHRAK 83
Cdd:COG0583     4 RQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELR 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314  84 QIAQKSPYLIRLGrSFLNPAQDFFP-LWHRFNQHYPQFKLEVVpfEDNQQSILETIkhLGQGFDLMVGAcDSLKWLEYVQ 162
Cdd:COG0583    84 ALRGGPRGTLRIG-APPSLARYLLPpLLARFRARHPGVRLELR--EGNSDRLVDAL--LEGELDLAIRL-GPPPDPGLVA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1417874314 163 lLPLKEAKLTCAMAKNHPLKGKACIqledLNDQDLI--MVKEGH 204
Cdd:COG0583   158 -RPLGEERLVLVASPDHPLARRAPL----VNSLEALlaAVAAGL 196
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
4-62 8.33e-25

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 93.99  E-value: 8.33e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1417874314   4 RKLEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAGH 62
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-228 1.69e-24

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 99.84  E-value: 1.69e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314   1 MYSRKLEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAGHSFYQDSLALIDQSQKAIH 80
Cdd:PRK09906    1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314  81 RAKQIAQKSPYLiRLGrsFLNPAQ-DFFP-LWHRFNQHYPQFKLEVVPFEDNQQsiletIKHLGQGfDLMVGACDSLKWL 158
Cdd:PRK09906   81 RARKIVQEDRQL-TIG--FVPSAEvNLLPkVLPMFRLRHPDTLIELVSLITTQQ-----EEKLRRG-ELDVGFMRHPVYS 151

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1417874314 159 EYVQLLPLKEAKLTCAMAKNHPLKGKACIQLEDLNDQDLIMVKEGHSQS-NDALRSYLKSHYRSIHIIDAA 228
Cdd:PRK09906  152 DEIDYLELLDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYSGSlAPIIKAWFAQHNSQPNIVQVA 222
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 93-292 2.01e-12

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: 64.54  E-value: 2.01e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314  93 IRLGrSFLNPAQDFFPLW-HRFNQHYPQFKLEVVpfEDNQQSILETIKHlGQgFDLMVGAC-DSLKWLEYVqllPLKEAK 170
Cdd:cd05466     2 LRIG-ASPSIAAYLLPPLlAAFRQRYPGVELSLV--EGGSSELLEALLE-GE-LDLAIVALpVDDPGLESE---PLFEEP 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314 171 LTCAMAKNHPLKGKACIQLEDLNDQDLIMVKEGhSQSNDALRSYLKSH---YRSIHIIDaayyyDLSTFNRCEQTG---A 244
Cdd:cd05466    74 LVLVVPPDHPLAKRKSVTLADLADEPLILFERG-SGLRRLLDRAFAEAgftPNIALEVD-----SLEAIKALVAAGlgiA 147

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1417874314 245 ILLSLDVWEDIHPSLITIPLAWSGPGVPYGIIYSKE--PNDQVAKFIKVL 292
Cdd:cd05466   148 LLPESAVEELADGGLVVLPLEDPPLSRTIGLVWRKGryLSPAARAFLELL 197
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
17-79 1.25e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 37.57  E-value: 1.25e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1417874314   17 SFSQAAQRLYISPTAVKKQIDRLEDlLGLDLFQRSSRG-----VKLTEAGHSFYQDSLALIDQSQKAI 79
Cdd:smart00347  26 SVSELAKRLGVSPSTVTRVLDRLEK-KGLVRREPSPEDrrsvlVSLTEEGRELIEQLLEARSETLAEL 92
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
4-204 8.60e-37

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 131.53  E-value: 8.60e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314   4 RKLEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAGHSFYQDSLALIDQSQKAIHRAK 83
Cdd:COG0583     4 RQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELR 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314  84 QIAQKSPYLIRLGrSFLNPAQDFFP-LWHRFNQHYPQFKLEVVpfEDNQQSILETIkhLGQGFDLMVGAcDSLKWLEYVQ 162
Cdd:COG0583    84 ALRGGPRGTLRIG-APPSLARYLLPpLLARFRARHPGVRLELR--EGNSDRLVDAL--LEGELDLAIRL-GPPPDPGLVA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1417874314 163 lLPLKEAKLTCAMAKNHPLKGKACIqledLNDQDLI--MVKEGH 204
Cdd:COG0583   158 -RPLGEERLVLVASPDHPLARRAPL----VNSLEALlaAVAAGL 196
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
4-62 8.33e-25

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 93.99  E-value: 8.33e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1417874314   4 RKLEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAGH 62
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-228 1.69e-24

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 99.84  E-value: 1.69e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314   1 MYSRKLEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAGHSFYQDSLALIDQSQKAIH 80
Cdd:PRK09906    1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314  81 RAKQIAQKSPYLiRLGrsFLNPAQ-DFFP-LWHRFNQHYPQFKLEVVPFEDNQQsiletIKHLGQGfDLMVGACDSLKWL 158
Cdd:PRK09906   81 RARKIVQEDRQL-TIG--FVPSAEvNLLPkVLPMFRLRHPDTLIELVSLITTQQ-----EEKLRRG-ELDVGFMRHPVYS 151

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1417874314 159 EYVQLLPLKEAKLTCAMAKNHPLKGKACIQLEDLNDQDLIMVKEGHSQS-NDALRSYLKSHYRSIHIIDAA 228
Cdd:PRK09906  152 DEIDYLELLDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYSGSlAPIIKAWFAQHNSQPNIVQVA 222
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-221 9.99e-21

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 89.63  E-value: 9.99e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314   1 MYSRKLEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAGHSFYQ-DSLAL--IDQSQK 77
Cdd:PRK11242    1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRyARRALqdLEAGRR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314  78 AIHRAKQIAQKS----------PYLIRlgrsflnpaqdffPLWHRFNQHYPQFKLEVvpFEDNQQSI----LETIKHLGQ 143
Cdd:PRK11242   81 AIHDVADLSRGSlrlamtptftAYLIG-------------PLIDAFHARYPGITLTI--REMSQERIeallADDELDVGI 145

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1417874314 144 GFDlMVGACDslkwleyVQLLPLKEAKLTCAMAKNHPLKGK-ACIQLEDLNDQDLIMVKEGHsqsndALRSYLKSHYRS 221
Cdd:PRK11242  146 AFA-PVHSPE-------IEAQPLFTETLALVVGRHHPLAARrKALTLDELADEPLVLLSAEF-----ATREQIDRYFRR 211
PRK09986 PRK09986
LysR family transcriptional regulator;
4-205 1.20e-18

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 84.00  E-value: 1.20e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314   4 RKLEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAGHSFYQDSLALIDQSQKAIHRAK 83
Cdd:PRK09986   10 KLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARVE 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314  84 QIAQKSPYLIRLGrsFLNPAqdffpLWH-------RFNQHYPQFKL---EVVPFEdnQQSILETiKHLGQGFDLMVGACD 153
Cdd:PRK09986   90 QIGRGEAGRIEIG--IVGTA-----LWGrlrpamrHFLKENPNVEWllrELSPSM--QMAALER-RELDAGIWRMADLEP 159

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1417874314 154 SlkwlEYVQLLPLKEAKLTCAMAKNHPLKGKACIQLEDLNDQDLIMVKEGHS 205
Cdd:PRK09986  160 N----PGFTSRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPFVHS 207
PRK09801 PRK09801
LysR family transcriptional regulator;
3-202 4.03e-17

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 80.08  E-value: 4.03e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314   3 SRKLEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAGHSFYQDSLALIDQSQKAIHRA 82
Cdd:PRK09801    8 AKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDV 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314  83 KQIAQKSPYLIRLGRSFLNPAQDFFPLWHRFNQHYPQFKLEVVPFeDNQQSILEtikhlgQGFDLMVGACDSLKWLeYVQ 162
Cdd:PRK09801   88 TQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELF-DRQIDLVQ------DNIDLDIRINDEIPDY-YIA 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1417874314 163 LLPLKEAKLTCAmAKNHPLKGKACIQLEDLNDQDLIMVKE 202
Cdd:PRK09801  160 HLLTKNKRILCA-APEYLQKYPQPQSLQELSRHDCLVTKE 198
rbcR CHL00180
LysR transcriptional regulator; Provisional
 4-207 5.03e-17

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 79.68  E-value: 5.03e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314   4 RKLEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAGHSFYQDS---LALIDQSQKAIH 80
Cdd:CHL00180    8 DQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGnriLALCEETCRALE 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314  81 RAKQIaqKSPYLIrLGRS-----FLNPAqdffpLWHRFNQHYPQ--FKLEVvpfeDNQQSILETIKHlGQgFDL-MVGAC 152
Cdd:CHL00180   88 DLKNL--QRGTLI-IGASqttgtYLMPR-----LIGLFRQRYPQinVQLQV----HSTRRIAWNVAN-GQ-IDIaIVGGE 153

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1417874314 153 DSLKWLEYVQLLPLKEAKLTCAMAKNHPLKGKACIQLEDLNDQDLIMVKEgHSQS 207
Cdd:CHL00180  154 VPTELKKILEITPYVEDELALIIPKSHPFAKLKKIQKEDLYRLNFITLDS-NSTI 207
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 4-224 9.80e-15

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 73.10  E-value: 9.80e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314   4 RKLEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRS-------SRGVKL-TEAGHSFYqdSLALIDQS 75
Cdd:PRK11013    7 RHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVrgrlhptVQGLRLfEEVQRSYY--GLDRIVSA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314  76 QKAIHRAKQiAQKSpyLIRLgrsflnP--AQDFFP-LWHRFNQHYPQFKLEVVPfednQQS-ILEtiKHL-GQGFDLmvG 150
Cdd:PRK11013   85 AESLREFRQ-GQLS--IACL------PvfSQSLLPgLCQPFLARYPDVSLNIVP----QESpLLE--EWLsAQRHDL--G 147

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1417874314 151 ACDSLKWLEYVQLLPLKEAKLTCAMAKNHPLKGKACIQLEDLNDQDLIMVkeghsQSNDALRSYLKSHYRSIHI 224
Cdd:PRK11013  148 LTETLHTPAGTERTELLTLDEVCVLPAGHPLAAKKVLTPDDFAGENFISL-----SRTDSYRQLLDQLFAEHGV 216
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
5-74 4.07e-14

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 71.19  E-value: 4.07e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1417874314   5 KLEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAGHSFY---QDSLALIDQ 74
Cdd:PRK10086   18 KLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFwalKSSLDTLNQ 90
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 6-123 6.31e-14

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 70.64  E-value: 6.31e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314   6 LEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAGHSFYQDSLALIDQSQKAIHRAKQI 85
Cdd:PRK11139   11 LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRAR 90

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1417874314  86 AQKSPYLIRLGRSFlnPAQDFFPLWHRFNQHYPQFKLE 123
Cdd:PRK11139   91 SAKGALTVSLLPSF--AIQWLVPRLSSFNEAHPDIDVR 126
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 4-224 9.60e-14

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 70.10  E-value: 9.60e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314   4 RKLEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAGHSFYQDSLALIDQSQKaihrAK 83
Cdd:PRK10837    6 RQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVE----IE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314  84 QIAQKSPYLIRLGRS-----FLNPaqdffPLWHRFNQHYPQFKLEVvpFEDNQQSILETIKHLGQGFDLMVGACD----- 153
Cdd:PRK10837   82 QLFREDNGALRIYASstignYILP-----AMIARYRRDYPQLPLEL--SVGNSQDVINAVLDFRVDIGLIEGPCHspeli 154

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1417874314 154 SLKWLeyvqllplkEAKLTCAMAKNHPLKGKAcIQLEDLNDQDLIMvKEGHSQSNDALRSYLKSHYRSIHI 224
Cdd:PRK10837  155 SEPWL---------EDELVVFAAPDSPLARGP-VTLEQLAAAPWIL-RERGSGTREIVDYLLLSHLPRFEL 214
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-211 1.61e-13

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 69.29  E-value: 1.61e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314   1 MYSRKLEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAGhsfyqdsLALIDQSQKAIH 80
Cdd:PRK11151    1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAG-------LLLVDQARTVLR 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314  81 RAK--------Q------------IAQKSPYLIRLgrsflnpaqdFFPLWHrfnQHYPqfKLEVVPFEDNQQSILEtikH 140
Cdd:PRK11151   74 EVKvlkemasqQgetmsgplhiglIPTVGPYLLPH----------IIPMLH---QTFP--KLEMYLHEAQTHQLLA---Q 135

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1417874314 141 LGQG-FDLMVGAcdSLKWLEYVQLLPLKEAKLTCAMAKNHPLKGKACIQLEDLNDQDLIMVKEGHSQSNDAL 211
Cdd:PRK11151  136 LDSGkLDCAILA--LVKESEAFIEVPLFDEPMLLAVYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAM 205
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 1-87 2.29e-13

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 68.82  E-value: 2.29e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314   1 MYSRK-LEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAGHSFYQDSLALIDQSQKAI 79
Cdd:PRK11074    1 MWSEYsLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETR 80


                  ....*...
gi 1417874314  80 HRAKQIAQ 87
Cdd:PRK11074   81 RQCQQVAN 88
PRK09791 PRK09791
LysR family transcriptional regulator;
5-199 5.11e-13

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 67.86  E-value: 5.11e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314   5 KLEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAGHSFYQDSlALI---------DQS 75
Cdd:PRK09791    9 QIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHA-SLIleelraaqeDIR 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314  76 QKAIHRAKQIAqkspylIRLGRSFlnpAQDFFP-LWHRFNQHYPQFKLEVVpfednQQSILETIKHLGQG-FDLMV---- 149
Cdd:PRK09791   88 QRQGQLAGQIN------IGMGASI---ARSLMPaVISRFHQQHPQVKVRIM-----EGQLVSMINELRQGeLDFTIntyy 153

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1417874314 150 -GACDSlkWLEYVQLLPlKEAKLTCamAKNHPLKGKAciQLEDLNDQDLIM 199
Cdd:PRK09791  154 qGPYDH--EFTFEKLLE-KQFAVFC--RPGHPAIGAR--SLKQLLDYSWTM 197
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 93-292 2.01e-12

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: 64.54  E-value: 2.01e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314  93 IRLGrSFLNPAQDFFPLW-HRFNQHYPQFKLEVVpfEDNQQSILETIKHlGQgFDLMVGAC-DSLKWLEYVqllPLKEAK 170
Cdd:cd05466     2 LRIG-ASPSIAAYLLPPLlAAFRQRYPGVELSLV--EGGSSELLEALLE-GE-LDLAIVALpVDDPGLESE---PLFEEP 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314 171 LTCAMAKNHPLKGKACIQLEDLNDQDLIMVKEGhSQSNDALRSYLKSH---YRSIHIIDaayyyDLSTFNRCEQTG---A 244
Cdd:cd05466    74 LVLVVPPDHPLAKRKSVTLADLADEPLILFERG-SGLRRLLDRAFAEAgftPNIALEVD-----SLEAIKALVAAGlgiA 147

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1417874314 245 ILLSLDVWEDIHPSLITIPLAWSGPGVPYGIIYSKE--PNDQVAKFIKVL 292
Cdd:cd05466   148 LLPESAVEELADGGLVVLPLEDPPLSRTIGLVWRKGryLSPAARAFLELL 197
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-61 1.87e-11

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 63.67  E-value: 1.87e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1417874314   6 LEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAG 61
Cdd:PRK10094    7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAG 62
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
4-61 1.74e-10

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 60.37  E-value: 1.74e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1417874314   4 RKLEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRsSRGVKLTEAG 61
Cdd:PRK13348    5 KQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAG 61
PRK10341 PRK10341
transcriptional regulator TdcA;
3-139 4.44e-10

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 59.49  E-value: 4.44e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314   3 SRKLEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAGHSFYQDSLALIDQSQKAIHRA 82
Cdd:PRK10341    9 TQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEI 88

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1417874314  83 KQIAQKSPYLIRLGRSFLNPAQDFFPLWHRFNQHYPqfKLEVVPFEDNQQSILETIK 139
Cdd:PRK10341   89 NGMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFP--KAQVSMYEAQLSSFLPAIR 143
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
4-66 1.48e-09

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 57.85  E-value: 1.48e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1417874314   4 RKLEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAGHSFYQ 66
Cdd:PRK10632    5 KRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQ 67
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-84 2.46e-09

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 57.00  E-value: 2.46e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314   1 MYSRKLEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAGHSFY---QDSLALIDQSQK 77
Cdd:PRK11233    1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYthaRAILRQCEQAQL 80


                  ....*..
gi 1417874314  78 AIHRAKQ 84
Cdd:PRK11233   81 AVHNVGQ 87
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 9-124 9.55e-09

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 55.38  E-value: 9.55e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314   9 FIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAGHSFYQDSLALIDQSQKAiHRAKQIAQK 88
Cdd:PRK14997   10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAA-QDAIAALQV 88

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1417874314  89 SPY-LIRLGRSFLNPAQDFFPLWHRFNQHYPQFKLEV 124
Cdd:PRK14997   89 EPRgIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQL 125
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
6-61 1.26e-08

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 54.78  E-value: 1.26e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1417874314   6 LEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRsSRGVKLTEAG 61
Cdd:PRK03635    7 LEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAG 61
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
26-123 2.41e-08

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 54.05  E-value: 2.41e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314  26 YISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAGHSFYQDSLALIDQSQKAIHrakQIAQKSPYL---IRL------G 96
Cdd:PRK11716    2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRH---TLDQQGPSLsgeLSLfcsvtaA 78

                          90       100
                  ....*....|....*....|....*....
gi 1417874314  97 RSFLnpaqdfFPLWHRFNQHYP--QFKLE 123
Cdd:PRK11716   79 YSHL------PPILDRFRAEHPlvEIKLT 101
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 93-293 2.61e-08

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: 53.06  E-value: 2.61e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314  93 IRLGrSFLNPAQDFFPLW-HRFNQHYPQFKLEVVpfEDNQQSILEtikHLGQG-FDLMVGAcDSLKWLEYVQLlPLKEAK 170
Cdd:pfam03466   4 LRIG-APPTLASYLLPPLlARFRERYPDVELELT--EGNSEELLD---LLLEGeLDLAIRR-GPPDDPGLEAR-PLGEEP 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314 171 LTCAMAKNHPLKGKACIQLEDLNDQDLIMVKEGHSqSNDALRSYLKSHYRSIHIidAAYYYDLSTFNRCEQTG---AILL 247
Cdd:pfam03466  76 LVLVAPPDHPLARGEPVSLEDLADEPLILLPPGSG-LRDLLDRALRAAGLRPRV--VLEVNSLEALLQLVAAGlgiALLP 152

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1417874314 248 SLDVWEDI-HPSLITIPLAWSGPGVPYGIIYSKE--PNDQVAKFIKVLA 293
Cdd:pfam03466 153 RSAVARELaDGRLVALPLPEPPLPRELYLVWRKGrpLSPAVRAFIEFLR 201
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
4-216 3.99e-08

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 53.48  E-value: 3.99e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314   4 RKLEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAGHSFYQDSLALIDQSQKAIHRAK 83
Cdd:PRK15421    5 KHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQACN 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314  84 QIAQKSpylIRLGRSFLNPAQDFFPLWHRFNQHYPQFKLEV---VPFeDNQQSiletikhLGQGFDLMVGACDSL--KWL 158
Cdd:PRK15421   85 EPQQTR---LRIAIECHSCIQWLTPALENFHKNWPQVEMDFksgVTF-DPQPA-------LQQGELDLVMTSDILprSGL 153

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1417874314 159 EYVqllPLKEAKLTCAMAKNHPLKGKACIQLEDLNDQDLIMVKEGHSQSnDALRSYLK 216
Cdd:PRK15421  154 HYS---PMFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRSRL-DVWRHFLQ 207
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 89-204 2.49e-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: 50.22  E-value: 2.49e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314  89 SPYLIrlgrsflnPAqdFFPLWHrfnQHYPQFKLEVVpfEDNQQSILEtikHLGQG-FDLMVGAcdslkwleyvqlLPLK 167
Cdd:cd08411    12 APYLL--------PR--LLPALR---QAYPKLRLYLR--EDQTERLLE---KLRSGeLDAALLA------------LPVD 61

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1417874314 168 EAKLTC----------AMAKNHPLKGKACIQLEDLNDQDLIMVKEGH 204
Cdd:cd08411    62 EPGLEEeplfdepfllAVPKDHPLAKRKSVTPEDLAGERLLLLEEGH 108
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 112-199 4.24e-07

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: 49.47  E-value: 4.24e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314 112 RFNQHYPQFKLEVVpfEDNQQSILEtikHLGQG-FDLMVgaCDSLKWLEYVQLLPLKEAKLTCAMAKNHPLKGKACIQLE 190
Cdd:cd08412    21 RFREAYPGVEVRVV--EGNQEELEE---GLRSGeLDLAL--TYDLDLPEDIAFEPLARLPPYVWLPADHPLAGKDEVSLA 93


                  ....*....
gi 1417874314 191 DLNDQDLIM 199
Cdd:cd08412    94 DLAAEPLIL 102
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 19-198 4.25e-07

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 50.38  E-value: 4.25e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314  19 SQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVK-LTEAGhsfyqdsLALIDQSQKAIHRAKQIAqkspyliRLGR 97
Cdd:PRK12682   20 TEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPG-------KAVLDVIERILREVGNIK-------RIGD 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314  98 SFLNP-------------AQDFFPL-WHRFNQHYPqfKLEVVPFEDNQQSILETIKHlGQGfDLMVgACDSLKWLEYVQL 163
Cdd:PRK12682   86 DFSNQdsgtltiatthtqARYVLPRvVAAFRKRYP--KVNLSLHQGSPDEIARMVIS-GEA-DIGI-ATESLADDPDLAT 160

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1417874314 164 LPLKEAKLTCAMAKNHPLKGKACIQLEDLNDQDLI 198
Cdd:PRK12682  161 LPCYDWQHAVIVPPDHPLAQEERITLEDLAEYPLI 195
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 6-61 4.81e-07

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 50.41  E-value: 4.81e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1417874314   6 LEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAG 61
Cdd:PRK15092   16 LRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHG 71
nhaR PRK11062
transcriptional activator NhaR; Provisional
 9-61 1.60e-06

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 48.47  E-value: 1.60e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1417874314   9 FIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAG 61
Cdd:PRK11062   12 FWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELG 64
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
11-198 3.66e-06

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 47.66  E-value: 3.66e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314  11 AVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQR-SSRGVKLTEAGhsfyqdslalidqsqKAIHR-AKQIAQK 88
Cdd:PRK12684   12 AVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRhGKRLRGLTEPG---------------RIILAsVERILQE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314  89 SPYLIRLGRSFLNPAQDFF--------------PLWHRFNQHYPQFKLEVvpFEDNQQSILETIKHlGQGfDLMVgACDS 154
Cdd:PRK12684   77 VENLKRVGKEFAAQDQGNLtiatthtqaryalpAAIKEFKKRYPKVRLSI--LQGSPTQIAEMVLH-GQA-DLAI-ATEA 151

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1417874314 155 LKWLEYVQLLPLKEAKLTCAMAKNHPLKGKACIQLEDLNDQDLI 198
Cdd:PRK12684  152 IADYKELVSLPCYQWNHCVVVPPDHPLLERKPLTLEDLAQYPLI 195
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 11-61 3.58e-05

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 44.65  E-value: 3.58e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1417874314  11 AVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRS-SRGVKLTEAG 61
Cdd:PRK12683   12 AVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRgKRLTGLTEPG 63
HTH_30 pfam13556
PucR C-terminal helix-turn-helix domain; This helix-turn-helix domain is often found at the ...
 6-47 6.68e-05

PucR C-terminal helix-turn-helix domain; This helix-turn-helix domain is often found at the C-terminus of PucR-like transcriptional regulators such as Swiss:O32138 and is likely to be DNA-binding.


Pssm-ID: 433305 [Multi-domain]  Cd Length: 56  Bit Score: 39.75  E-value: 6.68e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1417874314   6 LEIFIAvaQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDL 47
Cdd:pfam13556   2 LRAYLE--NGGNISATARALHVHRNTLRYRLRRIEELLGLDL 41
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 93-204 7.30e-05

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


Pssm-ID: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 42.91  E-value: 7.30e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314  93 IRLGrsFLNP-AQDFFP-LWHRFNQHYPQfklevVPFEDNQQSILETIKHLGQG-FDLMVgaCDSLKWLEYVQLLPLKEA 169
Cdd:cd08434     2 VRLG--FLHSlGTSLVPdLIRAFRKEYPN-----VTFELHQGSTDELLDDLKNGeLDLAL--CSPVPDEPDIEWIPLFTE 72

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1417874314 170 KLTCAMAKNHPLKGKACIQLEDLNDQDLIMVKEGH 204
Cdd:cd08434    73 ELVLVVPKDHPLAGRDSVDLAELADEPFVLLSPGF 107
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 93-292 1.10e-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: 42.11  E-value: 1.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314  93 IRLGrsFLNPA-QDFFPLW-HRFNQHYPQfkLEVVPFEDNQQSILETIKHlGQ---GFDLMVGACDSLkwleyvQLLPLK 167
Cdd:cd08414     2 LRIG--FVGSAlYGLLPRLlRRFRARYPD--VELELREMTTAEQLEALRA-GRldvGFVRPPPDPPGL------ASRPLL 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314 168 EAKLTCAMAKNHPLKGKACIQLEDLNDQDLIMV-KEGHSQSNDALRSYLKSHYRSIHIIDAAyyYDLSTfnrceqtgaiL 246
Cdd:cd08414    71 REPLVVALPADHPLAARESVSLADLADEPFVLFpREPGPGLYDQILALCRRAGFTPRIVQEA--SDLQT----------L 138

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1417874314 247 LSL------------DVWEDIHPSLITIPLAWSGPGVPYGIIYSK-EPNDQVAKFIKVL 292
Cdd:cd08414   139 LALvaaglgvalvpaSVARLQRPGVVYRPLADPPPRSELALAWRRdNASPALRAFLELA 197
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
6-61 1.51e-04

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 42.31  E-value: 1.51e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1417874314   6 LEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAG 61
Cdd:PRK03601    6 LKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAG 61
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
4-94 2.52e-04

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


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 39.80  E-value: 2.52e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314   4 RKLEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVK-----LTEAGHSFyqdsLALIDQSQKA 78
Cdd:COG2005    22 GRIELLEAIDETGSISAAAKAMGMSYKRAWDLIDAMNNLLGEPLVERQTGGKGgggarLTPEGRRL----LALYRRLEAE 97

                          90
                  ....*....|....*..
gi 1417874314  79 IHRA-KQIAQKSPYLIR 94
Cdd:COG2005    98 AQRAlAALFEELFALLR 114
PucR COG2508
DNA-binding transcriptional regulator, PucR/PutR family [Transcription];
6-47 4.79e-04

DNA-binding transcriptional regulator, PucR/PutR family [Transcription];


Pssm-ID: 441998 [Multi-domain]  Cd Length: 257  Bit Score: 40.75  E-value: 4.79e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1417874314   6 LEIFIAvaQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDL 47
Cdd:COG2508   195 LRAYLD--NGGNVSATARALHVHRNTVRYRLRRIEELLGRDL 234
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
1-66 5.17e-04

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 40.81  E-value: 5.17e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1417874314   1 MYSRKLEIFIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAGHSFYQ 66
Cdd:PRK15243    4 LINKKLKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQTIYR 69
cysB PRK12681
HTH-type transcriptional regulator CysB;
19-61 7.88e-04

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 40.27  E-value: 7.88e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1417874314  19 SQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVK-LTEAG 61
Cdd:PRK12681   20 SATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAG 63
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 93-199 9.95e-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: 39.46  E-value: 9.95e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314  93 IRLGRSFLNPAQDFFPLWHRFNQHYPQFKLEVVpfEDNQQSILETIKhlgQGfDLMVGAC----DSlkwlEYVQLLPLKE 168
Cdd:cd08438     2 LRLGLPPLGGSLLFAPLLAAFRQRYPNIELELV--EYGGKKVEQAVL---NG-ELDVGITvlpvDE----EEFDSQPLCN 71

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1417874314 169 AKLTCAMAKNHPLKGKACIQLEDLNDQDLIM 199
Cdd:cd08438    72 EPLVAVLPRGHPLAGRKTVSLADLADEPFIL 102
CdaR COG3835
Sugar diacid utilization regulator CdaR [Transcription, Signal transduction mechanisms];
6-47 1.24e-03

Sugar diacid utilization regulator CdaR [Transcription, Signal transduction mechanisms];


Pssm-ID: 443046 [Multi-domain]  Cd Length: 301  Bit Score: 39.63  E-value: 1.24e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1417874314   6 LEIFIAvaQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDL 47
Cdd:COG3835   243 LRAYFE--NNGNISETAEALFIHRNTLRYRLKKIEELTGLDL 282
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
17-79 1.25e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 37.57  E-value: 1.25e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1417874314   17 SFSQAAQRLYISPTAVKKQIDRLEDlLGLDLFQRSSRG-----VKLTEAGHSFYQDSLALIDQSQKAI 79
Cdd:smart00347  26 SVSELAKRLGVSPSTVTRVLDRLEK-KGLVRREPSPEDrrsvlVSLTEEGRELIEQLLEARSETLAEL 92
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
9-74 1.67e-03

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 39.27  E-value: 1.67e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1417874314   9 FIAVAQEGSFSQAAQRLYISPTAVKKQIDRLEDLLGLDLFQRSSRGVKLTEAGHSFYQDSLALIDQ 74
Cdd:PRK10082   19 FLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQ 84
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 111-203 1.88e-03

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


Pssm-ID: 176131 [Multi-domain]  Cd Length: 197  Bit Score: 38.66  E-value: 1.88e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314 111 HRFNQHYPQFKLEVvpFEDNQQSILETIKH----LGQGFdlMVGACDSLkwleyvQLLPLKEAKLTCAMAKNHPLKGKAC 186
Cdd:cd08440    20 AAFRRRHPGIRVRL--RDVSAEQVIEAVRSgevdFGIGS--EPEADPDL------EFEPLLRDPFVLVCPKDHPLARRRS 89

                          90
                  ....*....|....*..
gi 1417874314 187 IQLEDLNDQDLIMVKEG 203
Cdd:cd08440    90 VTWAELAGYPLIALGRG 106
PRK11886 PRK11886
bifunctional biotin--[acetyl-CoA-carboxylase] ligase/biotin operon repressor BirA;
2-102 5.06e-03

bifunctional biotin--[acetyl-CoA-carboxylase] ligase/biotin operon repressor BirA;


Pssm-ID: 237010 [Multi-domain]  Cd Length: 319  Bit Score: 37.84  E-value: 5.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314   2 YSRKLEIfIAVAQEG---SFSQAAQRLYISPTAVKKQIDRLEDlLGLDLFQRSSRGVKLTEaghsfyqdSLALIDqsqka 78
Cdd:PRK11886    3 YTVMLQL-LSLLADGdfhSGEQLGEELGISRAAIWKHIQTLEE-WGLDIFSVKGKGYRLAE--------PLDLLD----- 67

                          90       100
                  ....*....|....*....|....
gi 1417874314  79 ihrAKQIAQKSPylirLGRSFLNP 102
Cdd:PRK11886   68 ---PERISSQLP----PGRVTVLP 84
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 111-200 6.71e-03

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


Pssm-ID: 176142 [Multi-domain]  Cd Length: 199  Bit Score: 37.16  E-value: 6.71e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1417874314 111 HRFNQHYPQFKLEVVpfEDNQQSILETI--KHLGQGF-DLMVGACDSLkwleyvQLLPLKEAKLTCAMAKNHPLKGKACI 187
Cdd:cd08451    21 RRFREAYPDVELTLE--EANTAELLEALreGRLDAAFvRPPVARSDGL------VLELLLEEPMLVALPAGHPLARERSI 92

                          90
                  ....*....|...
gi 1417874314 188 QLEDLNDQDLIMV 200
Cdd:cd08451    93 PLAALADEPFILF 105
COG2345 COG2345
Predicted transcriptional regulator, ArsR family [Transcription];
19-74 9.58e-03

Predicted transcriptional regulator, ArsR family [Transcription];


Pssm-ID: 441914 [Multi-domain]  Cd Length: 217  Bit Score: 36.82  E-value: 9.58e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1417874314  19 SQAAQRLYISPTAVKKQIDRLEDlLGLDLFQRSSRGV-------KLTEAGHSF----YQD-SLALIDQ 74
Cdd:COG2345    31 AELAEALGLTPNAVRRHLDALEE-EGLVERETERRGRgrpaklyRLTEAGRARfpraYDDlAVALLDA 97
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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