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Conserved domains on  [gi|256556970|gb|ACU83592|]
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LysR-type transcriptional regulator [uncultured bacterium HF130_AEPn_2]

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 ...
 5-284 4.04e-109

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: 317.06  E-value: 4.04e-109
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970    5 QLRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKLAAITRSIFGLVDEAQTLLEA 84
Cdd:TIGR03339   1 QLKAFHAVARCGSFTRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRLELTDAGHRLLPIVERLFQQEAEAEFLLRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   85 NRQLLTGRLEVAADGPHMVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICA 164
Cdd:TIGR03339  81 SGALREGSLRIAATAPYYVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVSSEVVDDPRLDRVVLGNDPLVA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  165 LVPAGHPWlADPAGIRLEQLDQVIMVLREPSSITRRTFDDACAKASVQPRVLLELDSREAVTEAVAAELGVGVVSSVEVS 244
Cdd:TIGR03339 161 VVHRQHPL-AERESVTLEELAGQPLLMREPGSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAGLGVSVVSAAEVG 239

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 256556970  245 RDPRVHAIPIRGDGLLNQHMLGCMERRRELRLIQAFFELA 284
Cdd:TIGR03339 240 RDPRLRVLPIVGAEPTMDEYLYCLKERRGARLIAAFLELA 279
 
Name Accession Description Interval E-value
phn_lysR TIGR03339
aminoethylphosphonate catabolism associated LysR family transcriptional regulator; This group ...
 5-284 4.04e-109

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: 317.06  E-value: 4.04e-109
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970    5 QLRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKLAAITRSIFGLVDEAQTLLEA 84
Cdd:TIGR03339   1 QLKAFHAVARCGSFTRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRLELTDAGHRLLPIVERLFQQEAEAEFLLRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   85 NRQLLTGRLEVAADGPHMVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICA 164
Cdd:TIGR03339  81 SGALREGSLRIAATAPYYVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVSSEVVDDPRLDRVVLGNDPLVA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  165 LVPAGHPWlADPAGIRLEQLDQVIMVLREPSSITRRTFDDACAKASVQPRVLLELDSREAVTEAVAAELGVGVVSSVEVS 244
Cdd:TIGR03339 161 VVHRQHPL-AERESVTLEELAGQPLLMREPGSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAGLGVSVVSAAEVG 239

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 256556970  245 RDPRVHAIPIRGDGLLNQHMLGCMERRRELRLIQAFFELA 284
Cdd:TIGR03339 240 RDPRLRVLPIVGAEPTMDEYLYCLKERRGARLIAAFLELA 279
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-172 8.76e-46

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 154.64  E-value: 8.76e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   1 MNLFQLRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKLAAITRSIFGLVDEAQT 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  81 LLEANRQLLTGRLEVAAD---GPHMVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPL 157
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPpslARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170
                 ....*....|....*
gi 256556970 158 NESRICALVPAGHPW 172
Cdd:COG0583  161 GEERLVLVASPDHPL 175
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-231 2.12e-35

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: 128.89  E-value: 2.12e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   1 MNLFQLRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKLAAITRSIFGLVDEAQT 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  81 LLEANRQLLTGRLEVAAD---GPHMVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPL 157
Cdd:NF040786  81 EFDRYGKESKGVLRIGAStipGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 158 NESRICALVPAGHPW---LADPAGIrlEQLDQVIMVLREPSSITRRTFDDACAKASV---QPRVLLELDSREAVTEAVAA 231
Cdd:NF040786 161 YKDRLVLITPNGTEKyrmLKEEISI--SELQKEPFIMREEGSGTRKEAEKALKSLGIsleDLNVVASLGSTEAIKQSVEA 238
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 99-284 3.49e-28

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: 107.30  E-value: 3.49e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  99 GPHMVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICALVPAGHPwLADPAG 178
Cdd:cd05466   11 AAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPDHP-LAKRKS 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 179 IRLEQLDQVIMVLREPSSITRRTFDDACAKASVQPRVLLELDSREAVTEAVAAEL--GVGVVSSVEVSRDPRVHAIPIRG 256
Cdd:cd05466   90 VTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLgiALLPESAVEELADGGLVVLPLED 169

                        170       180
                 ....*....|....*....|....*...
gi 256556970 257 DGLLNQHMLGCMERRRELRLIQAFFELA 284
Cdd:cd05466  170 PPLSRTIGLVWRKGRYLSPAARAFLELL 197
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-233 2.10e-27

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 107.80  E-value: 2.10e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   3 LFQLRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKLAAITRSIFGLVDEAQTLL 82
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  83 EANRQLLTGRLEVAAD---GPHMVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVL-TEV--EPRKGVHLQP 156
Cdd:CHL00180  87 EDLKNLQRGTLIIGASqttGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVgGEVptELKKILEITP 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 157 LNESRICALVPAGHPWlADPAGIRLEQLDQVIMVLREPSSITRRTFDDACAKASVQPRVL---LELDSREAVTEAVAAEL 233
Cdd:CHL00180 167 YVEDELALIIPKSHPF-AKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGIDSKRFkieMELNSIEAIKNAVQSGL 245
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-284 1.72e-26

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 102.75  E-value: 1.72e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   90 TGRLEVAAD---GPHMVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICALV 166
Cdd:pfam03466   1 SGRLRIGAPptlASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  167 PAGHPwLADPAGIRLEQLDQVIMVLREPSSITRRTFDDACAKASVQPRVLLELDSREAVTEAVAAEL---GVGVVSSVEV 243
Cdd:pfam03466  81 PPDHP-LARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLgiaLLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 256556970  244 SRDPRVHAIPIRGDGLLNQHMLGCMERRRELRLIQAFFELA 284
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFL 200
 
Name Accession Description Interval E-value
phn_lysR TIGR03339
aminoethylphosphonate catabolism associated LysR family transcriptional regulator; This group ...
 5-284 4.04e-109

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: 317.06  E-value: 4.04e-109
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970    5 QLRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKLAAITRSIFGLVDEAQTLLEA 84
Cdd:TIGR03339   1 QLKAFHAVARCGSFTRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRLELTDAGHRLLPIVERLFQQEAEAEFLLRE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   85 NRQLLTGRLEVAADGPHMVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICA 164
Cdd:TIGR03339  81 SGALREGSLRIAATAPYYVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVSSEVVDDPRLDRVVLGNDPLVA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  165 LVPAGHPWlADPAGIRLEQLDQVIMVLREPSSITRRTFDDACAKASVQPRVLLELDSREAVTEAVAAELGVGVVSSVEVS 244
Cdd:TIGR03339 161 VVHRQHPL-AERESVTLEELAGQPLLMREPGSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAGLGVSVVSAAEVG 239

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 256556970  245 RDPRVHAIPIRGDGLLNQHMLGCMERRRELRLIQAFFELA 284
Cdd:TIGR03339 240 RDPRLRVLPIVGAEPTMDEYLYCLKERRGARLIAAFLELA 279
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-172 8.76e-46

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 154.64  E-value: 8.76e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   1 MNLFQLRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKLAAITRSIFGLVDEAQT 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  81 LLEANRQLLTGRLEVAAD---GPHMVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPL 157
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPpslARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170
                 ....*....|....*
gi 256556970 158 NESRICALVPAGHPW 172
Cdd:COG0583  161 GEERLVLVASPDHPL 175
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-231 2.12e-35

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: 128.89  E-value: 2.12e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   1 MNLFQLRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKLAAITRSIFGLVDEAQT 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  81 LLEANRQLLTGRLEVAAD---GPHMVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPL 157
Cdd:NF040786  81 EFDRYGKESKGVLRIGAStipGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 158 NESRICALVPAGHPW---LADPAGIrlEQLDQVIMVLREPSSITRRTFDDACAKASV---QPRVLLELDSREAVTEAVAA 231
Cdd:NF040786 161 YKDRLVLITPNGTEKyrmLKEEISI--SELQKEPFIMREEGSGTRKEAEKALKSLGIsleDLNVVASLGSTEAIKQSVEA 238
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 99-284 3.49e-28

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: 107.30  E-value: 3.49e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  99 GPHMVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICALVPAGHPwLADPAG 178
Cdd:cd05466   11 AAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPDHP-LAKRKS 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 179 IRLEQLDQVIMVLREPSSITRRTFDDACAKASVQPRVLLELDSREAVTEAVAAEL--GVGVVSSVEVSRDPRVHAIPIRG 256
Cdd:cd05466   90 VTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLgiALLPESAVEELADGGLVVLPLED 169

                        170       180
                 ....*....|....*....|....*...
gi 256556970 257 DGLLNQHMLGCMERRRELRLIQAFFELA 284
Cdd:cd05466  170 PPLSRTIGLVWRKGRYLSPAARAFLELL 197
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-233 2.10e-27

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 107.80  E-value: 2.10e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   3 LFQLRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKLAAITRSIFGLVDEAQTLL 82
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  83 EANRQLLTGRLEVAAD---GPHMVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVL-TEV--EPRKGVHLQP 156
Cdd:CHL00180  87 EDLKNLQRGTLIIGASqttGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVgGEVptELKKILEITP 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 157 LNESRICALVPAGHPWlADPAGIRLEQLDQVIMVLREPSSITRRTFDDACAKASVQPRVL---LELDSREAVTEAVAAEL 233
Cdd:CHL00180 167 YVEDELALIIPKSHPF-AKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGIDSKRFkieMELNSIEAIKNAVQSGL 245
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-284 1.72e-26

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 102.75  E-value: 1.72e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   90 TGRLEVAAD---GPHMVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICALV 166
Cdd:pfam03466   1 SGRLRIGAPptlASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  167 PAGHPwLADPAGIRLEQLDQVIMVLREPSSITRRTFDDACAKASVQPRVLLELDSREAVTEAVAAEL---GVGVVSSVEV 243
Cdd:pfam03466  81 PPDHP-LARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLgiaLLPRSAVARE 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 256556970  244 SRDPRVHAIPIRGDGLLNQHMLGCMERRRELRLIQAFFELA 284
Cdd:pfam03466 160 LADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFL 200
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-229 1.24e-25

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 102.73  E-value: 1.24e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   1 MNLFQLRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKLAAITRSIFGLVDEAQT 80
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  81 LLEANRQLLTGRLEVAAD---GPHMVMPMLAKLRARYPGITVNLRLGNaQETLAALLSEHA-DVAVLTEVEPRKGVHLQP 156
Cdd:PRK11242  81 AIHDVADLSRGSLRLAMTptfTAYLIGPLIDAFHARYPGITLTIREMS-QERIEALLADDElDVGIAFAPVHSPEIEAQP 159

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 256556970 157 LNESRICALVPAGHPWLADPAGIRLEQLDQVIMVLREPSSITRRTFDDACAKASVQPRVLLELDSREAVTEAV 229
Cdd:PRK11242 160 LFTETLALVVGRHHPLAARRKALTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIV 232
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-233 3.84e-24

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 98.99  E-value: 3.84e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   1 MNLFQLRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKLAAITRSIFGLVDEAQT 80
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  81 LLEANRQLLTGRLEVA-ADGP---HMVMPMLAKLRARYPGITVNLrlgnaQETLAALLSE-----HADVAVLTEVEPRKG 151
Cdd:PRK11233  81 AVHNVGQALSGQVSIGlAPGTaasSLTMPLLQAVRAEFPGIVLYL-----HENSGATLNEklmngQLDMAVIYEHSPVAG 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 152 VHLQPLNESRICALVPAGHPwladPAGIRLEQLDQVIMVLREPSSITRRTFDDACAKASVQPRVLLELDSREAVTEAVAA 231
Cdd:PRK11233 156 LSSQPLLKEDLFLVGTQDCP----GQSVDLAAVAQMNLFLPRDYSAVRLRVDEAFSLRRLTAKVIGEIESIATLTAAIAS 231


                 ..
gi 256556970 232 EL 233
Cdd:PRK11233 232 GM 233
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-221 6.52e-23

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 95.83  E-value: 6.52e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   1 MNLFQLR-AFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVE-LTEEGIKLAAITRSIFglvDEA 78
Cdd:PRK12682   1 MNLQQLRfVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERIL---REV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  79 QTLLEANRQLL---TGRLEVAADgpHM----VMP-MLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTE-VEPR 149
Cdd:PRK12682  78 GNIKRIGDDFSnqdSGTLTIATT--HTqaryVLPrVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATEsLADD 155

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 256556970 150 KGVHLQPLNESRICALVPAGHPwLADPAGIRLEQLDQVIMVLREPSSITRRTFDDACAKASVQPRVLLE-LDS 221
Cdd:PRK12682 156 PDLATLPCYDWQHAVIVPPDHP-LAQEERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEaIDS 227
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 6-142 6.13e-22

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 92.60  E-value: 6.13e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   6 LRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKLAAITRSIFglvdeaQTLLEAN 85
Cdd:PRK11139  11 LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIF------DQLAEAT 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 256556970  86 RQLLT----GRLEVAAdGP----HMVMPMLAKLRARYPGITVNLRlgnAQETLAALLSEHADVAV 142
Cdd:PRK11139  85 RKLRArsakGALTVSL-LPsfaiQWLVPRLSSFNEAHPDIDVRLK---AVDRLEDFLRDDVDVAI 145
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 99-255 6.45e-22

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: 90.29  E-value: 6.45e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  99 GPHMVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICALVPAGHPwLADPAG 178
Cdd:cd08434   11 GTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPKDHP-LAGRDS 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 256556970 179 IRLEQLDQVIMVLREPSSITRRTFDDACAKASVQPRVLLEldSREAVTEA--VAAELGVGVVSSVEVSRDPRVHAIPIR 255
Cdd:cd08434   90 VDLAELADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAFE--GEEDSTIAglVAAGLGVAILPEMTLLNPPGVKKIPIK 166
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 105-231 6.80e-22

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: 90.63  E-value: 6.80e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 105 PMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVlteVE---PRKGVHLQPLNESRICALVPAGHPWlADPAGIRL 181
Cdd:cd08420   17 RLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGL---VEgpvDHPDLIVEPFAEDELVLVVPPDHPL-AGRKEVTA 92

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 256556970 182 EQLDQVIMVLREPSSITRRTFDDACAKASV---QPRVLLELDSREAVTEAVAA 231
Cdd:cd08420   93 EELAAEPWILREPGSGTREVFERALAEAGLdglDLNIVMELGSTEAIKEAVEA 145
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 103-234 1.94e-21

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: 89.10  E-value: 1.94e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 103 VMP-MLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICALVPAGHPwLADPAGIRL 181
Cdd:cd08419   13 FAPrLLGAFCRRHPGVEVSLRVGNREQVLERLADNEDDLAIMGRPPEDLDLVAEPFLDNPLVVIAPPDHP-LAGQKRIPL 91

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 256556970 182 EQLDQVIMVLREPSSITRRTFDDACAKASVQPRVLLELDSREAVTEAVAAELG 234
Cdd:cd08419   92 ERLAREPFLLREPGSGTRLAMERFFAEHGVTLRVRMELGSNEAIKQAVMAGLG 144
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-221 8.25e-21

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 89.83  E-value: 8.25e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   1 MNLFQLRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKLAAITRSIFGLVDEAQT 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  81 L----LEANRQLLTGRLEVAADG--PHmVMPMlakLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHL 154
Cdd:PRK09906  81 RarkiVQEDRQLTIGFVPSAEVNllPK-VLPM---FRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDY 156

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 256556970 155 QPLNESRICALVPAGHPwLADPAGIRLEQLDQVIMVLREP--SSITRRTFDDACAKASVQPRVLLELDS 221
Cdd:PRK09906 157 LELLDEPLVVVLPVDHP-LAHEKEITAAQLDGVNFISTDPaySGSLAPIIKAWFAQHNSQPNIVQVATN 224
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
5-61 5.62e-20

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 81.28  E-value: 5.62e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 256556970    5 QLRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEG 61
Cdd:pfam00126   3 QLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
3-162 2.32e-19

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 85.82  E-value: 2.32e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   3 LFQLRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKLAAITRSIFGLVDeaQTLL 82
Cdd:PRK10086  16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLN--QEIL 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  83 EANRQLLTGRLEVAADgPHMV----MPMLAKLRARYPGITVNLRLGNaqeTLAALLSEHADVAVLTEVEPRKGVHLQPLN 158
Cdd:PRK10086  94 DIKNQELSGTLTVYSR-PSIAqcwlVPRLADFTRRYPSISLTILTGN---ENVNFQRAGIDLAIYFDDAPSAQLTHHFLM 169


                 ....
gi 256556970 159 ESRI 162
Cdd:PRK10086 170 DEEI 173
PRK09986 PRK09986
LysR family transcriptional regulator;
1-231 1.03e-18

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 84.00  E-value: 1.03e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   1 MNLFQLRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKLAAITRSIFglvDEAQT 80
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLL---DNAEQ 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  81 LLEANRQL---LTGRLEVAADGPHM---VMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEV--EPRKGV 152
Cdd:PRK09986  84 SLARVEQIgrgEAGRIEIGIVGTALwgrLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMAdlEPNPGF 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 153 HLQPLNESRICALVPAGHPwLADPAGIRLEQL-DQVIMVLREPSSITRRTFDDACAKASVQPRVLLELDSREAVTEAVAA 231
Cdd:PRK09986 164 TSRRLHESAFAVAVPEEHP-LASRSSVPLKALrNEYFITLPFVHSDWGKFLQRVCQQAGFSPQIIRQVNEPQTVLAMVSM 242
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-218 2.33e-17

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 80.41  E-value: 2.33e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   1 MNLFQLRAFDAVARDG-SFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARR-VELTEEGiklAAITRSIFGLVDEA 78
Cdd:PRK12684   1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRlRGLTEPG---RIILASVERILQEV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  79 QTLLE-----ANRQllTGRLEVAA---DGPHMVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTE-VEPR 149
Cdd:PRK12684  78 ENLKRvgkefAAQD--QGNLTIATthtQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATEaIADY 155

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 256556970 150 KGVHLQPLNESRICALVPAGHPWLADpAGIRLEQLDQVIMVLREPSSITRRTFDDACAKASVQPRVLLE 218
Cdd:PRK12684 156 KELVSLPCYQWNHCVVVPPDHPLLER-KPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGLKPDIVLE 223
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 106-256 5.73e-17

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: 77.26  E-value: 5.73e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 106 MLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVL-TEVEPRKGVHLQPLNESRICALVPAGHPwLADPAGIRLEQL 184
Cdd:cd08436   18 LLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVgLPERRPPGLASRELAREPLVAVVAPDHP-LAGRRRVALADL 96

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 256556970 185 DQVIMVLREPSSITRRTFDDACAKASVQPRVLLELDSREAVTEAVAAELGVGVVSSVEVSRDPRVHAIPIRG 256
Cdd:cd08436   97 ADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLPASVAARLPGLAALPLEP 168
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-217 2.12e-16

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 77.78  E-value: 2.12e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   1 MNLFQLRAF-DAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVE-LTEEGIKLAAITRSIfgLVDeA 78
Cdd:PRK12683   1 MNFQQLRIIrEAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERM--LLD-A 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  79 QTLLEANRQLL---TGRLEVAA---DGPHMVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTE-VEPRKG 151
Cdd:PRK12683  78 ENLRRLAEQFAdrdSGHLTVATthtQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEaLDREPD 157

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 256556970 152 VHLQPLNESRICALVPAGHPWLADPAgIRLEQLDQVIMVLREPSSITRRTFDDACAKASVQPRVLL 217
Cdd:PRK12683 158 LVSFPYYSWHHVVVVPKGHPLTGREN-LTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLVPDIVL 222
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-218 2.15e-14

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: 69.86  E-value: 2.15e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 105 PMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICALVPAGHPwLADPAGIRLEQL 184
Cdd:cd08440   17 PVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPKDHP-LARRRSVTWAEL 95

                         90       100       110
                 ....*....|....*....|....*....|....
gi 256556970 185 DQVIMVLREPSSITRRTFDDACAKASVQPRVLLE 218
Cdd:cd08440   96 AGYPLIALGRGSGVRALIDRALAAAGLTLRPAYE 129
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 105-233 2.58e-14

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: 69.84  E-value: 2.58e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 105 PMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICALVPAGHPwLADPAGIRLEQL 184
Cdd:cd08414   17 RLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALPADHP-LAARESVSLADL 95

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 256556970 185 DQVIMVL--REPSSITRRTFDDACAKASVQPRVLLELDSREAVTEAVAAEL 233
Cdd:cd08414   96 ADEPFVLfpREPGPGLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGL 146
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-233 3.03e-14

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 71.26  E-value: 3.03e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   3 LFQLRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKLAAITRSIFGLVDEAQTLL 82
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIEQLF 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  83 EANrqllTGRLEVAAD---GPHMVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNE 159
Cdd:PRK10837  85 RED----NGALRIYASstiGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPELISEPWLE 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 256556970 160 SRICALVPAGHPWLADPagIRLEQLDQVIMVLREPSSITRRTFDDACAKASVQPRVLLELDSREAVTEAVAAEL 233
Cdd:PRK10837 161 DELVVFAAPDSPLARGP--VTLEQLAAAPWILRERGSGTREIVDYLLLSHLPRFELAMELGNSEAIKHAVRHGL 232
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-172 4.92e-14

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 70.83  E-value: 4.92e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   1 MNLFQLRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKLAAITRSIfglVDEAQT 80
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTV---LREVKV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  81 LLE-ANRQ--LLTGRLEVA---ADGPHMVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLT---EVEPRKG 151
Cdd:PRK11151  78 LKEmASQQgeTMSGPLHIGlipTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILAlvkESEAFIE 157

                        170       180
                 ....*....|....*....|.
gi 256556970 152 VhlqPLNESRICALVPAGHPW 172
Cdd:PRK11151 158 V---PLFDEPMLLAVYEDHPW 175
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-259 6.45e-14

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: 68.87  E-value: 6.45e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 105 PMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICALVPAGHPwLADPAGIRLEQL 184
Cdd:cd08426   17 SLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVVPPGHP-LARQPSVTLAQL 95

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 256556970 185 DQVIMVLREPSSITRRTFDDACAKASVQPRVLLELDSREAVTEAVAAELGVGVVSSVEVSRDPR---VHAIPIRGDGL 259
Cdd:cd08426   96 AGYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTELAVRREIRrgqLVAVPLADPHM 173
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 104-231 2.99e-13

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: 66.85  E-value: 2.99e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 104 MPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICALVPAGHPwLADPAGIRLEQ 183
Cdd:cd08433   16 VPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGPADAP-LPRGAPVPLAE 94

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 256556970 184 LDQVIMVLREPSSITRRTFDDACAKASVQPRVLLELDSREAVTEAVAA 231
Cdd:cd08433   95 LARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAA 142
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 103-231 3.23e-13

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: 66.82  E-value: 3.23e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 103 VMP-MLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICALVPAGHPwLADPAGIRL 181
Cdd:cd08415   14 LLPrAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLPPGHP-LARKDVVTP 92

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 256556970 182 EQLDQVIMVLREPSSITRRTFDDACAKASVQPRVLLELDSREAVTEAVAA 231
Cdd:cd08415   93 ADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAA 142
PRK12680 PRK12680
LysR family transcriptional regulator;
1-217 4.02e-13

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 68.50  E-value: 4.02e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   1 MNLFQLRAFDAVA-RDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVE-LTEEGIKLAAITRSIFGLVDEA 78
Cdd:PRK12680   1 MTLTQLRYLVAIAdAELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  79 QTLLEANRQLLTGRLEVA---ADGPHMVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEV--EPRKGVH 153
Cdd:PRK12680  81 RTYAANQRRESQGQLTLTtthTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAggEPSAGIA 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 256556970 154 LqPLNESRICALVPAGHPWLADPAGIRLEQLDQVIMVLREPSSITRRTFDDACAKASVQPRVLL 217
Cdd:PRK12680 161 V-PLYRWRRLVVVPRGHALDTPRRAPDMAALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIAL 223
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-233 8.99e-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: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 65.70  E-value: 8.99e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 105 PMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPR-----KGVHLQPLNESRICALVPAGHPwLADPAGI 179
Cdd:cd08423   17 PALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFDYPVTpppddPGLTRVPLLDDPLDLVLPADHP-LAGREEV 95

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 256556970 180 RLEQLDQVIMVLREPSSITRRTFDDACAKASVQPRVLLELDSREAVTEAVAAEL 233
Cdd:cd08423   96 ALADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGL 149
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 105-221 5.15e-12

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: 63.41  E-value: 5.15e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 105 PMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEV--EPRKGVHLqPLNESRICALVPAGHPwLADPAGIRLE 182
Cdd:cd08413   17 PVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEAldDHPDLVTL-PCYRWNHCVIVPPGHP-LADLGPLTLE 94

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 256556970 183 QLDQVIMVLREPSSITRRTFDDACAKASVQPRVLLE-LDS 221
Cdd:cd08413   95 DLAQYPLITYDFGFTGRSSIDRAFARAGLEPNIVLTaLDA 134
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 102-231 1.04e-11

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: 62.56  E-value: 1.04e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 102 MVMP-MLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICALVPAGHPwLADPAGIR 180
Cdd:cd08412   13 YYLPgLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARLPPYVWLPADHP-LAGKDEVS 91

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 256556970 181 LEQLDQVIMV-LREPSSitRRTFDDACAKASVQPRVLLELDSREAVTEAVAA 231
Cdd:cd08412   92 LADLAAEPLIlLDLPHS--REYFLSLFAAAGLTPRIAYRTSSFEAVRSLVAN 141
cbl PRK12679
HTH-type transcriptional regulator Cbl;
1-217 1.29e-11

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 64.06  E-value: 1.29e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   1 MNLFQLRAFDAVAR-DGSFTRAAARLFISQPAVTGHIKALEEHYQITL-LRRTARRVELTEEGIKLAAITRSIFGLVDEA 78
Cdd:PRK12679   1 MNFQQLKIIREAARqDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIfIRRGKRLLGMTEPGKALLVIAERILNEASNV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  79 QTLLEANRQLLTGRLEVA---ADGPHMVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEveprkgvhlQ 155
Cdd:PRK12679  81 RRLADLFTNDTSGVLTIAtthTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASE---------R 151

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 256556970 156 PLNESRICA----------LVPAGHPwLADPAGIRLEQLDQVIMVLREPSSITRRTFDDACAKASVQPRVLL 217
Cdd:PRK12679 152 LSNDPQLVAfpwfrwhhslLVPHDHP-LTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVL 222
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 100-230 1.44e-11

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold; CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176116  Cd Length: 197  Bit Score: 62.35  E-value: 1.44e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 100 PHMVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVlTEVEPRK-GVHLQPLNESRICALVPAGHPWLADPAG 178
Cdd:cd08425   13 AYLIGPLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGI-AFAPVRSpDIDAQPLFDERLALVVGATHPLAQRRTA 91

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 256556970 179 IRLEQLDQVIMVLREPSSITRRTFDDACAKASVQPRVLLELDSREAVTEAVA 230
Cdd:cd08425   92 LTLDDLAAEPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVR 143
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
5-100 9.75e-11

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 60.94  E-value: 9.75e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   5 QLRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTaRRVELTEEGIKLAAITRsifglvdeaQT-LLE 83
Cdd:PRK03635   6 QLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQRLLRHAR---------QVrLLE 75

                         90
                 ....*....|....*..
gi 256556970  84 ANrqlLTGRLEVAADGP 100
Cdd:PRK03635  76 AE---LLGELPALDGTP 89
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-201 2.31e-10

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 60.21  E-value: 2.31e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   6 LRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKLAAITRSIFGLVDEAQTLLEAN 85
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  86 RQLLTGRLEVAADG----PHMVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAV-LTEVEPRK-GVHLQPLNE 159
Cdd:PRK10094  87 NDGVERQVNIVINNllynPQAVAQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIgVTGTEALAnTFSLDPLGS 166

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 256556970 160 SRICALVPAGHPWLADPAGIRLEQLDQVIMVLREPSS--ITRRT 201
Cdd:PRK10094 167 VQWRFVMAADHPLANVEEPLTEAQLRRFPAVNIEDSArtLTKRV 210
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
5-168 2.58e-10

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 59.98  E-value: 2.58e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   5 QLRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTaRRVELTEEGIKLAAITRSIFGLVDEAQ-TLLE 83
Cdd:PRK13348   6 QLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHLRQVALLEADLLsTLPA 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  84 ANRQLLTGRLEVAADG-PHMVMPMLAKLRARyPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESR- 161
Cdd:PRK13348  85 ERGSPPTLAIAVNADSlATWFLPALAAVLAG-ERILLELIVDDQDHTFALLERGEVVGCVSTQPKPMRGCLAEPLGTMRy 163


                 ....*..
gi 256556970 162 ICALVPA 168
Cdd:PRK13348 164 RCVASPA 170
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 2-231 2.99e-10

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 59.62  E-value: 2.99e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   2 NLFQLRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKL-AAITRSIFGLvDEAQT 80
Cdd:PRK11013   5 SLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLfEEVQRSYYGL-DRIVS 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  81 LLEANRQLLTGRLEVAAdGP---HMVMPMLAK-LRARYPGITVNLrlgNAQET------LAAL-----LSEHADVAVLTE 145
Cdd:PRK11013  84 AAESLREFRQGQLSIAC-LPvfsQSLLPGLCQpFLARYPDVSLNI---VPQESplleewLSAQrhdlgLTETLHTPAGTE 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 146 VEPrkgvhLQPLNEsrICALvPAGHPwLADPAGIRLEQLDQVIMVLREPSSITRRTFDDACAKASVQPRVLLELDSREAV 225
Cdd:PRK11013 160 RTE-----LLTLDE--VCVL-PAGHP-LAAKKVLTPDDFAGENFISLSRTDSYRQLLDQLFAEHGVKRRMVVETHSAASV 230


                 ....*.
gi 256556970 226 TEAVAA 231
Cdd:PRK11013 231 CAMVRA 236
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 101-233 3.29e-10

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: 58.34  E-value: 3.29e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 101 HMVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICALVPAGHPWlADPAGIR 180
Cdd:cd08438   13 LLFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPRGHPL-AGRKTVS 91

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 256556970 181 LEQL-DQVIMVLREPSSITRRtFDDACAKASVQPRVLLELDSREAVTEAVAAEL 233
Cdd:cd08438   92 LADLaDEPFILFNEDFALHDR-IIDACQQAGFTPNIAARSSQWDFIAELVAAGL 144
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 104-284 4.11e-10

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: 57.96  E-value: 4.11e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 104 MPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICALVPAGHPwLADPAGIRLEQ 183
Cdd:cd08441   16 MPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAPDHP-LAAKEFITPED 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 184 L-DQVIM---VLREPSSITRRTFDdacaKASVQPRVLLELDSREAVTEAVAAELGVGVV---SSVEVSRDPRVHAIPIRG 256
Cdd:cd08441   95 LaDETLItypVERERLDVFRHFLQ----PAGIEPKRRRTVELTLMILQLVASGRGVAALpnwAVREYLDQGLVVARPLGE 170

                        170       180
                 ....*....|....*....|....*...
gi 256556970 257 DGLLNQHMLGCMERRRELRLIQAFFELA 284
Cdd:cd08441  171 EGLWRTLYAAVRTEDADQPYLQDFLELA 198
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 95-218 6.53e-10

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: 57.67  E-value: 6.53e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  95 VAADGPHMVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAV--LTEVEPRKGVHLQPLNESRICALVPAGHPw 172
Cdd:cd08435    7 VPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIgrLADDEQPPDLASEELADEPLVVVARPGHP- 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 256556970 173 LADPAGIRLEQLDQVIMVLREPSSITRRTFDDACAKASVQ-PRVLLE 218
Cdd:cd08435   86 LARRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPlPRNVVE 132
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
9-124 2.08e-09

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 57.46  E-value: 2.08e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   9 FDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKLAAITRSIFGLVDEAQTLLEANRQL 88
Cdd:PRK10632  10 FAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAFNNT 89

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 256556970  89 LTGRLEVAAD---GPHMVMPMLAKLRARYPGITVNLRLG 124
Cdd:PRK10632  90 PIGTLRIGCSstmAQNVLAGLTAKMLKEYPGLSVNLVTG 128
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 111-218 4.72e-09

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: 54.88  E-value: 4.72e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 111 RARYPGITVNLRLGNAQETLAALLSEHADVAVL-TEVEPRKGVHLQPLNESRICALVPAGHPwLADPAGIRLEQL--DQV 187
Cdd:cd08451   24 REAYPDVELTLEEANTAELLEALREGRLDAAFVrPPVARSDGLVLELLLEEPMLVALPAGHP-LARERSIPLAALadEPF 102

                         90       100       110
                 ....*....|....*....|....*....|....
gi 256556970 188 IMVlrePSSITRRTFDD---ACAKASVQPRVLLE 218
Cdd:cd08451  103 ILF---PRPVGPGLYDAiiaACRRAGFTPRIGQE 133
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 6-145 2.09e-08

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 54.26  E-value: 2.09e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   6 LRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKLAAITRSIFGLVDEAQT-LLEA 84
Cdd:PRK15092  16 LRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACSsLMYS 95

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 256556970  85 NRQlltGRLEVAA--DGPHMVMP-MLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTE 145
Cdd:PRK15092  96 NLQ---GVLTIGAsdDTADTILPfLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTTH 156
PRK10341 PRK10341
transcriptional regulator TdcA;
5-160 2.39e-08

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 54.10  E-value: 2.39e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   5 QLRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKLAAITRSIfglVDEAQTLL-E 83
Cdd:PRK10341  11 HLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESI---TREMKNMVnE 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  84 ANRQLLTGRLEVAADGPHMV----MP-MLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAV--LTEVEPRKGVHLQP 156
Cdd:PRK10341  88 INGMSSEAVVDVSFGFPSLIgftfMSdMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIgtLSNEMKLQDLHVEP 167


                 ....
gi 256556970 157 LNES 160
Cdd:PRK10341 168 LFES 171
PRK09791 PRK09791
LysR family transcriptional regulator;
3-136 2.98e-08

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 53.61  E-value: 2.98e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   3 LFQLRAFDAVARDGSFtRAAAR-LFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKLAAITRSIFGLVDEAQTL 81
Cdd:PRK09791   7 IHQIRAFVEVARQGSI-RGASRmLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQED 85

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 256556970  82 LEANRQLLTGRLE--VAADGPHMVMP-MLAKLRARYPgiTVNLRLGNAQetLAALLSE 136
Cdd:PRK09791  86 IRQRQGQLAGQINigMGASIARSLMPaVISRFHQQHP--QVKVRIMEGQ--LVSMINE 139
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
5-171 3.04e-08

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 53.87  E-value: 3.04e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   5 QLRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKLAAITRSIFGLVDEAqtlLEA 84
Cdd:PRK15421   6 HLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQA---LQA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  85 NRQLLTGRLEVAADGPHMVM---PMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESR 161
Cdd:PRK15421  83 CNEPQQTRLRIAIECHSCIQwltPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYE 162

                        170
                 ....*....|
gi 256556970 162 ICALVPAGHP 171
Cdd:PRK15421 163 VRLVLAPDHP 172
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
 105-284 5.80e-08

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: 51.81  E-value: 5.80e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 105 PMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAV--LTEVEPRKgVHLQPLNESRICALVPAGHPWLADPAGIRLE 182
Cdd:cd08430   17 PILERFRAQHPQVEIKLHTGDPADAIDKVLNGEADIAIaaRPDKLPAR-LAFLPLATSPLVFIAPNIACAVTQQLSQGEI 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 183 QLDQVIMVLREpSSITRRTFDDACAKASVQPRVLLELDSREAVTEAVAAELGVGVVSSVEVSRDP---RVHAIPIRGDgl 259
Cdd:cd08430   96 DWSRLPFILPE-RGLARERLDQWFRRRGIKPNIYAQVAGHEAIVSMVALGCGVGIVPELVLDNSPlkdKVRILEVQPE-- 172

                        170       180
                 ....*....|....*....|....*..
gi 256556970 260 LNQHMLG--CMERRRELRLIQAFFELA 284
Cdd:cd08430  173 LEPFEVGlcCLKKRLNEPLIKAFWQVA 199
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
26-160 6.24e-08

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 52.51  E-value: 6.24e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  26 FISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKLAAITRSIFGLVDEAQTLLEANRQLLTGRLE----VAADGPH 101
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSlfcsVTAAYSH 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 256556970 102 MvMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAV--LTEVEPRKgVHLQPLNES 160
Cdd:PRK11716  82 L-PPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIaaKPETLPAS-VAFSPIDEI 140
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-282 1.01e-07

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


Pssm-ID: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 51.04  E-value: 1.01e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 105 PMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTE--VEPRKGVHLQPLNESRICALVPAGHPWlADPAgirlE 182
Cdd:cd08427   17 RALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEppFPLPKDLVWTPLVREPLVLIAPAELAG-DDPR----E 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 183 QLDQVIMVLREPSSITRRTFDDACAKASVQPRVLLELDSREAVTEAVAAEL--GVGVVSSVEVSRDPRVHAIPIRGDGLL 260
Cdd:cd08427   92 LLATQPFIRYDRSAWGGRLVDRFLRRQGIRVREVMELDSLEAIAAMVAQGLgvAIVPDIAVPLPAGPRVRVLPLGDPAFS 171

                        170       180
                 ....*....|....*....|....
gi 256556970 261 NQhmLGCMERRRELR--LIQAFFE 282
Cdd:cd08427  172 RR--VGLLWRRSSPRsrLIQALLE 193
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 9-179 1.30e-07

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 51.91  E-value: 1.30e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   9 FDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKLAAITRSIFGLVDEAQTLLEANRQL 88
Cdd:PRK14997  10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVE 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  89 LTG--RLEVAADGPHM-VMPMLAKLRARYPGITVNLRLGNAQetlAALLSEHADVAVltEVEPRkgvhlqPLNESRICAL 165
Cdd:PRK14997  90 PRGivKLTCPVTLLHVhIGPMLAKFMARYPDVSLQLEATNRR---VDVVGEGVDVAI--RVRPR------PFEDSDLVMR 158

                        170
                 ....*....|....*.
gi 256556970 166 VPA--GHPWLADPAGI 179
Cdd:PRK14997 159 VLAdrGHRLFASPDLI 174
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 95-216 1.49e-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: 50.72  E-value: 1.49e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  95 VAADGPHMVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICALVPAGHPwLA 174
Cdd:cd08447    7 TAASAYSFLPRLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFARPGLETRPLVREPLVAAVPAGHP-LA 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 256556970 175 DPAGIRLEQLDQVIMVLREPSSitRRTFDDACAK----ASVQPRVL 216
Cdd:cd08447   86 GAERLTLEDLDGQPFIMYSPTE--ARYFHDLVVRlfasAGVQPRYV 129
nhaR PRK11062
transcriptional activator NhaR; Provisional
 1-61 3.83e-07

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 50.39  E-value: 3.83e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 256556970   1 MNLFQLRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEG 61
Cdd:PRK11062   4 INYNHLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELG 64
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 10-71 6.68e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 49.56  E-value: 6.68e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 256556970  10 DAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKLAAITRSI 71
Cdd:PRK11074  11 DAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSV 72
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 107-231 1.65e-06

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


Pssm-ID: 176146 [Multi-domain]  Cd Length: 196  Bit Score: 47.48  E-value: 1.65e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 107 LAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICALVPAGHPwLADPAGIRLEQLDQ 186
Cdd:cd08457   19 LAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIETRSLPAVVAVPMGHP-LAQLDVVSPQDLAG 97

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 256556970 187 VIMVLREPSSITRRTFDDACAKASVQPRVLLELDSREAVTEAVAA 231
Cdd:cd08457   98 ERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVRE 142
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 112-231 2.51e-06

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


Pssm-ID: 176113  Cd Length: 198  Bit Score: 47.13  E-value: 2.51e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 112 ARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICALVPAGHPwLADPAGIRLEQ-LDQVIMV 190
Cdd:cd08421   24 AAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLETRPYRTDRLVVVVPRDHP-LAGRASVAFADtLDHDFVG 102

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 256556970 191 LREPSSITRRTfDDACAKASVQPRVLLELDSREAVTEAVAA 231
Cdd:cd08421  103 LPAGSALHTFL-REAAARLGRRLRLRVQVSSFDAVCRMVAA 142
PRK09801 PRK09801
LysR family transcriptional regulator;
6-164 3.73e-06

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 47.34  E-value: 3.73e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   6 LRAFDAVARDGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRVELTEEGIKlaaITRSIFGLVDEAQTLLEAN 85
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQR---CYEHALEILTQYQRLVDDV 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  86 RQLLT---GRLEVAAD---GPHMVMPMLAKLRARYPGITVNLRLGNAQETLAAlLSEHADVAVLTEVEPRKGVHLQPLNE 159
Cdd:PRK09801  88 TQIKTrpeGMIRIGCSfgfGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQ-DNIDLDIRINDEIPDYYIAHLLTKNK 166


                 ....*
gi 256556970 160 SRICA 164
Cdd:PRK09801 167 RILCA 171
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 101-231 4.91e-06

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: 46.05  E-value: 4.91e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 101 HMVMP-MLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICALVPAGHPWLADPagI 179
Cdd:cd08417   12 ALLLPpLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARKDHPLAGGP--L 89

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 256556970 180 RLEQ---LDQVIMVLREPSsitRRTFDDACAKASVQPRVLLELDSREAVTEAVAA 231
Cdd:cd08417   90 TLEDylaAPHVLVSPRGRG---HGLVDDALAELGLSRRVALTVPHFLAAPALVAG 141
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 91-162 1.06e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain; This CD represents the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA. 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: 176167 [Multi-domain]  Cd Length: 199  Bit Score: 45.41  E-value: 1.06e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 256556970  91 GRLEVAADGP---HMVMPMLAKLRARYPGITVNLrlgNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRI 162
Cdd:cd08478    3 GLLRVDAATPfvlHLLAPLIAKFRERYPDIELEL---VSNEGIIDLIERKTDVAIRIGELTDSTLHARPLGKSRL 74
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 106-193 1.20e-04

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: 42.13  E-value: 1.20e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 106 MLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICALVPAGHPwLADPAGIRLEQLD 185
Cdd:cd08411   19 LLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAVPKDHP-LAKRKSVTPEDLA 97


                 ....*....
gi 256556970 186 -QVIMVLRE 193
Cdd:cd08411   98 gERLLLLEE 106
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-215 2.38e-04

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 41.81  E-value: 2.38e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970   1 MNLFQLRAFDAVAR-DGSFTRAAARLFISQPAVTGHIKALEEHYQITLLRRTARRV-ELTEEGIKLAAITRSIFGLVDEA 78
Cdd:PRK12681   1 MKLQQLRYIVEVVNhNLNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLtQVTPAGEEIIRIAREILSKVESI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  79 QTLLEANRQLLTGRLEVA---ADGPHMVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEveprkGVHL- 154
Cdd:PRK12681  81 KSVAGEHTWPDKGSLYIAtthTQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAIATE-----ALHLy 155

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 155 -----QPLNESRICALVPAGHPwLADPAGIRLEQLDQ---VIMVLrepsSITRRT-FDDACAKASVQPRV 215
Cdd:PRK12681 156 ddlimLPCYHWNRSVVVPPDHP-LAKKKKLTIEELAQyplVTYVF----GFTGRSeLDTAFNRAGLTPRI 220
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 92-231 2.91e-04

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: 41.10  E-value: 2.91e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  92 RLEVAADGPHMVMPM---LAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHL--QPLNESRICALV 166
Cdd:cd08449    1 HLNIGMVGSVLWGGLgpaLRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFADTLNDPPLasELLWREPMVVAL 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 256556970 167 PAGHPwLADPAGIRLEQL-DQVIMVLREPSSITRRTFDDACAKASVQPRVLLELDSREAVTEAVAA 231
Cdd:cd08449   81 PEEHP-LAGRKSLTLADLrDEPFVFLRLANSRFADFLINCCLQAGFTPQITQEVVEPQTLMALVAA 145
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 105-238 3.02e-04

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: 41.01  E-value: 3.02e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 105 PMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTE-VEPRKGVHLQPLNESRICALVPAGHPwLADPAGIRLEQ 183
Cdd:cd08443   17 PVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEaLHDYDDLITLPCYHWNRCVVVKRDHP-LADKQSISIEE 95

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 256556970 184 LDQVIMVLREPSSITRRTFDDACAKASVQPRVLLELDSREAVTEAVAAELGVGVV 238
Cdd:cd08443   96 LATYPIVTYTFGFTGRSELDTAFNRAGLTPNIVLTATDADVIKTYVRLGLGVGVI 150
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 103-215 3.20e-04

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


Pssm-ID: 176139 [Multi-domain]  Cd Length: 197  Bit Score: 40.71  E-value: 3.20e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 103 VMP-MLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICALVPAGHPwLADPAGIRL 181
Cdd:cd08448   14 GLPrILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAGLSARLLHREPFVCCLPAGHP-LAARRRIDL 92

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 256556970 182 EQLDQVIMVL--REPSSITRRTFDDACAKASVQPRV 215
Cdd:cd08448   93 RELAGEPFVLfsREVSPDYYDQIIALCMDAGFHPKI 128
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
 101-219 8.11e-04

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


Pssm-ID: 176148 [Multi-domain]  Cd Length: 201  Bit Score: 39.48  E-value: 8.11e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 101 HMVM--PMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICALVPAGHPWLADPag 178
Cdd:cd08459   11 EMYFlpRLLAALREVAPGVRIETVRLPVDELEEALESGEIDLAIGYLPDLGAGFFQQRLFRERYVCLVRKDHPRIGST-- 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 256556970 179 IRLEQLDQVIMVLREPSSITRRTFDDACAKASVQPRVLLEL 219
Cdd:cd08459   89 LTLEQFLAARHVVVSASGTGHGLVEQALREAGIRRRIALRV 129
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 91-231 1.09e-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: 39.35  E-value: 1.09e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970  91 GRLEVAAD---GPHMVMPMLAKLRARYPGITVNLRLGNAqetLAALLSEHADVAVLTEVEPRKGVHLQPLNESR--ICA- 164
Cdd:cd08422    1 GRLRISAPvsfGRLHLAPLLAEFLARYPDVRLELVLSDR---LVDLVEEGFDLAIRIGELPDSSLVARRLGPVRrvLVAs 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 165 ---LvpAGHPWLADPAGirLEQLDqvIMVLREPSSITRRTFDDACAKASVQPRVLLELDSREAVTEAVAA 231
Cdd:cd08422   78 payL--ARHGTPQTPED--LARHR--CLGYRLPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALA 141
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 102-234 2.46e-03

The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold; AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. 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: 176143 [Multi-domain]  Cd Length: 197  Bit Score: 38.25  E-value: 2.46e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 102 MVMPMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICALVPAGHPwLADPAGIRL 181
Cdd:cd08452   14 FLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALHIETVQSSPCVLALPKQHP-LASKEEITI 92

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 256556970 182 EQL--DQVIMVLREPSSITRRTFDDACAKASVQPRVLLELDSREAVTEAVAAELG 234
Cdd:cd08452   93 EDLrdEPIITVAREAWPTLYDEIIQLCEQAGFRPKIVQEATEYQTVIGLVSAGIG 147
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 101-233 4.81e-03

The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold; LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The 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: 176145 [Multi-domain]  Cd Length: 196  Bit Score: 37.40  E-value: 4.81e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 101 HMVMP-MLAKLRARYPGITVNLRLGNAQeTLAALLSEH-ADVAVLTEVEPRKGVHLQPLNESRICALVPAGHPwLADPAG 178
Cdd:cd08456   12 QSFLPrAIKAFLQRHPDVTISIHTRDSP-TVEQWLSAQqCDLGLVSTLHEPPGIERERLLRIDGVCVLPPGHR-LAVKKV 89

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 256556970 179 IRLEQLDQVIMVLREPSSITRRTFDDACAKASVQPRVLLELDSREAVTEAVAAEL 233
Cdd:cd08456   90 LTPSDLEGEPFISLARTDGTRQRVDALFEQAGVKRRIVVETSYAATICALVAAGV 144
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 104-175 4.96e-03

The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176123 [Multi-domain]  Cd Length: 194  Bit Score: 37.17  E-value: 4.96e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 256556970 104 MPMLAKLRARYPGITVNLRlgnAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRicaLVPAGHPWLAD 175
Cdd:cd08432   16 IPRLARFQARHPDIDLRLS---TSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEE---LVPVCSPALLA 81
PBP2_SyrM cd08467
The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates ...
 106-176 5.55e-03

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


Pssm-ID: 176156 [Multi-domain]  Cd Length: 200  Bit Score: 37.03  E-value: 5.55e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 256556970 106 MLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICALVPAGHPWLADP 176
Cdd:cd08467   18 LAPRLRERAPGLDLRLCPIGDDLAERGLEQGTIDLAVGRFAVPPDGLVVRRLYDDGFACLVRHGHPALAQE 88
PBP2_DntR_like_2 cd08464
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-183 8.14e-03

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


Pssm-ID: 176153 [Multi-domain]  Cd Length: 200  Bit Score: 36.83  E-value: 8.14e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 105 PMLAKLRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPL-NESRICalvpaghpwLADPAGIRLEQ 183
Cdd:cd08464   17 PLLAALRAEAPGVRLVFRQVDPFNVGDMLDRGEIDLAIGVFGELPAWLKREVLyTEGYAC---------LFDPQQLSLSA 87
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 100-196 8.55e-03

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: 36.59  E-value: 8.55e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256556970 100 PHmVMPMLaklRARYPGITVNLRLGNAQETLAALLSEHADVAVLTEVEPRKGVHLQPLNESRICALVPAGHPwLADPAGI 179
Cdd:cd08450   16 PE-VLPIL---REEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGIDYQLLLKEPLIVVLPADHR-LAGREKI 90

                         90
                 ....*....|....*..
gi 256556970 180 RLEQLDQVIMVLREPSS 196
Cdd:cd08450   91 PPQDLAGENFISPAPTA 107
 
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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