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Conserved domains on  [gi|1916855015|ref|WP_192888759|]
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LysR family transcriptional regulator [Vibrio bathopelagicus]

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];
3-299 6.06e-44

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 150.79  E-value: 6.06e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015   3 LDINLLKTFVTLAEYKHFGKAANALHMTQPNVSLHLKQLEQLTRIKLIERSP--FQLTQAGERLLETSQRTLLELQICQA 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGrgLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  81 DLNAINDLKIGTLTIAVSDIISRFLLIRPFQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADLGFVIAkEQHNESLYFTK 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLG-PPPDPGLVARP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 161 LQELSWCALgdgldiqgsdCStenevkeaeadpeltlillghdtrtrdfideglPSLNLPNHRVMeVGSVDAQIDWAEAG 240
Cdd:COG0583   160 LGEERLVLV----------AS---------------------------------PDHPLARRAPL-VNSLEALLAAVAAG 195

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1916855015 241 FGVAIIPEFAISTKQHLNSKVT-PLTNFSST-SLGYIVRQNQVLSKATKQLLGWVNDEITQ 299
Cdd:COG0583   196 LGIALLPRFLAADELAAGRLVAlPLPDPPPPrPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
3-299 6.06e-44

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 150.79  E-value: 6.06e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015   3 LDINLLKTFVTLAEYKHFGKAANALHMTQPNVSLHLKQLEQLTRIKLIERSP--FQLTQAGERLLETSQRTLLELQICQA 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGrgLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  81 DLNAINDLKIGTLTIAVSDIISRFLLIRPFQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADLGFVIAkEQHNESLYFTK 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLG-PPPDPGLVARP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 161 LQELSWCALgdgldiqgsdCStenevkeaeadpeltlillghdtrtrdfideglPSLNLPNHRVMeVGSVDAQIDWAEAG 240
Cdd:COG0583   160 LGEERLVLV----------AS---------------------------------PDHPLARRAPL-VNSLEALLAAVAAG 195

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1916855015 241 FGVAIIPEFAISTKQHLNSKVT-PLTNFSST-SLGYIVRQNQVLSKATKQLLGWVNDEITQ 299
Cdd:COG0583   196 LGIALLPRFLAADELAAGRLVAlPLPDPPPPrPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 4-250 1.49e-28

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: 111.17  E-value: 1.49e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015   4 DINLLKTFVTLAEYKHFGKAANALHMTQPNVSLHLKQLEQLTRIKLIERSP--FQLTQAGERLLETSQRTL-LELQICQA 80
Cdd:NF040786    2 NLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTkeVSLTEDGKLLYEYAKEMLdLWEKLEEE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  81 DLNAINDLKiGTLTIAVSDIISRFLLIRPFQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADLGFViAKEQHNESLYFTK 160
Cdd:NF040786   82 FDRYGKESK-GVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFT-GTKLEKKRLVYTP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 161 LQElswcalgDGLDIQGSDCSTENEV-KEAEADPELT---LILL--GHDTRTRdfIDEGLPSLNLPN---HRVMEVGSVD 231
Cdd:NF040786  160 FYK-------DRLVLITPNGTEKYRMlKEEISISELQkepFIMReeGSGTRKE--AEKALKSLGISLedlNVVASLGSTE 230

                         250
                  ....*....|....*....
gi 1916855015 232 AQIDWAEAGFGVAIIPEFA 250
Cdd:NF040786  231 AIKQSVEAGLGISVISELA 249
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-296 7.49e-25

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: 98.90  E-value: 7.49e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  91 GTLTIAVSDIISRFLLIRPFQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADLGFVIAKEQHNEsLYFTKL--QELSWCA 168
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPG-LEARPLgeEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 169 -----LGDGLDIQGSDCSTEnevkeaeadpelTLILLGHDTRTRDFIDEGLPSLNLPNHRVMEVGSVDAQIDWAEAGFGV 243
Cdd:pfam03466  81 ppdhpLARGEPVSLEDLADE------------PLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGI 148

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1916855015 244 AIIPEFAIstKQHLNS---KVTPLTNFSSTS-LGYIVRQNQVLSKATKQLLGWVNDE 296
Cdd:pfam03466 149 ALLPRSAV--ARELADgrlVALPLPEPPLPReLYLVWRKGRPLSPAVRAFIEFLREA 203
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-290 3.35e-23

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: 94.59  E-value: 3.35e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  92 TLTIAVSDIISRFLLIRPFQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADLGFVIAkEQHNESLYFTKLQELS-WCALG 170
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVAL-PVDDPGLESEPLFEEPlVLVVP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 171 DGLDIQGSDCSTENEVKeaeadpELTLILLGHDTRTRDFIDEGLPSLNLPNHRVMEVGSVDAQIDWAEAGFGVAIIPEFA 250
Cdd:cd05466    80 PDHPLAKRKSVTLADLA------DEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESA 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1916855015 251 ISTKQHLNSKVTPLTNFS-STSLGYIVRQNQVLSKATKQLL 290
Cdd:cd05466   154 VEELADGGLVVLPLEDPPlSRTIGLVWRKGRYLSPAARAFL 194
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 11-255 1.65e-18

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 83.85  E-value: 1.65e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  11 FVTLAEYKHFGKAANALHMTQPNVSLHLKQLEQLTRIKLIERS--PFQLTQAGERLLETSQRTLLELQICQADLNAINDL 88
Cdd:PRK11242    9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSgrTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVADL 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  89 KIGTLTIAVSDIISRFL---LIRPFQkfkAQYPGIDLTLLNTTSSQASSLVKNAQADLGFVIAKEQHNE----SLYFTKL 161
Cdd:PRK11242   89 SRGSLRLAMTPTFTAYLigpLIDAFH---ARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEieaqPLFTETL 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 162 qelswcALGDGLDIQGSDCSTENEVKEAEADPeltLILLGHDTRTRDFIDEGLPSLNLPNHRVMEVGSVDAQIDWAEAGF 241
Cdd:PRK11242  166 ------ALVVGRHHPLAARRKALTLDELADEP---LVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRGR 236

                         250
                  ....*....|....
gi 1916855015 242 GVAIIPEfAISTKQ 255
Cdd:PRK11242  237 LATLLPA-AIAREH 249
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
3-299 6.06e-44

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 150.79  E-value: 6.06e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015   3 LDINLLKTFVTLAEYKHFGKAANALHMTQPNVSLHLKQLEQLTRIKLIERSP--FQLTQAGERLLETSQRTLLELQICQA 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGrgLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  81 DLNAINDLKIGTLTIAVSDIISRFLLIRPFQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADLGFVIAkEQHNESLYFTK 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLG-PPPDPGLVARP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 161 LQELSWCALgdgldiqgsdCStenevkeaeadpeltlillghdtrtrdfideglPSLNLPNHRVMeVGSVDAQIDWAEAG 240
Cdd:COG0583   160 LGEERLVLV----------AS---------------------------------PDHPLARRAPL-VNSLEALLAAVAAG 195

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1916855015 241 FGVAIIPEFAISTKQHLNSKVT-PLTNFSST-SLGYIVRQNQVLSKATKQLLGWVNDEITQ 299
Cdd:COG0583   196 LGIALLPRFLAADELAAGRLVAlPLPDPPPPrPLYLVWRRRRHLSPAVRAFLDFLREALAE 256
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 4-250 1.49e-28

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: 111.17  E-value: 1.49e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015   4 DINLLKTFVTLAEYKHFGKAANALHMTQPNVSLHLKQLEQLTRIKLIERSP--FQLTQAGERLLETSQRTL-LELQICQA 80
Cdd:NF040786    2 NLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTkeVSLTEDGKLLYEYAKEMLdLWEKLEEE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  81 DLNAINDLKiGTLTIAVSDIISRFLLIRPFQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADLGFViAKEQHNESLYFTK 160
Cdd:NF040786   82 FDRYGKESK-GVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFT-GTKLEKKRLVYTP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 161 LQElswcalgDGLDIQGSDCSTENEV-KEAEADPELT---LILL--GHDTRTRdfIDEGLPSLNLPN---HRVMEVGSVD 231
Cdd:NF040786  160 FYK-------DRLVLITPNGTEKYRMlKEEISISELQkepFIMReeGSGTRKE--AEKALKSLGISLedlNVVASLGSTE 230

                         250
                  ....*....|....*....
gi 1916855015 232 AQIDWAEAGFGVAIIPEFA 250
Cdd:NF040786  231 AIKQSVEAGLGISVISELA 249
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-296 7.49e-25

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: 98.90  E-value: 7.49e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  91 GTLTIAVSDIISRFLLIRPFQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADLGFVIAKEQHNEsLYFTKL--QELSWCA 168
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPG-LEARPLgeEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 169 -----LGDGLDIQGSDCSTEnevkeaeadpelTLILLGHDTRTRDFIDEGLPSLNLPNHRVMEVGSVDAQIDWAEAGFGV 243
Cdd:pfam03466  81 ppdhpLARGEPVSLEDLADE------------PLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGI 148

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1916855015 244 AIIPEFAIstKQHLNS---KVTPLTNFSSTS-LGYIVRQNQVLSKATKQLLGWVNDE 296
Cdd:pfam03466 149 ALLPRSAV--ARELADgrlVALPLPEPPLPReLYLVWRKGRPLSPAVRAFIEFLREA 203
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-290 3.35e-23

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: 94.59  E-value: 3.35e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  92 TLTIAVSDIISRFLLIRPFQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADLGFVIAkEQHNESLYFTKLQELS-WCALG 170
Cdd:cd05466     1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVAL-PVDDPGLESEPLFEEPlVLVVP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 171 DGLDIQGSDCSTENEVKeaeadpELTLILLGHDTRTRDFIDEGLPSLNLPNHRVMEVGSVDAQIDWAEAGFGVAIIPEFA 250
Cdd:cd05466    80 PDHPLAKRKSVTLADLA------DEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESA 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1916855015 251 ISTKQHLNSKVTPLTNFS-STSLGYIVRQNQVLSKATKQLL 290
Cdd:cd05466   154 VEELADGGLVVLPLEDPPlSRTIGLVWRKGRYLSPAARAFL 194
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 11-255 1.65e-18

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 83.85  E-value: 1.65e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  11 FVTLAEYKHFGKAANALHMTQPNVSLHLKQLEQLTRIKLIERS--PFQLTQAGERLLETSQRTLLELQICQADLNAINDL 88
Cdd:PRK11242    9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSgrTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVADL 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  89 KIGTLTIAVSDIISRFL---LIRPFQkfkAQYPGIDLTLLNTTSSQASSLVKNAQADLGFVIAKEQHNE----SLYFTKL 161
Cdd:PRK11242   89 SRGSLRLAMTPTFTAYLigpLIDAFH---ARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEieaqPLFTETL 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 162 qelswcALGDGLDIQGSDCSTENEVKEAEADPeltLILLGHDTRTRDFIDEGLPSLNLPNHRVMEVGSVDAQIDWAEAGF 241
Cdd:PRK11242  166 ------ALVVGRHHPLAARRKALTLDELADEP---LVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRGR 236

                         250
                  ....*....|....
gi 1916855015 242 GVAIIPEfAISTKQ 255
Cdd:PRK11242  237 LATLLPA-AIAREH 249
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-290 5.07e-18

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: 80.26  E-value: 5.07e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  92 TLTIAVSDIISRFLLIRPFQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADLGFVIAKEQHNEsLYFTKLQELSWCALGd 171
Cdd:cd08440     1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPD-LEFEPLLRDPFVLVC- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 172 gldIQGSDCSTENEVKEAEADPElTLILLGHDTRTRDFIDEGLPSLNLPNHRVMEVGSVDAQIDWAEAGFGVAIIPEFAI 251
Cdd:cd08440    79 ---PKDHPLARRRSVTWAELAGY-PLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALAL 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1916855015 252 STKQHLNSKVTPLTN-FSSTSLGYIVRQNQVLSKATKQLL 290
Cdd:cd08440   155 PLADHPGLVARPLTEpVVTRTVGLIRRRGRSLSPAAQAFL 194
rbcR CHL00180
LysR transcriptional regulator; Provisional
 8-146 7.74e-17

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 79.29  E-value: 7.74e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015   8 LKTFVTLAEYKHFGKAANALHMTQPNVSLHLKQLEQLTRIKLIERS--PFQLTQAGERLLETSQRTlleLQICQADLNAI 85
Cdd:CHL00180   10 LRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSknKASLTEAGELLLRYGNRI---LALCEETCRAL 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1916855015  86 NDLKI---GTLTIAVSDIISRFLLIRPFQKFKAQYPGIDLTL-LNTTSSQASSlVKNAQADLGFV 146
Cdd:CHL00180   87 EDLKNlqrGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLqVHSTRRIAWN-VANGQIDIAIV 150
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-62 1.01e-16

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 72.80  E-value: 1.01e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015   5 INLLKTFVTLAEYKHFGKAANALHMTQPNVSLHLKQLEQLTRIKLIERS--PFQLTQAGE 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTtrGVRLTEAGE 60
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 23-156 1.57e-16

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 78.49  E-value: 1.57e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  23 AANALHMTQPNVSLHLKQLEQLTRIKLIERSPFQL---TQAGERLLETSQRTLLELQICQ--ADLNAINDlkIGTLTIAV 97
Cdd:PRK12682   22 AAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLkglTEPGKAVLDVIERILREVGNIKriGDDFSNQD--SGTLTIAT 99

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1916855015  98 SDIISRFLLIRPFQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADLGfvIAKEQ--HNESL 156
Cdd:PRK12682  100 THTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIG--IATESlaDDPDL 158
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
22-150 3.86e-15

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 74.24  E-value: 3.86e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  22 KAANALHMTQPNVSLHLKQLEQLTRIKLIERSPFQ---LTQAGERLLETSQRTLLELQICQADLNAINDLKIGTLTIAVS 98
Cdd:PRK12684   21 EAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRlrgLTEPGRIILASVERILQEVENLKRVGKEFAAQDQGNLTIATT 100

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1916855015  99 DIISRFLLIRPFQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADLGfvIAKE 150
Cdd:PRK12684  101 HTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLA--IATE 150
PRK09986 PRK09986
LysR family transcriptional regulator;
3-145 7.08e-14

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 70.52  E-value: 7.08e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015   3 LDINLLKTFVTLAEYKHFGKAANALHMTQPNVSLHLKQLEQLTRIKLIERSP--FQLTQAGERLLETSQRTLleLQICQA 80
Cdd:PRK09986    7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSrsVVLTHAGKILMEESRRLL--DNAEQS 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1916855015  81 dLNAINDLKIGTLTIAVSDIISRFL---LIRPFQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADLGF 145
Cdd:PRK09986   85 -LARVEQIGRGEAGRIEIGIVGTALwgrLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGI 151
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-97 4.48e-13

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 68.07  E-value: 4.48e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015   2 MLDINLLKTFVTLAEYKHFGKAANALHMTQPNVSLHLKQLEQLTRIKLIER-SPFQLTQAGERLLetsqRTLLELQICQA 80
Cdd:PRK13348    1 MLDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRgRPCRPTPAGQRLL----RHLRQVALLEA 76

                          90       100
                  ....*....|....*....|..
gi 1916855015  81 DLnaINDLKIG-----TLTIAV 97
Cdd:PRK13348   77 DL--LSTLPAErgsppTLAIAV 96
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 23-150 5.72e-13

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 68.15  E-value: 5.72e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  23 AANALHMTQPNVSLHLKQLEQLTRIKLIERSPFQL---TQAGERLLETSQRTLLELQICQADLNAINDLKIGTLTIAVSD 99
Cdd:PRK12683   22 VANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLtglTEPGKELLQIVERMLLDAENLRRLAEQFADRDSGHLTVATTH 101

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1916855015 100 IISRFLLIRPFQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADLGfvIAKE 150
Cdd:PRK12683  102 TQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIG--IATE 150
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 92-290 1.92e-11

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: 62.12  E-value: 1.92e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  92 TLTIAVSDIISRFLLIRPFQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADLGFvIAKEQHNESLYFTKLQ--ELSW-CA 168
Cdd:cd08420     1 TLRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGL-VEGPVDHPDLIVEPFAedELVLvVP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 169 LGDGLdiqgsdcsTENEVKEAEADPELTLILLGHDTRTRDFIDEGLPSLNLPNHR---VMEVGSVDAQIDWAEAGFGVAI 245
Cdd:cd08420    80 PDHPL--------AGRKEVTAEELAAEPWILREPGSGTREVFERALAEAGLDGLDlniVMELGSTEAIKEAVEAGLGISI 151

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1916855015 246 IPEFAISTKQHLNS-KVTPLTNFSST-SLGYIVRQNQVLSKATKQLL 290
Cdd:cd08420   152 LSRLAVRKELELGRlVALPVEGLRLTrPFSLIYHKDKYLSPAAEAFL 198
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
28-266 2.60e-11

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 62.91  E-value: 2.60e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  28 HMTQPNVSLHLKQLEQLTRIKLIERS--PFQLTQAGERLLETSQRTLLELQICQADLNAINDLKIGTLTIAVSDIISRFL 105
Cdd:PRK11716    2 HVSPSTLSRQIQRLEEELGQPLFVRDnrSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSVTAAYSH 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 106 LIRPFQKFKAQYPGIDLTLlnTT--SSQASSLVKNAQADLGFVIAKEQHNESLYFTKLQE--LSWCALGDGldiqgsdCS 181
Cdd:PRK11716   82 LPPILDRFRAEHPLVEIKL--TTgdAADAVEKVQSGEADLAIAAKPETLPASVAFSPIDEipLVLIAPALP-------CP 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 182 TENEVKEAEAD-PELTLILLGHDT-RTRdfIDEGLPSLNL-PNhrvmevgsVDAQIDWAEA-------GFGVAIIPEFAI 251
Cdd:PRK11716  153 VRQQLSQEKPDwSRIPFILPEHGPaRRR--IDLWFRRHKIkPN--------IYATVSGHEAivsmvalGCGVGLLPEVVL 222

                         250
                  ....*....|....*..
gi 1916855015 252 --STkqhLNSKVTPLTN 266
Cdd:PRK11716  223 enSP---VRNRVQILER 236
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
3-65 7.08e-11

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 61.57  E-value: 7.08e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1916855015   3 LDINLLKTFVTLAEYKHFGKAANALHMTQPNVSLHLKQLE-QL-----TRikliERSPFQLTQAGERLL 65
Cdd:PRK03601    1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLEnQLgvnlfTR----HRNNIRLTAAGERLL 65
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 3-144 8.89e-11

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 61.58  E-value: 8.89e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015   3 LDINLLKTFVTLAEYKHFGKAANALHMTQPNVSLHLKQLEQLTRIKLIERSPFQL--TQAGERLLETSQRTLLELQICQA 80
Cdd:PRK11151    1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVlfTQAGLLLVDQARTVLREVKVLKE 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1916855015  81 DLNAINDLKIGTLTIAVSDIISRFLLIRPFQKFKAQYPGIDLTLlntTSSQASSLVknAQADLG 144
Cdd:PRK11151   81 MASQQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYL---HEAQTHQLL--AQLDSG 139
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
2-97 1.62e-10

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 60.56  E-value: 1.62e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015   2 MLDINLLKTFVTLAEYKHFGKAANALHMTQPNVSLHLKQLEQLTRIKLIERS-PFQLTQAGERLLETSQRT-LLELQIcQ 79
Cdd:PRK03635    1 MLDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRTqPCRPTEAGQRLLRHARQVrLLEAEL-L 79

                          90
                  ....*....|....*...
gi 1916855015  80 ADLNAINDLKIgTLTIAV 97
Cdd:PRK03635   80 GELPALDGTPL-TLSIAV 96
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
8-125 2.00e-10

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 60.40  E-value: 2.00e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015   8 LKTFVTLAEYKHFGKAANALHMTQPNVSLHLKQLEQLTRIKLIERSP--FQLTQAGERLLETSQRTLlelqicqADLN-A 84
Cdd:PRK10086   19 LHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHrkVELTEEGKRVFWALKSSL-------DTLNqE 91

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1916855015  85 INDLK----IGTLTIAVSDIISRFLLIRPFQKFKAQYPGIDLTLL 125
Cdd:PRK10086   92 ILDIKnqelSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTIL 136
cysB PRK12681
HTH-type transcriptional regulator CysB;
23-150 1.07e-09

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 58.37  E-value: 1.07e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  23 AANALHMTQPNVSLHLKQLEQLTRIKLIERSPFQLTQ---AGERLLETSQRTLLELQICQADLNAINDLKIGTLTIAVSD 99
Cdd:PRK12681   22 TAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTQvtpAGEEIIRIAREILSKVESIKSVAGEHTWPDKGSLYIATTH 101

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1916855015 100 IISRFLLIRPFQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADlgFVIAKE 150
Cdd:PRK12681  102 TQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNAD--FAIATE 150
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
2-87 1.18e-09

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 58.28  E-value: 1.18e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015   2 MLDINLLKTFVTLAEYKHFGKAANALHMTQPNVSLHLKQLEQLTRIKLIERS--PFQLTQAGERLLETSQRTLLELQICQ 79
Cdd:PRK10094    1 MFDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTtrSVTLTAAGEHLLSQARDWLSWLESMP 80


                  ....*...
gi 1916855015  80 ADLNAIND 87
Cdd:PRK10094   81 SELQQVND 88
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 92-265 3.21e-09

The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. LysR is the transcriptional activator of lysA gene encoding diaminopimelate decarboxylase, an enzyme that catalyses the decarboxylation of diaminopimelate to produce lysine. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176107 [Multi-domain]  Cd Length: 196  Bit Score: 55.65  E-value: 3.21e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  92 TLTIAVSDIISRFLLIRPFQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADLGFVIAkEQHNESLYFTKLQEL-SWCALG 170
Cdd:cd08415     1 TLRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASL-PLDHPGLESEPLASGrAVCVLP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 171 DGLDIQGSDcstenEVKEAEADPElTLILLGHDTRTRDFIDEGLPSLNLPNHRVMEVGSVDAQIDWAEAGFGVAIIPEFA 250
Cdd:cd08415    80 PGHPLARKD-----VVTPADLAGE-PLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIVDPLT 153

                         170
                  ....*....|....*
gi 1916855015 251 ISTKQHLNSKVTPLT 265
Cdd:cd08415   154 AAGYAGAGLVVRPFR 168
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 22-144 3.53e-09

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 56.92  E-value: 3.53e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  22 KAANALHMTQPNVSLHLKQLEQLTRIKLIERSPFQL--TQAGERLLETSQRTLLELQICQADLNAINDLKIGTLTIAVSD 99
Cdd:PRK11013   23 EAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLhpTVQGLRLFEEVQRSYYGLDRIVSAAESLREFRQGQLSIACLP 102

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1916855015 100 IISRFLLIRPFQKFKAQYPGIDLTLLnttsSQASSLVK---NAQA-DLG 144
Cdd:PRK11013  103 VFSQSLLPGLCQPFLARYPDVSLNIV----PQESPLLEewlSAQRhDLG 147
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 8-146 4.71e-09

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 56.32  E-value: 4.71e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015   8 LKTFVTLAEYKHFGKAANALHMTQPNVSLHLKQLEQLTRIKLIERSP--FQLTQAGERLLETSQRTL--------LELQI 77
Cdd:PRK09906    6 LRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKrkVALTAAGEVFLQDARAILeqaekaklRARKI 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1916855015  78 CQADLNaindLKIGTLTIAVSDIISRFLLIrpfqkFKAQYPGIDLTLLNTTSSQASSLVKNAQADLGFV 146
Cdd:PRK09906   86 VQEDRQ----LTIGFVPSAEVNLLPKVLPM-----FRLRHPDTLIELVSLITTQQEEKLRRGELDVGFM 145
cbl PRK12679
HTH-type transcriptional regulator Cbl;
24-151 5.50e-09

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 56.36  E-value: 5.50e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  24 ANALHMTQPNVSLHLKQLEQLTRIKLIERSPFQL---TQAGERLLETSQRTLLELQICQ--ADLNAiNDLKiGTLTIAVS 98
Cdd:PRK12679   23 ANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLlgmTEPGKALLVIAERILNEASNVRrlADLFT-NDTS-GVLTIATT 100

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1916855015  99 DIISRFLLIRPFQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADLGfvIAKEQ 151
Cdd:PRK12679  101 HTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIG--IASER 151
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
11-125 1.99e-08

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 54.77  E-value: 1.99e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  11 FVTLAEYKHFGKAANALHMTQPNVSLHLKQLEQLTRIKLIERSP--FQLTQAGERLLETSQRTLLELQICQADLNAINDL 88
Cdd:PRK10632   10 FAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTrsIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAFNNT 89

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1916855015  89 KIGTLTIAVSDIISRFLLIRPFQKFKAQYPGIDLTLL 125
Cdd:PRK10632   90 PIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLV 126
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-153 8.65e-08

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 52.72  E-value: 8.65e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015   1 MMLDINLLKTFVTLAEYKHFGKAANALHMTQPNVSLHLKQLEQLTRIKLIERSPFQ--LTQAGERLLETSQRTL-LELQI 77
Cdd:PRK15092    9 INLDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNklLTEHGIQLLGYARKILrFNDEA 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  78 CQADLnaINDLKiGTLTIAVSD----IISRFLLIRpfqkFKAQYPGIDLTLLNTTSSQASSLVKNAQADLgfVIAKEQHN 153
Cdd:PRK15092   89 CSSLM--YSNLQ-GVLTIGASDdtadTILPFLLNR----VSSVYPKLALDVRVKRNAFMMEMLESQEVDL--AVTTHRPS 159
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 2-127 8.93e-08

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 52.69  E-value: 8.93e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015   2 MLDINLLKTFVTLAEYKHFGKAANALHMTQPNVSLHLKQLEQLTRIKLIERSP--FQLTQAGERLLETSQRTLLELQICQ 79
Cdd:PRK14997    1 KTDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTrqFNVTEVGQTFYEHCKAMLVEAQAAQ 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1916855015  80 ADLNAINDLKIGTLTIAVSDIISRFLLIRPFQKFKAQYPGIDLTLLNT 127
Cdd:PRK14997   81 DAIAALQVEPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEAT 128
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 88-248 1.02e-06

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 48.37  E-value: 1.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  88 LKIGTLT----IAVSDIISRFllirpfqkfKAQYPGIDLTLLNTTSSQASSLVKNAQADLGFVIAKEQHNESLYFTKL-- 161
Cdd:cd08436     2 LAIGTITslaaVDLPELLARF---------HRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRPPGLASRELar 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 162 QEL-SWCALGDGLdiqgsdcSTENEVKEAEADPElTLILLGHDTRTRDFIDEGLPSLNLPNHRVMEVGSVDAQIDWAEAG 240
Cdd:cd08436    73 EPLvAVVAPDHPL-------AGRRRVALADLADE-PFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARG 144


                  ....*...
gi 1916855015 241 FGVAIIPE 248
Cdd:cd08436   145 LGVALLPA 152
PRK12680 PRK12680
LysR family transcriptional regulator;
23-253 1.67e-06

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 48.85  E-value: 1.67e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  23 AANALHMTQPNVSLHLKQLE-QLTRIKLIE--RSPFQLTQAGERLLETSQRTLLELQICQAdlNAINDLK--IGTLTIAV 97
Cdd:PRK12680   22 AAARVHATQPGLSKQLKQLEdELGFLLFVRkgRSLESVTPAGVEVIERARAVLSEANNIRT--YAANQRResQGQLTLTT 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  98 SDIISRFLLIRPFQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADLGFVIAKEQHNES-----LYftKLQELSWCALGDG 172
Cdd:PRK12680  100 THTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAgiavpLY--RWRRLVVVPRGHA 177

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 173 LDIQGSdcsteneVKEAEADPELTLILLGHDTRTRDFIDEGLPSLNLPNHRVMEVGSVDAQIDWAEAGFGVAIIPEFAIS 252
Cdd:PRK12680  178 LDTPRR-------APDMAALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLIKTYVRAGLGVGLLAEMAVN 250


                  .
gi 1916855015 253 T 253
Cdd:PRK12680  251 A 251
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
2-143 1.98e-06

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 48.48  E-value: 1.98e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015   2 MLDINLLKTFVTLAEYKHFGKAANALHMTQPNVSLHLKQLEQLTRIKLIER--SPFQLTQAGERLLETSQRTLleLQICQ 79
Cdd:PRK15421    1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRksQPLRFTPQGEILLQLANQVL--PQISQ 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1916855015  80 AdLNAINDLKIGTLTIAVSDIISRFLLIRPFQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADL 143
Cdd:PRK15421   79 A-LQACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDL 141
PRK09791 PRK09791
LysR family transcriptional regulator;
5-167 4.43e-06

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 47.45  E-value: 4.43e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015   5 INLLKTFVTLAEYKHFGKAANALHMTQPNVSLHLKQLEQLTRIKLIERSP--FQLTQAGERLLETSQRTLLELQICQADL 82
Cdd:PRK09791    7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSkgVTLTDAGESFYQHASLILEELRAAQEDI 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  83 NAINDLKIGTLTIAVSDIISRFLLIRPFQKFKAQYPGIDLTLlntTSSQASSLVKN-AQADLGFVI---AKEQHNESLYF 158
Cdd:PRK09791   87 RQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRI---MEGQLVSMINElRQGELDFTIntyYQGPYDHEFTF 163


                  ....*....
gi 1916855015 159 TKLQELSWC 167
Cdd:PRK09791  164 EKLLEKQFA 172
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 92-290 4.66e-06

The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176129 [Multi-domain]  Cd Length: 197  Bit Score: 46.40  E-value: 4.66e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  92 TLTIAVSDIISRFLLIRPFQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADLGFVIAKEQH---------NESLYFTkLQ 162
Cdd:cd08438     1 HLRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEeefdsqplcNEPLVAV-LP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 163 ELSWCALGDGLDIQgsdcstenEVKeaeadpELTLILLghdtrTRDFideglpSLnlpNHRVME----------VGSVDA 232
Cdd:cd08438    80 RGHPLAGRKTVSLA--------DLA------DEPFILF-----NEDF------AL---HDRIIDacqqagftpnIAARSS 131

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1916855015 233 QIDW----AEAGFGVAIIPEfAISTKQHLNS-KVTPLTNFS-STSLGYIVRQNQVLSKATKQLL 290
Cdd:cd08438   132 QWDFiaelVAAGLGVALLPR-SIAQRLDNAGvKVIPLTDPDlRWQLALIWRKGRYLSHAARAWL 194
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 90-251 6.08e-06

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


Pssm-ID: 176124  Cd Length: 198  Bit Score: 46.05  E-value: 6.08e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  90 IGtLTIAVSDIISRFLLirpfQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADLGfVI--AKEQHneSLYFTKLQELSWC 167
Cdd:cd08433     4 VG-LPPSAASVLAVPLL----RAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLA-LLygPPPIP--GLSTEPLLEEDLF 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 168 ALGDgldiQGSDCSTENEVKEAEADpELTLIL--LGHDTRTRdfIDEGLPSLNLPNHRVMEVGSVDAQIDWAEAGFGVAI 245
Cdd:cd08433    76 LVGP----ADAPLPRGAPVPLAELA-RLPLILpsRGHGLRRL--VDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTI 148


                  ....*.
gi 1916855015 246 IPEFAI 251
Cdd:cd08433   149 LPASAV 154
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 113-291 6.58e-06

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


Pssm-ID: 176133  Cd Length: 193  Bit Score: 46.06  E-value: 6.58e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 113 FKAQYPGIDLTLLNTTSSQASSLVKNAQADLGFVIAKEQHnESLYFTKL--QELSWCALGDGLDIQGsdcstenevkeAE 190
Cdd:cd08442    22 YHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEH-PRLEQEPVfqEELVLVSPKGHPPVSR-----------AE 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 191 ADPELTLILLGHDTRTRDFIDEGLPSLNLPNHRVMEVGSVDAQIDWAEAGFGVAIIPEFAISTKQHLNS-KVTPLTNFSS 269
Cdd:cd08442    90 DLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAGMGIALLPRSVLDSLQGRGSvSIHPLPEPFA 169

                         170       180
                  ....*....|....*....|..
gi 1916855015 270 TSLGYIVRQNQVLSKATKQLLG 291
Cdd:cd08442   170 DVTTWLVWRKDSFTAALQAFLD 191
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 6-129 6.68e-06

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 46.76  E-value: 6.68e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015   6 NLLKTFVTLAEYKHFGKAANALHMTQPNVSLHLKQLEQLTRIKLIER--SPFQLTQAGERLLETSQRTLLELQICQADLN 83
Cdd:PRK11139    9 NALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRrnRSLLLTEEGQRYFLDIREIFDQLAEATRKLR 88

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1916855015  84 AINDlkIGTLTIAV-SDIISRFLLIRPFqKFKAQYPGIDLTLLNTTS 129
Cdd:PRK11139   89 ARSA--KGALTVSLlPSFAIQWLVPRLS-SFNEAHPDIDVRLKAVDR 132
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 88-250 1.57e-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: 44.81  E-value: 1.57e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  88 LKIGTLTIAVSDIISRFLlirpfQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADLGFVIAKEQHnESLYFTKLQELSWC 167
Cdd:cd08414     2 LRIGFVGSALYGLLPRLL-----RRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDP-PGLASRPLLREPLV 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 168 -ALGDgldiqGSDCSTENEVKEAE-ADpeLTLILLGHDTRT--RDFIDEGLPSLNLPNHRVMEVGSVDAQIDWAEAGFGV 243
Cdd:cd08414    76 vALPA-----DHPLAARESVSLADlAD--EPFVLFPREPGPglYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGV 148


                  ....*..
gi 1916855015 244 AIIPEFA 250
Cdd:cd08414   149 ALVPASV 155
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
8-156 2.59e-05

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 45.05  E-value: 2.59e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015   8 LKTFVTLAEYKHFGKAANALHMTQPNVSLHLKQLEQLTRIKLIER--SPFQLTQAGeRLLETSQRTLL-ELQICQADLNA 84
Cdd:PRK10082   16 LYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRqvTPLQLSEQG-KIFHSQIRHLLqQLESNLAELRG 94

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1916855015  85 INDLKIGTLTIAVSDIISRFLLIRPFQKFKAQYP----GIDLtllnttsSQASSLVKNAQADLGFVIakeqHNESL 156
Cdd:PRK10082   95 GSDYAQRKIKIAAAHSLSLGLLPSIISQMPPLFTwaieAIDV-------DEAVDKLREGQSDCIFSF----HDEDL 159
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 92-150 2.62e-05

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: 44.15  E-value: 2.62e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1916855015  92 TLTIAVSDIISRFLLIRPFQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADLGfvIAKE 150
Cdd:cd08413     1 QLTIATTHTQARYVLPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIA--IATE 57
PRK10341 PRK10341
transcriptional regulator TdcA;
2-118 1.43e-04

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 42.93  E-value: 1.43e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015   2 MLDINLLKT-----FVTLAEYKHFGKAANALHMTQPNVSLHLKQLEQLTRIKLIER--SPFQLTQAGERLLETSQRTLLE 74
Cdd:PRK10341    1 MSTILLPKTqhlvvFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRknTGVTLTPAGQVLLSRSESITRE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1916855015  75 LQICQADLNAINDLKIGTLTIAVSDIISRFLLIRPFQKFKAQYP 118
Cdd:PRK10341   81 MKNMVNEINGMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFP 124
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
 93-150 2.12e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold; Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonation enzyme. Both Cbl and CysB require expression of the tau and ssu genes. Like many other members of the LTTR family, the Cbl is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176135  Cd Length: 198  Bit Score: 41.72  E-value: 2.12e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1916855015  93 LTIAVSDIISRFLLIRPFQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADLGfvIAKE 150
Cdd:cd08444     2 LTIATTHTQARYALPWVVQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIG--IATE 57
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 8-250 1.06e-03

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 40.05  E-value: 1.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015   8 LKTFVTLAEYKHFGKAANALHMTQPNVSLHLKQLEQLTRIKLIERSP--FQLTQAGeRLLETSQRTLLElQICQADLNAI 85
Cdd:PRK11233    6 LKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKrgVTPTEAG-KILYTHARAILR-QCEQAQLAVH 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  86 NdlkIG-TLTIAVS---------DIISRFLLirpfQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADLGfVIAKEQHNES 155
Cdd:PRK11233   84 N---VGqALSGQVSiglapgtaaSSLTMPLL----QAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMA-VIYEHSPVAG 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 156 LYFTKLqelswcaLGDGLDIQGSDCSTENEVKEAE-ADPELTLILLGHDTRTRdfIDEGLPSLNLPNHRVMEVGSVDAQI 234
Cdd:PRK11233  156 LSSQPL-------LKEDLFLVGTQDCPGQSVDLAAvAQMNLFLPRDYSAVRLR--VDEAFSLRRLTAKVIGEIESIATLT 226

                         250
                  ....*....|....*.
gi 1916855015 235 DWAEAGFGVAIIPEFA 250
Cdd:PRK11233  227 AAIASGMGVTVLPESA 242
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
 112-266 2.00e-03

The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic bindin; In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-independent manner. 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: 176121  Cd Length: 199  Bit Score: 38.71  E-value: 2.00e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 112 KFKAQYPGIDLTLlnTTSSQASSL--VKNAQADLGFVIAKEQHNESLYFTKLQE--LSWCALGDgldiqgsDCSTENEVK 187
Cdd:cd08430    21 RFRAQHPQVEIKL--HTGDPADAIdkVLNGEADIAIAARPDKLPARLAFLPLATspLVFIAPNI-------ACAVTQQLS 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 188 EAEAD-PELTLILLGHDTrTRDFIDEGLPSLNL-PNhrvmevgsVDAQIDWAEA-------GFGVAIIPEFAIStKQHLN 258
Cdd:cd08430    92 QGEIDwSRLPFILPERGL-ARERLDQWFRRRGIkPN--------IYAQVAGHEAivsmvalGCGVGIVPELVLD-NSPLK 161


                  ....*...
gi 1916855015 259 SKVTPLTN 266
Cdd:cd08430   162 DKVRILEV 169
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 211-253 2.86e-03

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: 37.99  E-value: 2.86e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1916855015 211 DEGLPSLNLPnhRVMEVGSVDAQIDWAEAGFGVAIIPEFAIST 253
Cdd:cd08476   115 DGGDPELRLP--TALVCNNIEALIEFALQGLGIACLPDFSVRE 155
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 92-250 3.47e-03

The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176146 [Multi-domain]  Cd Length: 196  Bit Score: 37.85  E-value: 3.47e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015  92 TLTIAVSDIISRFLLIRPFQKFKAQYPGIDLTLLNTTSSQASSLVKNAQADLGFVIAKEQHNE-SLYFTKlQELSWCALG 170
Cdd:cd08457     1 TLRIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQgFLIETR-SLPAVVAVP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1916855015 171 DGLDIQGSDCSTENEVKEAEadpeltLILLGHDTRTRDFIDEGLPSLNLPNHRVMEVGSVDAQIDWAEAGFGVAIIPEFA 250
Cdd:cd08457    80 MGHPLAQLDVVSPQDLAGER------IITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGIAIIDPAT 153
 
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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