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Conserved domains on  [gi|694086219|ref|WP_032431001|]
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MULTISPECIES: LysR family transcriptional regulator [Klebsiella]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

LysR family transcriptional regulator containing an N-terminal HTH (helix-turn-helix) DNA-binding domain and a C-terminal substrate binding domain, which is structurally homologous to the type 2 periplasmic-binding (PBP2) fold proteins

CATH:  3.40.190.10
Gene Ontology:  GO:0003700|GO:0003677|GO:0006355
PubMed:  19047729|8257110|15808743
SCOP:  4000316

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
4-292 5.25e-43

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 147.71  E-value: 5.25e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219   4 LIHLRTFLEAYRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATEAADEL---ARAISPYIDGLAEKL 80
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLlerARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  81 SSLRAGAEsgGTVNLAGPPDFIHSRLGAVMAPLMKE--GYRLRFHTGNKQRIYSLLQEGSVDLAVTASMPDDRLYGYAHL 158
Cdd:COG0583   83 RALRGGPR--GTLRIGAPPSLARYLLPPLLARFRARhpGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 159 LTERMLLVHSPRLtetlgtqpsaatlasvPLIAYDEELPlirmvwtamfqrapdmqasftiqDLRIIRDLVRDGHGWSVL 238
Cdd:COG0583  161 GEERLVLVASPDH----------------PLARRAPLVN-----------------------SLEALLAAVAAGLGIALL 201

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 694086219 239 PDYHCLDDLKSGRLVSVTKAETAPVNHLYLAWNKSNANNRRTAYVRDYILNAFP 292
Cdd:COG0583  202 PRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
4-292 5.25e-43

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 147.71  E-value: 5.25e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219   4 LIHLRTFLEAYRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATEAADEL---ARAISPYIDGLAEKL 80
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLlerARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  81 SSLRAGAEsgGTVNLAGPPDFIHSRLGAVMAPLMKE--GYRLRFHTGNKQRIYSLLQEGSVDLAVTASMPDDRLYGYAHL 158
Cdd:COG0583   83 RALRGGPR--GTLRIGAPPSLARYLLPPLLARFRARhpGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 159 LTERMLLVHSPRLtetlgtqpsaatlasvPLIAYDEELPlirmvwtamfqrapdmqasftiqDLRIIRDLVRDGHGWSVL 238
Cdd:COG0583  161 GEERLVLVASPDH----------------PLARRAPLVN-----------------------SLEALLAAVAAGLGIALL 201

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 694086219 239 PDYHCLDDLKSGRLVSVTKAETAPVNHLYLAWNKSNANNRRTAYVRDYILNAFP 292
Cdd:COG0583  202 PRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 4-289 6.34e-25

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: 101.15  E-value: 6.34e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219   4 LIHLRTFLEAYRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATEAADEL---ARAISPYIDGLAEKL 80
Cdd:NF040786   3 LKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLyeyAKEMLDLWEKLEEEF 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  81 SslRAGAESGGTVNLAG---PPDFIhsrLGAVMAPLMKEGYRLRFH--TGNKQRIYSLLQEGSVDLAVTASMPDDRLYGY 155
Cdd:NF040786  83 D--RYGKESKGVLRIGAstiPGQYL---LPELLKKFKEKYPNVRFKlmISDSIKVIELLLEGEVDIGFTGTKLEKKRLVY 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 156 AHLLTERMLLV---HSPRLTETLGTQpSAATLASVPLIaYDEELPLIRMVWTAMFQRA----PDMQASFTIQDLRIIRDL 228
Cdd:NF040786 158 TPFYKDRLVLItpnGTEKYRMLKEEI-SISELQKEPFI-MREEGSGTRKEAEKALKSLgislEDLNVVASLGSTEAIKQS 235

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 694086219 229 VRDGHGWSVLPDYHCLDDLKSGRLVSVtKAETAPVN-HLYLAWNKSNANNRRTAYVRDYILN 289
Cdd:NF040786 236 VEAGLGISVISELAAEKEVERGRVLIF-PIPGLPKNrDFYLVYNKNRQLSPTAEAFLQFVKE 296
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-292 1.95e-23

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: 95.05  E-value: 1.95e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219   91 GTVNLAGPPDFIHSRLGAVMAPLMKE--GYRLRFHTGNKQRIYSLLQEGSVDLAVTASMPDDRLYGYAHLLTERMLLVHS 168
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERypDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  169 PRLTETLGTQPSAATLASVPLIAYDEELPLiRMVWTAMFQRAP-DMQASFTIQDLRIIRDLVRDGHGWSVLPDYHCLDDL 247
Cdd:pfam03466  82 PDHPLARGEPVSLEDLADEPLILLPPGSGL-RDLLDRALRAAGlRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 694086219  248 KSGRLVSVTKAETAPVNHLYLAWNKSNANNRRTAYVRDYILNAFP 292
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-287 4.44e-16

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: 74.94  E-value: 4.44e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  92 TVNLAGPPDFIHSRLGAVMAPLMKE--GYRLRFHTGNKQRIYSLLQEGSVDLAVTASMPDDRLYGYAHLLTERMLLVHSP 169
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRypGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 170 RLTETLGTQPSAATLASVPLIAYDEELPLIRMVWTAMFQRAPDMQASFTIQDLRIIRDLVRDGHGWSVLPDyHCLDDLKS 249
Cdd:cd05466   81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPE-SAVEELAD 159

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 694086219 250 GRLVSVTKAETAPVNHLYLAWNKSNANNRRTAYVRDYI 287
Cdd:cd05466  160 GGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
6-256 1.22e-13

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 69.80  E-value: 1.22e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219   6 HLRTFLEAYRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIReARGVKATEAADELARAISPYidGL--AEKLSSL 83
Cdd:PRK03635   6 QLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQV--RLleAELLGEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  84 RAGAESGGTVNLAGPPDFIHSRLGAVMAPLMKE-GYRLRFHTGNKQRIYSLLQEGSVDLAVTASmpDDRLYGY-AHLL-T 160
Cdd:PRK03635  83 PALDGTPLTLSIAVNADSLATWFLPALAPVLARsGVLLDLVVEDQDHTAELLRRGEVVGAVTTE--PQPVQGCrVDPLgA 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 161 ERMLLVHSPRLTET-LGTQPSAATLASVPLIAYDeelplirmvwtamfqRAPDMQASFTIQDLRIIR------------- 226
Cdd:PRK03635 161 MRYLAVASPAFAARyFPDGVTAEALAKAPAVVFN---------------RKDDLQDRFLRQAFGLPPgsvpchyvpssea 225

                        250       260       270
                 ....*....|....*....|....*....|..
gi 694086219 227 --DLVRDGHGWSVLPDYHCLDDLKSGRLVSVT 256
Cdd:PRK03635 226 fvRAALAGLGWGMIPELQIEPELASGELVDLT 257
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
4-292 5.25e-43

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 147.71  E-value: 5.25e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219   4 LIHLRTFLEAYRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATEAADEL---ARAISPYIDGLAEKL 80
Cdd:COG0583    3 LRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLlerARRILAELEEAEAEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  81 SSLRAGAEsgGTVNLAGPPDFIHSRLGAVMAPLMKE--GYRLRFHTGNKQRIYSLLQEGSVDLAVTASMPDDRLYGYAHL 158
Cdd:COG0583   83 RALRGGPR--GTLRIGAPPSLARYLLPPLLARFRARhpGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 159 LTERMLLVHSPRLtetlgtqpsaatlasvPLIAYDEELPlirmvwtamfqrapdmqasftiqDLRIIRDLVRDGHGWSVL 238
Cdd:COG0583  161 GEERLVLVASPDH----------------PLARRAPLVN-----------------------SLEALLAAVAAGLGIALL 201

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 694086219 239 PDYHCLDDLKSGRLVSVTKAETAPVNHLYLAWNKSNANNRRTAYVRDYILNAFP 292
Cdd:COG0583  202 PRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 4-289 6.34e-25

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: 101.15  E-value: 6.34e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219   4 LIHLRTFLEAYRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATEAADEL---ARAISPYIDGLAEKL 80
Cdd:NF040786   3 LKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLyeyAKEMLDLWEKLEEEF 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  81 SslRAGAESGGTVNLAG---PPDFIhsrLGAVMAPLMKEGYRLRFH--TGNKQRIYSLLQEGSVDLAVTASMPDDRLYGY 155
Cdd:NF040786  83 D--RYGKESKGVLRIGAstiPGQYL---LPELLKKFKEKYPNVRFKlmISDSIKVIELLLEGEVDIGFTGTKLEKKRLVY 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 156 AHLLTERMLLV---HSPRLTETLGTQpSAATLASVPLIaYDEELPLIRMVWTAMFQRA----PDMQASFTIQDLRIIRDL 228
Cdd:NF040786 158 TPFYKDRLVLItpnGTEKYRMLKEEI-SISELQKEPFI-MREEGSGTRKEAEKALKSLgislEDLNVVASLGSTEAIKQS 235

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 694086219 229 VRDGHGWSVLPDYHCLDDLKSGRLVSVtKAETAPVN-HLYLAWNKSNANNRRTAYVRDYILN 289
Cdd:NF040786 236 VEAGLGISVISELAAEKEVERGRVLIF-PIPGLPKNrDFYLVYNKNRQLSPTAEAFLQFVKE 296
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-292 1.95e-23

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: 95.05  E-value: 1.95e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219   91 GTVNLAGPPDFIHSRLGAVMAPLMKE--GYRLRFHTGNKQRIYSLLQEGSVDLAVTASMPDDRLYGYAHLLTERMLLVHS 168
Cdd:pfam03466   2 GRLRIGAPPTLASYLLPPLLARFRERypDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  169 PRLTETLGTQPSAATLASVPLIAYDEELPLiRMVWTAMFQRAP-DMQASFTIQDLRIIRDLVRDGHGWSVLPDYHCLDDL 247
Cdd:pfam03466  82 PDHPLARGEPVSLEDLADEPLILLPPGSGL-RDLLDRALRAAGlRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 694086219  248 KSGRLVSVTKAETAPVNHLYLAWNKSNANNRRTAYVRDYILNAFP 292
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
6-62 1.46e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 77.43  E-value: 1.46e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 694086219    6 HLRTFLEAYRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATEAA 62
Cdd:pfam00126   3 QLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 92-287 4.44e-16

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: 74.94  E-value: 4.44e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  92 TVNLAGPPDFIHSRLGAVMAPLMKE--GYRLRFHTGNKQRIYSLLQEGSVDLAVTASMPDDRLYGYAHLLTERMLLVHSP 169
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRypGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 170 RLTETLGTQPSAATLASVPLIAYDEELPLIRMVWTAMFQRAPDMQASFTIQDLRIIRDLVRDGHGWSVLPDyHCLDDLKS 249
Cdd:cd05466   81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPE-SAVEELAD 159

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 694086219 250 GRLVSVTKAETAPVNHLYLAWNKSNANNRRTAYVRDYI 287
Cdd:cd05466  160 GGLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
6-256 1.22e-13

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 69.80  E-value: 1.22e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219   6 HLRTFLEAYRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIReARGVKATEAADELARAISPYidGL--AEKLSSL 83
Cdd:PRK03635   6 QLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQV--RLleAELLGEL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  84 RAGAESGGTVNLAGPPDFIHSRLGAVMAPLMKE-GYRLRFHTGNKQRIYSLLQEGSVDLAVTASmpDDRLYGY-AHLL-T 160
Cdd:PRK03635  83 PALDGTPLTLSIAVNADSLATWFLPALAPVLARsGVLLDLVVEDQDHTAELLRRGEVVGAVTTE--PQPVQGCrVDPLgA 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 161 ERMLLVHSPRLTET-LGTQPSAATLASVPLIAYDeelplirmvwtamfqRAPDMQASFTIQDLRIIR------------- 226
Cdd:PRK03635 161 MRYLAVASPAFAARyFPDGVTAEALAKAPAVVFN---------------RKDDLQDRFLRQAFGLPPgsvpchyvpssea 225

                        250       260       270
                 ....*....|....*....|....*....|..
gi 694086219 227 --DLVRDGHGWSVLPDYHCLDDLKSGRLVSVT 256
Cdd:PRK03635 226 fvRAALAGLGWGMIPELQIEPELASGELVDLT 257
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
7-267 1.14e-11

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 63.84  E-value: 1.14e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219   7 LRTFLEAYRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREaRGVKATEAADELARAISpYIDGL-AEKLSSLRA 85
Cdd:PRK13348   7 LEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHLR-QVALLeADLLSTLPA 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  86 GAESGGTVNLAGPPDFIHSRLGAVMAPLMKEGyRLRF--------HTgnkqriYSLLQEGSVDLAVTASMPDDRLYGYAH 157
Cdd:PRK13348  85 ERGSPPTLAIAVNADSLATWFLPALAAVLAGE-RILLelivddqdHT------FALLERGEVVGCVSTQPKPMRGCLAEP 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 158 LLTERMLLVHSPRLTETLGTQP-SAATLASVPLIAYDeelplirmvwtamfqRAPDMQASFTIQ--DLRIIR-------- 226
Cdd:PRK13348 158 LGTMRYRCVASPAFAARYFAQGlTRHSALKAPAVAFN---------------RKDTLQDSFLEQlfGLPVGAyprhyvps 222

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 694086219 227 -----DLVRDGHGWSVLPDYHCLDDLKSGRLVSVTKAETAPVNhLY 267
Cdd:PRK13348 223 thahlAAIRHGLGYGMVPELLIGPLLAAGRLVDLAPGHPVDVA-LY 267
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
2-176 1.14e-11

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 64.25  E-value: 1.14e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219   2 SHLIHLRTFLEAYRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATEAADELARAISPYIDGLAEKLS 81
Cdd:PRK10086  14 WQLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEIL 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  82 SLRaGAESGGTVNLAGPPDFIHS----RLGAvmaplMKEGY---RLRFHTGNKqriYSLLQEGSVDLAVTAS-MPDDRLY 153
Cdd:PRK10086  94 DIK-NQELSGTLTVYSRPSIAQCwlvpRLAD-----FTRRYpsiSLTILTGNE---NVNFQRAGIDLAIYFDdAPSAQLT 164

                        170       180
                 ....*....|....*....|...
gi 694086219 154 GYaHLLTERMLLVHSPRLTETLG 176
Cdd:PRK10086 165 HH-FLMDEEILPVCSPEYAERHA 186
PRK10341 PRK10341
transcriptional regulator TdcA;
6-272 1.19e-11

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 64.11  E-value: 1.19e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219   6 HLRTFLEAYRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATEAADELARAISPYIDGLAEKLSSLRa 85
Cdd:PRK10341  11 HLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN- 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  86 gAESGGTVNLA--GPPDFIHSRLGAVMAPLMKEGY---RLRFHTGNKQRIYSLLQEGSVDLAVTASMPDDRLYGY-AHLL 159
Cdd:PRK10341  90 -GMSSEAVVDVsfGFPSLIGFTFMSDMINKFKEVFpkaQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMKLQDLhVEPL 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 160 TERMLLVHSPRLTETLGTQpsaaTLASVPliayDEE--LPLIRMVW----TAMFQRAP-DMQASFTIQDLRIIRDLVRDG 232
Cdd:PRK10341 169 FESEFVLVASKSRTCTGTT----TLESLK----NEQwvLPQTNMGYyselLTTLQRNGiSIENIVKTDSVVTIYNLVLNA 240

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 694086219 233 HGWSVLPdYHCLDDLKSGRLVSVTKAETAPVNHLYLAWNK 272
Cdd:PRK10341 241 DFLTVIP-CDMTSPFGSNQFITIPIEETLPVAQYAAVWSK 279
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 91-270 3.20e-11

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: 61.30  E-value: 3.20e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  91 GTVNLAGPPDFIHSRLGAVMAPLMKEgY---RLRFHTGNkqRIYSLLQEGsVDLAV-TASMPDDRLYgyAHLLTE-RMLL 165
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLAR-YpdvRLELVLSD--RLVDLVEEG-FDLAIrIGELPDSSLV--ARRLGPvRRVL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 166 VHSPRLTETLGTQPSAATLASVPLIAYDeeLPLIRMVWTamFQRA-----PDMQASFTIQDLRIIRDLVRDGHGWSVLPD 240
Cdd:cd08422   75 VASPAYLARHGTPQTPEDLARHRCLGYR--LPGRPLRWR--FRRGggeveVRVRGRLVVNDGEALRAAALAGLGIALLPD 150

                        170       180       190
                 ....*....|....*....|....*....|
gi 694086219 241 YHCLDDLKSGRLVSVTKAETAPVNHLYLAW 270
Cdd:cd08422  151 FLVAEDLASGRLVRVLPDWRPPPLPIYAVY 180
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 97-270 3.39e-10

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: 58.38  E-value: 3.39e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  97 GPPDFIHSRLGAVMAPLMKEGY---RLRFHTGNKQRIYSLLQEGSVDLAVtasmpddrLYGYAH--------LLTERMLL 165
Cdd:cd08433    5 GLPPSAASVLAVPLLRAVRRRYpgiRLRIVEGLSGHLLEWLLNGRLDLAL--------LYGPPPipglstepLLEEDLFL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 166 VHSPRLTETLGTQPSAATLASVPLIaydeeLP-----LIRMVWTAMFQRAPDMQASFTIQDLRIIRDLVRDGHGWSVLPD 240
Cdd:cd08433   77 VGPADAPLPRGAPVPLAELARLPLI-----LPsrghgLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPA 151

                        170       180       190
                 ....*....|....*....|....*....|
gi 694086219 241 YHCLDDLKSGRLVSVTKAETAPVNHLYLAW 270
Cdd:cd08433  152 SAVAAEVAAGRLVAAPIVDPALTRTLSLAT 181
PRK09801 PRK09801
LysR family transcriptional regulator;
7-255 4.78e-10

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 59.28  E-value: 4.78e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219   7 LRTFLEAYRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATEAAD---ELARAISPYIDGLAEKLSSL 83
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQrcyEHALEILTQYQRLVDDVTQI 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  84 RAGAEsgGTVNLAGPPDFIHSRLGAVMAPLMKEGYRLRFHTGNKQRIYSLLQEG-SVDLAVTASMPDdrlYGYAHLLTE- 161
Cdd:PRK09801  91 KTRPE--GMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNiDLDIRINDEIPD---YYIAHLLTKn 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 162 RMLLVHSPrltETLGTQPSAATLASvpLIAYD----EELPLIRMVW---TAMFQRAPDMQASFTIQDLRIIRDLVRDGHG 234
Cdd:PRK09801 166 KRILCAAP---EYLQKYPQPQSLQE--LSRHDclvtKERDMTHGIWelgNGQEKKSVKVSGHLSSNSGEIVLQWALEGKG 240

                        250       260
                 ....*....|....*....|.
gi 694086219 235 WSVLPDYHCLDDLKSGRLVSV 255
Cdd:PRK09801 241 IMLRSEWDVLPFLESGKLVQV 261
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 92-240 7.40e-10

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: 57.16  E-value: 7.40e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  92 TVNLAgppdFIHSrLGAVMAPLMKEGYRLR-------FHTGNKQRIYSLLQEGSVDLAVTASMPDDRLYGYAHLLTERML 164
Cdd:cd08434    1 TVRLG----FLHS-LGTSLVPDLIRAFRKEypnvtfeLHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELV 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 165 LVHSP--RLTEtlGTQPSAATLASVPLIAYDEELPLIRMVWtAMFQRA---PDMqaSFTIQDLRIIRDLVRDGHGWSVLP 239
Cdd:cd08434   76 LVVPKdhPLAG--RDSVDLAELADEPFVLLSPGFGLRPIVD-ELCAAAgftPKI--AFEGEEDSTIAGLVAAGLGVAILP 150


                 .
gi 694086219 240 D 240
Cdd:cd08434  151 E 151
PRK09791 PRK09791
LysR family transcriptional regulator;
7-95 2.49e-09

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 57.08  E-value: 2.49e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219   7 LRTFLEAYRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATEAADELARAISPYIDGL--AEKLSSLR 84
Cdd:PRK09791  10 IRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELraAQEDIRQR 89

                         90
                 ....*....|.
gi 694086219  85 AGaESGGTVNL 95
Cdd:PRK09791  90 QG-QLAGQINI 99
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
7-88 2.56e-09

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 57.12  E-value: 2.56e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219   7 LRTFLEAYRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATEAADEL---ARAISPYIDGLAEKLSSL 83
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLlsqARDWLSWLESMPSELQQV 86


                 ....*
gi 694086219  84 RAGAE 88
Cdd:PRK10094  87 NDGVE 91
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 4-63 1.29e-08

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 54.96  E-value: 1.29e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219   4 LIHLRTFLEAYRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATEAAD 63
Cdd:PRK11242   3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGE 62
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 7-150 1.60e-08

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 54.65  E-value: 1.60e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219   7 LRTFLEAYRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATEAADEL---ARAISPYIDglaEKLSS- 82
Cdd:PRK15092  16 LRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLlgyARKILRFND---EACSSl 92

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 694086219  83 --------LRAGAeSGGTVNLAGPpdFIHSRLGAVMaPLMKEGYRLRFHtgnkQRIYSLLQEGSVDLAVTASMPDD 150
Cdd:PRK15092  93 mysnlqgvLTIGA-SDDTADTILP--FLLNRVSSVY-PKLALDVRVKRN----AFMMEMLESQEVDLAVTTHRPSS 160
rbcR CHL00180
LysR transcriptional regulator; Provisional
 4-67 5.39e-08

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 53.10  E-value: 5.39e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 694086219   4 LIHLRTFLEAYRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATEAADELAR 67
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLR 70
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 7-69 6.80e-08

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 52.76  E-value: 6.80e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 694086219   7 LRTFLEAYRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATEAADEL---ARAI 69
Cdd:PRK11233   6 LKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILythARAI 71
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 7-190 1.38e-07

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 51.77  E-value: 1.38e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219   7 LRTFLEAYRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATEAADELARAISPYIDGLAEKLSSLRAG 86
Cdd:PRK11139  11 LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKLRAR 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  87 AESGG-TVNLagPPDF-IH---SRLGavmaplmkegyrlRFHTGNKQ---RIYSLLQ-EGS----VDLAVTasmpddrlY 153
Cdd:PRK11139  91 SAKGAlTVSL--LPSFaIQwlvPRLS-------------SFNEAHPDidvRLKAVDRlEDFlrddVDVAIR--------Y 147

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 694086219 154 GYAH--------LLTERMLLVHSPRLteTLGTQP--SAATLASVPLI 190
Cdd:PRK11139 148 GRGNwpglrvekLLDEYLLPVCSPAL--LNGGKPlkTPEDLARHTLL 192
PRK12680 PRK12680
LysR family transcriptional regulator;
22-240 1.93e-07

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 51.55  E-value: 1.93e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  22 AAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKA-TEAADEL---ARAISPYIDGLAEKLSSLRAgaESGGTVNLAG 97
Cdd:PRK12680  22 AAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLESvTPAGVEVierARAVLSEANNIRTYAANQRR--ESQGQLTLTT 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  98 ppdfIHSRLGAVMAP---LMKEGYR---LRFHTGNKQRIYSLLQEGSVDLAVTASMPDDRLYGYAHLLTERMLLVHSPR- 170
Cdd:PRK12680 100 ----THTQARFVLPPavaQIKQAYPqvsVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAGIAVPLYRWRRLVVVPRg 175

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 694086219 171 -LTETLGTQPSAATLASVPLIAYDEELPLIRMVWTAMFQRAPDMQASFTIQDLRIIRDLVRDGHGWSVLPD 240
Cdd:PRK12680 176 hALDTPRRAPDMAALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLIKTYVRAGLGVGLLAE 246
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
7-259 3.17e-07

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 50.82  E-value: 3.17e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219   7 LRTFLEAYRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATEAADELARAISPYIDGLAEKLSSLRAG 86
Cdd:PRK10082  16 LYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNLAELRGG 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  87 AE---------SGGTVNLAGPPDFIHSrlgavMAPLmkegYRLRFHTGNKQRIYSLLQEGSVDLAVtaSMPDDRL----Y 153
Cdd:PRK10082  96 SDyaqrkikiaAAHSLSLGLLPSIISQ-----MPPL----FTWAIEAIDVDEAVDKLREGQSDCIF--SFHDEDLleapF 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 154 GYAHLLTERMLLV-HSPRLTETLGT--QPsaatlaSVPLIAYDEELPLIRMVWTAMFQRAPDMQASFTIQDL-RIIRDLV 229
Cdd:PRK10082 165 DHIRLFESQLFPVcASDEHGEALFNlaQP------HFPLLNYSRNSYMGRLINRTLTRHSELSFSTFFVSSMsELLKQVA 238

                        250       260       270
                 ....*....|....*....|....*....|
gi 694086219 230 RDGHGWSVLPDYHCLDDLKSGRLVSVTKAE 259
Cdd:PRK10082 239 LDGCGIAWLPEYAIQQEIRSGQLVVLNRDE 268
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 91-255 5.15e-07

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 4. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176162 [Multi-domain]  Cd Length: 202  Bit Score: 49.09  E-value: 5.15e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  91 GTVNLAGPPDFIHSRLGAVMAPLMKE--GYRLRFHTGNkqRIYSLLQEGsVDLA--VTASMPDD-----RLYGYAHLLte 161
Cdd:cd08473    3 GTVRVSCPPALAQELLAPLLPRFMAAypQVRLQLEATN--RRVDLIEEG-IDVAlrVRFPPLEDsslvmRVLGQSRQR-- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 162 rmlLVHSPRLTETLGTQPSAATLASVPLIAYDEELPliRMVWTamFQRAPDMQASFTIQ------DLRIIRDLVRDGHGW 235
Cdd:cd08473   78 ---LVASPALLARLGRPRSPEDLAGLPTLSLGDVDG--RHSWR--LEGPDGESITVRHRprlvtdDLLTLRQAALAGVGI 150

                        170       180
                 ....*....|....*....|
gi 694086219 236 SVLPDYHCLDDLKSGRLVSV 255
Cdd:cd08473  151 ALLPDHLCREALRAGRLVRV 170
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-259 9.57e-07

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 49.25  E-value: 9.57e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219   1 MSHLIHLRTfLEAYR-SGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATEAAD---ELARAISPYIDGL 76
Cdd:PRK15421   1 MIEVKHLKT-LQALRnCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEillQLANQVLPQISQA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  77 AE-----KLSSLRAGAESGGTVNLAGPP-DFIHSRLGAVmaplmkegyRLRFHTGNKQRIYSLLQEGSVDLAVTAS-MPD 149
Cdd:PRK15421  80 LQacnepQQTRLRIAIECHSCIQWLTPAlENFHKNWPQV---------EMDFKSGVTFDPQPALQQGELDLVMTSDiLPR 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 150 DRLYgYAHLLTERMLLVHSPRLTETLGTQPSAATLASVPLIAYdeelPLIRM---VWTAMFQRAPDMQASFTIQDLRIIR 226
Cdd:PRK15421 151 SGLH-YSPMFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIY----PVQRSrldVWRHFLQPAGVSPSLKSVDNTLLLI 225

                        250       260       270
                 ....*....|....*....|....*....|...
gi 694086219 227 DLVRDGHGWSVLPDYHCLDDLKSGRLVSVTKAE 259
Cdd:PRK15421 226 QMVAARMGIAALPHWVVESFERQGLVVTKTLGE 258
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 4-69 1.04e-06

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 49.00  E-value: 1.04e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 694086219   4 LIHLRTFLEAYRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATEAAD---ELARAI 69
Cdd:PRK09906   3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEvflQDARAI 71
PRK09986 PRK09986
LysR family transcriptional regulator;
7-240 1.64e-06

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 48.57  E-value: 1.64e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219   7 LRTFLEAYRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATEAADELARAISPYIDGLAEKLSSLRA- 85
Cdd:PRK09986  12 LRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARVEQi 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  86 GAESGGTVNLAgppdFIHSRLGAVMAPLMKegyRLRFHTGN---------KQRIYSLLQEGSVDLAVTASMPDDRLYGYA 156
Cdd:PRK09986  92 GRGEAGRIEIG----IVGTALWGRLRPAMR---HFLKENPNvewllrelsPSMQMAALERRELDAGIWRMADLEPNPGFT 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 157 HL-LTERMLLVHSPRltetlgtQPSAATLASVPLIAYDEE----LPLIRMVWTAMFQRAPdMQASFTIQDLRIIRD---- 227
Cdd:PRK09986 165 SRrLHESAFAVAVPE-------EHPLASRSSVPLKALRNEyfitLPFVHSDWGKFLQRVC-QQAGFSPQIIRQVNEpqtv 236

                        250
                 ....*....|....*
gi 694086219 228 --LVRDGHGWSVLPD 240
Cdd:PRK09986 237 laMVSMGIGITLLPD 251
leuO PRK09508
leucine transcriptional activator; Reviewed
 20-65 6.56e-06

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 46.94  E-value: 6.56e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 694086219  20 SRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATEAADEL 65
Cdd:PRK09508  40 TRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARARQL 85
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 7-287 1.92e-05

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 45.37  E-value: 1.92e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219   7 LRTFLEAYRSG-SFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATEaadELARAISPYIDGLAEKLSSLRA 85
Cdd:PRK12682   6 LRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKGLT---EPGKAVLDVIERILREVGNIKR 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  86 GAE-----SGGTVNLAGppdfIHSRLGAVMAPLMKEgYRLRF-------HTGNKQRIYSLLQEGSVDLA-VTASMPDD-- 150
Cdd:PRK12682  83 IGDdfsnqDSGTLTIAT----THTQARYVLPRVVAA-FRKRYpkvnlslHQGSPDEIARMVISGEADIGiATESLADDpd 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 151 ----RLYGYAH--LLTERMLLVHSPRLTetlgtqpsAATLASVPLIAYDEELPLiRMVWTAMFQRA---PDMqaSFTIQD 221
Cdd:PRK12682 158 latlPCYDWQHavIVPPDHPLAQEERIT--------LEDLAEYPLITYHPGFTG-RSRIDRAFAAAglqPDI--VLEAID 226

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 694086219 222 LRIIRDLVRDGHGWSVLPDYhCLDDLKSGRLVSVtkaetaPVNHLYLAwNKSNANNRRTAYVRDYI 287
Cdd:PRK12682 227 SDVIKTYVRLGLGVGIVAEM-AYRPDRDGDLVAL------PAGHLFGP-NTAWVALKRGAYLRNYV 284
cbl PRK12679
HTH-type transcriptional regulator Cbl;
7-268 2.80e-05

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 44.80  E-value: 2.80e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219   7 LRTFLEAYRSG-SFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIReaRGvKATEAADELARAISPYIDGLAEKLSSLRA 85
Cdd:PRK12679   6 LKIIREAARQDyNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIR--RG-KRLLGMTEPGKALLVIAERILNEASNVRR 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  86 GA-----ESGGTVNLAGppdfIHSRLGAVMAPLMKE------GYRLRFHTGNKQRIYSLLQEGSVDLAVTASM--PDDRL 152
Cdd:PRK12679  83 LAdlftnDTSGVLTIAT----THTQARYSLPEVIKAfrelfpEVRLELIQGTPQEIATLLQNGEADIGIASERlsNDPQL 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 153 YGYAHLLTERMLLVhsPRLTETLGTQP-SAATLASVPLIAYDEELPLiRMVWTAMFQRA---PDMQASftIQDLRIIRDL 228
Cdd:PRK12679 159 VAFPWFRWHHSLLV--PHDHPLTQITPlTLESIAKWPLITYRQGITG-RSRIDDAFARKgllADIVLS--AQDSDVIKTY 233

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 694086219 229 VRDGHGWSVLPDYHClDDLKSGRLVSVTKAETAPVNHLYL 268
Cdd:PRK12679 234 VALGLGIGLVAEQSS-GEQEESNLIRLDTRHLFDANTVWL 272
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
7-294 3.38e-05

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 44.62  E-value: 3.38e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219   7 LRTFLEAYRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATEAADELAraisPYidglAEKLSS--LR 84
Cdd:PRK03601   6 LKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLL----PY----AETLMNtwQA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  85 AGAESGGT-----VNLAGPPDFIHSRLGAVMAPLMKEGYRLRFHTGNKQRiYSL---LQEGSVDLAVTASMPddrlygya 156
Cdd:PRK03601  78 AKKEVAHTsqhneLSIGASASLWECMLTPWLGRLYQNQEALQFEARIAQR-QSLvkqLHERQLDLLITTEAP-------- 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 157 hllteRMLLVHSPRLTE-TLGTQPSAATLASvpliaydEELPLIRMVWTAMFQR------APDMQASFTIQDLRIIRDLV 229
Cdd:PRK03601 149 -----KMDEFSSQLLGHfTLALYTSAPSKKK-------SELNYIRLEWGADFQQheagliGADEVPILTTSSAELARQLL 216

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 694086219 230 RDGHGWSVLPDYHCldDLKSGrLVSVTKAETApVNHLYLAWNKsnaNNRRTAYVRDyiLNAFPLN 294
Cdd:PRK03601 217 ATLNGCAFLPVHWA--KEKGG-LHTVPDSTTL-SRPLYAIWLQ---NSDKQALIRD--LLKTPVL 272
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 102-286 3.45e-05

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


Pssm-ID: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 43.72  E-value: 3.45e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 102 IHSRLGAVMAPLMKEGYRLRFH--TGNKQRIYSLLQEGSVDLAVTA--SMPDDRLYGYAHLLTERMLLVHSPRLTETlgt 177
Cdd:cd08427   11 LTGLLPRALARLRRRHPDLEVHivPGLSAELLARVDAGELDAAIVVepPFPLPKDLVWTPLVREPLVLIAPAELAGD--- 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 178 qPSAATLASVPLIAYDEELPLIRMVWTAMFQRAPDMQASFTIQDLRIIRDLVRDGHGWSVLPDYhCLDDLKSGRLVSVTK 257
Cdd:cd08427   88 -DPRELLATQPFIRYDRSAWGGRLVDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAIVPDI-AVPLPAGPRVRVLPL 165

                        170       180
                 ....*....|....*....|....*....
gi 694086219 258 AETAPVNHLYLAWNKSNANNRRTAYVRDY 286
Cdd:cd08427  166 GDPAFSRRVGLLWRRSSPRSRLIQALLEA 194
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 129-270 1.63e-04

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 7. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176165  Cd Length: 197  Bit Score: 41.85  E-value: 1.63e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 129 RIYSLLQEGsVDLAV-TASMPDDRLYGYAhLLTERMLLVHSPRLTETLGTQPSAATLASVPLIAYD-------EELPLIR 200
Cdd:cd08476   37 RLVDVIDEG-FDAVIrTGELPDSRLMSRR-LGSFRMVLVASPDYLARHGTPETPADLAEHACLRYRfpttgklEPWPLRG 114

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 201 MVWTAmfqrAPDMQASFTIQDLRIIRDLVRDGHGWSVLPDYHCLDDLKSGRLVSVTKAETAPVNHLYLAW 270
Cdd:cd08476  115 DGGDP----ELRLPTALVCNNIEALIEFALQGLGIACLPDFSVREALADGRLVTVLDDYVEERGQFRLLW 180
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 119-272 4.52e-04

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: 40.55  E-value: 4.52e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 119 RLRFHTGNKQRIYSLLQEGSVDLAVTASMPDDRLYGYAHLLTERMLLVHSPRLTETLGTQPSAATLASVPLIAYDE---- 194
Cdd:cd08420   30 RVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDHPLAGRKEVTAEELAAEPWILREPgsgt 109

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 694086219 195 -ElpLIRMVWTAMFQRAPDMQASFTIQDLRIIRDLVRDGHGWSVLPDYHCLDDLKSGRLVSVTKAETAPVNHLYLAWNK 272
Cdd:cd08420  110 rE--VFERALAEAGLDGLDLNIVMELGSTEAIKEAVEAGLGISILSRLAVRKELELGRLVALPVEGLRLTRPFSLIYHK 186
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
7-194 5.02e-04

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 41.12  E-value: 5.02e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219   7 LRTFLEAYRSG-SFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREA-RGVKATEAadelARAISPYIDGLAEKLSSLR 84
Cdd:PRK12684   6 LRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGkRLRGLTEP----GRIILASVERILQEVENLK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  85 -----AGAESGGTVNLAGPPDFIHSRLGAVMAPLMKEgY---RLRFHTGNKQRIYSLLQEGSVDLAV-TASMPDDR---- 151
Cdd:PRK12684  82 rvgkeFAAQDQGNLTIATTHTQARYALPAAIKEFKKR-YpkvRLSILQGSPTQIAEMVLHGQADLAIaTEAIADYKelvs 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 694086219 152 LYGYAHlltERMLLV---HsPRLTE---TLgtqpsaATLASVPLIAYDE 194
Cdd:PRK12684 161 LPCYQW---NHCVVVppdH-PLLERkplTL------EDLAQYPLITYDF 199
PRK11482 PRK11482
DNA-binding transcriptional regulator;
5-83 7.65e-04

DNA-binding transcriptional regulator;


Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 40.48  E-value: 7.65e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219   5 IHLRTFLEA-YRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATEAADELARAISpyiDGLAEKLSSL 83
Cdd:PRK11482  31 LNLLTIFEAvYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHEYIS---QGLESILGAL 107
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 212-255 1.12e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 5. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176163 [Multi-domain]  Cd Length: 202  Bit Score: 39.37  E-value: 1.12e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 694086219 212 DMQASFTIQDLRIIRDLVRDGHGWSVLPDYHCLDDLKSGRLVSV 255
Cdd:cd08474  127 DVEGPLILNDSDLMLDAALDGLGIAYLFEDLVAEHLASGRLVRV 170
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 4-51 1.17e-03

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 39.67  E-value: 1.17e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 694086219   4 LIHLRTFLEAYRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIR 51
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDR 52
nhaR PRK11062
transcriptional activator NhaR; Provisional
 1-60 1.21e-03

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 39.61  E-value: 1.21e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 694086219   1 MSHLI--HLRTFLEAYRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATE 60
Cdd:PRK11062   1 MSHINynHLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTE 62
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 101-276 2.01e-03

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: 38.64  E-value: 2.01e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 101 FIHSRLGAVMAPLMKE------GYRLRFHTGNKQRIYSLLQEGSVDLAVTASMPDDRLYGYAHLLTERMLLV----HspR 170
Cdd:cd08414    6 FVGSALYGLLPRLLRRfrarypDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVAlpadH--P 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 171 LTEtlGTQPSAATLASVPLIAYD-EELPLIRMVWTAMFQRA---PdmQASFTIQDLRIIRDLVRDGHGWSVLPDyhCLDD 246
Cdd:cd08414   84 LAA--RESVSLADLADEPFVLFPrEPGPGLYDQILALCRRAgftP--RIVQEASDLQTLLALVAAGLGVALVPA--SVAR 157

                        170       180       190
                 ....*....|....*....|....*....|
gi 694086219 247 LKSGRLVSVTKAETAPVNHLYLAWNKSNAN 276
Cdd:cd08414  158 LQRPGVVYRPLADPPPRSELALAWRRDNAS 187
PBP2_DntR_like_2 cd08464
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 97-171 2.42e-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: 38.37  E-value: 2.42e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 694086219  97 GPPDFIHSRLGAVMAPLMKE---GYRLRFHTGNKQRIYSLLQEGSVDLAVTASMPDDRLYGYAHLLTERMLLVHSPRL 171
Cdd:cd08464    5 GLSDDVESWLAPPLLAALRAeapGVRLVFRQVDPFNVGDMLDRGEIDLAIGVFGELPAWLKREVLYTEGYACLFDPQQ 82
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 117-276 2.69e-03

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 37.97  E-value: 2.69e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 117 GYRLRFHTGNKQRIYSLLQEGSVDLAVtASMPDDRLYGYAH--LLTERMLLVHSP--RLTETlgTQPSAATLASVPLIAY 192
Cdd:cd08436   28 GVDIRLRQAGSDDLLAAVREGRLDLAF-VGLPERRPPGLASreLAREPLVAVVAPdhPLAGR--RRVALADLADEPFVDF 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 193 DEELPLIRMVWTAmFQRA---PDMQasFTIQDLRIIRDLVRDGHGWSVLPDYHCLDDlksGRLVSVTkAETAPVNHLYLA 269
Cdd:cd08436  105 PPGTGARRQVDRA-FAAAgvrRRVA--FEVSDVDLLLDLVARGLGVALLPASVAARL---PGLAALP-LEPAPRRRLYLA 177


                 ....*..
gi 694086219 270 WNKSNAN 276
Cdd:cd08436  178 WSAPPPS 184
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
1-73 3.44e-03

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 38.50  E-value: 3.44e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 694086219   1 MSHLIH--LRTFLEAYRSGSFSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATEAADELARAI-SPYI 73
Cdd:PRK15243   1 MDFLINkkLKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQTIYRKVkSHYI 76
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 19-165 3.72e-03

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 38.47  E-value: 3.72e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  19 FSRAAQVLGISQPAASQHIQSLEVLTGKRLFIREARGVKATEAADEL---ARAISPYIDGLAEkLSSLRAGAESG----G 91
Cdd:PRK11151  18 FRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLvdqARTVLREVKVLKE-MASQQGETMSGplhiG 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219  92 TVNLAGP---PDFIhsrlgavmaPLMKEGY---RLRFHTGNKQRIYSLLQEGSVDLAVTASMPDDRLYGYAHLLTERMLL 165
Cdd:PRK11151  97 LIPTVGPyllPHII---------PMLHQTFpklEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFIEVPLFDEPMLL 167
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 119-286 6.56e-03

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: 37.14  E-value: 6.56e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 119 RLRFHTGNKQRIYSLLQEGSVDLAVTASMPDDRLYGYAHLLT-ERMLLVH-SPRLTEtlGTQPSAATLASVPLIAYDeeL 196
Cdd:cd08412   30 EVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARlPPYVWLPaDHPLAG--KDEVSLADLAAEPLILLD--L 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 197 PLIRMVWTAMFQRAPDM-QASFTIQDLRIIRDLVRDGHGWSVLPD----YHCLDdlkSGRLVSVTKAETAPVNHLYLAWN 271
Cdd:cd08412  106 PHSREYFLSLFAAAGLTpRIAYRTSSFEAVRSLVANGLGYSLLNDrpyrPWSYD---GKRLVRRPLADPVPPLRLGLAWR 182

                        170
                 ....*....|....*
gi 694086219 272 KSNANNRRTAYVRDY 286
Cdd:cd08412  183 RGARLTRAARAFVDF 197
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 129-287 6.74e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 6. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176164 [Multi-domain]  Cd Length: 199  Bit Score: 36.76  E-value: 6.74e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 129 RIYSLLQEGsVDLAVTASMPDDRLYGYAHLL-TERMLLVHSPRLTETLGTQPSAATLASVPLIAYDEELPLIRmvWtamf 207
Cdd:cd08475   39 RFVDLIEEG-IDLAVRIGELADSTGLVARRLgTQRMVLCASPAYLARHGTPRTLEDLAEHQCIAYGRGGQPLP--W---- 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694086219 208 qRAPDMQASFT---------IQDLRIIRDLVRDGHGWSVLPDYHCLDDLKSGRLVSVTKAETAPVNHLYLAWNKSNANNR 278
Cdd:cd08475  112 -RLADEQGRLVrfrpaprlqFDDGEAIADAALAGLGIAQLPTWLVADHLQRGELVEVLPELAPEGLPIHAVWPRTRHLPP 190


                 ....*....
gi 694086219 279 RTAYVRDYI 287
Cdd:cd08475  191 KVRAAVDAL 199
 
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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