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Conserved domains on  [gi|504531872|ref|WP_014718974|]
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MULTISPECIES: LysR substrate-binding domain-containing protein [Pseudomonas]

Protein Classification

type 2 periplasmic-binding domain-containing protein( domain architecture ID 229383)

type 2 periplasmic-binding protein (PBP2) is typically comprised of two globular subdomains connected by a flexible hinge; it binds its ligand in the cleft between these domains in a manner resembling a Venus flytrap; similar to the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Periplasmic_Binding_Protein_Type_2 super family cl21456
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
 7-285 4.07e-130

Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1 (PBP1), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The origin of PBP module can be traced across the distant phyla, including eukaryotes, archebacteria, and prokaryotes. The majority of PBP2 proteins are involved in the uptake of a variety of soluble substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. 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 family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. The substrate binding domain of the LysR transcriptional regulators and the oligopeptide-like transport systems also contain the type 2 periplasmic binding fold and thus they are significantly homologous to that of the PBP2; however, these two families are grouped into a separate hierarchy of the PBP2 superfamily due to the large number of protein sequences.


The actual alignment was detected with superfamily member TIGR03339:

Pssm-ID: 473866 [Multi-domain]  Cd Length: 279  Bit Score: 370.99  E-value: 4.07e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872    7 QLKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLGITQRLFVIEAEAEELLQD 86
Cdd:TIGR03339   1 QLKAFHAVARCGSFTRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRLELTDAGHRLLPIVERLFQQEAEAEFLLRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   87 SRALLTGTLTLAVDAPVHVLPQIARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLA 166
Cdd:TIGR03339  81 SGALREGSLRIAATAPYYVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVSSEVVDDPRLDRVVLGNDPLVA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  167 FVARDHAWAGRESICLADLDNTPLVLRETGSVTRQTLEQEMRQAGLRIRPAIQVEGREAAREAVVVGIGVGVVSAAEFGA 246
Cdd:TIGR03339 161 VVHRQHPLAERESVTLEELAGQPLLMREPGSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAGLGVSVVSAAEVGR 240

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 504531872  247 DARVYAMPIRDCTQRMKETLVCLKEQSSRRVVATFLEIV 285
Cdd:TIGR03339 241 DPRLRVLPIVGAEPTMDEYLYCLKERRGARLIAAFLELA 279
 
Name Accession Description Interval E-value
phn_lysR TIGR03339
aminoethylphosphonate catabolism associated LysR family transcriptional regulator; This group ...
 7-285 4.07e-130

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


Pssm-ID: 132382 [Multi-domain]  Cd Length: 279  Bit Score: 370.99  E-value: 4.07e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872    7 QLKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLGITQRLFVIEAEAEELLQD 86
Cdd:TIGR03339   1 QLKAFHAVARCGSFTRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRLELTDAGHRLLPIVERLFQQEAEAEFLLRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   87 SRALLTGTLTLAVDAPVHVLPQIARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLA 166
Cdd:TIGR03339  81 SGALREGSLRIAATAPYYVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVSSEVVDDPRLDRVVLGNDPLVA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  167 FVARDHAWAGRESICLADLDNTPLVLRETGSVTRQTLEQEMRQAGLRIRPAIQVEGREAAREAVVVGIGVGVVSAAEFGA 246
Cdd:TIGR03339 161 VVHRQHPLAERESVTLEELAGQPLLMREPGSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAGLGVSVVSAAEVGR 240

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 504531872  247 DARVYAMPIRDCTQRMKETLVCLKEQSSRRVVATFLEIV 285
Cdd:TIGR03339 241 DPRLRVLPIVGAEPTMDEYLYCLKERRGARLIAAFLELA 279
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-181 2.76e-49

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 163.88  E-value: 2.76e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   7 QLKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLGITQRLFVIEAEAEELLQD 86
Cdd:COG0583    5 QLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRA 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  87 SRALLTGTLTLAVD---APVHVLPQIARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQ 163
Cdd:COG0583   85 LRGGPRGTLRIGAPpslARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPLGEER 164

                        170
                 ....*....|....*...
gi 504531872 164 LLAFVARDHAWAGRESIC 181
Cdd:COG0583  165 LVLVASPDHPLARRAPLV 182
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 7-215 1.36e-42

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: 148.15  E-value: 1.36e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   7 QLKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLGITQRLFVIEAEAEELLQD 86
Cdd:NF040786   5 QLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDR 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  87 SRALLTGTLTLAVDA-P-VHVLPQI-ARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQ 163
Cdd:NF040786  85 YGKESKGVLRIGASTiPgQYLLPELlKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPFYKDR 164

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 504531872 164 LLAFVARDHAWAGR--ESICLADLDNTPLVLRETGSVTRQTLEQEMRQAGLRIR 215
Cdd:NF040786 165 LVLITPNGTEKYRMlkEEISISELQKEPFIMREEGSGTRKEAEKALKSLGISLE 218
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 104-229 3.48e-32

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: 117.98  E-value: 3.48e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 104 HVLPQ-IARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAFVARDHAWAGRESICL 182
Cdd:cd08420   13 YLLPRlLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDHPLAGRKEVTA 92

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 504531872 183 ADLDNTPLVLRETGSVTRQTLEQEMRQAGL---RIRPAIQVEGREAAREA 229
Cdd:cd08420   93 EELAAEPWILREPGSGTREVFERALAEAGLdglDLNIVMELGSTEAIKEA 142
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 11-221 3.04e-31

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 118.14  E-value: 3.04e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  11 FHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLGITQRLFVIEAEAEELLQDSRAL 90
Cdd:PRK11242   9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVADL 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  91 LTGTLTLAVD---APVHVLPQIARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAF 167
Cdd:PRK11242  89 SRGSLRLAMTptfTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQPLFTETLALV 168

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 504531872 168 VARDHAWAGRES-ICLADLDNTPLVLRETGSVTRQTLEQEMRQAGlrIRPAIQVE 221
Cdd:PRK11242 169 VGRHHPLAARRKaLTLDELADEPLVLLSAEFATREQIDRYFRRHG--VTPRVAIE 221
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 92-289 4.65e-31

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: 115.08  E-value: 4.65e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   92 TGTLTLAVD---APVHVLPQIARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAFV 168
Cdd:pfam03466   1 SGRLRIGAPptlASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  169 ARDHAWAGRESICLADLDNTPLVLRETGSVTRQTLEQEMRQAGLRIRPAIQVEGREAAREAVVVGI---GVGVVSAAEFG 245
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLgiaLLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 504531872  246 ADARVYAMPIRDCTQRMKETLVCLKEQSSRRVVATFLEIVRESL 289
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREAL 204
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 8-211 1.30e-13

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 69.77  E-value: 1.30e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   8 LKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLGITQRLFVIEAEAEELL--- 84
Cdd:NF041036   6 LKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMDELksf 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  85 -QDSRALLTGTLTLAVdapVHvLPQI-ARFCQRYPGI-SVKIETGNTDESLSRLYNYQADLALLGRDVDDP--RLLSLPL 159
Cdd:NF041036  86 kGRQRLSICCTPTFGM---AH-LPGVlNRFMLRNADVvDLKFLFHSPAQALEGIQNKEFDLAIIEHCADLDlgRFHTYPL 161

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 504531872 160 PDDQLLaFVARDHAWAGRESICLADLDNTPLVLRETGSVTRQTLEQEMRQAG 211
Cdd:NF041036 162 PQDELV-FVSAPSLGLPTPNVTLERLLELCLITRRDGCSSRDLLRRNLAEQG 212
 
Name Accession Description Interval E-value
phn_lysR TIGR03339
aminoethylphosphonate catabolism associated LysR family transcriptional regulator; This group ...
 7-285 4.07e-130

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


Pssm-ID: 132382 [Multi-domain]  Cd Length: 279  Bit Score: 370.99  E-value: 4.07e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872    7 QLKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLGITQRLFVIEAEAEELLQD 86
Cdd:TIGR03339   1 QLKAFHAVARCGSFTRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRLELTDAGHRLLPIVERLFQQEAEAEFLLRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   87 SRALLTGTLTLAVDAPVHVLPQIARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLA 166
Cdd:TIGR03339  81 SGALREGSLRIAATAPYYVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVSSEVVDDPRLDRVVLGNDPLVA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  167 FVARDHAWAGRESICLADLDNTPLVLRETGSVTRQTLEQEMRQAGLRIRPAIQVEGREAAREAVVVGIGVGVVSAAEFGA 246
Cdd:TIGR03339 161 VVHRQHPLAERESVTLEELAGQPLLMREPGSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAGLGVSVVSAAEVGR 240

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 504531872  247 DARVYAMPIRDCTQRMKETLVCLKEQSSRRVVATFLEIV 285
Cdd:TIGR03339 241 DPRLRVLPIVGAEPTMDEYLYCLKERRGARLIAAFLELA 279
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-181 2.76e-49

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 163.88  E-value: 2.76e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   7 QLKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLGITQRLFVIEAEAEELLQD 86
Cdd:COG0583    5 QLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEAELRA 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  87 SRALLTGTLTLAVD---APVHVLPQIARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQ 163
Cdd:COG0583   85 LRGGPRGTLRIGAPpslARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPLGEER 164

                        170
                 ....*....|....*...
gi 504531872 164 LLAFVARDHAWAGRESIC 181
Cdd:COG0583  165 LVLVASPDHPLARRAPLV 182
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 7-215 1.36e-42

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: 148.15  E-value: 1.36e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   7 QLKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLGITQRLFVIEAEAEELLQD 86
Cdd:NF040786   5 QLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDR 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  87 SRALLTGTLTLAVDA-P-VHVLPQI-ARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQ 163
Cdd:NF040786  85 YGKESKGVLRIGASTiPgQYLLPELlKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPFYKDR 164

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 504531872 164 LLAFVARDHAWAGR--ESICLADLDNTPLVLRETGSVTRQTLEQEMRQAGLRIR 215
Cdd:NF040786 165 LVLITPNGTEKYRMlkEEISISELQKEPFIMREEGSGTRKEAEKALKSLGISLE 218
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 104-229 3.48e-32

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: 117.98  E-value: 3.48e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 104 HVLPQ-IARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAFVARDHAWAGRESICL 182
Cdd:cd08420   13 YLLPRlLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDHPLAGRKEVTA 92

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 504531872 183 ADLDNTPLVLRETGSVTRQTLEQEMRQAGL---RIRPAIQVEGREAAREA 229
Cdd:cd08420   93 EELAAEPWILREPGSGTREVFERALAEAGLdglDLNIVMELGSTEAIKEA 142
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 11-221 3.04e-31

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 118.14  E-value: 3.04e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  11 FHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLGITQRLFVIEAEAEELLQDSRAL 90
Cdd:PRK11242   9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHDVADL 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  91 LTGTLTLAVD---APVHVLPQIARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAF 167
Cdd:PRK11242  89 SRGSLRLAMTptfTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQPLFTETLALV 168

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 504531872 168 VARDHAWAGRES-ICLADLDNTPLVLRETGSVTRQTLEQEMRQAGlrIRPAIQVE 221
Cdd:PRK11242 169 VGRHHPLAARRKaLTLDELADEPLVLLSAEFATREQIDRYFRRHG--VTPRVAIE 221
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 92-289 4.65e-31

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: 115.08  E-value: 4.65e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   92 TGTLTLAVD---APVHVLPQIARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAFV 168
Cdd:pfam03466   1 SGRLRIGAPptlASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  169 ARDHAWAGRESICLADLDNTPLVLRETGSVTRQTLEQEMRQAGLRIRPAIQVEGREAAREAVVVGI---GVGVVSAAEFG 245
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLgiaLLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 504531872  246 ADARVYAMPIRDCTQRMKETLVCLKEQSSRRVVATFLEIVRESL 289
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREAL 204
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 94-285 5.87e-31

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: 114.62  E-value: 5.87e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  94 TLTLAVDAPV--HVLPQ-IARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAFVAR 170
Cdd:cd05466    1 TLRIGASPSIaaYLLPPlLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 171 DHAWAGRESICLADLDNTPLVLRETGSVTRQTLEQEMRQAGLRIRPAIQVEGREAAREAVVVGI--GVGVVSAAEFGADA 248
Cdd:cd05466   81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLgiALLPESAVEELADG 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 504531872 249 RVYAMPIRDCTQRMKETLVCLKEQSSRRVVATFLEIV 285
Cdd:cd05466  161 GLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
rbcR CHL00180
LysR transcriptional regulator; Provisional
 7-212 9.10e-29

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 111.65  E-value: 9.10e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   7 QLKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLGITQRLFVIEAEAEELLQD 86
Cdd:CHL00180   9 QLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRALED 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  87 SRALLTGTLTLAVDAPV--HVLPQ-IARFCQRYPGISVKIETgNTDESLS-RLYNYQADLALLGRDVDDP--RLLSL-PL 159
Cdd:CHL00180  89 LKNLQRGTLIIGASQTTgtYLMPRlIGLFRQRYPQINVQLQV-HSTRRIAwNVANGQIDIAIVGGEVPTElkKILEItPY 167

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 504531872 160 PDDQLLAFVARDHAWAGRESICLADLDNTPLVLRETGSVTRQTLEQEMRQAGL 212
Cdd:CHL00180 168 VEDELALIIPKSHPFAKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGI 220
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
6-173 4.45e-25

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 102.00  E-value: 4.45e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   6 AQLKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLGITQRLFviEAEAEELLQ 85
Cdd:PRK10086  17 SKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSL--DTLNQEILD 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  86 DSRALLTGTLTLAVD---APVHVLPQIARFCQRYPGISVKIETGNTDESLSRlynYQADLALLGRDVDDPRLLSLPLPDD 162
Cdd:PRK10086  95 IKNQELSGTLTVYSRpsiAQCWLVPRLADFTRRYPSISLTILTGNENVNFQR---AGIDLAIYFDDAPSAQLTHHFLMDE 171

                        170
                 ....*....|.
gi 504531872 163 QLLAFVARDHA 173
Cdd:PRK10086 172 EILPVCSPEYA 182
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 94-229 8.15e-25

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: 98.35  E-value: 8.15e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  94 TLTLAVDAPVH-VLPQ-IARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAFVARD 171
Cdd:cd08419    1 RLRLAVVSTAKyFAPRlLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGRPPEDLDLVAEPFLDNPLVVIAPPD 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 504531872 172 HAWAGRESICLADLDNTPLVLRETGSVTRQTLEQEMRQAGLRIRPAIQVEGREAAREA 229
Cdd:cd08419   81 HPLAGQKRIPLERLAREPFLLREPGSGTRLAMERFFAEHGVTLRVRMELGSNEAIKQA 138
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 8-134 1.05e-24

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 100.69  E-value: 1.05e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   8 LKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGER-LLGITQRLFVIeAEAEELLQD 86
Cdd:PRK11139  11 LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRyFLDIREIFDQL-AEATRKLRA 89

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 504531872  87 SRAllTGTLTlaVDAPVH-----VLPQIARFCQRYPGISVKIETGNTDESLSR 134
Cdd:PRK11139  90 RSA--KGALT--VSLLPSfaiqwLVPRLSSFNEAHPDIDVRLKAVDRLEDFLR 138
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 7-213 3.15e-22

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 93.90  E-value: 3.15e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   7 QLKAFHAVAIHG-SFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRN-KRSVRLTDLGERLLGITQRLFV----IEAEA 80
Cdd:PRK12682   5 QLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHgKRLKGLTEPGKAVLDVIERILRevgnIKRIG 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  81 EELL-QDSralltGTLTLAVdapVH-----VLPQ-IARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDV-DDP 152
Cdd:PRK12682  85 DDFSnQDS-----GTLTIAT---THtqaryVLPRvVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATESLaDDP 156

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 504531872 153 RLLSLPLPDDQLLAFVARDHAWAGRESICLADLDNTPLVLRETGSVTRQTLEQEMRQAGLR 213
Cdd:PRK12682 157 DLATLPCYDWQHAVIVPPDHPLAQEERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQ 217
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-64 1.66e-21

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 85.51  E-value: 1.66e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 504531872    7 QLKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGE 64
Cdd:pfam00126   3 QLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 1-204 3.76e-21

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 90.90  E-value: 3.76e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   1 MSVSHAQLKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLGITQRLFVIEAEA 80
Cdd:PRK10837   1 MHITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  81 EELLQDSrallTGTLTLAVDAPV--HVLPQ-IARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSL 157
Cdd:PRK10837  81 EQLFRED----NGALRIYASSTIgnYILPAmIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPELISE 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 504531872 158 PLPDDQLLAFVARDHAWAGREsICLADLDNTPLVLRETGSVTRQTLE 204
Cdd:PRK10837 157 PWLEDELVVFAAPDSPLARGP-VTLEQLAAAPWILRERGSGTREIVD 202
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 104-221 5.35e-21

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: 88.35  E-value: 5.35e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 104 HVLPQ-IARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAFVARDHAWAGRESICL 182
Cdd:cd08440   13 TLLPPvLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPKDHPLARRRSVTW 92

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 504531872 183 ADLDNTPLVLRETGSVTRQTLEQEMRQAGLRIRPAIQVE 221
Cdd:cd08440   93 AELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVS 131
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
33-225 2.77e-19

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 85.26  E-value: 2.77e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  33 AISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLGITQRlfvIEAEAEEL---LQDSRALLTGTLTL--AVDAPVHVLP 107
Cdd:PRK11716   7 TLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQ---TLLQWQQLrhtLDQQGPSLSGELSLfcSVTAAYSHLP 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 108 QI-ARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAFVARDHA-----WAGRESIc 181
Cdd:PRK11716  84 PIlDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETLPASVAFSPIDEIPLVLIAPALPcpvrqQLSQEKP- 162

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 504531872 182 laDLDNTPLVLRETGsVTRQTLEQEMRQagLRIRPAI--QVEGREA 225
Cdd:PRK11716 163 --DWSRIPFILPEHG-PARRRIDLWFRR--HKIKPNIyaTVSGHEA 203
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-187 3.05e-18

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 82.90  E-value: 3.05e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   1 MSVSHaqLKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLGiTQRLFVIEAE- 79
Cdd:PRK09906   1 MELRH--LRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQ-DARAILEQAEk 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  80 ----AEELLQDSRALLTGTLTLavdAPVHVLPQ-IARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRL 154
Cdd:PRK09906  78 aklrARKIVQEDRQLTIGFVPS---AEVNLLPKvLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEI 154

                        170       180       190
                 ....*....|....*....|....*....|...
gi 504531872 155 LSLPLPDDQLLAFVARDHAWAGRESICLADLDN 187
Cdd:PRK09906 155 DYLELLDEPLVVVLPVDHPLAHEKEITAAQLDG 187
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
7-212 6.93e-18

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 81.95  E-value: 6.93e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   7 QLKAFHAVAIHG-SFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRN-KRSVRLTDLGERLLGITQRlfvIEAEAEELL 84
Cdd:PRK12684   5 QLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHgKRLRGLTEPGRIILASVER---ILQEVENLK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  85 Q---DSRALLTGTLTLAVdapVH-----VLPQ-IARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDD-PRL 154
Cdd:PRK12684  82 RvgkEFAAQDQGNLTIAT---THtqaryALPAaIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATEAIADyKEL 158

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 504531872 155 LSLPLPDDQLLAFVARDHAWAGRESICLADLDNTPLVLRETGSVTRQTLEQEMRQAGL 212
Cdd:PRK12684 159 VSLPCYQWNHCVVVPPDHPLLERKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGL 216
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
5-117 4.07e-17

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 79.43  E-value: 4.07e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   5 HAQLKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNkRSVRLTDLGERLLGITQRLFVIEAEAEELL 84
Cdd:PRK03635   4 YKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQRLLRHARQVRLLEAELLGEL 82

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 504531872  85 QDSRALLTgTLTLAVDA---PVHVLPQIARFCQRYP 117
Cdd:PRK03635  83 PALDGTPL-TLSIAVNAdslATWFLPALAPVLARSG 117
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
6-101 7.72e-16

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 76.16  E-value: 7.72e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   6 AQLKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNkRSVRLTDLGERLLGITQRLFVIEAEAEELLQ 85
Cdd:PRK13348   5 KQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHLRQVALLEADLLSTLP 83

                         90
                 ....*....|....*.
gi 504531872  86 DSRALLTgTLTLAVDA 101
Cdd:PRK13348  84 AERGSPP-TLAIAVNA 98
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 103-224 1.19e-15

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: 73.72  E-value: 1.19e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 103 VHVLPQ-IARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAFVARDHAWAGRESIC 181
Cdd:cd08434   12 TSLVPDlIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPKDHPLAGRDSVD 91

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 504531872 182 LADLDNTPLVLRETGSVTRQTLEQEMRQAGlrIRPAIQVEGRE 224
Cdd:cd08434   92 LAELADEPFVLLSPGFGLRPIVDELCAAAG--FTPKIAFEGEE 132
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 21-212 1.46e-15

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 75.46  E-value: 1.46e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  21 TGAAERLFLTQPAISDQVRKLEERFGVLLFHR-NKRSVRLTDLGERLLGITQRLFVieaEAEELLQDSRALL---TGTLT 96
Cdd:PRK12683  20 TEVANALYTSQSGVSKQIKDLEDELGVEIFIRrGKRLTGLTEPGKELLQIVERMLL---DAENLRRLAEQFAdrdSGHLT 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  97 LAVdapVH-----VLPQIAR-FCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDD-PRLLSLPLPDDQLLAFVA 169
Cdd:PRK12683  97 VAT---THtqaryALPKVVRqFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALDRePDLVSFPYYSWHHVVVVP 173

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 504531872 170 RDHAWAGRESICLADLDNTPLVLRETGSVTRQTLEQEMRQAGL 212
Cdd:PRK12683 174 KGHPLTGRENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGL 216
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 105-220 1.50e-15

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: 73.36  E-value: 1.50e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 105 VLPQ-IARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAFVARDHAWAGRESICLA 183
Cdd:cd08415   14 LLPRaIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLPPGHPLARKDVVTPA 93

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 504531872 184 DLDNTPLVLRETGSVTRQTLEQEMRQAGLRIRPAIQV 220
Cdd:cd08415   94 DLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIET 130
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 96-220 7.59e-15

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: 71.48  E-value: 7.59e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  96 TLAVDAPVHVLPQIARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPR-LLSLPLPDDQLLAFVARDHAW 174
Cdd:cd08436    6 TITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRPPgLASRELAREPLVAVVAPDHPL 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 504531872 175 AGRESICLADLDNTPLVLRETGSVTRQTLEQEMRQAGLRIRPAIQV 220
Cdd:cd08436   86 AGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEV 131
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 105-226 8.83e-15

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: 71.38  E-value: 8.83e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 105 VLPQ-IARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAFVARDHAWAGRESICLA 183
Cdd:cd08414   14 LLPRlLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALPADHPLAARESVSLA 93

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 504531872 184 DLDNTPLVL--RETGSVTRQTLEQEMRQAGLRIRPAIQVEGREAA 226
Cdd:cd08414   94 DLADEPFVLfpREPGPGLYDQILALCRRAGFTPRIVQEASDLQTL 138
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 13-203 1.29e-14

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 72.75  E-value: 1.29e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  13 AVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGerLLGITQ-RLFVIEAeaeELLQDSRALL 91
Cdd:PRK11151  11 ALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAG--LLLVDQaRTVLREV---KVLKEMASQQ 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  92 TGTLTlavdAPVHV----------LPQI-ARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLP 160
Cdd:PRK11151  86 GETMS----GPLHIgliptvgpylLPHIiPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFIEVPLF 161

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 504531872 161 DDQLLAFVARDHAWAGRESICLADLDNTPLVLRETGSVTR-QTL 203
Cdd:PRK11151 162 DEPMLLAVYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRdQAM 205
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 93-221 2.83e-14

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: 69.99  E-value: 2.83e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  93 GTLTLAVDapvHVLPQ-IARFCQRYPGISVKIETGNTDESLSRLYNYQADLAL--LGRDVDDPRLLSLPLPDDQLLAFVA 169
Cdd:cd08435    5 GAVPAAAP---VLLPPaIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIgrLADDEQPPDLASEELADEPLVVVAR 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 504531872 170 RDHAWAGRESICLADLDNTPLVLRETGSVTRQTLEQEMRQAGLRiRPAIQVE 221
Cdd:cd08435   82 PGHPLARRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLP-LPRNVVE 132
PRK09791 PRK09791
LysR family transcriptional regulator;
7-126 6.60e-14

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 70.56  E-value: 6.60e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   7 QLKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLgitQRLFVIEAE---AEEL 83
Cdd:PRK09791   9 QIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFY---QHASLILEElraAQED 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 504531872  84 LQDSRALLTGTLTLAVDAPV--HVLPQ-IARFCQRYPGISVKIETG 126
Cdd:PRK09791  86 IRQRQGQLAGQINIGMGASIarSLMPAvISRFHQQHPQVKVRIMEG 131
cysB PRK12681
HTH-type transcriptional regulator CysB;
7-212 1.14e-13

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 69.93  E-value: 1.14e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   7 QLKAFHAVAIHG-SFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRN-KRSVRLTDLGERLLGITQRLFV----IEAEA 80
Cdd:PRK12681   5 QLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSgKHLTQVTPAGEEIIRIAREILSkvesIKSVA 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  81 EELLQDSRalltGTLTLAVdapVH-----VLPQ-IARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRdvddprl 154
Cdd:PRK12681  85 GEHTWPDK----GSLYIAT---THtqaryALPPvIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAIATE------- 150

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 504531872 155 lSLPLPDDQLL---------AFVARDHAWAGRESICLADLDNTPLVLRETGSVTRQTLEQEMRQAGL 212
Cdd:PRK12681 151 -ALHLYDDLIMlpcyhwnrsVVVPPDHPLAKKKKLTIEELAQYPLVTYVFGFTGRSELDTAFNRAGL 216
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 8-211 1.30e-13

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 69.77  E-value: 1.30e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   8 LKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLGITQRLFVIEAEAEELL--- 84
Cdd:NF041036   6 LKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMDELksf 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  85 -QDSRALLTGTLTLAVdapVHvLPQI-ARFCQRYPGI-SVKIETGNTDESLSRLYNYQADLALLGRDVDDP--RLLSLPL 159
Cdd:NF041036  86 kGRQRLSICCTPTFGM---AH-LPGVlNRFMLRNADVvDLKFLFHSPAQALEGIQNKEFDLAIIEHCADLDlgRFHTYPL 161

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 504531872 160 PDDQLLaFVARDHAWAGRESICLADLDNTPLVLRETGSVTRQTLEQEMRQAG 211
Cdd:NF041036 162 PQDELV-FVSAPSLGLPTPNVTLERLLELCLITRRDGCSSRDLLRRNLAEQG 212
PRK09986 PRK09986
LysR family transcriptional regulator;
8-191 2.18e-13

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 68.98  E-value: 2.18e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   8 LKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLGITQRLFvieAEAEELLQDS 87
Cdd:PRK09986  12 LRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLL---DNAEQSLARV 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  88 RALLTGTLTLAVDAPV------HVLPQIARFCQRYPgisvkietgNTDESLSRLYNYQADLALLGRDVD----------- 150
Cdd:PRK09986  89 EQIGRGEAGRIEIGIVgtalwgRLRPAMRHFLKENP---------NVEWLLRELSPSMQMAALERRELDagiwrmadlep 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 504531872 151 DPRLLSLPLPDDQLLAFVARDHAWAGRESICLADLDNTPLV 191
Cdd:PRK09986 160 NPGFTSRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFI 200
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 107-227 2.39e-13

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: 67.16  E-value: 2.39e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 107 PQIARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAFVARDHAWAGRESICLADLD 186
Cdd:cd08421   17 EDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLETRPYRTDRLVVVVPRDHPLAGRASVAFADTL 96

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 504531872 187 NTPLV-LRETGSVTRQtLEQEMRQAGLRIRPAIQVEGREAAR 227
Cdd:cd08421   97 DHDFVgLPAGSALHTF-LREAAARLGRRLRLRVQVSSFDAVC 137
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
8-85 1.80e-12

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 66.37  E-value: 1.80e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504531872   8 LKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLG-ITQRLFVIEAEAEELLQ 85
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSqARDWLSWLESMPSELQQ 85
PRK12680 PRK12680
LysR family transcriptional regulator;
21-218 1.81e-12

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 66.57  E-value: 1.81e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  21 TGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVR-LTDLGERLLGITQRLFV----IEAEAEELLQDSRALLTGTl 95
Cdd:PRK12680  20 TLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSeannIRTYAANQRRESQGQLTLT- 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  96 TLAVDAPVHVLPQIARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRL-LSLPLPDDQLLAFVARDHAW 174
Cdd:PRK12680  99 TTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAgIAVPLYRWRRLVVVPRGHAL 178

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 504531872 175 -AGRESICLADLDNTPLVLRETGSVTRQTLEQEMRQAGLRIRPAI 218
Cdd:PRK12680 179 dTPRRAPDMAALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIAL 223
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 109-215 1.32e-11

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: 62.19  E-value: 1.32e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 109 IARFCQRYPGISVKI--ETGNTDESLsrLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAFVARDHAWAGRESICLADLD 186
Cdd:cd08438   19 LAAFRQRYPNIELELveYGGKKVEQA--VLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPRGHPLAGRKTVSLADLA 96

                         90       100
                 ....*....|....*....|....*....
gi 504531872 187 NTPLVLRETGSVTRQTLEQEMRQAGLRIR 215
Cdd:cd08438   97 DEPFILFNEDFALHDRIIDACQQAGFTPN 125
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 13-123 1.53e-11

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 63.81  E-value: 1.53e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  13 AVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGErllgitqrLFVIEAEA-----EELLQDS 87
Cdd:PRK11074  12 AVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGE--------WFVKEARSvikkmQETRRQC 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 504531872  88 RALLTG---TLTLAVDAPV---HVLPQIARFCQRYPGISVKI 123
Cdd:PRK11074  84 QQVANGwrgQLSIAVDNIVrpdRTRQLIVDFYRHFDDVELII 125
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 104-196 2.06e-11

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: 61.77  E-value: 2.06e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 104 HVLPQIArfcQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAFVARDHAWAGRESICLA 183
Cdd:cd08411   18 RLLPALR---QAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAVPKDHPLAKRKSVTPE 94

                         90
                 ....*....|...
gi 504531872 184 DLDNTPLVLRETG 196
Cdd:cd08411   95 DLAGERLLLLEEG 107
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 101-222 2.22e-11

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: 61.84  E-value: 2.22e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 101 APVHVLPQIARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAFVARDHAWAGRESI 180
Cdd:cd08433   11 ASVLAVPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGPADAPLPRGAPV 90

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 504531872 181 CLADLDNTPLVLRETGSVTRQTLEQEMRQAGLRIRPAIQVEG 222
Cdd:cd08433   91 PLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDS 132
cbl PRK12679
HTH-type transcriptional regulator Cbl;
7-212 3.77e-11

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 62.52  E-value: 3.77e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   7 QLKAFHAVA-IHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLF-HRNKRSVRLTDLGERLLGITQRLFViEAE----- 79
Cdd:PRK12679   5 QLKIIREAArQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFiRRGKRLLGMTEPGKALLVIAERILN-EASnvrrl 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  80 AEELLQDSRALLTgTLTLAVDAPVHVLPQIARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLG-RDVDDPRLLSLP 158
Cdd:PRK12679  84 ADLFTNDTSGVLT-IATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASeRLSNDPQLVAFP 162

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 504531872 159 LPDDQLLAFVARDHAWAGRESICLADLDNTPLVLRETGSVTRQTLEQEMRQAGL 212
Cdd:PRK12679 163 WFRWHHSLLVPHDHPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGL 216
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
7-192 6.86e-11

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 61.96  E-value: 6.86e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   7 QLKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLGITQRLFVIEAEAeelLQD 86
Cdd:PRK15421   6 HLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQA---LQA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  87 SRALLTGTLTLAVDAPVHV---LPQIARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQ 163
Cdd:PRK15421  83 CNEPQQTRLRIAIECHSCIqwlTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYE 162

                        170       180
                 ....*....|....*....|....*....
gi 504531872 164 LLAFVARDHAWAGRESICLADLDNTPLVL 192
Cdd:PRK15421 163 VRLVLAPDHPLAAKTRITPEDLASETLLI 191
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 8-229 9.65e-11

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 61.20  E-value: 9.65e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   8 LKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLGITQRLFVIEAEAEELLQDS 87
Cdd:PRK15092  16 LRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACSSLMYS 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  88 RalLTGTLTLAV--DAPVHVLPQI-ARFCQRYPGISVKIETGNTDESLSRLYNYQADLAL-LGRDVDDPRLLslpLPDDQ 163
Cdd:PRK15092  96 N--LQGVLTIGAsdDTADTILPFLlNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVtTHRPSSFPALN---LRTSP 170

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 504531872 164 LLAFVARDHAWAGRESIcladldntPLVLRETGSVTRQTLEQEMRQAGLRIRPAIQVEGREAAREA 229
Cdd:PRK15092 171 TLWYCAAEYVLQKGEPI--------PLVLLDEPSPFRDMALATLNAAGIPWRIAYVASTLSAVRAA 228
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 11-127 1.20e-10

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 61.16  E-value: 1.20e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  11 FHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLGITQRLFVIEAEAEELLQDSRAL 90
Cdd:PRK14997  10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVE 89

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 504531872  91 LTGTLTLAVDAP---VHVLPQIARFCQRYPGISVKIETGN 127
Cdd:PRK14997  90 PRGIVKLTCPVTllhVHIGPMLAKFMARYPDVSLQLEATN 129
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 1-226 1.29e-10

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 61.16  E-value: 1.29e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   1 MSVSHAQLKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLGITQRLFV----I 76
Cdd:PRK11013   2 AAVSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSYYgldrI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  77 EAEAEELlqdsRALLTGTLTLAVdAPV---HVLPQI-ARFCQRYPGISVKI---ETGNTDESLSRlynYQADLALLGRDV 149
Cdd:PRK11013  82 VSAAESL----REFRQGQLSIAC-LPVfsqSLLPGLcQPFLARYPDVSLNIvpqESPLLEEWLSA---QRHDLGLTETLH 153

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504531872 150 DDPRLLSLPLPDDQLLAFVARDHAWAGRESICLADLDNTPLV-LRETGSVtRQTLEQEMRQAGLRIRpaIQVEGREAA 226
Cdd:PRK11013 154 TPAGTERTELLTLDEVCVLPAGHPLAAKKVLTPDDFAGENFIsLSRTDSY-RQLLDQLFAEHGVKRR--MVVETHSAA 228
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 101-227 1.90e-10

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: 59.10  E-value: 1.90e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 101 APVhVLPQ-IARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAFVARDHAWAGRES 179
Cdd:cd08412   11 APY-YLPGlLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARLPPYVWLPADHPLAGKDE 89

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 504531872 180 ICLADLDNTPLVLReTGSVTRQTLEQEMRQAGLRIRPAIQVEGREAAR 227
Cdd:cd08412   90 VSLADLAAEPLILL-DLPHSREYFLSLFAAAGLTPRIAYRTSSFEAVR 136
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
 106-225 5.73e-10

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: 57.59  E-value: 5.73e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 106 LPQI-ARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDP-RLLSLPLpDDQLLAFVARDHAWAGRESICLA 183
Cdd:cd08430   15 LPPIlERFRAQHPQVEIKLHTGDPADAIDKVLNGEADIAIAARPDKLPaRLAFLPL-ATSPLVFIAPNIACAVTQQLSQG 93

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 504531872 184 DLD--NTPLVLRETGsVTRQTLEQEMRQagLRIRPAI--QVEGREA 225
Cdd:cd08430   94 EIDwsRLPFILPERG-LARERLDQWFRR--RGIKPNIyaQVAGHEA 136
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 109-228 8.65e-10

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: 57.32  E-value: 8.65e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 109 IARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAFVARDHAWAGRESICLADLDNT 188
Cdd:cd08426   19 IARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVVPPGHPLARQPSVTLAQLAGY 98

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 504531872 189 PLVLRETGSVTRQTLEQEMRQAGLRIRPAIQVEGREAARE 228
Cdd:cd08426   99 PLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQ 138
nhaR PRK11062
transcriptional activator NhaR; Provisional
 11-104 9.20e-10

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 58.48  E-value: 9.20e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  11 FHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLGITQRLFVIEAEA---------E 81
Cdd:PRK11062  12 FWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKMFTLSQEMldivnyrkeS 91

                         90       100       110
                 ....*....|....*....|....*....|..
gi 504531872  82 ELLQD-------SRALLTGTLTLAV--DAPVH 104
Cdd:PRK11062  92 NLLFDvgvadalSKRLVSRVLLTAVpeDESIH 123
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
8-67 1.41e-09

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 57.72  E-value: 1.41e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   8 LKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLL 67
Cdd:PRK03601   6 LKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLL 65
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 107-226 2.83e-09

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: 55.68  E-value: 2.83e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 107 PQIARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDV-----DDPRLLSLPLPDDQLLAFVARDHAWAGRESIC 181
Cdd:cd08423   17 PALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFDYPvtpppDDPGLTRVPLLDDPLDLVLPADHPLAGREEVA 96

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 504531872 182 LADLDNTPLVLRETGSVTRQTLEQEMRQAGLRIRPAIQVEGREAA 226
Cdd:cd08423   97 LADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATV 141
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 93-221 2.87e-09

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: 55.80  E-value: 2.87e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  93 GTLTLAVD---APVHVLPQIARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAFVA 169
Cdd:cd08425    1 GSLRLAMTptfTAYLIGPLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDAQPLFDERLALVVG 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 504531872 170 RDHAWAGRE-SICLADLDNTPLVLRETGSVTRQTLEQEMRQAGlrIRPAIQVE 221
Cdd:cd08425   81 ATHPLAQRRtALTLDDLAAEPLALLSPDFATRQHIDRYFQKQG--IKPRIAIE 131
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 8-221 4.37e-09

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 56.23  E-value: 4.37e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   8 LKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLGITQ---------RLFVIEA 78
Cdd:PRK11233   6 LKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARailrqceqaQLAVHNV 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  79 EAEELLQDSRALLTGTLTLAVDAPvhvLPQIARfcQRYPGISVKIETgNTDESLS-RLYNYQADLALLGRDVDDPRLLSL 157
Cdd:PRK11233  86 GQALSGQVSIGLAPGTAASSLTMP---LLQAVR--AEFPGIVLYLHE-NSGATLNeKLMNGQLDMAVIYEHSPVAGLSSQ 159

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 504531872 158 PLPDDQLLAFVARDhawAGRESICLADLDNTPLVLRETGSVTRQTLEQEMRQAGLRIRPAIQVE 221
Cdd:PRK11233 160 PLLKEDLFLVGTQD---CPGQSVDLAAVAQMNLFLPRDYSAVRLRVDEAFSLRRLTAKVIGEIE 220
PRK10341 PRK10341
transcriptional regulator TdcA;
7-221 1.51e-08

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 54.87  E-value: 1.51e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   7 QLKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLGitqRLFVIEAEAEELLQD 86
Cdd:PRK10341  11 HLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLS---RSESITREMKNMVNE 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  87 SRALLTGTLT-LAVDAP----VHVLPQ-IARFCQRYPGISVKIETGNTDESLSRLYNYQADLAlLGRDVDDPRLLSL--- 157
Cdd:PRK10341  88 INGMSSEAVVdVSFGFPsligFTFMSDmINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFA-IGTLSNEMKLQDLhve 166

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 504531872 158 PLPDDQLLAFVARDHAWAGreSICLADLDNTPLVLRETGSVTRQTLEQEMRQAGLRIRPAIQVE 221
Cdd:PRK10341 167 PLFESEFVLVASKSRTCTG--TTTLESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTD 228
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
11-126 1.79e-08

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 54.77  E-value: 1.79e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  11 FHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLGITQRLFVIEAEAEELLQDSRAL 90
Cdd:PRK10632  10 FAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAFNNT 89

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 504531872  91 LTGTLTLAVDAPV--HVL-PQIARFCQRYPGISVKIETG 126
Cdd:PRK10632  90 PIGTLRIGCSSTMaqNVLaGLTAKMLKEYPGLSVNLVTG 128
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 106-212 2.87e-08

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: 52.61  E-value: 2.87e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 106 LPQI-ARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAFVARDHAWAGResicLAD 184
Cdd:cd08442   15 LPPLlAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSPKGHPPVSR----AED 90

                         90       100
                 ....*....|....*....|....*...
gi 504531872 185 LDNTPLVLRETGSVTRQTLEQEMRQAGL 212
Cdd:cd08442   91 LAGSTLLAFRAGCSYRRRLEDWLAEEGV 118
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 104-212 3.96e-08

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: 52.24  E-value: 3.96e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 104 HVLPQ-IARFCQRYPGISVKIETGNTDESLSRLYNYQADLALL-GRDVDDPRLLSLPLPDDQLLAFVARDHAWAGRESIC 181
Cdd:cd08413   13 YVLPPvIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIAtEALDDHPDLVTLPCYRWNHCVIVPPGHPLADLGPLT 92

                         90       100       110
                 ....*....|....*....|....*....|.
gi 504531872 182 LADLDNTPLVLRETGSVTRQTLEQEMRQAGL 212
Cdd:cd08413   93 LEDLAQYPLITYDFGFTGRSSIDRAFARAGL 123
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 104-212 2.41e-07

The C-terminal substrate domain of LysR-type transcriptional regulator CysB 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.


Pssm-ID: 176134  Cd Length: 198  Bit Score: 50.25  E-value: 2.41e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 104 HVLPQ-IARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDD-PRLLSLPLPDDQLLAFVARDHAWAGRESIC 181
Cdd:cd08443   13 YVLPPvIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHDyDDLITLPCYHWNRCVVVKRDHPLADKQSIS 92

                         90       100       110
                 ....*....|....*....|....*....|.
gi 504531872 182 LADLDNTPLVLRETGSVTRQTLEQEMRQAGL 212
Cdd:cd08443   93 IEELATYPIVTYTFGFTGRSELDTAFNRAGL 123
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-191 5.50e-07

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: 49.18  E-value: 5.50e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 105 VLPQ-IARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAFVARDHAWAGRESICLA 183
Cdd:cd08447   14 FLPRlLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFARPGLETRPLVREPLVAAVPAGHPLAGAERLTLE 93


                 ....*...
gi 504531872 184 DLDNTPLV 191
Cdd:cd08447   94 DLDGQPFI 101
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 109-215 1.45e-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: 1.45e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 109 IARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPR-LLSLPLPDDQLLAFVARDHAWAGRESICLADLDN 187
Cdd:cd08451   20 IRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARSDgLVLELLLEEPMLVALPAGHPLARERSIPLAALAD 99

                         90       100       110
                 ....*....|....*....|....*....|
gi 504531872 188 TPLVL--RETGSVTRQTLEQEMRQAGLRIR 215
Cdd:cd08451  100 EPFILfpRPVGPGLYDAIIAACRRAGFTPR 129
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 107-192 1.99e-06

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: 47.27  E-value: 1.99e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 107 PQIARFCQRYPGISVKIETGNTDESLSRLYNYQADLALL--GRDVDDPRLLSLPLPDDQLLAFVARDHAWAGRESICLAD 184
Cdd:cd08449   17 PALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVrfADTLNDPPLASELLWREPMVVALPEEHPLAGRKSLTLAD 96


                 ....*...
gi 504531872 185 LDNTPLVL 192
Cdd:cd08449   97 LRDEPFVF 104
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 101-216 6.28e-06

The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold; HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. 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: 176141 [Multi-domain]  Cd Length: 196  Bit Score: 45.83  E-value: 6.28e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 101 APVHVLPQIAR-FCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAFVARDHAWAGRES 179
Cdd:cd08450   10 AEVQWLPEVLPiLREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGIDYQLLLKEPLIVVLPADHRLAGREK 89

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 504531872 180 ICLADLDNTPLVLRE-TGSVTRQTLEQEMRQAGLRIRP 216
Cdd:cd08450   90 IPPQDLAGENFISPApTAPVLQQVIENYAAQHNIQPNI 127
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 104-192 6.53e-06

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: 46.11  E-value: 6.53e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 104 HVLPQI-ARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAFVARDHAWAGRESICL 182
Cdd:cd08448   13 RGLPRIlRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAGLSARLLHREPFVCCLPAGHPLAARRRIDL 92

                         90
                 ....*....|
gi 504531872 183 ADLDNTPLVL 192
Cdd:cd08448   93 RELAGEPFVL 102
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 105-220 6.01e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 42.97  E-value: 6.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 105 VLPQI-ARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAFVARDHAWAGREsICLA 183
Cdd:cd08417   14 LLPPLlARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARKDHPLAGGP-LTLE 92

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 504531872 184 DLDNTPLVLRETGSVTRQTLEQEMRQAGLRIRPAIQV 220
Cdd:cd08417   93 DYLAAPHVLVSPRGRGHGLVDDALAELGLSRRVALTV 129
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-225 6.91e-05

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


Pssm-ID: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 42.95  E-value: 6.91e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 105 VLPQI-ARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDV--DDPRLLSLPLPDDQLLAFVARDHAWAGRESIc 181
Cdd:cd08427   14 LLPRAlARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPPfpLPKDLVWTPLVREPLVLIAPAELAGDDPREL- 92

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 504531872 182 ladLDNTPLVLRETGSVTRQTLEQEMRQAGLRIRPAIQVEGREA 225
Cdd:cd08427   93 ---LATQPFIRYDRSAWGGRLVDRFLRRQGIRVREVMELDSLEA 133
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 106-197 7.28e-05

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: 42.95  E-value: 7.28e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 106 LPQIARFCQRYPGISVKIETGNTDESLSRlynYQADLALLGRDVDDPRLLSLPLPDDQLLAFVARDHAwAGRESICLADL 185
Cdd:cd08432   16 IPRLARFQARHPDIDLRLSTSDRLVDFAR---EGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALL-AGLPLLSPADL 91

                         90
                 ....*....|..
gi 504531872 186 DNTPLvLRETGS 197
Cdd:cd08432   92 ARHTL-LHDATR 102
PBP2_NocR cd08458
The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the ...
 109-218 1.43e-04

The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the catabolism of nopaline, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator NocR, which is involved in the catabolism of nopaline. 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, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. 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: 176147  Cd Length: 196  Bit Score: 42.01  E-value: 1.43e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 109 IARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAFVARDHAWAGRESICLADLDNT 188
Cdd:cd08458   19 IQTFIADRPDVSVYLDTVPSQTVLELVSLQHYDLGISILAGDYPGLTTEPVPSFRAVCLLPPGHRLEDKETVHATDLEGE 98

                         90       100       110
                 ....*....|....*....|....*....|
gi 504531872 189 PLVLRETGSVTRQTLEQEMRQAGLRIRPAI 218
Cdd:cd08458   99 SLICLSPVSLLRMQTDAALDSCGVHCNRRI 128
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
19-171 3.73e-04

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 41.58  E-value: 3.73e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  19 SFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLG-ITQRLFVIEAEAEELLQDSR-ALLTGTLT 96
Cdd:PRK10082  27 NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSqIRHLLQQLESNLAELRGGSDyAQRKIKIA 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  97 LAVDAPVHVLPQIARfcQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDdprLLSLP-----LPDDQLLAFVARD 171
Cdd:PRK10082 107 AAHSLSLGLLPSIIS--QMPPLFTWAIEAIDVDEAVDKLREGQSDCIFSFHDED---LLEAPfdhirLFESQLFPVCASD 181
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 106-191 4.61e-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: 40.63  E-value: 4.61e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 106 LPQIARFCQRYPGISVKIETGNTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLLAFVARDHAWAGRESICLADL 185
Cdd:cd08441   16 MPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAPDHPLAAKEFITPEDL 95


                 ....*.
gi 504531872 186 DNTPLV 191
Cdd:cd08441   96 ADETLI 101
PRK09801 PRK09801
LysR family transcriptional regulator;
18-150 5.51e-04

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 40.79  E-value: 5.51e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  18 GSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLgitQRLFVIEAEAEELLQDSRALLT---GT 94
Cdd:PRK09801  21 GSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCY---EHALEILTQYQRLVDDVTQIKTrpeGM 97

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 504531872  95 LTLAVD---APVHVLPQIARFCQRYPGISVKIEtgntdeslsrLYNYQADLALLGRDVD 150
Cdd:PRK09801  98 IRIGCSfgfGRSHIAPAITELMRNYPELQVHFE----------LFDRQIDLVQDNIDLD 146
leuO PRK09508
leucine transcriptional activator; Reviewed
 8-172 1.29e-03

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 39.62  E-value: 1.29e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872   8 LKAFHAVAIHGSFTGAAERLFLTQPAISDQVRKLEERFGVLLFHRNKRSVRLTDLGERLLG-ITQRLFVIEAEAE----E 82
Cdd:PRK09508  27 LTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARARQLFGpVRQALQLVQNELPgsgfE 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  83 LLQDSRalltgTLTLAVDAPVHVL--PQI-ARFCQRYPGISVKIET---GNTDESLsrlyNYQ-ADLALLGRDVDDPRLL 155
Cdd:PRK09508 107 PESSER-----VFNLCICSPLDIRltSQIyNRIEQIAPNIHVVFKSslnQNIEHQL----RYQeTEFVISYEEFDRPEFT 177

                        170
                 ....*....|....*..
gi 504531872 156 SLPLPDDQLLAFVARDH 172
Cdd:PRK09508 178 SVPLFKDELVLVASKNH 194
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 104-221 2.83e-03

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: 38.03  E-value: 2.83e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872 104 HVLPQ-IARFCQRYPGISVKIETGNTDESL------------SRLYNYQADLALlgRDVDDPRLLslplpddqlLAfVAR 170
Cdd:cd08446   14 DTVPRlLRAFLTARPDVTVSLHNMTKDEQIealragrihigfGRFYPVEPDIAV--ENVAQERLY---------LA-VPK 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 504531872 171 DHAWAGRESICLADLDNTPLVLRETGSvtRQTLEQE----MRQAGLRIRPAIQVE 221
Cdd:cd08446   82 SHPLAARPAVSLADLRNEPLILFPRGG--RPSFADEvlglFRRAGVEPRVAQEVE 134
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 96-229 3.10e-03

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: 37.81  E-value: 3.10e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504531872  96 TLAVDAPV-----HVLPQIARFCQRYPGISVKIEtgnTDESLSRLYNYQADLALLGRDVDDPRLLSLPLPDDQLL----- 165
Cdd:cd08422    2 RLRISAPVsfgrlHLAPLLAEFLARYPDVRLELV---LSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVlvasp 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 504531872 166 AFVARdhawAGR-ESicLADLDNTP-LVLRETGSVTRQTLEQEMRQAGLRIRPAIQVEGREAAREA 229
Cdd:cd08422   79 AYLAR----HGTpQT--PEDLARHRcLGYRLPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAA 138
 
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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