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Conserved domains on  [gi|1582640192|gb|TBE20600|]
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LysR family transcriptional regulator (plasmid) [Rhizobium ruizarguesonis]

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];
7-298 1.18e-47

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 160.42  E-value: 1.18e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192   7 DLRSLTVFRAVVDHKSFLGAQIALGLSQSAVSFHIKALEDRLGFKLCQRGRSGFELTDRGAIVHERSKGLFLALNAFESD 86
Cdd:COG0583     2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  87 IGALKNRITGTLRLGLVDnTITDSDLPihRVIARISERAPEARVELAIDTPDALLSEIANGGLDIALLPETQPYQGLKLS 166
Cdd:COG0583    82 LRALRGGPRGTLRIGAPP-SLARYLLP--PLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVAR 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192 167 RFREEIHSLYCAQGHPLfrqaeaeltiehvetfdfvvrpyanmrelqffpkARARAIASNMEAQAMFVMSGHYLGYLPDH 246
Cdd:COG0583   159 PLGEERLVLVASPDHPL----------------------------------ARRAPLVNSLEALLAAVAAGLGIALLPRF 204

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1582640192 247 YARGWVQKGRFRQLMPEETRIHSTFVIATRSTEKPSTILDFFIRELAGIASE 298
Cdd:COG0583   205 LAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-298 1.18e-47

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 160.42  E-value: 1.18e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192   7 DLRSLTVFRAVVDHKSFLGAQIALGLSQSAVSFHIKALEDRLGFKLCQRGRSGFELTDRGAIVHERSKGLFLALNAFESD 86
Cdd:COG0583     2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  87 IGALKNRITGTLRLGLVDnTITDSDLPihRVIARISERAPEARVELAIDTPDALLSEIANGGLDIALLPETQPYQGLKLS 166
Cdd:COG0583    82 LRALRGGPRGTLRIGAPP-SLARYLLP--PLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVAR 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192 167 RFREEIHSLYCAQGHPLfrqaeaeltiehvetfdfvvrpyanmrelqffpkARARAIASNMEAQAMFVMSGHYLGYLPDH 246
Cdd:COG0583   159 PLGEERLVLVASPDHPL----------------------------------ARRAPLVNSLEALLAAVAAGLGIALLPRF 204

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1582640192 247 YARGWVQKGRFRQLMPEETRIHSTFVIATRSTEKPSTILDFFIRELAGIASE 298
Cdd:COG0583   205 LAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 95-293 3.16e-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: 83.88  E-value: 3.16e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  95 TGTLRLGLVDnTITDSDLPihRVIARISERAPEARVELAIDTPDALLSEIANGGLDIALLPETQPYQGLKLSRFREEIHS 174
Cdd:pfam03466   1 SGRLRIGAPP-TLASYLLP--PLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192 175 LYCAQGHPLFRQaeAELTIEHVETFDFVVRP---------YANMRELQFFPKARARaiASNMEAQAMFVMSGHYLGYLPD 245
Cdd:pfam03466  78 LVAPPDHPLARG--EPVSLEDLADEPLILLPpgsglrdllDRALRAAGLRPRVVLE--VNSLEALLQLVAAGLGIALLPR 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1582640192 246 HYARGWVQKGRFRQLMPEETRIHSTFVIATRSTEKPSTILDFFIRELA 293
Cdd:pfam03466 154 SAVARELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLR 201
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 7-204 6.30e-19

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 84.98  E-value: 6.30e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192   7 DLRSLTVFRAVVDHKSFLGAQIALGLSQSAVSFHIKALEDRLGFKLCQRGRSGFELTDRGAIVHERSKG-LFLALNAfES 85
Cdd:NF040786    2 NLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEmLDLWEKL-EE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  86 DIGALKNRITGTLRLGlVDNTITDSDLPihRVIARISERAPEARVELAIDTPDALLSEIANGGLDIALLPETQPYQGLKL 165
Cdd:NF040786   81 EFDRYGKESKGVLRIG-ASTIPGQYLLP--ELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVY 157

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1582640192 166 SRFREEIHSLYCAQGHPLFRQAEAELTIEHVETFDFVVR 204
Cdd:NF040786  158 TPFYKDRLVLITPNGTEKYRMLKEEISISELQKEPFIMR 196
rbcR CHL00180
LysR transcriptional regulator; Provisional
 8-182 2.46e-13

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 69.28  E-value: 2.46e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192   8 LRSLTVFRAVVDHKSFLGAQIALGLSQSAVSFHIKALEDRLGFKLCQRGRSGFELTDRGAIVHERSkGLFLALnAFESD- 86
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYG-NRILAL-CEETCr 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  87 -IGALKNRITGTLRLGlVDNTITDSDLPihRVIARISERAPEARVELAIDTPDALLSEIANGGLDIALLPETQP---YQG 162
Cdd:CHL00180   85 aLEDLKNLQRGTLIIG-ASQTTGTYLMP--RLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGEVPtelKKI 161

                         170       180
                  ....*....|....*....|
gi 1582640192 163 LKLSRFREEIHSLYCAQGHP 182
Cdd:CHL00180  162 LEITPYVEDELALIIPKSHP 181
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 97-292 6.78e-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: 63.39  E-value: 6.78e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  97 TLRLGLVDnTITDSDLPihRVIARISERAPEARVELAIDTPDALLSEIANGGLDIALLPETQPYQGLKLSRFREEIHSLY 176
Cdd:cd05466     1 TLRIGASP-SIAAYLLP--PLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192 177 CAQGHPLFRQaeAELTIEHVETFDFVVRPYANMRELQFFPKARARAIA-------SNMEAQAMFVMSGHYLGYLPDHYAR 249
Cdd:cd05466    78 VPPDHPLAKR--KSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTpnialevDSLEAIKALVAAGLGIALLPESAVE 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1582640192 250 GwVQKGRFRQLMPEETRIHSTFVIATRSTEKPSTILDFFIREL 292
Cdd:cd05466   156 E-LADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-298 1.18e-47

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 160.42  E-value: 1.18e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192   7 DLRSLTVFRAVVDHKSFLGAQIALGLSQSAVSFHIKALEDRLGFKLCQRGRSGFELTDRGAIVHERSKGLFLALNAFESD 86
Cdd:COG0583     2 DLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  87 IGALKNRITGTLRLGLVDnTITDSDLPihRVIARISERAPEARVELAIDTPDALLSEIANGGLDIALLPETQPYQGLKLS 166
Cdd:COG0583    82 LRALRGGPRGTLRIGAPP-SLARYLLP--PLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVAR 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192 167 RFREEIHSLYCAQGHPLfrqaeaeltiehvetfdfvvrpyanmrelqffpkARARAIASNMEAQAMFVMSGHYLGYLPDH 246
Cdd:COG0583   159 PLGEERLVLVASPDHPL----------------------------------ARRAPLVNSLEALLAAVAAGLGIALLPRF 204

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1582640192 247 YARGWVQKGRFRQLMPEETRIHSTFVIATRSTEKPSTILDFFIRELAGIASE 298
Cdd:COG0583   205 LAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 95-293 3.16e-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: 83.88  E-value: 3.16e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  95 TGTLRLGLVDnTITDSDLPihRVIARISERAPEARVELAIDTPDALLSEIANGGLDIALLPETQPYQGLKLSRFREEIHS 174
Cdd:pfam03466   1 SGRLRIGAPP-TLASYLLP--PLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192 175 LYCAQGHPLFRQaeAELTIEHVETFDFVVRP---------YANMRELQFFPKARARaiASNMEAQAMFVMSGHYLGYLPD 245
Cdd:pfam03466  78 LVAPPDHPLARG--EPVSLEDLADEPLILLPpgsglrdllDRALRAAGLRPRVVLE--VNSLEALLQLVAAGLGIALLPR 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1582640192 246 HYARGWVQKGRFRQLMPEETRIHSTFVIATRSTEKPSTILDFFIRELA 293
Cdd:pfam03466 154 SAVARELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLR 201
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 7-204 6.30e-19

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


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 84.98  E-value: 6.30e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192   7 DLRSLTVFRAVVDHKSFLGAQIALGLSQSAVSFHIKALEDRLGFKLCQRGRSGFELTDRGAIVHERSKG-LFLALNAfES 85
Cdd:NF040786    2 NLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEmLDLWEKL-EE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  86 DIGALKNRITGTLRLGlVDNTITDSDLPihRVIARISERAPEARVELAIDTPDALLSEIANGGLDIALLPETQPYQGLKL 165
Cdd:NF040786   81 EFDRYGKESKGVLRIG-ASTIPGQYLLP--ELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVY 157

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1582640192 166 SRFREEIHSLYCAQGHPLFRQAEAELTIEHVETFDFVVR 204
Cdd:NF040786  158 TPFYKDRLVLITPNGTEKYRMLKEEISISELQKEPFIMR 196
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
8-66 1.95e-16

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 72.03  E-value: 1.95e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1582640192   8 LRSLTVFRAVVDHKSFLGAQIALGLSQSAVSFHIKALEDRLGFKLCQRGRSGFELTDRG 66
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
rbcR CHL00180
LysR transcriptional regulator; Provisional
 8-182 2.46e-13

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 69.28  E-value: 2.46e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192   8 LRSLTVFRAVVDHKSFLGAQIALGLSQSAVSFHIKALEDRLGFKLCQRGRSGFELTDRGAIVHERSkGLFLALnAFESD- 86
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYG-NRILAL-CEETCr 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  87 -IGALKNRITGTLRLGlVDNTITDSDLPihRVIARISERAPEARVELAIDTPDALLSEIANGGLDIALLPETQP---YQG 162
Cdd:CHL00180   85 aLEDLKNLQRGTLIIG-ASQTTGTYLMP--RLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGEVPtelKKI 161

                         170       180
                  ....*....|....*....|
gi 1582640192 163 LKLSRFREEIHSLYCAQGHP 182
Cdd:CHL00180  162 LEITPYVEDELALIIPKSHP 181
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 7-298 6.62e-12

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 65.01  E-value: 6.62e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192   7 DLRSLTVFRAVVDHKSFLGAQIALGLSQSAVSFHIKALEDRLGFKLCQRGRSGFELTDRGAIVHERSKGLFLALNAFESD 86
Cdd:PRK14997    3 DLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  87 IGALKNRITGTLRLGLvdnTITDSDLPIHRVIARISERAPEARVELAIDTPDAllsEIANGGLDIALLPETQPYQGLKLs 166
Cdd:PRK14997   83 IAALQVEPRGIVKLTC---PVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRV---DVVGEGVDVAIRVRPRPFEDSDL- 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192 167 rfreeIHSLYCAQGHPLFR-----------QAEAELTI---------EHVETFDfVVRPYANMRELQFFPkaraRAIASN 226
Cdd:PRK14997  156 -----VMRVLADRGHRLFAspdliarmgipSAPAELSHwpglslasgKHIHRWE-LYGPQGARAEVHFTP----RMITTD 225

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1582640192 227 MEAQAMFVMSGHYLGYLPDHYARGWVQKGRFRQLM----PEETRIHSTFviATRSTEKPS--TILDFFIRELAGIASE 298
Cdd:PRK14997  226 MLALREAAMAGVGLVQLPVLMVKEQLAAGELVAVLeewePRREVIHAVF--PSRRGLLPSvrALVDFLTEEYARMVEE 301
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 97-292 6.78e-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: 63.39  E-value: 6.78e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  97 TLRLGLVDnTITDSDLPihRVIARISERAPEARVELAIDTPDALLSEIANGGLDIALLPETQPYQGLKLSRFREEIHSLY 176
Cdd:cd05466     1 TLRIGASP-SIAAYLLP--PLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192 177 CAQGHPLFRQaeAELTIEHVETFDFVVRPYANMRELQFFPKARARAIA-------SNMEAQAMFVMSGHYLGYLPDHYAR 249
Cdd:cd05466    78 VPPDHPLAKR--KSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTpnialevDSLEAIKALVAAGLGIALLPESAVE 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1582640192 250 GwVQKGRFRQLMPEETRIHSTFVIATRSTEKPSTILDFFIREL 292
Cdd:cd05466   156 E-LADGGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 8-171 1.84e-10

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 60.63  E-value: 1.84e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192   8 LRSLTVFRAVVDHKSFLGAQIALGLSQSAVSFHIKALEDRLGFKLCQR-GRSgFELTDRGAIVHERSKGLFLALNAfesd 86
Cdd:PRK11139    8 LNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRrNRS-LLLTEEGQRYFLDIREIFDQLAE---- 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  87 igalknrITGTLRLGLVDNTITDSDLP---IHRVIARIS---ERAPEARVEL-AIDTPDALLSEiangGLDIALLPETQP 159
Cdd:PRK11139   83 -------ATRKLRARSAKGALTVSLLPsfaIQWLVPRLSsfnEAHPDIDVRLkAVDRLEDFLRD----DVDVAIRYGRGN 151

                         170
                  ....*....|..
gi 1582640192 160 YQGLKLSRFREE 171
Cdd:PRK11139  152 WPGLRVEKLLDE 163
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
2-98 5.03e-10

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 59.63  E-value: 5.03e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192   2 LLAQSDLRSLTVFRAVVDHKSFLGAQIALGLSQSAVSFHIKALEDRLGFKLCQRGRSGFELTDRGAIVHERSKGLFLALN 81
Cdd:PRK10086   10 LLNGWQLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLN 89

                          90
                  ....*....|....*...
gi 1582640192  82 AfesDIGALKNR-ITGTL 98
Cdd:PRK10086   90 Q---EILDIKNQeLSGTL 104
PRK09791 PRK09791
LysR family transcriptional regulator;
4-183 6.01e-09

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 56.31  E-value: 6.01e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192   4 AQSDLRSLTVFRAVVDHKSFLGAQIALGLSQSAVSFHIKALEDRLGFKLCQRGRSGFELTDRGAIVHERSKGLFLALNAF 83
Cdd:PRK09791    3 FQVKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  84 ESDIGALKNRITGTLRLGlVDNTITDSDLPihRVIARISERAPEARVELAIDTPDALLSEIANGGLDIALLPETQ-PYQG 162
Cdd:PRK09791   83 QEDIRQRQGQLAGQINIG-MGASIARSLMP--AVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYYQgPYDH 159

                         170       180
                  ....*....|....*....|..
gi 1582640192 163 -LKLSRFREEIHSLYCAQGHPL 183
Cdd:PRK09791  160 eFTFEKLLEKQFAVFCRPGHPA 181
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
7-86 2.25e-08

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 54.21  E-value: 2.25e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192   7 DLRSLTVFRAVVDHKSFLGAQIALGLSQSAVSFHIKALEDRLGFKLCQRGRSgFELTDRGaivhERSKGLFLALNAFESD 86
Cdd:PRK13348    3 DYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRP-CRPTPAG----QRLLRHLRQVALLEAD 77
PRK09986 PRK09986
LysR family transcriptional regulator;
7-249 3.16e-08

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 53.96  E-value: 3.16e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192   7 DLRSLTVFRAVVDHKSFLGAQIALGLSQSAVSFHIKALEDRLGFKLCQRGRSGFELTDRGAIVHERSKGLFLALNAFESD 86
Cdd:PRK09986    8 DLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLAR 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  87 IGALKNRITGTLRLGLVDNTITDSDLPIHRviaRISERAPEARVELAIDTPDALLSEIANGGLDIAL--LPETQPYQGLK 164
Cdd:PRK09986   88 VEQIGRGEAGRIEIGIVGTALWGRLRPAMR---HFLKENPNVEWLLRELSPSMQMAALERRELDAGIwrMADLEPNPGFT 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192 165 LSRFREEIHSLYCAQGHPLFRQAEAELTIEHVETF--------DFVVRPYANMRELQFFPKararAIASNMEAQAM--FV 234
Cdd:PRK09986  165 SRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFitlpfvhsDWGKFLQRVCQQAGFSPQ----IIRQVNEPQTVlaMV 240

                         250
                  ....*....|....*
gi 1582640192 235 MSGHYLGYLPDHYAR 249
Cdd:PRK09986  241 SMGIGITLLPDSYAQ 255
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 8-204 3.63e-08

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 53.54  E-value: 3.63e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192   8 LRSLTVFRAVVDHKSFLGAQIALGLSQSAVSFHIKALEDRLGFKLcqrgrsgFELTDRGAIVHERSKGLF---LALNAFE 84
Cdd:PRK10837    5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQL-------FDRVGKRLVVNEHGRLLYpraLALLEQA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  85 SDIGALKNRITGTLRLGlVDNTITDSDLPihRVIARISERAPEARVELAIDTPDALLSEIANGGLDIALL------PE-- 156
Cdd:PRK10837   78 VEIEQLFREDNGALRIY-ASSTIGNYILP--AMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIegpchsPEli 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1582640192 157 TQPYqglklsrfREEIHSLYCAQGHPLFRQaeaELTIEHVETFDFVVR 204
Cdd:PRK10837  155 SEPW--------LEDELVVFAAPDSPLARG---PVTLEQLAAAPWILR 191
PRK10341 PRK10341
transcriptional regulator TdcA;
9-160 4.97e-08

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 53.33  E-value: 4.97e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192   9 RSLTVFRAVVDHKSFLGAQIALGLSQSAVSFHIKALEDRLGFKLCQRGRSGFELTDRGAIVHERSKGLFLALNAFESDIG 88
Cdd:PRK10341   10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN 89

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1582640192  89 ALKNRITGTLRLG---LVDNTITDSdlpihrVIARISERAPEARVELAIDTPDALLSEIANGGLDIA---LLPETQPY 160
Cdd:PRK10341   90 GMSSEAVVDVSFGfpsLIGFTFMSD------MINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAigtLSNEMKLQ 161
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
8-153 6.21e-08

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 53.23  E-value: 6.21e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192   8 LRSLTVFRAVVDHKSFLGAQIALGLSQSAVSFHIKALEDRLGFKLCQRGRSGFELTDRGAIVHERSKGLFLALNAFESDI 87
Cdd:PRK10632    4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1582640192  88 GALKNRITGTLRLGlvdntitDSDLPIHRVIARISERA----PEARVEL--AIDTPDAllseIANgGLDIAL 153
Cdd:PRK10632   84 YAFNNTPIGTLRIG-------CSSTMAQNVLAGLTAKMlkeyPGLSVNLvtGIPAPDL----IAD-GLDVVI 143
PRK12680 PRK12680
LysR family transcriptional regulator;
33-183 7.37e-08

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 53.09  E-value: 7.37e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  33 SQSAVSFHIKALEDRLGFKL-CQRGRSGFELTDRGAIVHERSKGLFLALNAFESDIGALKNRITGTLRLglvDNTITDSD 111
Cdd:PRK12680   29 TQPGLSKQLKQLEDELGFLLfVRKGRSLESVTPAGVEVIERARAVLSEANNIRTYAANQRRESQGQLTL---TTTHTQAR 105

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1582640192 112 LPIHRVIARISERAPEARVELAIDTPDALLSEIANGGLDIALLPE--TQPYQGLKLSRFREEiHSLYCAQGHPL 183
Cdd:PRK12680  106 FVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTagGEPSAGIAVPLYRWR-RLVVVPRGHAL 178
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 29-199 1.11e-07

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 52.35  E-value: 1.11e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  29 ALGLSQSAVSFHIKALEDRLGFKLCQR-GRSGFELTDRGAIVHERSKGLFLALNAFESDIGALKNRITGTLrlgLVDNTI 107
Cdd:PRK12683   25 ALYTSQSGVSKQIKDLEDELGVEIFIRrGKRLTGLTEPGKELLQIVERMLLDAENLRRLAEQFADRDSGHL---TVATTH 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192 108 TDSDLPIHRVIARISERAPEARVELAIDTPDALLSEIANGGLDIALLPET-QPYQGLKLSRFREEIHSLYCAQGHPLfrQ 186
Cdd:PRK12683  102 TQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEAlDREPDLVSFPYYSWHHVVVVPKGHPL--T 179

                         170
                  ....*....|...
gi 1582640192 187 AEAELTIEHVETF 199
Cdd:PRK12683  180 GRENLTLEAIAEY 192
cbl PRK12679
HTH-type transcriptional regulator Cbl;
33-202 1.25e-07

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 52.12  E-value: 1.25e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  33 SQSAVSFHIKALEDRLGFKL-CQRGRSGFELTDRGA--------IVHERSKGLFLALNAFESDIGALKnritgtlrlglV 103
Cdd:PRK12679   29 SQSGVSRHIRELEDELGIEIfIRRGKRLLGMTEPGKallviaerILNEASNVRRLADLFTNDTSGVLT-----------I 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192 104 DNTITDSDLPIHRVIARISERAPEARVELAIDTPDALLSEIANGGLDIALLPE-TQPYQGLKLSRFREEIHSLYCAQGHP 182
Cdd:PRK12679   98 ATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASErLSNDPQLVAFPWFRWHHSLLVPHDHP 177

                         170       180
                  ....*....|....*....|
gi 1582640192 183 LfrQAEAELTIEHVETFDFV 202
Cdd:PRK12679  178 L--TQITPLTLESIAKWPLI 195
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
7-57 5.26e-07

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 50.16  E-value: 5.26e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1582640192   7 DLRSLTVFRAVVDHKSFLGAQIALGLSQSAVSFHIKALEDRLGFKLCQRGR 57
Cdd:PRK03635    3 DYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRTQ 53
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 8-152 1.42e-06

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 48.80  E-value: 1.42e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192   8 LRSLTVFRAVVDHKSFLGAQIALGLSQSAVSFHIKALEDRLGFKLCQRGRSGFELTDRGAIVHERSKGLFLALNAFESDI 87
Cdd:PRK11242    3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAI 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1582640192  88 GALKNRITGTLRLGLvdnTITDSDLPIHRVIARISERAPEARVELAIDTPDALLSEIANGGLDIA 152
Cdd:PRK11242   83 HDVADLSRGSLRLAM---TPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVG 144
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 117-292 1.69e-06

The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 47.65  E-value: 1.69e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192 117 VIARISERAPEARVELAIDTPDALLSEIANGGLDIAL--LPETQPYQGLKLSRFREEIHSLYCAQGHPLFRqaEAELTIE 194
Cdd:cd08435    18 AIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIgrLADDEQPPDLASEELADEPLVVVARPGHPLAR--RARLTLA 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192 195 HVETFDFVV-RPYANMREL--QFFPKARARAIASNMEAQAMF-----VMSGHYLGYLPDHYARGWVQKGRFRQLMPEETR 266
Cdd:cd08435    96 DLADYPWVLpPPGTPLRQRleQLFAAAGLPLPRNVVETASISallalLARSDMLAVLPRSVAEDELRAGVLRELPLPLPT 175

                         170       180
                  ....*....|....*....|....*.
gi 1582640192 267 IHSTFVIATRSTEKPSTILDFFIREL 292
Cdd:cd08435   176 SRRPIGITTRRGGPLSPAARALLDAL 201
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 96-192 3.10e-06

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: 47.13  E-value: 3.10e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  96 GTLRLGlVDNTITDSDLPihRVIARISERAPEARVELAIDTPDALLSEIANGGLDIALLPEtqPYQGLKLSR---FREEI 172
Cdd:cd08411     1 GPLRLG-VIPTIAPYLLP--RLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLAL--PVDEPGLEEeplFDEPF 75

                          90       100
                  ....*....|....*....|
gi 1582640192 173 HsLYCAQGHPLFRQAEAELT 192
Cdd:cd08411    76 L-LAVPKDHPLAKRKSVTPE 94
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 97-292 2.44e-05

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: 44.42  E-value: 2.44e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  97 TLRLGLVDnTITDSDLPihRVIARISERAPEARVELAIDTPDALLSEIANGGLDIALLPETQPYQGLKLSRFREEihSLY 176
Cdd:cd08414     1 RLRIGFVG-SALYGLLP--RLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLRE--PLV 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192 177 CA--QGHPLFRQAE---AELTIEHVETFDFVVRPYANMRELQFFPKA----RARAIASNMEAQAMFVMSGHYLGYLPDHY 247
Cdd:cd08414    76 VAlpADHPLAARESvslADLADEPFVLFPREPGPGLYDQILALCRRAgftpRIVQEASDLQTLLALVAAGLGVALVPASV 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1582640192 248 ARGWVQKGRFRQLmpEETRIHSTFVIATRSTEkPSTILDFFIREL 292
Cdd:cd08414   156 ARLQRPGVVYRPL--ADPPPRSELALAWRRDN-ASPALRAFLELA 197
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 29-194 2.49e-05

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 44.98  E-value: 2.49e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  29 ALGLSQSAVSFHIKALEDRLGFKLCQrgRSGFELTDrgaiVHERSKGLFLALNAFESDIGALK-------NRITGTLRLG 101
Cdd:PRK12682   25 ALHTSQPGVSKAIIELEEELGIEIFI--RHGKRLKG----LTEPGKAVLDVIERILREVGNIKrigddfsNQDSGTLTIA 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192 102 lVDNTITDSDLPihRVIARISERAPEARVELAIDTPDALLSEIANGGLDIALLPET-QPYQGLKLSRFREEIHSLYCAQG 180
Cdd:PRK12682   99 -TTHTQARYVLP--RVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATESlADDPDLATLPCYDWQHAVIVPPD 175

                         170
                  ....*....|....
gi 1582640192 181 HPLfRQAEaELTIE 194
Cdd:PRK12682  176 HPL-AQEE-RITLE 187
COG4742 COG4742
Predicted transcriptional regulator, contains HTH domain [Transcription];
29-153 3.55e-05

Predicted transcriptional regulator, contains HTH domain [Transcription];


Pssm-ID: 443776 [Multi-domain]  Cd Length: 267  Bit Score: 44.50  E-value: 3.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  29 ALGLSQSAVSFHIKALEDRlgfKLCQRGRSGFELTDRGAIVHERSKGLFLALNAFESDIGALKNRITGTL------RLG- 101
Cdd:COG4742    38 SLDVSRSTILRQLKELEER---GLIERDDGEYELTTLGRLVVEEMEPLLDTLEVLEENRDYWETHDLSAIppelllRIGe 114

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1582640192 102 LVDNTITDSDL-----PIHRVIARISErAPEARVELAIDTPD--ALLSEIANGGLDIAL 153
Cdd:COG4742   115 LGDATVIEPDLtdpfePVERFLELLRE-SKRVRGVSPVFHPDypELFSELVEKGVEVEL 172
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 112-292 5.35e-05

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: 43.25  E-value: 5.35e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192 112 LPihRVIARISERAPEARVELAIDTPDALLSEIANGGLDIALLPETQPYQGLKLSRFREEIHSLYCAQGHPLFRQaeAEL 191
Cdd:cd08420    15 LP--RLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDHPLAGR--KEV 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192 192 TIEHVETFDFVVR-PYANMREL--QFFPKARARAIA-------SNMEA--QAmfVMSGHYLGYLPDHYARGWVQKGRFRQ 259
Cdd:cd08420    91 TAEELAAEPWILRePGSGTREVfeRALAEAGLDGLDlnivmelGSTEAikEA--VEAGLGISILSRLAVRKELELGRLVA 168

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1582640192 260 LMPEETRIHSTFVIATRSTEKPSTILDFFIREL 292
Cdd:cd08420   169 LPVEGLRLTRPFSLIYHKDKYLSPAAEAFLEFL 201
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-202 8.68e-05

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: 42.59  E-value: 8.68e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  97 TLRLGLVdNTITDSDLPihRVIARISERAPEARVELAIDTPDALLSEIANGGLDIAL--LPETQPyQGLKLSRFREEIHS 174
Cdd:cd08436     1 RLAIGTI-TSLAAVDLP--ELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFvgLPERRP-PGLASRELAREPLV 76

                          90       100
                  ....*....|....*....|....*....
gi 1582640192 175 LYCAQGHPLFRQAEAELTIEHVETF-DFV 202
Cdd:cd08436    77 AVVAPDHPLAGRRRVALADLADEPFvDFP 105
PRK09801 PRK09801
LysR family transcriptional regulator;
9-101 1.37e-04

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 43.10  E-value: 1.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192   9 RSLTVFRAVVDHKSFLGAQIALGLSQSAVSFHIKALEDRLGFKLCQRGRSGFELTDRGAIVHERSKGLFLALNAFESDIG 88
Cdd:PRK09801    9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                          90
                  ....*....|...
gi 1582640192  89 ALKNRITGTLRLG 101
Cdd:PRK09801   89 QIKTRPEGMIRIG 101
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 116-262 1.48e-04

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: 42.20  E-value: 1.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192 116 RVIARISERAPEARVELAIDTPDALLSEIANGGLDIALLPETQPYQGLKLSRFREEIHSLYCAQGHPLFRQA---EAELT 192
Cdd:cd08417    17 PLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARKDHPLAGGPltlEDYLA 96

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1582640192 193 IEHVetfdfVVRPYANMREL--QFFPKA----RARAIASNMEAQAMFVMSGHYLGYLPDHYARGWVQKGRFRQLMP 262
Cdd:cd08417    97 APHV-----LVSPRGRGHGLvdDALAELglsrRVALTVPHFLAAPALVAGTDLIATVPRRLAEALAERLGLRVLPL 167
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 7-249 1.77e-04

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 42.36  E-value: 1.77e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192   7 DLRSLTVFRAVVDHKSFLGAQIALGLSQSAVSFHIKALEDRLGFKLCQRGRSGFELTDRGAIVHERSKGLFLALNAFESD 86
Cdd:PRK11233    2 NFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  87 IGALKNRITGTLRLGLVDNTITDS-DLPIhrvIARISERAPEARVELAIDTPDALLSEIANGGLDIALLPETQPYQGLK- 164
Cdd:PRK11233   82 VHNVGQALSGQVSIGLAPGTAASSlTMPL---LQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYEHSPVAGLSs 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192 165 LSRFREEIHsLYCAQGHP-----LFRQAEAELtiehvetfdFVVRPYANMREL--QFFPKAR--ARAIASnMEAQAMF-- 233
Cdd:PRK11233  159 QPLLKEDLF-LVGTQDCPgqsvdLAAVAQMNL---------FLPRDYSAVRLRvdEAFSLRRltAKVIGE-IESIATLta 227

                         250
                  ....*....|....*..
gi 1582640192 234 -VMSGHYLGYLPDHYAR 249
Cdd:PRK11233  228 aIASGMGVTVLPESAAR 244
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 7-154 3.14e-04

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 41.68  E-value: 3.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192   7 DLRSLTVFRAVVDHKSFLGAQIALGLSQSAVSFHIKALEDRLGFKLCQRGRSGFELTDRGAIVHERS--------KGLFL 78
Cdd:PRK09906    2 ELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDAraileqaeKAKLR 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1582640192  79 ALNAFESDIgalknritgTLRLGLV---DNTITDSDLPIHRViariseRAPEARVELAIDTPDALLSEIANGGLDIALL 154
Cdd:PRK09906   82 ARKIVQEDR---------QLTIGFVpsaEVNLLPKVLPMFRL------RHPDTLIELVSLITTQQEEKLRRGELDVGFM 145
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
21-299 3.15e-04

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 41.96  E-value: 3.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  21 KSFLGAQIALGLSQSAVSFHIKALEDRLGFKLCQRGRSGFELTDRGAIVHERSKGLFLAL--NAFE----SDIGALKNRI 94
Cdd:PRK10082   26 RNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLesNLAElrggSDYAQRKIKI 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  95 TG--TLRLGLVDNTItdSDLPIHRVIARISERAPEARVELAIDTPDALLSEianggLDIALLpeTQPYQGLKLsrFREEI 172
Cdd:PRK10082  106 AAahSLSLGLLPSII--SQMPPLFTWAIEAIDVDEAVDKLREGQSDCIFSF-----HDEDLL--EAPFDHIRL--FESQL 174

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192 173 HSLyCA---QGHPLFRQAEAELTIEHVETFDF----VVRPYANMRELQFfpkaRARAIASNMEAQAMFVMSGHYLGYLPD 245
Cdd:PRK10082  175 FPV-CAsdeHGEALFNLAQPHFPLLNYSRNSYmgrlINRTLTRHSELSF----STFFVSSMSELLKQVALDGCGIAWLPE 249

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1582640192 246 HYARGWVQKGRFRQLMPEETRIhSTFVIATRSTEKPSTILDFFIRELAGIASEA 299
Cdd:PRK10082  250 YAIQQEIRSGQLVVLNRDELVI-PIQAYAYRMNTRMNPVAERFWRELRELEIVL 302
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 112-199 4.52e-04

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


Pssm-ID: 176105 [Multi-domain]  Cd Length: 198  Bit Score: 40.68  E-value: 4.52e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192 112 LPihRVIARISERAPEARVELAIDTPDALLSEIANGGLDIALLPET--QPYQGLKLSRFREEiHSLYCAQGHPLfrQAEA 189
Cdd:cd08413    15 LP--PVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEAldDHPDLVTLPCYRWN-HCVIVPPGHPL--ADLG 89

                          90
                  ....*....|
gi 1582640192 190 ELTIEHVETF 199
Cdd:cd08413    90 PLTLEDLAQY 99
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
29-66 7.53e-04

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 40.39  E-value: 7.53e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1582640192  29 ALGLSQSAVSFHIKALEDRLGFKLCQRGRSGFELTDRG 66
Cdd:PRK03601   24 SLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAG 61
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 216-273 8.01e-04

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 7. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. 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: 176165  Cd Length: 197  Bit Score: 39.92  E-value: 8.01e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1582640192 216 PKARARAIASNMEAQAMFVMSGHYLGYLPDHYARGWVQKGRFRQLMPEETRIHSTFVI 273
Cdd:cd08476   121 LRLPTALVCNNIEALIEFALQGLGIACLPDFSVREALADGRLVTVLDDYVEERGQFRL 178
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 7-182 1.95e-03

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 39.24  E-value: 1.95e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192   7 DLRSLTVFRAVVDHKSFLGAQIALGLSQSAVSFHIKALEDRLGFKLCQRGRSGFELTDRGAIVHERSKGLFLALNAFESD 86
Cdd:PRK11151    2 NIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKEM 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  87 IGALKNRITGTLRLGLVDnTITDSDLPIhrVIARISERAPEARVELAIDTPDALLSEIANGGLD---IALLPETQPYQGL 163
Cdd:PRK11151   82 ASQQGETMSGPLHIGLIP-TVGPYLLPH--IIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDcaiLALVKESEAFIEV 158

                         170
                  ....*....|....*....
gi 1582640192 164 KLsrFREEIhSLYCAQGHP 182
Cdd:PRK11151  159 PL--FDEPM-LLAVYEDHP 174
PRK11482 PRK11482
DNA-binding transcriptional regulator;
7-244 5.64e-03

DNA-binding transcriptional regulator;


Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 37.78  E-value: 5.64e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192   7 DLRSLTVFRAVVDHKSFLGAQIALGLSQSAVSFHIKALEDRLGFKLCQRGRSGFELTDRGAIVHER-SKGLflalnafES 85
Cdd:PRK11482   30 DLNLLTIFEAVYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHEYiSQGL-------ES 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192  86 DIGALKnrITGTL---RLGLVDNTITDSDLPIHRVIARISERAPEARVE-LAIDTPDALLSEianggLDIALLPETQPYQ 161
Cdd:PRK11482  103 ILGALD--ITGSYdkqRTITIATTPSVGALVMPVIYQAIKTHYPQLLLRnIPISDAENQLSQ-----FQTDLIIDTHSCS 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1582640192 162 GLKLSR---FREEIhSLYCAQGHPLFRqaeAELTIEHVETFDFVV-------RPYANMRELQFFPKARARAIASNMEAQA 231
Cdd:PRK11482  176 NRTIQHhvlFTDNV-VLVCRQGHPLLS---LEDDEETLDNAEHTLllpegqnFSGLRQRLQEMFPDRQISFSSYNILTIA 251

                         250
                  ....*....|...
gi 1582640192 232 MFVMSGHYLGYLP 244
Cdd:PRK11482  252 ALIASSDMLGIMP 264
 
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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