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Conserved domains on  [gi|2473439716|gb|WFA10481|]
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LysR family transcriptional regulator [Tissierella sp. Yu-01]

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];
1-166 2.63e-46

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 156.57  E-value: 2.63e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   1 MEYFVMVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIRRV-PLELTYAGEVFLRYALGFQQSHQAMKKEFCDI 79
Cdd:COG0583     6 LRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGrGLRLTEAGERLLERARRILAELEEAEAELRAL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  80 TANQKGILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEI 159
Cdd:COG0583    86 RGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPLGEERL 165


                  ....*..
gi 2473439716 160 VLLISKE 166
Cdd:COG0583   166 VLVASPD 172
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 85-271 3.42e-26

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: 102.37  E-value: 3.42e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  85 GILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLIS 164
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716 165 KellsgiyeegfESKIAQG---NLSALQECPFVLGNPEDIGGQIGRSMIKHSGFQPIVKAQSDNIETLLSLCVRGIGACF 241
Cdd:pfam03466  82 P-----------DHPLARGepvSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIAL 150

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2473439716 242 CPINLVQATLPAKQLSKLRM----FRFDNYAAYP 271
Cdd:pfam03466 151 LPRSAVARELADGRLVALPLpeppLPRELYLVWR 184
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-166 2.63e-46

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 156.57  E-value: 2.63e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   1 MEYFVMVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIRRV-PLELTYAGEVFLRYALGFQQSHQAMKKEFCDI 79
Cdd:COG0583     6 LRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGrGLRLTEAGERLLERARRILAELEEAEAELRAL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  80 TANQKGILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEI 159
Cdd:COG0583    86 RGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPLGEERL 165


                  ....*..
gi 2473439716 160 VLLISKE 166
Cdd:COG0583   166 VLVASPD 172
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 2-195 1.00e-37

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: 135.44  E-value: 1.00e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   2 EYFVMVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIRRV-PLELTYAGEVFLRYALGFQQSHQAMKKEFCDIT 80
Cdd:NF040786    7 EAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTkEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDRYG 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  81 ANQKGILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLA-VGSFPESlPDVELRDFYQEEI 159
Cdd:NF040786   87 KESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGfTGTKLEK-KRLVYTPFYKDRL 165

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2473439716 160 VLLISKELlsgiyeEGFESKIAQGNLSALQECPFVL 195
Cdd:NF040786  166 VLITPNGT------EKYRMLKEEISISELQKEPFIM 195
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 3-236 1.21e-32

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 121.99  E-value: 1.21e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   3 YFVMVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIR--RVpLELTYAGEVFLRYALGFQQSHQAMKKEFCDIT 80
Cdd:PRK11242    8 YFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRsgRT-VRLTDAGEVYLRYARRALQDLEAGRRAIHDVA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  81 ANQKGILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIV 160
Cdd:PRK11242   87 DLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQPLFTETLA 166

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2473439716 161 LLISKellsgiyEEGFESKIAQGNLSALQECPFVLGNPEDIG-GQIGRSMIKHsGFQPIVKAQSDNIETLLSLCVRG 236
Cdd:PRK11242  167 LVVGR-------HHPLAARRKALTLDELADEPLVLLSAEFATrEQIDRYFRRH-GVTPRVAIEANSISAVLEIVRRG 235
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 85-271 3.42e-26

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: 102.37  E-value: 3.42e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  85 GILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLIS 164
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716 165 KellsgiyeegfESKIAQG---NLSALQECPFVLGNPEDIGGQIGRSMIKHSGFQPIVKAQSDNIETLLSLCVRGIGACF 241
Cdd:pfam03466  82 P-----------DHPLARGepvSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIAL 150

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2473439716 242 CPINLVQATLPAKQLSKLRM----FRFDNYAAYP 271
Cdd:pfam03466 151 LPRSAVARELADGRLVALPLpeppLPRELYLVWR 184
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 87-293 1.28e-24

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: 98.06  E-value: 1.28e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  87 LRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLISKE 166
Cdd:cd05466     2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716 167 -LLSGiyeegfESKIAqgnLSALQECPFVLGNPEDIGGQIGRSMIKHSGFQPIVKAQSDNIETLLSLCVRGIGACFCPin 245
Cdd:cd05466    82 hPLAK------RKSVT---LADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLP-- 150

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 2473439716 246 lvQATLPAKQLSKLRMFRFDNYAAY-PIRFGYQRNPYQWSIISEFIKIA 293
Cdd:cd05466   151 --ESAVEELADGGLVVLPLEDPPLSrTIGLVWRKGRYLSPAARAFLELL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
1-56 5.44e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 76.27  E-value: 5.44e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2473439716   1 MEYFVMVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIRRV-PLELTYAGE 56
Cdd:pfam00126   4 LRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTrGVRLTEAGE 60
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 87-243 1.58e-16

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: 76.01  E-value: 1.58e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  87 LRVGvsFTRSRV--IMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLIS 164
Cdd:cd08414     2 LRIG--FVGSALygLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716 165 KE--LLSgiyeegfESKIAqgnLSALQECPFVLGNPEDIGG---QIgRSMIKHSGFQPIVKAQSDNIETLLSLCVRGIGA 239
Cdd:cd08414    80 ADhpLAA-------RESVS---LADLADEPFVLFPREPGPGlydQI-LALCRRAGFTPRIVQEASDLQTLLALVAAGLGV 148


                  ....
gi 2473439716 240 CFCP 243
Cdd:cd08414   149 ALVP 152
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
12-84 7.66e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 35.26  E-value: 7.66e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   12 SFTKAAEQLHITQQTLSAHIssveKELECQLLIRRVP---------LELTYAGEVFLRYALgfQQSHQAMKKEFCDITAN 82
Cdd:smart00347  26 SVSELAKRLGVSPSTVTRVL----DRLEKKGLVRREPspedrrsvlVSLTEEGRELIEQLL--EARSETLAELLAGLTAE 99


                   ..
gi 2473439716   83 QK 84
Cdd:smart00347 100 EQ 101
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-166 2.63e-46

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 156.57  E-value: 2.63e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   1 MEYFVMVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIRRV-PLELTYAGEVFLRYALGFQQSHQAMKKEFCDI 79
Cdd:COG0583     6 LRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGrGLRLTEAGERLLERARRILAELEEAEAELRAL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  80 TANQKGILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEI 159
Cdd:COG0583    86 RGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPLGEERL 165


                  ....*..
gi 2473439716 160 VLLISKE 166
Cdd:COG0583   166 VLVASPD 172
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 2-195 1.00e-37

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: 135.44  E-value: 1.00e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   2 EYFVMVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIRRV-PLELTYAGEVFLRYALGFQQSHQAMKKEFCDIT 80
Cdd:NF040786    7 EAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTkEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDRYG 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  81 ANQKGILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLA-VGSFPESlPDVELRDFYQEEI 159
Cdd:NF040786   87 KESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGfTGTKLEK-KRLVYTPFYKDRL 165

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2473439716 160 VLLISKELlsgiyeEGFESKIAQGNLSALQECPFVL 195
Cdd:NF040786  166 VLITPNGT------EKYRMLKEEISISELQKEPFIM 195
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 3-236 1.21e-32

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 121.99  E-value: 1.21e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   3 YFVMVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIR--RVpLELTYAGEVFLRYALGFQQSHQAMKKEFCDIT 80
Cdd:PRK11242    8 YFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRsgRT-VRLTDAGEVYLRYARRALQDLEAGRRAIHDVA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  81 ANQKGILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIV 160
Cdd:PRK11242   87 DLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQPLFTETLA 166

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2473439716 161 LLISKellsgiyEEGFESKIAQGNLSALQECPFVLGNPEDIG-GQIGRSMIKHsGFQPIVKAQSDNIETLLSLCVRG 236
Cdd:PRK11242  167 LVVGR-------HHPLAARRKALTLDELADEPLVLLSAEFATrEQIDRYFRRH-GVTPRVAIEANSISAVLEIVRRG 235
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 85-271 3.42e-26

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: 102.37  E-value: 3.42e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  85 GILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLIS 164
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716 165 KellsgiyeegfESKIAQG---NLSALQECPFVLGNPEDIGGQIGRSMIKHSGFQPIVKAQSDNIETLLSLCVRGIGACF 241
Cdd:pfam03466  82 P-----------DHPLARGepvSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIAL 150

                         170       180       190
                  ....*....|....*....|....*....|....
gi 2473439716 242 CPINLVQATLPAKQLSKLRM----FRFDNYAAYP 271
Cdd:pfam03466 151 LPRSAVARELADGRLVALPLpeppLPRELYLVWR 184
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 87-293 1.28e-24

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: 98.06  E-value: 1.28e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  87 LRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLISKE 166
Cdd:cd05466     2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716 167 -LLSGiyeegfESKIAqgnLSALQECPFVLGNPEDIGGQIGRSMIKHSGFQPIVKAQSDNIETLLSLCVRGIGACFCPin 245
Cdd:cd05466    82 hPLAK------RKSVT---LADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLP-- 150

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 2473439716 246 lvQATLPAKQLSKLRMFRFDNYAAY-PIRFGYQRNPYQWSIISEFIKIA 293
Cdd:cd05466   151 --ESAVEELADGGLVVLPLEDPPLSrTIGLVWRKGRYLSPAARAFLELL 197
rbcR CHL00180
LysR transcriptional regulator; Provisional
 7-165 3.47e-23

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 96.63  E-value: 3.47e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   7 VARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIR-RVPLELTYAGEVFLRYA---LGF-QQSHQAMKkefcDITA 81
Cdd:CHL00180   16 IATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRsKNKASLTEAGELLLRYGnriLALcEETCRALE----DLKN 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  82 NQKGILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAV--GSFPESLPDV-ELRDFYQEE 158
Cdd:CHL00180   92 LQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIvgGEVPTELKKIlEITPYVEDE 171


                  ....*..
gi 2473439716 159 IVLLISK 165
Cdd:CHL00180  172 LALIIPK 178
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
1-56 5.44e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 76.27  E-value: 5.44e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2473439716   1 MEYFVMVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIRRV-PLELTYAGE 56
Cdd:pfam00126   4 LRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTrGVRLTEAGE 60
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-243 7.17e-17

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 79.04  E-value: 7.17e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   1 MEYFVMVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIR-RVPLELTYAGEVFLRYA-LGFQQSHQAmkKEFCD 78
Cdd:PRK09906    6 LRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRdKRKVALTAAGEVFLQDArAILEQAEKA--KLRAR 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  79 ITANQKGILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEE 158
Cdd:PRK09906   84 KIVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLELLDEP 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716 159 IVLLISKEllsgiYEEGFESKIAqgnLSALQECPFVLGNPEDIG--GQIGRSMIKHSGFQPIVKAQSDNIETLLSLCVRG 236
Cdd:PRK09906  164 LVVVLPVD-----HPLAHEKEIT---AAQLDGVNFISTDPAYSGslAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMG 235


                  ....*..
gi 2473439716 237 IGACFCP 243
Cdd:PRK09906  236 LGCTIIP 242
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 87-243 1.58e-16

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: 76.01  E-value: 1.58e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  87 LRVGvsFTRSRV--IMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLIS 164
Cdd:cd08414     2 LRIG--FVGSALygLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716 165 KE--LLSgiyeegfESKIAqgnLSALQECPFVLGNPEDIGG---QIgRSMIKHSGFQPIVKAQSDNIETLLSLCVRGIGA 239
Cdd:cd08414    80 ADhpLAA-------RESVS---LADLADEPFVLFPREPGPGlydQI-LALCRRAGFTPRIVQEASDLQTLLALVAAGLGV 148


                  ....
gi 2473439716 240 CFCP 243
Cdd:cd08414   149 ALVP 152
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 8-170 3.69e-16

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 76.81  E-value: 3.69e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   8 ARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIRR-VPLELTYAGEvflRYALG----FQQSHQAMKKEfcdITAN 82
Cdd:PRK11139   18 ARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRnRSLLLTEEGQ---RYFLDireiFDQLAEATRKL---RARS 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  83 QKGILRVGV--SFTrSRVIMPDLiSAFQEKYPNIEITImeSSNDAMHKYLIDgEIDLAVGSFPESLPDVELRDFYQEEIV 160
Cdd:PRK11139   92 AKGALTVSLlpSFA-IQWLVPRL-SSFNEAHPDIDVRL--KAVDRLEDFLRD-DVDVAIRYGRGNWPGLRVEKLLDEYLL 166

                         170
                  ....*....|
gi 2473439716 161 LLISKELLSG 170
Cdd:PRK11139  167 PVCSPALLNG 176
PRK09791 PRK09791
LysR family transcriptional regulator;
4-151 7.47e-15

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 73.26  E-value: 7.47e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   4 FVMVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIRRVP-LELTYAGEVFLRYALGFQQSHQAMKKEFCDITAN 82
Cdd:PRK09791   13 FVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKgVTLTDAGESFYQHASLILEELRAAQEDIRQRQGQ 92

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2473439716  83 QKGILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVEL 151
Cdd:PRK09791   93 LAGQINIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYYQGPYDHEF 161
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 89-232 5.73e-14

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


Pssm-ID: 176125 [Multi-domain]  Cd Length: 195  Bit Score: 69.10  E-value: 5.73e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  89 VGVSFTRS---RVImPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLISK 165
Cdd:cd08434     2 VRLGFLHSlgtSLV-PDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPK 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2473439716 166 E-LLSGiyeegfESKIAqgnLSALQECPFVLGNPEDIGGQIGRSMIKHSGFQPIVKAQSDNIETLLSL 232
Cdd:cd08434    81 DhPLAG------RDSVD---LAELADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAFEGEEDSTIAGL 139
PRK09986 PRK09986
LysR family transcriptional regulator;
1-243 8.07e-14

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 70.14  E-value: 8.07e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   1 MEYFVMVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIRRV-PLELTYAGEVFLRYA-LGFQQSHQAMKKeFCD 78
Cdd:PRK09986   12 LRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSrSVVLTHAGKILMEESrRLLDNAEQSLAR-VEQ 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  79 ITANQKGILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAV--GSFPESLPDVELRDFYQ 156
Cdd:PRK09986   91 IGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIwrMADLEPNPGFTSRRLHE 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716 157 EEIVLLISKE-LLSGiyeegfESKIAqgnLSALQECPFVL--GNPEDIGGQIGRSMIKHsGFQPIVKAQSDNIETLLSLC 233
Cdd:PRK09986  171 SAFAVAVPEEhPLAS------RSSVP---LKALRNEYFITlpFVHSDWGKFLQRVCQQA-GFSPQIIRQVNEPQTVLAMV 240

                         250
                  ....*....|
gi 2473439716 234 VRGIGACFCP 243
Cdd:PRK09986  241 SMGIGITLLP 250
PRK10341 PRK10341
transcriptional regulator TdcA;
4-195 1.22e-13

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 69.89  E-value: 1.22e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   4 FVMVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIRR-VPLELTYAGEVFLRYALGFQQSHQAMKKEFCDITAN 82
Cdd:PRK10341   15 FQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKnTGVTLTPAGQVLLSRSESITREMKNMVNEINGMSSE 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  83 QKgilrVGVSFTRSRVI----MPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSF--PESLPDVELRDFYQ 156
Cdd:PRK10341   95 AV----VDVSFGFPSLIgftfMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLsnEMKLQDLHVEPLFE 170

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2473439716 157 EEIVLLISKellsgiyeegfeSKIAQG--NLSALQECPFVL 195
Cdd:PRK10341  171 SEFVLVASK------------SRTCTGttTLESLKNEQWVL 199
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
21-148 2.03e-13

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 68.69  E-value: 2.03e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  21 HITQQTLSAHISSVEKELECQLLIR---RVplELTYAGEVFLRYALGFQQSHQAMKKEFCDITANQKGILRVGVSFTRSR 97
Cdd:PRK11716    2 HVSPSTLSRQIQRLEEELGQPLFVRdnrSV--TLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLFCSVTAAY 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2473439716  98 VIMPDLISAFQEKYPNIEITImeSSND---AMHKyLIDGEIDLAVGSFPESLPD 148
Cdd:PRK11716   80 SHLPPILDRFRAEHPLVEIKL--TTGDaadAVEK-VQSGEADLAIAAKPETLPA 130
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 99-162 2.69e-12

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: 64.47  E-value: 2.69e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2473439716  99 IMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLL 162
Cdd:cd08440    14 LLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLV 77
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 87-254 4.33e-12

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: 63.73  E-value: 4.33e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  87 LRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLISKe 166
Cdd:cd08438     2 LRLGLPPLGGSLLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPR- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716 167 llsgiyeegfESKIAQG---NLSALQECPFVLGNPEDIGGQIGRSMIKHSGFQPIVKAQSDNIETLLSLCVRGIGACFCP 243
Cdd:cd08438    81 ----------GHPLAGRktvSLADLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLP 150

                         170
                  ....*....|.
gi 2473439716 244 INLVQATLPAK 254
Cdd:cd08438   151 RSIAQRLDNAG 161
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-139 5.88e-12

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 65.09  E-value: 5.88e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   1 MEYFVMVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIRR----VPLEltyAGEVFLRYALG-FQQSHQAmkke 75
Cdd:PRK11233    6 LKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTkrgvTPTE---AGKILYTHARAiLRQCEQA---- 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2473439716  76 fcditanQKGILRVG------VSF------TRSRVIMPdLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAV 139
Cdd:PRK11233   79 -------QLAVHNVGqalsgqVSIglapgtAASSLTMP-LLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAV 146
PBP2_ToxR cd08465
The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates ...
 86-168 1.50e-11

The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates the expression of the toxoflavin biosynthesis genes; contains the type 2 periplasmic bindinig fold; In soil bacterium Burkholderia glumae, ToxR regulates the toxABCDE and toxFGHI operons in the presence of toxoflavin as a coinducer. Additionally, the expression of both operons requires a transcriptional activator, ToxJ, whose expression is regulated by the TofI or TofR quorum-sensing system. The biosynthesis of toxoflavin is suggested to be synthesized in a pathway common to the synthesis of riboflavin. 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: 176154  Cd Length: 200  Bit Score: 62.33  E-value: 1.50e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  86 ILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLISK 165
Cdd:cd08465     1 VFRLAMSDYGARLVLPALMRQLRAEAPGIDLAVSQASREAMLAQVADGEIDLALGVFPELPEELHAETLFEERFVCLADR 80


                  ...
gi 2473439716 166 ELL 168
Cdd:cd08465    81 ATL 83
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 14-150 1.93e-11

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 63.47  E-value: 1.93e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  14 TKAAEQLHITQQTLSAHISSVEKELECQLLIRRVP--LELTYAGEVFLRYALGFQQSHQAMKKEFCDITANQKGILRVGV 91
Cdd:PRK12682   20 TEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKrlKGLTEPGKAVLDVIERILREVGNIKRIGDDFSNQDSGTLTIAT 99

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2473439716  92 SFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSfpESLPDVE 150
Cdd:PRK12682  100 THTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIAT--ESLADDP 156
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 6-140 3.25e-11

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 62.65  E-value: 3.25e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   6 MVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIRR---VplELTYAGEVFLRYALGFQQSHQAMKKEfCDITAN 82
Cdd:PRK11074   12 AVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRhrdV--ELTPAGEWFVKEARSVIKKMQETRRQ-CQQVAN 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2473439716  83 Q-KGILRVGVsftrSRVIMPD----LISAFQEKYPNIEITI-MESSN---DAmhkyLIDGEIDLAVG 140
Cdd:PRK11074   89 GwRGQLSIAV----DNIVRPDrtrqLIVDFYRHFDDVELIIrQEVFNgvwDA----LADGRVDIAIG 147
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 85-236 3.31e-11

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold; CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR 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 (PBP2). The PBP2 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: 176116  Cd Length: 197  Bit Score: 61.19  E-value: 3.31e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  85 GILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLIS 164
Cdd:cd08425     1 GSLRLAMTPTFTAYLIGPLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDAQPLFDERLALVVG 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2473439716 165 KellsGIYEEGFESKIAqgnLSALQECPFVLGNPEDIG-GQIGRSMIKHsGFQPIVKAQSDNIETLLSLCVRG 236
Cdd:cd08425    81 A----THPLAQRRTALT---LDDLAAEPLALLSPDFATrQHIDRYFQKQ-GIKPRIAIEANSISAVLEVVRRG 145
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 87-195 4.48e-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: 60.97  E-value: 4.48e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  87 LRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLA-VGSFPESlPDVELRDFYQEEIVLLISK 165
Cdd:cd08420     2 LRIGASTTIGEYLLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGlVEGPVDH-PDLIVEPFAEDELVLVVPP 80

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2473439716 166 EL-LSGIYEEGFEskiaqgnlsALQECPFVL 195
Cdd:cd08420    81 DHpLAGRKEVTAE---------ELAAEPWIL 102
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 88-165 5.35e-11

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


Pssm-ID: 176110 [Multi-domain]  Cd Length: 201  Bit Score: 60.83  E-value: 5.35e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  88 RVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDvelRDFYQE-----EIVLL 162
Cdd:cd08418     3 SIGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYL---KELISEplfesDFVVV 79


                  ...
gi 2473439716 163 ISK 165
Cdd:cd08418    80 ARK 82
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-166 6.39e-11

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 61.97  E-value: 6.39e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   1 MEYFVMVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLL---IRRVpleltyagevfLRYALGFQQSHQAMK---- 73
Cdd:PRK11151    6 LEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLertSRKV-----------LFTQAGLLLVDQARTvlre 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  74 -KEFCDITANQ----KGILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAV-GSFPESLP 147
Cdd:PRK11151   75 vKVLKEMASQQgetmSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAIlALVKESEA 154

                         170
                  ....*....|....*....
gi 2473439716 148 DVELrDFYQEEIVLLISKE 166
Cdd:PRK11151  155 FIEV-PLFDEPMLLAVYED 172
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 98-165 4.66e-10

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: 57.99  E-value: 4.66e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2473439716  98 VIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLISK 165
Cdd:cd08417    13 LLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARK 80
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
3-147 4.78e-10

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 59.22  E-value: 4.78e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   3 YFVMVARER-SFTKAAEQLHITQQTLSAHISSVEKELECQLLIR---RVpLELTYAGEVFLRYALGFQQSHQAMKKEFCD 78
Cdd:PRK12684    8 FVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRhgkRL-RGLTEPGRIILASVERILQEVENLKRVGKE 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2473439716  79 ITANQKGILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVG-----SFPE--SLP 147
Cdd:PRK12684   87 FAAQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIAteaiaDYKElvSLP 162
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
4-139 7.81e-10

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 58.86  E-value: 7.81e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   4 FVMVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLI---RRVplELTYAGE-VFlrYALgfQQSHQAMKKEFCDI 79
Cdd:PRK10086   22 FEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVrshRKV--ELTEEGKrVF--WAL--KSSLDTLNQEILDI 95

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2473439716  80 tANQK--GILRVGV--SFTRSrVIMPDlISAFQEKYPNIEITIMeSSNDamhkyLID---GEIDLAV 139
Cdd:PRK10086   96 -KNQElsGTLTVYSrpSIAQC-WLVPR-LADFTRRYPSISLTIL-TGNE-----NVNfqrAGIDLAI 153
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 86-239 1.07e-09

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: 56.83  E-value: 1.07e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  86 ILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLISK 165
Cdd:cd08433     1 RVSVGLPPSAASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGPA 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2473439716 166 ELLsgiyeegfESKIAQGNLSALQECPFVLgnPEdiGGQIGRSMIKHSGFQ----PIVKAQSDNIETLLSLCVRGIGA 239
Cdd:cd08433    81 DAP--------LPRGAPVPLAELARLPLIL--PS--RGHGLRRLVDEAAARagltLNVVVEIDSVATLKALVAAGLGY 146
cbl PRK12679
HTH-type transcriptional regulator Cbl;
9-141 2.88e-09

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 57.13  E-value: 2.88e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   9 RERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIRRVP--LELTYAGEVFLRYALGFQQSHQAMKKeFCDITANQ-KG 85
Cdd:PRK12679   15 QDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKrlLGMTEPGKALLVIAERILNEASNVRR-LADLFTNDtSG 93

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2473439716  86 ILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGS 141
Cdd:PRK12679   94 VLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIAS 149
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 85-166 3.63e-09

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: 55.61  E-value: 3.63e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  85 GILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLIS 164
Cdd:cd08411     1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAVP 80


                  ..
gi 2473439716 165 KE 166
Cdd:cd08411    81 KD 82
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 87-238 1.40e-08

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


Pssm-ID: 176104 [Multi-domain]  Cd Length: 198  Bit Score: 53.70  E-value: 1.40e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  87 LRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVgsfpesLPDVELRDFYQEEI------- 159
Cdd:cd08412     2 LRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLAL------TYDLDLPEDIAFEPlarlppy 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716 160 VLLISKELLSGiyeegfESKIaqgNLSALQECPFV-LGNPEdiGGQIGRSMIKHSGFQPIVKAQSDNIETLLSLCVRGIG 238
Cdd:cd08412    76 VWLPADHPLAG------KDEV---SLADLAAEPLIlLDLPH--SREYFLSLFAAAGLTPRIAYRTSSFEAVRSLVANGLG 144
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-62 1.47e-08

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 54.59  E-value: 1.47e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2473439716   2 EYFVMVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIRRVPLELTYAGEVFLRYA 62
Cdd:PRK13348    8 EALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRPCRPTPAGQRLLRHL 68
PRK12680 PRK12680
LysR family transcriptional regulator;
1-147 1.53e-08

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 55.01  E-value: 1.53e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   1 MEYFVMVA-RERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIRR-VPLE-LTYAGEVFLRYAlgfqqshQAMKKEFC 77
Cdd:PRK12680    6 LRYLVAIAdAELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKgRSLEsVTPAGVEVIERA-------RAVLSEAN 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2473439716  78 DI---TANQK----GILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLP 147
Cdd:PRK12680   79 NIrtyAANQRresqGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEP 155
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 87-249 2.00e-08

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: 53.37  E-value: 2.00e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  87 LRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPD-VELRDFYQEEIVLLISK 165
Cdd:cd08436     2 LAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRPPgLASRELAREPLVAVVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716 166 E-LLSGiyeegfeskIAQGNLSALQECPFVlGNPEDIGgqiGRSMIKH----SGFQPIVKAQSDNIETLLSLCVRGIGAC 240
Cdd:cd08436    82 DhPLAG---------RRRVALADLADEPFV-DFPPGTG---ARRQVDRafaaAGVRRRVAFEVSDVDLLLDLVARGLGVA 148


                  ....*....
gi 2473439716 241 FCPINLVQA 249
Cdd:cd08436   149 LLPASVAAR 157
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
6-62 2.95e-08

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 54.01  E-value: 2.95e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2473439716   6 MVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIRRVPLELTYAGEVFLRYA 62
Cdd:PRK03635   12 AVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRTQPCRPTEAGQRLLRHA 68
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 7-166 3.10e-08

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 53.89  E-value: 3.10e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   7 VARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIRRVP--LELTYAGEVFLRYALGFQQSHQAMKKEFCDITANQK 84
Cdd:PRK12683   13 VRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKrlTGLTEPGKELLQIVERMLLDAENLRRLAEQFADRDS 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  85 GILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSfpESL---PDVELRDFYQEEIVL 161
Cdd:PRK12683   93 GHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIAT--EALdrePDLVSFPYYSWHHVV 170


                  ....*
gi 2473439716 162 LISKE 166
Cdd:PRK12683  171 VVPKG 175
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 87-253 4.14e-08

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


Pssm-ID: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 52.60  E-value: 4.14e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  87 LRVGvSF-TRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAV-----GSFPESLPDVELRDFYQEEIV 160
Cdd:cd08423     2 LRVG-AFpTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVvfdypVTPPPDDPGLTRVPLLDDPLD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716 161 LLISKE-LLSGiyeegfESKIAqgnLSALQECPFVLGNPEDIGGQIGRSMIKHSGFQPIVKAQSDNIETLLSLCVRGIGA 239
Cdd:cd08423    81 LVLPADhPLAG------REEVA---LADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGV 151

                         170
                  ....*....|....
gi 2473439716 240 CFCPiNLVQATLPA 253
Cdd:cd08423   152 ALVP-RLALGARPP 164
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 4-152 4.58e-08

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 53.49  E-value: 4.58e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   4 FVMVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIR--RVPLeLTYAGEVFLRYA---LGFQQshqamkkEFCD 78
Cdd:PRK15092   19 FVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARhgRNKL-LTEHGIQLLGYArkiLRFND-------EACS 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2473439716  79 --ITANQKGILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSF-PESLPDVELR 152
Cdd:PRK15092   91 slMYSNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTTHrPSSFPALNLR 167
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 86-238 6.03e-08

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: 51.79  E-value: 6.03e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  86 ILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLI-- 163
Cdd:cd08415     1 TLRIAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLpp 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716 164 -----SKELLSgiyeegfeskiaqgnLSALQECPFVLGNPEDIGGQIGRSMIKHSGFQPIVKAQSDNIETLLSLCVRGIG 238
Cdd:cd08415    81 ghplaRKDVVT---------------PADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLG 145
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 87-243 1.37e-07

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 50.77  E-value: 1.37e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  87 LRVGVSFTRSrvIMPDLISAFQEKYPNIEITI-MESSNDAMHKyLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLISK 165
Cdd:cd08426     4 VATGEGLAAE--LLPSLIARFRQRYPGVFFTVdVASTADVLEA-VLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVVPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716 166 EllsgiyeegfESKIAQG--NLSALQECPFVLGNPEDIGGQIGRSMIKHSGFQPIVKAQSDNIETLLSLCVRGIGACFCP 243
Cdd:cd08426    81 G----------HPLARQPsvTLAQLAGYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLT 150
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 86-238 1.55e-07

The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold; In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. 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: 176140 [Multi-domain]  Cd Length: 197  Bit Score: 50.73  E-value: 1.55e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  86 ILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRD--FYQEEIVLLI 163
Cdd:cd08449     1 HLNIGMVGSVLWGGLGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFADTLNDPPLASelLWREPMVVAL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2473439716 164 SKE-LLSGiyeegfeSKIAQgnLSALQECPFVLGNPED--IGGQIGRSMIKhSGFQPIVKAQSDNIETLLSLCVRGIG 238
Cdd:cd08449    81 PEEhPLAG-------RKSLT--LADLRDEPFVFLRLANsrFADFLINCCLQ-AGFTPQITQEVVEPQTLMALVAAGFG 148
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 85-243 1.92e-07

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tfdA and tfdB gene expression. These genes encode enzymes for the conversion of 2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenol. 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: 176137 [Multi-domain]  Cd Length: 198  Bit Score: 50.36  E-value: 1.92e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  85 GILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLIS 164
Cdd:cd08446     1 GELDVGYFGSAILDTVPRLLRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFYPVEPDIAVENVAQERLYLAVP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716 165 KELlsgiyEEGFESKIAqgnLSALQECPFVL----GNPEDIGGQIGrsMIKHSGFQPIVKAQSDNIETLLSLCVRGIGAC 240
Cdd:cd08446    81 KSH-----PLAARPAVS---LADLRNEPLILfprgGRPSFADEVLG--LFRRAGVEPRVAQEVEDVVAALALVAAGFGVC 150


                  ...
gi 2473439716 241 FCP 243
Cdd:cd08446   151 IVP 153
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
4-75 4.50e-07

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 50.02  E-value: 4.50e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2473439716   4 FVMVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIR-RVPLELTYAGEVFLRYALGFQQSHQAMKKE 75
Cdd:PRK03601    9 FLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRhRNNIRLTAAGERLLPYAETLMNTWQAAKKE 81
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 87-161 5.40e-07

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: 49.19  E-value: 5.40e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2473439716  87 LRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDF--YQEEIVL 161
Cdd:cd08435     2 VRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLADDEQPPDLASEelADEPLVV 78
cysB PRK12681
HTH-type transcriptional regulator CysB;
3-139 5.76e-07

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 50.28  E-value: 5.76e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   3 YFVMVARER-SFTKAAEQLHITQQTLSAHISSVEKELECQLLIR------RVplelTYAGEVFLRYA---LGFQQSHQAM 72
Cdd:PRK12681    8 YIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARsgkhltQV----TPAGEEIIRIAreiLSKVESIKSV 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2473439716  73 KKEFcdiTANQKGILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAV 139
Cdd:PRK12681   84 AGEH---TWPDKGSLYIATTHTQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAI 147
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 87-238 1.40e-06

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


Pssm-ID: 176142 [Multi-domain]  Cd Length: 199  Bit Score: 47.94  E-value: 1.40e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  87 LRVGvsFTRSRV---IMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFP-ESLPDVELRDFYQEEIVL- 161
Cdd:cd08451     2 LRVG--FTSSAAfhpLVPGLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPvARSDGLVLELLLEEPMLVa 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716 162 LISKELLSGiyeegfESKIAqgnLSALQECPFVLGNPEdiggqIGRSM---IKHS----GFQPIVKAQSDNIETLLSLCV 234
Cdd:cd08451    80 LPAGHPLAR------ERSIP---LAALADEPFILFPRP-----VGPGLydaIIAAcrraGFTPRIGQEAPQMASAINLVA 145


                  ....
gi 2473439716 235 RGIG 238
Cdd:cd08451   146 AGLG 149
PBP2_SyrM cd08467
The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates ...
 98-166 2.03e-06

The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold; Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176156 [Multi-domain]  Cd Length: 200  Bit Score: 47.43  E-value: 2.03e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2473439716  98 VIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLISKE 166
Cdd:cd08467    13 ALLPRLAPRLRERAPGLDLRLCPIGDDLAERGLEQGTIDLAVGRFAVPPDGLVVRRLYDDGFACLVRHG 81
nhaR PRK11062
transcriptional activator NhaR; Provisional
 3-62 2.78e-06

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 48.08  E-value: 2.78e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2473439716   3 YFVMVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIRR----VPLELtyaGEVFLRYA 62
Cdd:PRK11062   11 YFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKgrglEPTEL---GELVFRYA 71
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
12-145 3.15e-06

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 47.70  E-value: 3.15e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  12 SFTKAAEQLHITQQTLSAHISSVEKELECQLLIRRV-PLELTYAGEVFLRYAlgfQQSHQAMKKEFCDITANQKGILRVG 90
Cdd:PRK15421   18 SLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSqPLRFTPQGEILLQLA---NQVLPQISQALQACNEPQQTRLRIA 94

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2473439716  91 VSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGS--FPES 145
Cdd:PRK15421   95 IECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSdiLPRS 151
PRK09801 PRK09801
LysR family transcriptional regulator;
1-138 3.24e-06

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 47.72  E-value: 3.24e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   1 MEYFVMVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIRRVP-LELTYAGEVFLRYALGFQQSHQAMKKEFCDI 79
Cdd:PRK09801   11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARgVALTESGQRCYEHALEILTQYQRLVDDVTQI 90

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2473439716  80 TANQKGILRVGVSFTRSRVIMPDLISAFQEKYPNIEItimessndamHKYLIDGEIDLA 138
Cdd:PRK09801   91 KTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQV----------HFELFDRQIDLV 139
PBP2_MdcR cd08416
The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which ...
 87-243 3.28e-06

The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold; This family includes the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and 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 (PBP2). The PBP2 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: 176108  Cd Length: 199  Bit Score: 46.95  E-value: 3.28e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  87 LRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESL--PDVELRDFYQEEIVLLIS 164
Cdd:cd08416     2 LRLGSLYSLTVNTVPRIIMGLKLRRPELDIELTLGSNKDLLKKLKDGELDAILVATPEGLndPDFEVVPLFEDDIFLAVP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716 165 KellsgiyeegfESKIAQG---NLSALQECPFVLGNPEDIGGQIGRSMIKHSGFQPIVKAQSDNIETLLSLCVRGIGACF 241
Cdd:cd08416    82 A-----------TSPLAASseiDLRDLKDEKFVTLSEGFATYRGFDEAFEIAGFEPNVVMRVNDIFSLMSMVSGGVGYAL 150


                  ..
gi 2473439716 242 CP 243
Cdd:cd08416   151 LP 152
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 87-161 3.64e-06

The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). 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: 176111  Cd Length: 197  Bit Score: 46.73  E-value: 3.64e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2473439716  87 LRVGVSFTrSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVL 161
Cdd:cd08419     2 LRLAVVST-AKYFAPRLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGRPPEDLDLVAEPFLDNPLVV 75
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
 98-165 7.25e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate of the oxidative degradation of the aromatic ring in soil bacteria. LinR positively regulates expression of the genes (linD and linE) encoding enzymes for gamma-hexachlorocyclohexane (a haloorganic insecticide) degradation. Expression of linD and linE are induced by their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ) and chlorohydroquinone (CHQ). The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176148 [Multi-domain]  Cd Length: 201  Bit Score: 46.03  E-value: 7.25e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2473439716  98 VIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLISK 165
Cdd:cd08459    13 YFLPRLLAALREVAPGVRIETVRLPVDELEEALESGEIDLAIGYLPDLGAGFFQQRLFRERYVCLVRK 80
PBP2_DntR_like_3 cd08461
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-203 8.28e-06

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. 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: 176150 [Multi-domain]  Cd Length: 198  Bit Score: 45.74  E-value: 8.28e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  97 RVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVgSFPESLPDvEL--RDFYQEEIVLLISKellsgiyee 174
Cdd:cd08461    12 KAILPPLLAALRQEAPGVRVAIRDLESDNLEAQLERGEVDLAL-TTPEYAPD-GLrsRPLFEERYVCVTRR--------- 80

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2473439716 175 gfESKIAQGNLSALQEC--PFVLGNPeDIGG 203
Cdd:cd08461    81 --GHPLLQGPLSLDQFCalDHIVVSP-SGGG 108
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 3-151 8.66e-06

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 46.52  E-value: 8.66e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   3 YFVMVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIRRV-PLELTYAGEVFLRYALGFQQSHQAMKKEFCDITA 81
Cdd:PRK14997    9 WFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTrQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQV 88

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2473439716  82 NQKGILRVGVSFTRSRVIMPDLISAFQEKYPNIEITiMESSNdamHKYLIDGE-IDLAVGSFPESLPDVEL 151
Cdd:PRK14997   89 EPRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQ-LEATN---RRVDVVGEgVDVAIRVRPRPFEDSDL 155
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
4-62 1.73e-05

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 45.57  E-value: 1.73e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   4 FVMVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIRRV-PLELTYAGEVFLRYA 62
Cdd:PRK10094   10 FIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTrSVTLTAAGEHLLSQA 69
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 87-252 2.19e-05

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176139 [Multi-domain]  Cd Length: 197  Bit Score: 44.57  E-value: 2.19e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  87 LRVGvsFTRSRV--IMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLIS 164
Cdd:cd08448     2 LRIG--FVGSMLyrGLPRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAGLSARLLHREPFVCCLP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716 165 KellsgiyeegfESKIAQ---GNLSALQECPFVLGNPEDIGG---QIgRSMIKHSGFQPIVKAQSDNIETLLSLCVRGIG 238
Cdd:cd08448    80 A-----------GHPLAArrrIDLRELAGEPFVLFSREVSPDyydQI-IALCMDAGFHPKIRHEVRHWLTVVALVAAGMG 147

                         170
                  ....*....|....
gi 2473439716 239 ACFCPINLVQATLP 252
Cdd:cd08448   148 VALVPRSLARAGLA 161
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
 87-147 7.85e-05

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: 42.57  E-value: 7.85e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2473439716  87 LRVGVSFTRSRVIMPDLISAFQEKYPNIEITiMESSN--DAMHKyLIDGEIDLAVGSFPESLP 147
Cdd:cd08430     2 LSLYCSVTASYSFLPPILERFRAQHPQVEIK-LHTGDpaDAIDK-VLNGEADIAIAARPDKLP 62
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 1-114 8.13e-05

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 43.52  E-value: 8.13e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   1 MEYFVMVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIR---RvpLELTYAGEVFLRYALGFQQshQAMKKEfc 77
Cdd:PRK10837    8 LEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRvgkR--LVVNEHGRLLYPRALALLE--QAVEIE-- 81

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2473439716  78 DITANQKGILRVGVSFTRSRVIMPDLISAFQEKYPNI 114
Cdd:PRK10837   82 QLFREDNGALRIYASSTIGNYILPAMIARYRRDYPQL 118
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-118 9.28e-05

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 43.21  E-value: 9.28e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   1 MEYFVMVARERSFTKAAEQLHITQQTLSAHISSVEKELECQLLIRRV-PLELTYAGEVFLRYALGFQQSHQAMKKEFCDI 79
Cdd:PRK10632    7 MSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTrSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAF 86

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2473439716  80 TANQKGILRVGVSFTRSRVIMPDLISAFQEKYPNIEITI 118
Cdd:PRK10632   87 NNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNL 125
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 88-243 1.11e-04

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176138 [Multi-domain]  Cd Length: 198  Bit Score: 42.25  E-value: 1.11e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  88 RVGVSFTRSRV--IMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLISK 165
Cdd:cd08447     1 SLRIGFTAASAysFLPRLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFARPGLETRPLVREPLVAAVPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716 166 ellsgiyeegfESKIAQGNLSALQEC---PFVLGNPEDiggqiGR-------SMIKHSGFQPIVKAQSDNIETLLSLCVR 235
Cdd:cd08447    81 -----------GHPLAGAERLTLEDLdgqPFIMYSPTE-----ARyfhdlvvRLFASAGVQPRYVQYLSQIHTMLALVRA 144


                  ....*...
gi 2473439716 236 GIGACFCP 243
Cdd:cd08447   145 GLGVALVP 152
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 87-169 2.06e-04

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


Pssm-ID: 176133  Cd Length: 193  Bit Score: 41.44  E-value: 2.06e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  87 LRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLISKE 166
Cdd:cd08442     2 LRLGSMETTAAVRLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSPKG 81


                  ...
gi 2473439716 167 LLS 169
Cdd:cd08442    82 HPP 84
PBP2_LrhA_like cd08439
The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of ...
 86-152 2.57e-04

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


Pssm-ID: 176130  Cd Length: 185  Bit Score: 41.16  E-value: 2.57e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2473439716  86 ILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPES-LPDVELR 152
Cdd:cd08439     1 TLRIGCPDDYADTILPFLLNRFASVYPRLAIEVVCKRTPRLMEMLERGEVDLALITHPPPgASATILR 68
PBP2_DntR_like_2 cd08464
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-169 2.69e-04

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. 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: 176153 [Multi-domain]  Cd Length: 200  Bit Score: 41.06  E-value: 2.69e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2473439716  98 VIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLISKELLS 169
Cdd:cd08464    13 WLAPPLLAALRAEAPGVRLVFRQVDPFNVGDMLDRGEIDLAIGVFGELPAWLKREVLYTEGYACLFDPQQLS 84
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 85-139 4.81e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. 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 further 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: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 40.50  E-value: 4.81e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2473439716  85 GILRVG--VSFTRsRVIMPdLISAFQEKYPNIEITImeSSNDAMHKyLIDGEIDLAV 139
Cdd:cd08422     1 GRLRISapVSFGR-LHLAP-LLAEFLARYPDVRLEL--VLSDRLVD-LVEEGFDLAI 52
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 100-293 7.20e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mechanisms. In Escherichia coli and Salmonella enterica serovar Typhimurium, MetJ and MetR regulate the expression of methionine biosynthetic genes. The MetJ repressor negatively regulates the E. coli met genes, except for metH. Several of these genes are also under the positive control of MetR with homocysteine as a co-inducer. In Bacillus subtilis, the met genes are controlled by S-box termination-antitermination system. 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: 176132  Cd Length: 198  Bit Score: 39.86  E-value: 7.20e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716 100 MPdLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLISKEllsgiyeegfesk 179
Cdd:cd08441    16 MP-VLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAPD------------- 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716 180 iaqgnlSALQECPFVlgNPEDIGGQ------IGRSMI---KH----SGFQPIVKAQSDNIETLLSLCVRGIGACFCPINL 246
Cdd:cd08441    82 ------HPLAAKEFI--TPEDLADEtlitypVERERLdvfRHflqpAGIEPKRRRTVELTLMILQLVASGRGVAALPNWA 153

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2473439716 247 V-----QATLPAKQLSKLRMFRfDNYAAYpiRFGYQRNPYqwsiISEFIKIA 293
Cdd:cd08441   154 VreyldQGLVVARPLGEEGLWR-TLYAAV--RTEDADQPY----LQDFLELA 198
PBP2_PnbR cd08469
The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is ...
 98-148 8.39e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold; PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. 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: 176158  Cd Length: 221  Bit Score: 40.08  E-value: 8.39e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2473439716  98 VIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFpESLPD 148
Cdd:cd08469    13 VLLPALVRRLETEAPGIDLRIRPVTRLDLAEQLDLGRIDLVIGIF-EQIPP 62
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 87-148 9.59e-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: 39.53  E-value: 9.59e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2473439716  87 LRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSfpESLPD 148
Cdd:cd08413     2 LTIATTHTQARYVLPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIAT--EALDD 61
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 87-239 9.96e-04

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


Pssm-ID: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 39.48  E-value: 9.96e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  87 LRVGVSFTRSRVIMPDLISAFQEKYPNIEITI-MESSNDAMHKyLIDGEIDLAVGSFPESL--PDVELRDFYQEEIVLLI 163
Cdd:cd08427     2 LRLGAIATVLTGLLPRALARLRRRHPDLEVHIvPGLSAELLAR-VDAGELDAAIVVEPPFPlpKDLVWTPLVREPLVLIA 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2473439716 164 SKELlsgiyeegfeskiAQGN-LSALQECPFVLGNPEDIGGQIGRSMIKHSGFQPIVKAQSDNIETLLSLCVRGIGA 239
Cdd:cd08427    81 PAEL-------------AGDDpRELLATQPFIRYDRSAWGGRLVDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGV 144
PBP2_ClcR cd08485
The C-terminal substrate binding domain of LysR-type transcriptional regulator ClcR involved ...
 85-252 1.01e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator ClcR involved in the chlorocatechol catabolism, contains type 2 periplasmic binding fold; In soil bacterium Pseudomonas putida, the ortho-pathways of catechol and 3-chlorocatechol are central catabolic pathways that convert aromatic and chloroaromaric compounds to tricarboxylic acid (TCA) cycle intermediates. The 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR and an intermediate of the pathway, 2-chloromuconate, as an inducer for activation. 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: 176174 [Multi-domain]  Cd Length: 198  Bit Score: 39.68  E-value: 1.01e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  85 GILRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFpesLPdvelrdfYQEEIVL--L 162
Cdd:cd08485     1 GELRVAYFGTVVLHTLPLLLRQLLSVAPSATVSLTQMSKNRQIEALDAGTIDIGFGRF---YP-------YQEGVVVrnV 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716 163 ISKELLSGIYEEGFESKIAQGNLSALQECPFVL----GNPEDIGGQIGrsMIKHSGFQPIVKAQSDNIETLLSLCVRGIG 238
Cdd:cd08485    71 TNERLFLGAQKSRARSFGEQVHCSALRNEPLILfpreGRPSFADEVIG--VFKNARVEPKVVAIVEDVNAAMALALAGVG 148

                         170
                  ....*....|....
gi 2473439716 239 ACFCPINLVQATLP 252
Cdd:cd08485   149 VTIVPETVAMISWP 162
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 86-170 1.13e-03

The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. 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: 176123 [Multi-domain]  Cd Length: 194  Bit Score: 39.10  E-value: 1.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  86 ILRVGV--SFTrSRVIMPDLiSAFQEKYPNIEITImESSNDAMHkyLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLI 163
Cdd:cd08432     1 VLTVSVtpSFA-ARWLIPRL-ARFQARHPDIDLRL-STSDRLVD--FAREGIDLAIRYGDGDWPGLEAERLMDEELVPVC 75


                  ....*..
gi 2473439716 164 SKELLSG 170
Cdd:cd08432    76 SPALLAG 82
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
 87-146 1.43e-03

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


Pssm-ID: 176135  Cd Length: 198  Bit Score: 39.02  E-value: 1.43e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  87 LRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSfpESL 146
Cdd:cd08444     2 LTIATTHTQARYALPWVVQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIGIAT--EAL 59
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 100-162 2.18e-03

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: 176113  Cd Length: 198  Bit Score: 38.27  E-value: 2.18e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2473439716 100 MPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLL 162
Cdd:cd08421    15 LPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLETRPYRTDRLVVV 77
PBP2_DntR_like_4 cd08463
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 98-165 2.43e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. 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: 176152 [Multi-domain]  Cd Length: 203  Bit Score: 38.45  E-value: 2.43e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716  98 VIMPDLISAFQEKYPNIEITI--MESSNDAMHKyLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLISK 165
Cdd:cd08463    13 LFLPELVARFRREAPGARLEIhpLGPDFDYERA-LASGELDLVIGNWPEPPEHLHLSPLFSDEIVCLMRA 81
PBP2_LeuO cd08466
The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an ...
 112-166 2.74e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold; LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse model of Salmonella. In Vibrio cholerae, LeuO is involved in control of biofilm formation and in the stringent response. 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: 176155 [Multi-domain]  Cd Length: 200  Bit Score: 38.00  E-value: 2.74e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2473439716 112 PNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLISKE 166
Cdd:cd08466    27 PNISLRESPSSEEDLFEDLRLQEVDLVIDYVPFRDPSFKSELLFEDELVCVARKD 81
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 87-163 6.37e-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: 37.08  E-value: 6.37e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2473439716  87 LRVGVSFTRSRVIMPDLISAFQEKYPNIEITIMESSNDAMHKYLIDGEIDLAVGSFPESLPDVELRDFYQEEIVLLI 163
Cdd:cd08457     2 LRIAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIETRSLPAVVAV 78
HTH_MARR smart00347
helix_turn_helix multiple antibiotic resistance protein;
12-84 7.66e-03

helix_turn_helix multiple antibiotic resistance protein;


Pssm-ID: 197670 [Multi-domain]  Cd Length: 101  Bit Score: 35.26  E-value: 7.66e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2473439716   12 SFTKAAEQLHITQQTLSAHIssveKELECQLLIRRVP---------LELTYAGEVFLRYALgfQQSHQAMKKEFCDITAN 82
Cdd:smart00347  26 SVSELAKRLGVSPSTVTRVL----DRLEKKGLVRREPspedrrsvlVSLTEEGRELIEQLL--EARSETLAELLAGLTAE 99


                   ..
gi 2473439716   83 QK 84
Cdd:smart00347 100 EQ 101
 
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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