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Conserved domains on  [gi|446345343|ref|WP_000423198|]
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LysR family transcriptional regulator [Bacillus cereus]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-284 1.24e-59

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 190.46  E-value: 1.24e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   1 MELRHLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDVYN 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  81 EIFELKGVKRGVITIgGLLEDL--TYLTPYIMKFQQHYPNIVVKIIE--SEVAVNQIVDKNIDIGITRSAQIPDTLTSTL 156
Cdd:COG0583   81 ELRALRGGPRGTLRI-GAPPSLarYLLPPLLARFRARHPGVRLELREgnSDRLVDALLEGELDLAIRLGPPPDPGLVARP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 157 LYSEELVLVIPKNHPLNETSFVSFrelvglsrimvscscresikiycerlglslseanietkSSISLLSLVYNGHGVAII 236
Cdd:COG0583  160 LGEERLVLVASPDHPLARRAPLVN--------------------------------------SLEALLAAVAAGLGIALL 201

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 446345343 237 PLSLV-DFVNNDTLSIVRIIDPTSRQDINLIHFDDKFLSFAARIFMQKL 284
Cdd:COG0583  202 PRFLAaDELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFL 250
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-284 1.24e-59

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 190.46  E-value: 1.24e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   1 MELRHLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDVYN 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  81 EIFELKGVKRGVITIgGLLEDL--TYLTPYIMKFQQHYPNIVVKIIE--SEVAVNQIVDKNIDIGITRSAQIPDTLTSTL 156
Cdd:COG0583   81 ELRALRGGPRGTLRI-GAPPSLarYLLPPLLARFRARHPGVRLELREgnSDRLVDALLEGELDLAIRLGPPPDPGLVARP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 157 LYSEELVLVIPKNHPLNETSFVSFrelvglsrimvscscresikiycerlglslseanietkSSISLLSLVYNGHGVAII 236
Cdd:COG0583  160 LGEERLVLVASPDHPLARRAPLVN--------------------------------------SLEALLAAVAAGLGIALL 201

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 446345343 237 PLSLV-DFVNNDTLSIVRIIDPTSRQDINLIHFDDKFLSFAARIFMQKL 284
Cdd:COG0583  202 PRFLAaDELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFL 250
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-286 3.00e-46

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: 157.39  E-value: 3.00e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   1 MELRHLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDVYN 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  81 EIFELKGVKRGVITIGGLLEDLTYLTPYIMK-FQQHYPNIVVKIIE--SEVAVNQIVDKNIDIGITRSAQIPDTLTSTLL 157
Cdd:NF040786  81 EFDRYGKESKGVLRIGASTIPGQYLLPELLKkFKEKYPNVRFKLMIsdSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 158 YSEELVLVIPKNHPLNE--TSFVSFRELVGLSRIMvscscRE-------SIKIYCERLGLSLSEANI--ETKSSISLLSL 226
Cdd:NF040786 161 YKDRLVLITPNGTEKYRmlKEEISISELQKEPFIM-----REegsgtrkEAEKALKSLGISLEDLNVvaSLGSTEAIKQS 235

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446345343 227 VYNGHGVAIIP-LSLVDFVNNDTLSIVRIIDPTSRQDINLIHFDDKFLSFAARIFMQKLNE 286
Cdd:NF040786 236 VEAGLGISVISeLAAEKEVERGRVLIFPIPGLPKNRDFYLVYNKNRQLSPTAEAFLQFVKE 296
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-282 3.43e-37

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 133.54  E-value: 3.43e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   1 MELRHLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDVYN 80
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  81 EIFELKGVKRGVITIGGLLEDLTYLT-PYIMKFQQHYPNIVVKIIE--SEVAVNQIVDKNIDIGI----TRSAQIpdtlT 153
Cdd:PRK11242  81 AIHDVADLSRGSLRLAMTPTFTAYLIgPLIDAFHARYPGITLTIREmsQERIEALLADDELDVGIafapVHSPEI----E 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 154 STLLYSEELVLVIPKNHPL-NETSFVSFRELVGLSRIMVSCS--CRESIKIYCERLGLS---LSEANietksSIS-LLSL 226
Cdd:PRK11242 157 AQPLFTETLALVVGRHHPLaARRKALTLDELADEPLVLLSAEfaTREQIDRYFRRHGVTprvAIEAN-----SISaVLEI 231

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446345343 227 VYNGHGVAIIPLSLVdfVNNDTLSIVRIIDPTSRQDINLIHFDDKFLSFAARIFMQ 282
Cdd:PRK11242 232 VRRGRLATLLPAAIA--REHDGLCAIPLDPPLPQRTAALLRRKGAYRSAAARAFIE 285
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 102-282 4.88e-32

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: 117.32  E-value: 4.88e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 102 LTYLTPYIMKFQQHYPNIVVKIIE--SEVAVNQIVDKNIDIGITRSAQIPDTLTSTLLYSEELVLVIPKNHPLNETSFVS 179
Cdd:cd05466   12 AYLLPPLLAAFRQRYPGVELSLVEggSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPDHPLAKRKSVT 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 180 FRELVGLSRIMVS--CSCRESIKIYCERLGLSLSEAnIETKSSISLLSLVYNGHGVAIIPLSLVDFVNNDTLSIVRIIDP 257
Cdd:cd05466   92 LADLADEPLILFErgSGLRRLLDRAFAEAGFTPNIA-LEVDSLEAIKALVAAGLGIALLPESAVEELADGGLVVLPLEDP 170

                        170       180
                 ....*....|....*....|....*
gi 446345343 258 TSRQDINLIHFDDKFLSFAARIFMQ 282
Cdd:cd05466  171 PLSRTIGLVWRKGRYLSPAARAFLE 195
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-286 8.18e-29

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: 109.30  E-value: 8.18e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   90 RGVITIGgLLEDL--TYLTPYIMKFQQHYPNIVVKIIE--SEVAVNQIVDKNIDIGITRSAQIPDTLTSTLLYSEELVLV 165
Cdd:pfam03466   1 SGRLRIG-APPTLasYLLPPLLARFRERYPDVELELTEgnSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  166 IPKNHPLNETSFVSFRELVGLSRIMVS--CSCRESIKIYCERLGLSLsEANIETKSSISLLSLVYNGHGVAIIPLSLV-D 242
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADEPLILLPpgSGLRDLLDRALRAAGLRP-RVVLEVNSLEALLQLVAAGLGIALLPRSAVaR 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 446345343  243 FVNNDTLSIVRIIDPTSRQDINLIHFDDKFLSFAARIFMQKLNE 286
Cdd:pfam03466 159 ELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLRE 202
TF_pcaQ TIGR02424
pca operon transcription factor PcaQ; Members of this family are LysR-family transcription ...
 1-284 2.20e-26

pca operon transcription factor PcaQ; Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria. [Energy metabolism, Other, Regulatory functions, DNA interactions]


Pssm-ID: 274127 [Multi-domain]  Cd Length: 300  Bit Score: 105.18  E-value: 2.20e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343    1 MELRHLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDVYN 80
Cdd:TIGR02424   3 IKFRHLQCFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGTPLFERDRRGIRLTRYGELFLRHAGASLAALRQGVA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   81 EIFELKGVKRGVITIGGLLEDLTYLTPYIMK-FQQHYPNIVVKII--ESEVAVNQIVDKNIDIGITRSAQiPDT---LTS 154
Cdd:TIGR02424  83 SLSQLGEGEGPTVRIGALPTVAARLMPEVVKrFLARAPRLRVRIMtgPNAYLLDQLRVGALDLVVGRLGA-PETmqgLSF 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  155 TLLYSEELVLVIPKNHPLNETSFVSFRELVGLSRIMVSCScrESIKIYCERL----GLSLSEANIETKSSISLLSLVYNG 230
Cdd:TIGR02424 162 EHLYNEPVVFVVRAGHPLLAAPSLPVASLADYPVLLPPEG--SAIRPLAERLfiacGIPPPPQRIETVSGSFGRRYVQES 239

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 446345343  231 HGVAIIPLSLVDF-VNNDTLSIVRIIDPTSRQDINLIHFDDKFLSFAARIFMQKL 284
Cdd:TIGR02424 240 DAIWIISRGVVALdLADGTLVELPFDTRETGGPVGLCTRPDTQLSRAAQLFVDAL 294
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-284 1.24e-59

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 190.46  E-value: 1.24e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   1 MELRHLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDVYN 80
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  81 EIFELKGVKRGVITIgGLLEDL--TYLTPYIMKFQQHYPNIVVKIIE--SEVAVNQIVDKNIDIGITRSAQIPDTLTSTL 156
Cdd:COG0583   81 ELRALRGGPRGTLRI-GAPPSLarYLLPPLLARFRARHPGVRLELREgnSDRLVDALLEGELDLAIRLGPPPDPGLVARP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 157 LYSEELVLVIPKNHPLNETSFVSFrelvglsrimvscscresikiycerlglslseanietkSSISLLSLVYNGHGVAII 236
Cdd:COG0583  160 LGEERLVLVASPDHPLARRAPLVN--------------------------------------SLEALLAAVAAGLGIALL 201

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 446345343 237 PLSLV-DFVNNDTLSIVRIIDPTSRQDINLIHFDDKFLSFAARIFMQKL 284
Cdd:COG0583  202 PRFLAaDELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFL 250
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-286 3.00e-46

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: 157.39  E-value: 3.00e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   1 MELRHLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDVYN 80
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  81 EIFELKGVKRGVITIGGLLEDLTYLTPYIMK-FQQHYPNIVVKIIE--SEVAVNQIVDKNIDIGITRSAQIPDTLTSTLL 157
Cdd:NF040786  81 EFDRYGKESKGVLRIGASTIPGQYLLPELLKkFKEKYPNVRFKLMIsdSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 158 YSEELVLVIPKNHPLNE--TSFVSFRELVGLSRIMvscscRE-------SIKIYCERLGLSLSEANI--ETKSSISLLSL 226
Cdd:NF040786 161 YKDRLVLITPNGTEKYRmlKEEISISELQKEPFIM-----REegsgtrkEAEKALKSLGISLEDLNVvaSLGSTEAIKQS 235

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446345343 227 VYNGHGVAIIP-LSLVDFVNNDTLSIVRIIDPTSRQDINLIHFDDKFLSFAARIFMQKLNE 286
Cdd:NF040786 236 VEAGLGISVISeLAAEKEVERGRVLIFPIPGLPKNRDFYLVYNKNRQLSPTAEAFLQFVKE 296
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-282 3.43e-37

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 133.54  E-value: 3.43e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   1 MELRHLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDVYN 80
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  81 EIFELKGVKRGVITIGGLLEDLTYLT-PYIMKFQQHYPNIVVKIIE--SEVAVNQIVDKNIDIGI----TRSAQIpdtlT 153
Cdd:PRK11242  81 AIHDVADLSRGSLRLAMTPTFTAYLIgPLIDAFHARYPGITLTIREmsQERIEALLADDELDVGIafapVHSPEI----E 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 154 STLLYSEELVLVIPKNHPL-NETSFVSFRELVGLSRIMVSCS--CRESIKIYCERLGLS---LSEANietksSIS-LLSL 226
Cdd:PRK11242 157 AQPLFTETLALVVGRHHPLaARRKALTLDELADEPLVLLSAEfaTREQIDRYFRRHGVTprvAIEAN-----SISaVLEI 231

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446345343 227 VYNGHGVAIIPLSLVdfVNNDTLSIVRIIDPTSRQDINLIHFDDKFLSFAARIFMQ 282
Cdd:PRK11242 232 VRRGRLATLLPAAIA--REHDGLCAIPLDPPLPQRTAALLRRKGAYRSAAARAFIE 285
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 102-282 4.88e-32

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: 117.32  E-value: 4.88e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 102 LTYLTPYIMKFQQHYPNIVVKIIE--SEVAVNQIVDKNIDIGITRSAQIPDTLTSTLLYSEELVLVIPKNHPLNETSFVS 179
Cdd:cd05466   12 AYLLPPLLAAFRQRYPGVELSLVEggSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPDHPLAKRKSVT 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 180 FRELVGLSRIMVS--CSCRESIKIYCERLGLSLSEAnIETKSSISLLSLVYNGHGVAIIPLSLVDFVNNDTLSIVRIIDP 257
Cdd:cd05466   92 LADLADEPLILFErgSGLRRLLDRAFAEAGFTPNIA-LEVDSLEAIKALVAAGLGIALLPESAVEELADGGLVVLPLEDP 170

                        170       180
                 ....*....|....*....|....*
gi 446345343 258 TSRQDINLIHFDDKFLSFAARIFMQ 282
Cdd:cd05466  171 PLSRTIGLVWRKGRYLSPAARAFLE 195
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-286 3.31e-31

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 118.20  E-value: 3.31e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   3 LRHLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDVYNEI 82
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  83 FELKGVKRGVITIGGLLEDLTYLTPYIMK-FQQHYPNIVVKI-IESE--VAVNqIVDKNIDIGITrSAQIPDTLTSTL-- 156
Cdd:CHL00180  87 EDLKNLQRGTLIIGASQTTGTYLMPRLIGlFRQRYPQINVQLqVHSTrrIAWN-VANGQIDIAIV-GGEVPTELKKILei 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 157 --LYSEELVLVIPKNHPLNETSFVSFRELVGLSRIMV--SCSCRESIKIYCERLGLSLSEANIETK--SSISLLSLVYNG 230
Cdd:CHL00180 165 tpYVEDELALIIPKSHPFAKLKKIQKEDLYRLNFITLdsNSTIRKVIDNILIQNGIDSKRFKIEMElnSIEAIKNAVQSG 244

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446345343 231 HGVAIIPLSLVDF-VNNDTLSIVRIIDPTSRQDINLIHFDDKFLSFAARIFMQKLNE 286
Cdd:CHL00180 245 LGAAFVSVSAIEKeLELGLLHWIKIENITIKRMLSIITNPNRYKSKASETFYNEILT 301
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 90-286 8.18e-29

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: 109.30  E-value: 8.18e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   90 RGVITIGgLLEDL--TYLTPYIMKFQQHYPNIVVKIIE--SEVAVNQIVDKNIDIGITRSAQIPDTLTSTLLYSEELVLV 165
Cdd:pfam03466   1 SGRLRIG-APPTLasYLLPPLLARFRERYPDVELELTEgnSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  166 IPKNHPLNETSFVSFRELVGLSRIMVS--CSCRESIKIYCERLGLSLsEANIETKSSISLLSLVYNGHGVAIIPLSLV-D 242
Cdd:pfam03466  80 APPDHPLARGEPVSLEDLADEPLILLPpgSGLRDLLDRALRAAGLRP-RVVLEVNSLEALLQLVAAGLGIALLPRSAVaR 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 446345343  243 FVNNDTLSIVRIIDPTSRQDINLIHFDDKFLSFAARIFMQKLNE 286
Cdd:pfam03466 159 ELADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLRE 202
TF_pcaQ TIGR02424
pca operon transcription factor PcaQ; Members of this family are LysR-family transcription ...
 1-284 2.20e-26

pca operon transcription factor PcaQ; Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria. [Energy metabolism, Other, Regulatory functions, DNA interactions]


Pssm-ID: 274127 [Multi-domain]  Cd Length: 300  Bit Score: 105.18  E-value: 2.20e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343    1 MELRHLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDVYN 80
Cdd:TIGR02424   3 IKFRHLQCFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGTPLFERDRRGIRLTRYGELFLRHAGASLAALRQGVA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   81 EIFELKGVKRGVITIGGLLEDLTYLTPYIMK-FQQHYPNIVVKII--ESEVAVNQIVDKNIDIGITRSAQiPDT---LTS 154
Cdd:TIGR02424  83 SLSQLGEGEGPTVRIGALPTVAARLMPEVVKrFLARAPRLRVRIMtgPNAYLLDQLRVGALDLVVGRLGA-PETmqgLSF 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  155 TLLYSEELVLVIPKNHPLNETSFVSFRELVGLSRIMVSCScrESIKIYCERL----GLSLSEANIETKSSISLLSLVYNG 230
Cdd:TIGR02424 162 EHLYNEPVVFVVRAGHPLLAAPSLPVASLADYPVLLPPEG--SAIRPLAERLfiacGIPPPPQRIETVSGSFGRRYVQES 239

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 446345343  231 HGVAIIPLSLVDF-VNNDTLSIVRIIDPTSRQDINLIHFDDKFLSFAARIFMQKL 284
Cdd:TIGR02424 240 DAIWIISRGVVALdLADGTLVELPFDTRETGGPVGLCTRPDTQLSRAAQLFVDAL 294
phn_lysR TIGR03339
aminoethylphosphonate catabolism associated LysR family transcriptional regulator; This group ...
 6-262 3.83e-26

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: 104.05  E-value: 3.83e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343    6 LEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDVYNEIFEL 85
Cdd:TIGR03339   2 LKAFHAVARCGSFTRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRLELTDAGHRLLPIVERLFQQEAEAEFLLRES 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   86 KGVKRGVITIGGllEDLTYLTPYIMKFQQHYPNIVVK--IIESEVAVNQIVDKNIDIGItrSAQIPDT--LTSTLLYSEE 161
Cdd:TIGR03339  82 GALREGSLRIAA--TAPYYVLDLVARFRQRYPGIEVSvrIGNSQEVLQALQSYRVDVAV--SSEVVDDprLDRVVLGNDP 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  162 LVLVIPKNHPLNETSFVSFRELVGLSRIM--VSCSCRESIKIYCERLGLSLSEAnIETKSSISLLSLVYNGHGVAIIPLS 239
Cdd:TIGR03339 158 LVAVVHRQHPLAERESVTLEELAGQPLLMrePGSVTRQTTEEALAAAGVAPRPA-LEIGSREAIREAVLAGLGVSVVSAA 236

                         250       260
                  ....*....|....*....|...
gi 446345343  240 lvDFVNNDTLSIVRIIDPTSRQD 262
Cdd:TIGR03339 237 --EVGRDPRLRVLPIVGAEPTMD 257
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-62 9.64e-25

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 93.99  E-value: 9.64e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343    3 LRHLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGK 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-258 2.56e-24

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 99.76  E-value: 2.56e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   1 MELRHLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDVYN 80
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  81 EIFELKGVKRGVITIG---GLLEDLTYLtPYIMKFQQHYPNIVVKIIESEVAV--NQIVDKNIDIGITRSAQIPDTLTST 155
Cdd:PRK11233  81 AVHNVGQALSGQVSIGlapGTAASSLTM-PLLQAVRAEFPGIVLYLHENSGATlnEKLMNGQLDMAVIYEHSPVAGLSSQ 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 156 LLYSEELVLVIPKNHPLNETSFVSFREL-VGLSRIMvsCSCRESIKIYCERLGLSlseANI--ETKSSISLLSLVYNGHG 232
Cdd:PRK11233 160 PLLKEDLFLVGTQDCPGQSVDLAAVAQMnLFLPRDY--SAVRLRVDEAFSLRRLT---AKVigEIESIATLTAAIASGMG 234

                        250       260
                 ....*....|....*....|....*..
gi 446345343 233 VAIIPLSLVDFVNNDTLS-IVRIIDPT 258
Cdd:PRK11233 235 VTVLPESAARSLCGAVNGwMARITTPS 261
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-237 5.05e-24

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 98.69  E-value: 5.05e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   1 MELRHLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDVYN 80
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  81 EIFELKGVKRgVITIGGLLEDLTYLTPYIM-KFQQHYPNIVVKII-----ESEVAVNQivdKNIDIGITRSAQIPDTLTS 154
Cdd:PRK09906  81 RARKIVQEDR-QLTIGFVPSAEVNLLPKVLpMFRLRHPDTLIELVslittQQEEKLRR---GELDVGFMRHPVYSDEIDY 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 155 TLLYSEELVLVIPKNHPLNETSFVSFRELVGLSRIMV----SCSCRESIKIYCERLGLSLSeaNIETKSSISL-LSLVYN 229
Cdd:PRK09906 157 LELLDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTdpaySGSLAPIIKAWFAQHNSQPN--IVQVATNILVtMNLVGM 234


                 ....*...
gi 446345343 230 GHGVAIIP 237
Cdd:PRK09906 235 GLGCTIIP 242
PRK09986 PRK09986
LysR family transcriptional regulator;
3-239 1.42e-22

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 94.79  E-value: 1.42e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   3 LRHLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDVYNEI 82
Cdd:PRK09986   9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLARV 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  83 FELKGVKRGVITIGGLLEDL-TYLTPYIMKFQQHYPNIVVKIIESEVAVnQIV---DKNIDIGITRSA--QIPDTLTSTL 156
Cdd:PRK09986  89 EQIGRGEAGRIEIGIVGTALwGRLRPAMRHFLKENPNVEWLLRELSPSM-QMAaleRRELDAGIWRMAdlEPNPGFTSRR 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 157 LYSEELVLVIPKNHPLNETSFVSFRELVGlsRIMVSCSCRES-----IKIYCERLGLSlSEANIETKSSISLLSLVYNGH 231
Cdd:PRK09986 168 LHESAFAVAVPEEHPLASRSSVPLKALRN--EYFITLPFVHSdwgkfLQRVCQQAGFS-PQIIRQVNEPQTVLAMVSMGI 244


                 ....*...
gi 446345343 232 GVAIIPLS 239
Cdd:PRK09986 245 GITLLPDS 252
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 1-267 7.00e-21

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 90.09  E-value: 7.00e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   1 MELRHLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFdDVYN 80
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREV-KVLK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  81 EIFELKG------VKRGVI-TIGglledlTYLTPYIM-KFQQHYPNIVVKIIESEVA--VNQIVDKNIDIGITRSAQIPD 150
Cdd:PRK11151  80 EMASQQGetmsgpLHIGLIpTVG------PYLLPHIIpMLHQTFPKLEMYLHEAQTHqlLAQLDSGKLDCAILALVKESE 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 151 TLTSTLLYSEELVLVIPKNHPLNETSFVSFRELVGLSRIMVS---CsCRESIKIYCERLGLSLSE----ANIETkssisL 223
Cdd:PRK11151 154 AFIEVPLFDEPMLLAVYEDHPWANRDRVPMSDLAGEKLLMLEdghC-LRDQAMGFCFEAGADEDThfraTSLET-----L 227

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 446345343 224 LSLVYNGHGVAIIP-LSLVDFVNNDTLSIVRIIDPTSRQDINLIH 267
Cdd:PRK11151 228 RNMVAAGSGITLLPaLAVPNERKRDGVCYLPCIKPEPRRTIGLVY 272
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 94-284 1.77e-20

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: 86.78  E-value: 1.77e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  94 TIGglledlTYLTPYIM-KFQQHYPNIVVKIIE--SEVAVNQIVDKNIDIGITRSAQIPDTLTSTLLYSEELVLVIPKNH 170
Cdd:cd08420    9 TIG------EYLLPRLLaRFRKRYPEVRVSLTIgnTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDH 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 171 PLNETSFVSFRELVGLSRIMV---SCScRESIKIYCERLGLSLSEANI--ETKSSISLLSLVYNGHGVAIIP-LSLVDFV 244
Cdd:cd08420   83 PLAGRKEVTAEELAAEPWILRepgSGT-REVFERALAEAGLDGLDLNIvmELGSTEAIKEAVEAGLGISILSrLAVRKEL 161

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 446345343 245 NNDTLSIVRIIDPTSRQDINLIHFDDKFLSFAARIFMQKL 284
Cdd:cd08420  162 ELGRLVALPVEGLRLTRPFSLIYHKDKYLSPAAEAFLEFL 201
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 103-282 1.25e-19

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: 84.50  E-value: 1.25e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 103 TYLTPYIMKFQQHYPNIVVKIIEseVAVNQIVDK----NIDIGI-TRSAQIPDtLTSTLLYSEELVLVIPKNHPLNETSF 177
Cdd:cd08440   13 TLLPPVLAAFRRRHPGIRVRLRD--VSAEQVIEAvrsgEVDFGIgSEPEADPD-LEFEPLLRDPFVLVCPKDHPLARRRS 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 178 VSFRELVGLSRIMVS-CSC-RESIKIYCERLGLSLSeANIETKSSISLLSLVYNGHGVAIIPLSLVDFVNNDTLSIVRII 255
Cdd:cd08440   90 VTWAELAGYPLIALGrGSGvRALIDRALAAAGLTLR-PAYEVSHMSTALGMVAAGLGVAVLPALALPLADHPGLVARPLT 168

                        170       180
                 ....*....|....*....|....*..
gi 446345343 256 DPTSRQDINLIHFDDKFLSFAARIFMQ 282
Cdd:cd08440  169 EPVVTRTVGLIRRRGRSLSPAAQAFLD 195
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 4-242 1.64e-19

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 86.05  E-value: 1.64e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   4 RHLeyfiqvcnnnSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDVYNEIf 83
Cdd:PRK11139  19 RHL----------SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAEATRKL- 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  84 eLKGVKRGVITIgGLLEDLT--YLTPYIMKFQQHYPNIVVKIieseVAVNQIVD---KNIDIGITRSAQIPDTLTSTLLY 158
Cdd:PRK11139  88 -RARSAKGALTV-SLLPSFAiqWLVPRLSSFNEAHPDIDVRL----KAVDRLEDflrDDVDVAIRYGRGNWPGLRVEKLL 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 159 SEELVLV-----IPKNHPLNETSfvsfrELVGLSRIMVscSCRESIKIYCERLGlsLSEANIETKSSISLLSLVY----N 229
Cdd:PRK11139 162 DEYLLPVcspalLNGGKPLKTPE-----DLARHTLLHD--DSREDWRAWFRAAG--LDDLNVQQGPIFSHSSMALqaaiH 232

                        250
                 ....*....|...
gi 446345343 230 GHGVAIIPLSLVD 242
Cdd:PRK11139 233 GQGVALGNRVLAQ 245
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 112-267 2.06e-18

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: 81.01  E-value: 2.06e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 112 FQQHYPNIVVKIIE--SEVAVNQIVDKNIDIGITRSAQIPDTLTSTLLYSEELVLVIPKNHPLNETSFVSFRELVGLSRI 189
Cdd:cd08414   22 FRARYPDVELELREmtTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALPADHPLAARESVSLADLADEPFV 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 190 M----VSCSCRESIKIYCERLGLSLSEAnIETKSSISLLSLVYNGHGVAIIPLSLVDFVNNDtLSIVRIIDPTSRQDINL 265
Cdd:cd08414  102 LfprePGPGLYDQILALCRRAGFTPRIV-QEASDLQTLLALVAAGLGVALVPASVARLQRPG-VVYRPLADPPPRSELAL 179


                 ..
gi 446345343 266 IH 267
Cdd:cd08414  180 AW 181
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 105-278 4.51e-18

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: 80.29  E-value: 4.51e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 105 LTPYIMKFQQHYPNIVVKIIE--SEVAVNQIVDKNIDIGITRSAQIPDTLTSTLLYSEELVLVIPKNHP----------- 171
Cdd:cd08438   15 FAPLLAAFRQRYPNIELELVEygGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPRGHPlagrktvslad 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 172 LNETSFVSFRELVGLSRIMVSCscresikiyCERLGLSLseaNIETKSS-ISLL-SLVYNGHGVAIIPLSLVDFVNNDTL 249
Cdd:cd08438   95 LADEPFILFNEDFALHDRIIDA---------CQQAGFTP---NIAARSSqWDFIaELVAAGLGVALLPRSIAQRLDNAGV 162

                        170       180
                 ....*....|....*....|....*....
gi 446345343 250 SIVRIIDPTSRQDINLIHFDDKFLSFAAR 278
Cdd:cd08438  163 KVIPLTDPDLRWQLALIWRKGRYLSHAAR 191
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 103-280 9.51e-18

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: 79.50  E-value: 9.51e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 103 TYLTP-YIMKFQQHYPNIVVKIIE--SEVAVNQIVDKNIDIGITRSAQIPDTLTSTLLYSEELVLVIPKNHPLNETSFVS 179
Cdd:cd08434   12 TSLVPdLIRAFRKEYPNVTFELHQgsTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPKDHPLAGRDSVD 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 180 FRELVGLSRIMVS--CSCRESIKIYCERLGLSLSEAnIETKSSISLLSLVYNGHGVAIIPLSlvDFVNNDTLSIVRIIDP 257
Cdd:cd08434   92 LAELADEPFVLLSpgFGLRPIVDELCAAAGFTPKIA-FEGEEDSTIAGLVAAGLGVAILPEM--TLLNPPGVKKIPIKDP 168

                        170       180
                 ....*....|....*....|...
gi 446345343 258 TSRQDINLIHFDDKFLSFAARIF 280
Cdd:cd08434  169 DAERTIGLAWLKDRYLSPAARRF 191
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 3-260 1.83e-17

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 80.81  E-value: 1.83e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   3 LRHLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDVYNEI 82
Cdd:PRK11013   6 LRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSYYGLDRIVSAA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  83 FELKGVKRGVITIGGL-LEDLTYLTPYIMKFQQHYPNIVVKII--ESEVAVNQIVDKNIDIGITRSAQIPDTLTSTLLYS 159
Cdd:PRK11013  86 ESLREFRQGQLSIACLpVFSQSLLPGLCQPFLARYPDVSLNIVpqESPLLEEWLSAQRHDLGLTETLHTPAGTERTELLT 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 160 EELVLVIPKNHPLNETSFVSFRELVGLSRIMVScscreSIKIYCERLGLSLSEANI------ETKSSISLLSLVYNGHGV 233
Cdd:PRK11013 166 LDEVCVLPAGHPLAAKKVLTPDDFAGENFISLS-----RTDSYRQLLDQLFAEHGVkrrmvvETHSAASVCAMVRAGVGV 240

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 446345343 234 AII-PLSLVDFVNND------TLSI---VRIIDPTSR 260
Cdd:PRK11013 241 SIVnPLTALDYAGSGlvvrrfSISVpftVSLIRPLHR 277
PRK09801 PRK09801
LysR family transcriptional regulator;
4-164 3.58e-16

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 77.00  E-value: 3.58e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   4 RHLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDVYNEIF 83
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  84 ELKGVKRGVITIGGLLE-DLTYLTPYIMKFQQHYPNIVVKIiesEVAVNQI--VDKNIDIGITRSAQIPDTLTSTLLYSE 160
Cdd:PRK09801  89 QIKTRPEGMIRIGCSFGfGRSHIAPAITELMRNYPELQVHF---ELFDRQIdlVQDNIDLDIRINDEIPDYYIAHLLTKN 165


                 ....
gi 446345343 161 ELVL 164
Cdd:PRK09801 166 KRIL 169
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-288 9.24e-16

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 75.49  E-value: 9.24e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   3 LRHLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDVYNEI 82
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIEQLF 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  83 FELKGVKR--GVITIGGLLedltyLTPYIMKFQQHYPNIVVK--IIESEVAVNQIVDKNIDIG-ITRSAQIPDTLTSTLL 157
Cdd:PRK10837  85 REDNGALRiyASSTIGNYI-----LPAMIARYRRDYPQLPLElsVGNSQDVINAVLDFRVDIGlIEGPCHSPELISEPWL 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 158 ySEELVLVIPKNHPLNETSfVSFRELVGLSRIM--VSCSCRESIkiycERLGLS-LSEANI--ETKSSISLLSLVYngHG 232
Cdd:PRK10837 160 -EDELVVFAAPDSPLARGP-VTLEQLAAAPWILreRGSGTREIV----DYLLLShLPRFELamELGNSEAIKHAVR--HG 231

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 446345343 233 VAIIPLS---LVDFVNNDTLSIVRIIDPTSRQDINLIHFDDKFLSFAARIFMQKLNEPE 288
Cdd:PRK10837 232 LGISCLSrrvIADQLQAGTLVEVAVPLPRLMRTLYRIHHRQKHLSNALQRFLSYCQEAN 290
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 105-282 2.50e-15

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: 72.58  E-value: 2.50e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 105 LTPYIM-----KFQQHYPNIVVKIIE--SEVAVNQIVDKNIDIGITRSAQIPDTLTSTLLYSEELVLVIPKNHPLNETSF 177
Cdd:cd08412   10 LAPYYLpgllrRFREAYPGVEVRVVEgnQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARLPPYVWLPADHPLAGKDE 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 178 VSFRELVGLSRIM----VScscRESIKIYCERLGLS----LSEANIETkssisLLSLVYNGHGVAIIPLSLVDFVNNDTL 249
Cdd:cd08412   90 VSLADLAAEPLILldlpHS---REYFLSLFAAAGLTpriaYRTSSFEA-----VRSLVANGLGYSLLNDRPYRPWSYDGK 161

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 446345343 250 SIVR--IIDPTSRQDINLIHFDDKFLSFAARIFMQ 282
Cdd:cd08412  162 RLVRrpLADPVPPLRLGLAWRRGARLTRAARAFVD 196
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-172 9.19e-15

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 73.10  E-value: 9.19e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   1 MELRHLEYFIQVCNNN-SFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIK-MTEAGKLLFDKGKFIMQQFDDV 78
Cdd:PRK12682   1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  79 YNEIFELKGVKRGVITIGGLLEDLTYLTPYIMK-FQQHYPNI-----------VVKIIESEVAvnqivdkniDIGITRSA 146
Cdd:PRK12682  81 KRIGDDFSNQDSGTLTIATTHTQARYVLPRVVAaFRKRYPKVnlslhqgspdeIARMVISGEA---------DIGIATES 151

                        170       180
                 ....*....|....*....|....*..
gi 446345343 147 QIPDTLTSTLLYSE-ELVLVIPKNHPL 172
Cdd:PRK12682 152 LADDPDLATLPCYDwQHAVIVPPDHPL 178
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 104-284 1.81e-14

The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 70.38  E-value: 1.81e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 104 YLTPYIMKFQQHYPNIVVKIIE--SEVAVNQIVDKNID--IGITRSAQIPDTLTSTLLYSEELVLVIPKNHPLNETSFVS 179
Cdd:cd08435   14 LLPPAIARLLARHPRLTVRVVEgtSDELLEGLRAGELDlaIGRLADDEQPPDLASEELADEPLVVVARPGHPLARRARLT 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 180 FRELVGLSRIM--VSCSCRESIKIYCERLGLSLSEANIETKSSISLLSLVYNGHGVAIIPLSLVDFVNND-TLSIVRIID 256
Cdd:cd08435   94 LADLADYPWVLppPGTPLRQRLEQLFAAAGLPLPRNVVETASISALLALLARSDMLAVLPRSVAEDELRAgVLRELPLPL 173

                        170       180
                 ....*....|....*....|....*...
gi 446345343 257 PTSRQDINLIHFDDKFLSFAARIFMQKL 284
Cdd:cd08435  174 PTSRRPIGITTRRGGPLSPAARALLDAL 201
nhaR PRK11062
transcriptional activator NhaR; Provisional
 5-65 4.28e-14

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 70.81  E-value: 4.28e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446345343   5 HLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLF 65
Cdd:PRK11062   8 HLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVF 68
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-172 5.49e-14

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 70.99  E-value: 5.49e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   6 LEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDVYNEIFEL 85
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  86 K-GVKRGV-ITIGGLLEDLTYLTPYIMKFQQHYPNIVVKIIES------EVAVNQivDKNIDIGITRSAQIPDTLTSTLL 157
Cdd:PRK10094  87 NdGVERQVnIVINNLLYNPQAVAQLLAWLNERYPFTQFHISRQiymgvwDSLLYE--GFSLAIGVTGTEALANTFSLDPL 164

                        170
                 ....*....|....*
gi 446345343 158 YSEELVLVIPKNHPL 172
Cdd:PRK10094 165 GSVQWRFVMAADHPL 179
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 107-242 1.94e-13

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: 67.68  E-value: 1.94e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 107 PYIMK-FQQHYPNIVVKIIE--SEVAVNQIVDKNIDIGITRSAQIPDTLTSTLLYSEELVLVIPKNHPLNETSFVSFREL 183
Cdd:cd08448   16 PRILRaFRAEYPGIEVALHEmsSAEQIEALLRGELDLGFVHSRRLPAGLSARLLHREPFVCCLPAGHPLAARRRIDLREL 95

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446345343 184 VGLSRIM----VSCSCRESIKIYCERLGLSlseANI--ETKSSISLLSLVYNGHGVAIIPLSLVD 242
Cdd:cd08448   96 AGEPFVLfsreVSPDYYDQIIALCMDAGFH---PKIrhEVRHWLTVVALVAAGMGVALVPRSLAR 157
PRK10341 PRK10341
transcriptional regulator TdcA;
4-256 2.77e-13

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 68.74  E-value: 2.77e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   4 RHLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDVYNEIF 83
Cdd:PRK10341  10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  84 ELKGVKRGVITIG-GLLEDLTYLTPYIMKFQQHYPNIVVKIIESEVA--VNQIVDKNID--IGITRSAQIPDTLTSTLLY 158
Cdd:PRK10341  90 GMSSEAVVDVSFGfPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSsfLPAIRDGRLDfaIGTLSNEMKLQDLHVEPLF 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 159 SEELVLVIPKNHPLNETsfVSFRELVGLSRIM-VSC-SCRESIKIYCERLGLSLSEAnIETKSSISLLSLVYNGHGVAII 236
Cdd:PRK10341 170 ESEFVLVASKSRTCTGT--TTLESLKNEQWVLpQTNmGYYSELLTTLQRNGISIENI-VKTDSVVTIYNLVLNADFLTVI 246

                        250       260
                 ....*....|....*....|
gi 446345343 237 PLSLVDFVNNDTLSIVRIID 256
Cdd:PRK10341 247 PCDMTSPFGSNQFITIPIEE 266
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-172 3.12e-13

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 68.46  E-value: 3.12e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   1 MELRHLEYFIQVCNNN-SFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVG-RGIKMTEAGKLLFDKGKFIMQQFDDV 78
Cdd:PRK12684   1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGkRLRGLTEPGRIILASVERILQEVENL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  79 YNEIFELKGVKRGVITIGGLLEDLTYLTPYIMK-FQQHYPNIVVKIIE---SEVAvNQIVDKNIDIGI-TRSAQIPDTLT 153
Cdd:PRK12684  81 KRVGKEFAAQDQGNLTIATTHTQARYALPAAIKeFKKRYPKVRLSILQgspTQIA-EMVLHGQADLAIaTEAIADYKELV 159

                        170
                 ....*....|....*....
gi 446345343 154 STLLYSEELVLVIPKNHPL 172
Cdd:PRK12684 160 SLPCYQWNHCVVVPPDHPL 178
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 92-284 4.05e-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: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 66.56  E-value: 4.05e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  92 VITIGGLLEDLtyLTPYIMKFQQHYPNIVVKIIESEVA--VNQIVDKNIDIGITRSAQIPDTLTSTLLYSEELVLVIPKN 169
Cdd:cd08426    4 VATGEGLAAEL--LPSLIARFRQRYPGVFFTVDVASTAdvLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVVPPG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 170 HPLNETSFVSFRELVGLSRIMV--SCSCRESIKIYCERLGLSLSEAnIETKSSISLLSLVYNGHGVAIIP-LSLVDFVNN 246
Cdd:cd08426   82 HPLARQPSVTLAQLAGYPLALPppSFSLRQILDAAFARAGVQLEPV-LISNSIETLKQLVAAGGGISLLTeLAVRREIRR 160

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 446345343 247 DTLSIVRIIDPTSR-QDINLIHFDDKFLSFAARIFMQKL 284
Cdd:cd08426  161 GQLVAVPLADPHMNhRQLELQTRAGRQLPAAASAFLQLL 199
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 107-284 7.35e-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: 66.08  E-value: 7.35e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 107 PYIMKFQQHYPNIVVKIIE--SEVAVNQIVDKNIDIGITRSAQIPDTLTSTLLYSEELVLVIPKNHPLNETSFVSFRELV 184
Cdd:cd08433   17 PLLRAVRRRYPGIRLRIVEglSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGPADAPLPRGAPVPLAELA 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 185 GLSRIMVSC--SCRESIKIYCERLGLSLSEAnIETKSSISLLSLVYNGHGVAIIPLSLVDF-VNNDTLSIVRIIDPTSRQ 261
Cdd:cd08433   97 RLPLILPSRghGLRRLVDEAAARAGLTLNVV-VEIDSVATLKALVAAGLGYTILPASAVAAeVAAGRLVAAPIVDPALTR 175

                        170       180
                 ....*....|....*....|...
gi 446345343 262 DINLIHFDDKFLSFAARIFMQKL 284
Cdd:cd08433  176 TLSLATPRDRPLSPAALAVRDLL 198
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
16-165 1.44e-12

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 66.56  E-value: 1.44e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  16 NSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKfimQQFDDVYNEIFELKGVK-RGVIT 94
Cdd:PRK10086  29 QSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALK---SSLDTLNQEILDIKNQElSGTLT 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  95 IgglledltY---------LTPYIMKFQQHYPNIVVKIIESevavNQIVDKN---IDIGITRSAQIPDTLTSTLLYSEEL 162
Cdd:PRK10086 106 V--------YsrpsiaqcwLVPRLADFTRRYPSISLTILTG----NENVNFQragIDLAIYFDDAPSAQLTHHFLMDEEI 173


                 ...
gi 446345343 163 VLV 165
Cdd:PRK10086 174 LPV 176
PRK09791 PRK09791
LysR family transcriptional regulator;
1-184 1.83e-12

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 66.32  E-value: 1.83e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   1 MELRHLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDVYN 80
Cdd:PRK09791   5 VKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQE 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  81 EIFELKGVKRGVITIG-GLLEDLTYLTPYIMKFQQHYPNIVVKIIESEVA--VNQIVDKNIDIGITRSAQIP--DTLTST 155
Cdd:PRK09791  85 DIRQRQGQLAGQINIGmGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVsmINELRQGELDFTINTYYQGPydHEFTFE 164

                        170       180
                 ....*....|....*....|....*....
gi 446345343 156 LLYSEELVLVIPKNHPLNETSfvSFRELV 184
Cdd:PRK09791 165 KLLEKQFAVFCRPGHPAIGAR--SLKQLL 191
leuO PRK09508
leucine transcriptional activator; Reviewed
 19-252 9.03e-12

leucine transcriptional activator; Reviewed


Pssm-ID: 181918 [Multi-domain]  Cd Length: 314  Bit Score: 64.27  E-value: 9.03e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  19 TKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKgkfIMQQFDDVYNEI----FELKGVKRGV-I 93
Cdd:PRK09508  40 TRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARARQLFGP---VRQALQLVQNELpgsgFEPESSERVFnL 116

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  94 TIGGLLEdlTYLTPYIM-KFQQHYPNIVVKIiESEVAVN---QIVDKNID--IGITRSAQiPDtLTSTLLYSEELVLVIP 167
Cdd:PRK09508 117 CICSPLD--IRLTSQIYnRIEQIAPNIHVVF-KSSLNQNiehQLRYQETEfvISYEEFDR-PE-FTSVPLFKDELVLVAS 191

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 168 KNHPLNETSfVSFRELVGLSRIMVSCSCRESIKIYCERLGLSLSEANIETKSSISLLSLVYNGHGVAIIPLSLVD-FVNN 246
Cdd:PRK09508 192 KNHPRIKGP-ITEEQLYNEQHAVVSLDRFASFSQPWYDTVDKQASIAYQGTALSSVLNVVSQTHLVAIAPRWLAEeFAES 270


                 ....*.
gi 446345343 247 DTLSIV 252
Cdd:PRK09508 271 LELQIL 276
cbl PRK12679
HTH-type transcriptional regulator Cbl;
19-183 2.28e-11

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 63.29  E-value: 2.28e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  19 TKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVG-RGIKMTEAGKLLFDKGKFIMQQFDDVYNEIFELKGVKRGVITIGG 97
Cdd:PRK12679  20 TEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGkRLLGMTEPGKALLVIAERILNEASNVRRLADLFTNDTSGVLTIAT 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  98 LLEDLTYLTPYIMK-FQQHYPNIVVKIIE---SEVaVNQIVDKNIDIGITrSAQIPD--TLTSTLLYSEELVLVIPKNHP 171
Cdd:PRK12679 100 THTQARYSLPEVIKaFRELFPEVRLELIQgtpQEI-ATLLQNGEADIGIA-SERLSNdpQLVAFPWFRWHHSLLVPHDHP 177

                        170
                 ....*....|..
gi 446345343 172 LNETSFVSFREL 183
Cdd:PRK12679 178 LTQITPLTLESI 189
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 109-267 2.68e-11

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: 61.42  E-value: 2.68e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 109 IMKFQQHYPNIVVKI-------IESEVAVNQIvdkniDIGITRSAQIPDTLTSTLLYSEELVLVIPKNHPLNETSFVSFR 181
Cdd:cd08415   19 IARFRARHPDVRISLhtlssstVVEAVLSGQA-----DLGLASLPLDHPGLESEPLASGRAVCVLPPGHPLARKDVVTPA 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 182 ELVGLSRIMVSCSC--RESIKIYCERLGLSLSeANIETKSSISLLSLVYNGHGVAII-PLSLVDFVNNDTlsIVRIIDPT 258
Cdd:cd08415   94 DLAGEPLISLGRGDplRQRVDAAFERAGVEPR-IVIETQLSHTACALVAAGLGVAIVdPLTAAGYAGAGL--VVRPFRPA 170


                 ....*....
gi 446345343 259 SRQDINLIH 267
Cdd:cd08415  171 IPFEFALVR 179
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-170 3.29e-11

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 62.86  E-value: 3.29e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   1 ME-LRHLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDVY 79
Cdd:PRK10632   1 MErLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVH 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  80 NEIFELKGVKRGVITIGG---LLEDLtyLTPYIMKFQQHYPNIVVKIIESEVAVNQIVDkNIDIGITRSAQIPDTLTSTL 156
Cdd:PRK10632  81 EQLYAFNNTPIGTLRIGCsstMAQNV--LAGLTAKMLKEYPGLSVNLVTGIPAPDLIAD-GLDVVIRVGALQDSSLFSRR 157

                        170
                 ....*....|....
gi 446345343 157 LYSEELVLVIPKNH 170
Cdd:PRK10632 158 LGAMPMVVCAAKSY 171
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-172 1.48e-10

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 60.83  E-value: 1.48e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   1 MELRHLEYFIQVCNNN-SFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVG-RGIKMTEAGKLLFDKGKFIMQQFDDV 78
Cdd:PRK12683   1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGkRLTGLTEPGKELLQIVERMLLDAENL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  79 YNEIFELKGVKRGVITIGGLLEDLTYLTPYIMK-FQQHYPNivVKIIESEVAVNQIV----DKNIDIGITRSA--QIPDt 151
Cdd:PRK12683  81 RRLAEQFADRDSGHLTVATTHTQARYALPKVVRqFKEVFPK--VHLALRQGSPQEIAemllNGEADIGIATEAldREPD- 157

                        170       180
                 ....*....|....*....|.
gi 446345343 152 LTSTLLYSEELVLVIPKNHPL 172
Cdd:PRK12683 158 LVSFPYYSWHHVVVVPKGHPL 178
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-183 4.83e-10

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 59.14  E-value: 4.83e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   1 MELRHLEYFIQVCNNN-SFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIK-MTEAGKLLFDKGKFIMQQFDDV 78
Cdd:PRK12681   1 MKLQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSKVESI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  79 YNEIFELKGVKRGVITIGGLLEDLTY-LTPYIMKFQQHYPNIVVKIIE------SEVAvnqiVDKNIDIGITRSAQipdt 151
Cdd:PRK12681  81 KSVAGEHTWPDKGSLYIATTHTQARYaLPPVIKGFIERYPRVSLHMHQgsptqiAEAA----AKGNADFAIATEAL---- 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 446345343 152 ltstLLYSEELVL---------VIPKNHPLNETSFVSFREL 183
Cdd:PRK12681 153 ----HLYDDLIMLpcyhwnrsvVVPPDHPLAKKKKLTIEEL 189
PRK12680 PRK12680
LysR family transcriptional regulator;
1-173 9.89e-10

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 58.48  E-value: 9.89e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   1 MELRHLEYFIQVCNNN-SFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIK-MTEAGKLLFDKGKFIMQQFDDV 78
Cdd:PRK12680   1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  79 YNEIFELKGVKRGVITIGGLLEDLTY-LTPYIMKFQQHYPNIVVKIIES--EVAVNQIVDKNIDIGITRSA-QIPDTLTS 154
Cdd:PRK12680  81 RTYAANQRRESQGQLTLTTTHTQARFvLPPAVAQIKQAYPQVSVHLQQAaeSAALDLLGQGDADIAIVSTAgGEPSAGIA 160

                        170
                 ....*....|....*....
gi 446345343 155 TLLYSEELVLVIPKNHPLN 173
Cdd:PRK12680 161 VPLYRWRRLVVVPRGHALD 179
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 112-240 1.62e-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: 56.42  E-value: 1.62e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 112 FQQHYPNIVVKIIESEVA--VNQIVDKNIDIGITRSA-QIPDTLTSTLLYSEELVLVIPKNHPLNETSFVSFRELVGLSR 188
Cdd:cd08451   23 FREAYPDVELTLEEANTAelLEALREGRLDAAFVRPPvARSDGLVLELLLEEPMLVALPAGHPLARERSIPLAALADEPF 102

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 446345343 189 IMVScscRE-------SIKIYCERLGLSLSEANiETKSSISLLSLVYNGHGVAIIPLSL 240
Cdd:cd08451  103 ILFP---RPvgpglydAIIAACRRAGFTPRIGQ-EAPQMASAINLVAAGLGVSIVPASM 157
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 105-239 2.24e-09

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: 56.13  E-value: 2.24e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 105 LTPYIMKFQQHYPNIVVKIIE--SEVAVNQIVDKNIDIGITRSA---QIPDtLTSTLLYSEELVLVIPKNHPLNETSFVS 179
Cdd:cd08449   15 LGPALRRFKRQYPNVTVRFHElsPEAQKAALLSKRIDLGFVRFAdtlNDPP-LASELLWREPMVVALPEEHPLAGRKSLT 93

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446345343 180 FREL-----VGLSR--------IMVSCscresIKI-YCERLGLSLSEANietkssiSLLSLVYNGHGVAIIPLS 239
Cdd:cd08449   94 LADLrdepfVFLRLansrfadfLINCC-----LQAgFTPQITQEVVEPQ-------TLMALVAAGFGVALVPES 155
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
27-168 9.20e-09

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 55.21  E-value: 9.20e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  27 ISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDVYNEIFELKGVKRGVITIgglledltY-- 104
Cdd:PRK11716   3 VSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSL--------Fcs 74

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446345343 105 -------LTPYIMKFQQHYPNIVVKII--ESEVAVNQIVDKNIDIGItrsAQIPDTLTSTLLYSE----ELVLVIPK 168
Cdd:PRK11716  75 vtaayshLPPILDRFRAEHPLVEIKLTtgDAADAVEKVQSGEADLAI---AAKPETLPASVAFSPideiPLVLIAPA 148
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 112-284 1.17e-08

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


Pssm-ID: 176113  Cd Length: 198  Bit Score: 54.06  E-value: 1.17e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 112 FQQHYPNIVVKIIE--SEVAVNQIVDKNIDIGITRSAQIPDTLTsTLLYSE-ELVLVIPKNHPLNETSFVSFREL----- 183
Cdd:cd08421   22 FLAAHPDVRIDLEErlSADIVRAVAEGRADLGIVAGNVDAAGLE-TRPYRTdRLVVVVPRDHPLAGRASVAFADTldhdf 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 184 VGLSRimvSCSCRESIKIYCERLGLSLSeANIETKSSISLLSLVYNGHGVAIIPLSLVD-FVNNDTLSIVRIIDPTSRQD 262
Cdd:cd08421  101 VGLPA---GSALHTFLREAAARLGRRLR-LRVQVSSFDAVCRMVAAGLGIGIVPESAARrYARALGLRVVPLDDAWARRR 176

                        170       180
                 ....*....|....*....|..
gi 446345343 263 INLIHFDDKFLSFAARIFMQKL 284
Cdd:cd08421  177 LLLCVRSFDALPPAARALVDHL 198
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-142 3.61e-08

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 53.46  E-value: 3.61e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   1 MELRHLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDVYN 80
Cdd:PRK14997   2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQD 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446345343  81 EIFELKGVKRGVITIGGLLEDL-TYLTPYIMKFQQHYPNIVVKIIESEVAVNqIVDKNIDIGI 142
Cdd:PRK14997  82 AIAALQVEPRGIVKLTCPVTLLhVHIGPMLAKFMARYPDVSLQLEATNRRVD-VVGEGVDVAI 143
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-237 5.76e-08

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


Pssm-ID: 176115 [Multi-domain]  Cd Length: 200  Bit Score: 51.83  E-value: 5.76e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 105 LTPYIMKFQQHYPNIVVKIIESEVA--VNQIVDKNIDIGI-----TRSAQIPDTLTSTLLYSEELVLVIPKNHPLNETSF 177
Cdd:cd08423   15 LPPALAALRARHPGLEVRLREAEPPesLDALRAGELDLAVvfdypVTPPPDDPGLTRVPLLDDPLDLVLPADHPLAGREE 94

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446345343 178 VSFRELVGLSRIM--VSCSCRESIKIYCERLGLslsEANI--ETKSSISLLSLVYNGHGVAIIP 237
Cdd:cd08423   95 VALADLADEPWIAgcPGSPCHRWLVRACRAAGF---TPRIahEADDYATVLALVAAGLGVALVP 155
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-178 8.51e-08

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 52.34  E-value: 8.51e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   1 MELRHLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDD--- 77
Cdd:PRK15092  11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEacs 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  78 --VYNEIfelkgvkRGVITIGGLLEDLTYLTPYIM-KFQQHYPNIVvkiiesevavnqivdknIDIGITRSAQIPDtlts 154
Cdd:PRK15092  91 slMYSNL-------QGVLTIGASDDTADTILPFLLnRVSSVYPKLA-----------------LDVRVKRNAFMME---- 142

                        170       180
                 ....*....|....*....|....
gi 446345343 155 tLLYSEELVLVIPKNHPLNETSFV 178
Cdd:PRK15092 143 -MLESQEVDLAVTTHRPSSFPALN 165
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 92-238 1.98e-07

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: 50.45  E-value: 1.98e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  92 VITIGGLLEDLTYLTPYIMK-FQQHYPNIVVKII-----ESEVAVNQivdKNIDIGITRSAQIPDTLTSTLLYSEELVLV 165
Cdd:cd08450    1 VLTIGFLPGAEVQWLPEVLPiLREEHPDLDVELSslfspQLAEALMR---GKLDVAFMRPEIQSDGIDYQLLLKEPLIVV 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446345343 166 IPKNHPLNETSFVSFRELVGLSRIMVSCSCR---ESIKIYCERLGLSLSEanIETKSSISL-LSLVYNGHGVAIIPL 238
Cdd:cd08450   78 LPADHRLAGREKIPPQDLAGENFISPAPTAPvlqQVIENYAAQHNIQPNI--IQEADNLLSaMSLVASTLGCALLPL 152
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 91-266 2.91e-07

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: 49.83  E-value: 2.91e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  91 GVI-TIGglledlTYLTPYIMK-FQQHYPNIVVKIIE--SEVAVNQIVDKNIDIGITRSAQIPDTLTSTLLYSEELVLVI 166
Cdd:cd08411    6 GVIpTIA------PYLLPRLLPaLRQAYPKLRLYLREdqTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 167 PKNHPLNETSFVSFRELVGLSRIMVS---CsCRESIKIYCERLGLSLSE----ANIETkssisLLSLVYNGHGVAIIPLS 239
Cdd:cd08411   80 PKDHPLAKRKSVTPEDLAGERLLLLEeghC-LRDQALELCRLAGAREQTdfeaTSLET-----LRQMVAAGLGITLLPEL 153

                        170       180
                 ....*....|....*....|....*....
gi 446345343 240 LVDFVNN--DTLSIVRIIDPTSRQDINLI 266
Cdd:cd08411  154 AVPSEELrgDRLVVRPFAEPAPSRTIGLV 182
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 104-282 3.40e-07

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: 49.81  E-value: 3.40e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 104 YLTPYIM-KFQQHYPNIVVKIIES--EVAVNQIVDKNIDIGITrsAQIPDTL--TSTLLYSEELVLVIPKNHPLNETSFV 178
Cdd:cd08419   12 YFAPRLLgAFCRRHPGVEVSLRVGnrEQVLERLADNEDDLAIM--GRPPEDLdlVAEPFLDNPLVVIAPPDHPLAGQKRI 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 179 SFRELVGLSRIMvscscRE-------SIKIYCERLGLSLSEAnIETKSSISLLSLVYNGHGVAIIPL-SLVDFVNNDTLS 250
Cdd:cd08419   90 PLERLAREPFLL-----REpgsgtrlAMERFFAEHGVTLRVR-MELGSNEAIKQAVMAGLGLSVLSLhTLALELATGRLA 163

                        170       180       190
                 ....*....|....*....|....*....|...
gi 446345343 251 IVRIID-PTSRQdINLIHFDDKFLSFAARIFMQ 282
Cdd:cd08419  164 VLDVEGfPIRRQ-WYVVHRKGKRLSPAAQAFLD 195
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 102-267 4.96e-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: 49.11  E-value: 4.96e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 102 LTYLTPYIMK-FQQHYPNIVVKIIE--SEVAVNQIVDKNIDIGI-TR-SAQIPDTLTSTLLYSEELVLVIPKNHP----- 171
Cdd:cd08427   11 LTGLLPRALArLRRRHPDLEVHIVPglSAELLARVDAGELDAAIvVEpPFPLPKDLVWTPLVREPLVLIAPAELAgddpr 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 172 --LNETSFVSFRELVGLSRImvscscresIKIYCERLGLSLSEAnIETKSSISLLSLVYNGHGVAIIPLSLVDFVNNDTL 249
Cdd:cd08427   91 elLATQPFIRYDRSAWGGRL---------VDRFLRRQGIRVREV-MELDSLEAIAAMVAQGLGVAIVPDIAVPLPAGPRV 160

                        170
                 ....*....|....*...
gi 446345343 250 SIVRIIDPTSRQDINLIH 267
Cdd:cd08427  161 RVLPLGDPAFSRRVGLLW 178
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
17-64 5.42e-07

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 49.77  E-value: 5.42e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 446345343  17 SFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRvGRGIKMTEAGKLL 64
Cdd:PRK03635  18 SFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRL 64
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 105-274 7.61e-07

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


Pssm-ID: 176133  Cd Length: 193  Bit Score: 48.76  E-value: 7.61e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 105 LTPYIMKFQQHYPN--IVVKIIESEVAVNQIVDKNIDIG-ITRSAQIPDtLTSTLLYSEELVLVIPKNHP-------LNE 174
Cdd:cd08442   15 LPPLLAAYHARYPKvdLSLSTGTTGALIQAVLEGRLDGAfVAGPVEHPR-LEQEPVFQEELVLVSPKGHPpvsraedLAG 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 175 TSFVSFRElvglsrimvSCSCRESIKIYCERLGLSLSEAnIETKSSISLLSLVYNGHGVAIIPLSLVD-FVNNDTLSIVR 253
Cdd:cd08442   94 STLLAFRA---------GCSYRRRLEDWLAEEGVSPGKI-MEFGSYHAILGCVAAGMGIALLPRSVLDsLQGRGSVSIHP 163

                        170       180
                 ....*....|....*....|.
gi 446345343 254 IIDPTSRQDINLIHFDDKFLS 274
Cdd:cd08442  164 LPEPFADVTTWLVWRKDSFTA 184
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 103-281 8.44e-07

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: 48.48  E-value: 8.44e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 103 TYLT-PYIMKFQQHYPNIVVKIIE-SEVAVNQ-IVDKNIDIGITRSAQIPDTLTSTLLYSEELVLVIPKNHPL-NETSFV 178
Cdd:cd08425   13 AYLIgPLIDRFHARYPGIALSLREmPQERIEAaLADDRLDLGIAFAPVRSPDIDAQPLFDERLALVVGATHPLaQRRTAL 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 179 SFRELVGLSRIMVSCS--CRESIKIYCERLGLSLSEAnIETKSSISLLSLVYNGHGVAIIPLSLVdfVNNDTLSIVRIID 256
Cdd:cd08425   93 TLDDLAAEPLALLSPDfaTRQHIDRYFQKQGIKPRIA-IEANSISAVLEVVRRGRLATILPDAIA--REQPGLCAVALEP 169

                        170       180
                 ....*....|....*....|....*
gi 446345343 257 PTSRQDINLIHFDDKFLSFAARIFM 281
Cdd:cd08425  170 PLPGRTAALLRRKGAYRSAAARAFA 194
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
1-157 9.08e-07

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 49.25  E-value: 9.08e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   1 MELRHLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDVYN 80
Cdd:PRK03601   1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  81 EIF------ELkgvkrgviTIGG---LLEdlTYLTPYIMKFQQHYPNIVvkiIESEVA-----VNQIVDKNIDIGITRSA 146
Cdd:PRK03601  81 EVAhtsqhnEL--------SIGAsasLWE--CMLTPWLGRLYQNQEALQ---FEARIAqrqslVKQLHERQLDLLITTEA 147

                        170
                 ....*....|.
gi 446345343 147 QIPDTLTSTLL 157
Cdd:PRK03601 148 PKMDEFSSQLL 158
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-255 1.36e-06

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 48.86  E-value: 1.36e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   1 MELRHLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDVYN 80
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQ 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  81 EIFELKGVK-RGVITIGGLLEdltYLTPYIMKFQQHYPNIVVKI-----IESEVAVNQivdKNIDIGITRSAQIPDTLTS 154
Cdd:PRK15421  82 ACNEPQQTRlRIAIECHSCIQ---WLTPALENFHKNWPQVEMDFksgvtFDPQPALQQ---GELDLVMTSDILPRSGLHY 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 155 TLLYSEELVLVIPKNHPLNETSFVSFRELVGLSRIM--VSCSCRESIKIYCERLGLSLSEANIEtkSSISLLSLVYNGHG 232
Cdd:PRK15421 156 SPMFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIypVQRSRLDVWRHFLQPAGVSPSLKSVD--NTLLLIQMVAARMG 233

                        250       260
                 ....*....|....*....|...
gi 446345343 233 VAIIPLSLVDFVNNDTLSIVRII 255
Cdd:PRK15421 234 IAALPHWVVESFERQGLVVTKTL 256
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
1-87 1.99e-06

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 48.51  E-value: 1.99e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343   1 MELRHLEYFIQVCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDdvyN 80
Cdd:PRK10082  11 IETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLE---S 87


                 ....*..
gi 446345343  81 EIFELKG 87
Cdd:PRK10082  88 NLAELRG 94
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 112-284 5.89e-06

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


Pssm-ID: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 46.06  E-value: 5.89e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 112 FQQHYPNIVVKIIE--SEVAVNQIVDKNIDIGI-TRSAQIPDTLTSTLLYSEELVLVIPKNHPLNETSFVSFRELVGlsR 188
Cdd:cd08436   22 FHRRHPGVDIRLRQagSDDLLAAVREGRLDLAFvGLPERRPPGLASRELAREPLVAVVAPDHPLAGRRRVALADLAD--E 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 189 IMV----SCSCRESIKIYCERLGLslsEANI--ETKSSISLLSLVYNGHGVAIIPLSLVDfvNNDTLSIVRIIDPTSRQd 262
Cdd:cd08436  100 PFVdfppGTGARRQVDRAFAAAGV---RRRVafEVSDVDLLLDLVARGLGVALLPASVAA--RLPGLAALPLEPAPRRR- 173

                        170       180
                 ....*....|....*....|..
gi 446345343 263 INLIHFDDKfLSFAARIFMQKL 284
Cdd:cd08436  174 LYLAWSAPP-PSPAARAFLELL 194
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 109-244 7.54e-06

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: 45.87  E-value: 7.54e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 109 IMKFQQHYPNIVVKII--ESEVaVNQIVD-KNIDIGITRSAQIPDTLTSTLLYSEELVLVIPKNHPLNETSFVSFRELVG 185
Cdd:cd08456   19 IKAFLQRHPDVTISIHtrDSPT-VEQWLSaQQCDLGLVSTLHEPPGIERERLLRIDGVCVLPPGHRLAVKKVLTPSDLEG 97

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446345343 186 LSRIMVSCS--CRESIKIYCERLGLSlSEANIETKSSISLLSLVYNGHGVAII-PLSLVDFV 244
Cdd:cd08456   98 EPFISLARTdgTRQRVDALFEQAGVK-RRIVVETSYAATICALVAAGVGVSVVnPLTALDYA 158
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 12-78 1.09e-05

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 46.09  E-value: 1.09e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446345343  12 VCNNNSFTKAAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDKGKFIMQQFDDV 78
Cdd:PRK11074  13 VARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQET 79
PBP2_BenM_CatM_CatR cd08445
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 109-271 1.26e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold; This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes of the ortho-pathway required for benzoate catabolism: muconate lactonizing enzyme I, muconolactone isomerase, and catechol 1,2-dioxygenase. CatR normally responds to benzoate and cis,cis-muconate, an inducer molecule, to activate transcription of the catBCA operon, whose gene products convert benzoate to catechol. 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: 176136  Cd Length: 203  Bit Score: 45.30  E-value: 1.26e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 109 IMKFQQHYPNIVVKIIESeVAVNQI---VDKNIDIGITRsAQIPDT-LTSTLLYSEELVLVIPKNHPLNETSF-VSFREL 183
Cdd:cd08445   20 IRRFRQAAPDVEIELIEM-TTVQQIealKEGRIDVGFGR-LRIEDPaIRRIVLREEPLVVALPAGHPLAQEKApLTLAQL 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 184 VGLSRIMVSCSCRESIKIYC----ERLGLSLSEANiETKSSISLLSLVYNGHGVAIIPLSLVDFvnndtlsivriidptS 259
Cdd:cd08445   98 ADEPLILYPASPRPSFADQVlslfRDHGLRPRVIQ-EVRELQTALGLVAAGEGVTLVPASVQRL---------------R 161

                        170
                 ....*....|..
gi 446345343 260 RQDINLIHFDDK 271
Cdd:cd08445  162 RDDVVYRPLLDP 173
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 104-242 1.44e-05

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


Pssm-ID: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 44.90  E-value: 1.44e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 104 YLTPYIMK-FQQHYPNIVVKI--IESEVAVNQIVDKNIDIGITRSAQIPDTLTSTLLYSEELVLVIPKNHPLNETSfVSF 180
Cdd:cd08417   13 LLLPPLLArLRQEAPGVRLRFvpLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARKDHPLAGGP-LTL 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446345343 181 RELVGLSRIMVSC--SCRESIKIYCERLGLSLSEAnIETKSSISLLSLVYNGHGVAIIPLSLVD 242
Cdd:cd08417   92 EDYLAAPHVLVSPrgRGHGLVDDALAELGLSRRVA-LTVPHFLAAPALVAGTDLIATVPRRLAE 154
PBP2_LeuO cd08466
The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an ...
 104-242 3.09e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold; LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse model of Salmonella. In Vibrio cholerae, LeuO is involved in control of biofilm formation and in the stringent response. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176155 [Multi-domain]  Cd Length: 200  Bit Score: 43.78  E-value: 3.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 104 YLTPYIMK-FQQHYPNIVVKI--IESEVAVNQI----VDKNIDIGITRSAQIpdtlTSTLLYSEELVLVIPKNHP-LNET 175
Cdd:cd08466   13 LLLPRLLArLKQLAPNISLREspSSEEDLFEDLrlqeVDLVIDYVPFRDPSF----KSELLFEDELVCVARKDHPrIQGS 88

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446345343 176 sfVSFRELVGLSRIMVScSCRESI---KIYCERlglSLSEANI--ETKSSISLLSLVYNGHGVAIIPLSLVD 242
Cdd:cd08466   89 --LSLEQYLAEKHVVLS-LRRGNLsalDLLTEE---VLPQRNIayEVSSLLSMLAVVSQTDLIAIAPRWLAD 154
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 103-282 3.10e-05

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


Pssm-ID: 176110 [Multi-domain]  Cd Length: 201  Bit Score: 43.88  E-value: 3.10e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 103 TYLTPYIMKFQQHYPNIVVKIIESEVA--VNQIVDKNIDIGI-TRSAQIPD-TLTSTLLYSEELVLVIPKNHPLNETSfv 178
Cdd:cd08418   13 TLMPAVINRFKEQFPDVQISIYEGQLSslLPELRDGRLDFAIgTLPDEMYLkELISEPLFESDFVVVARKDHPLQGAR-- 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 179 SFRELVGLSRIM-VSC-----SCRESIKiyceRLGLSLSEAnIETKSSISLLSLVYNGHGVAIIPLSLV-DFVNNDTLSI 251
Cdd:cd08418   91 SLEELLDASWVLpGTRmgyynNLLEALR----RLGYNPRVA-VRTDSIVSIINLVEKADFLTILSRDMGrGPLDSFRLIT 165

                        170       180       190
                 ....*....|....*....|....*....|.
gi 446345343 252 VRIIDPTSRQDINLIHFDDKFLSFAARIFMQ 282
Cdd:cd08418  166 IPVEEPLPSADYYLIYRKKSRLTPLAEQLVE 196
PBP2_DntR_like_3 cd08461
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-192 5.99e-05

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


Pssm-ID: 176150 [Multi-domain]  Cd Length: 198  Bit Score: 43.04  E-value: 5.99e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 105 LTPYIMKFQQHYPN--IVVKIIESEVAVNQIVDKNIDIGITRSAQIPDTLTSTLLYSEELVLVIPKNHPLNETSfVSFRE 182
Cdd:cd08461   15 LPPLLAALRQEAPGvrVAIRDLESDNLEAQLERGEVDLALTTPEYAPDGLRSRPLFEERYVCVTRRGHPLLQGP-LSLDQ 93

                         90
                 ....*....|
gi 446345343 183 LVGLSRIMVS 192
Cdd:cd08461   94 FCALDHIVVS 103
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 108-243 9.89e-05

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: 42.48  E-value: 9.89e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 108 YIMKFQQHYPNIVVKI--IESEVAVNQIVDKNIDIGITRSAQIPDTLTSTLLYSEELVLVIPKNHPLNETSFVSFRELVG 185
Cdd:cd08457   18 FLAAFLRLRPNLHLSLmgLSSSQVLEAVASGRADLGIADGPLEERQGFLIETRSLPAVVAVPMGHPLAQLDVVSPQDLAG 97

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446345343 186 lSRIMVSCS---CRESIKIYCERLGLSLSeANIETKSSISLLSLVYNGHGVAII-PLSLVDF 243
Cdd:cd08457   98 -ERIITLENgylFRMRVEVALGKIGVKRR-PIIEVNLSHTALSLVREGLGIAIIdPATAIGL 157
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 104-247 1.25e-04

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: 42.10  E-value: 1.25e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 104 YLTPYIMKFQQHYPNIVVKI--IESEVAVNQIVDKNIDIGITRSAQIPDTLTSTLLYSEELVLVIPKNHPLNETSFVSFR 181
Cdd:cd08452   14 FLPPIVREYRKKFPSVKVELreLSSPDQVEELLKGRIDIGFLHPPIQHTALHIETVQSSPCVLALPKQHPLASKEEITIE 93

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446345343 182 ELVGLSRIMVSCSC----RESIKIYCERLGLSlseANI--ETKSSISLLSLVYNGHGVAIIPLSLVDFVNND 247
Cdd:cd08452   94 DLRDEPIITVAREAwptlYDEIIQLCEQAGFR---PKIvqEATEYQTVIGLVSAGIGVTFVPSSAKKLFNLE 162
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 112-271 2.50e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tfdA and tfdB gene expression. These genes encode enzymes for the conversion of 2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenol. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176137 [Multi-domain]  Cd Length: 198  Bit Score: 41.11  E-value: 2.50e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 112 FQQHYP--NIVVKIIESEVAVNQIVDKNIDIGITR-SAQIPDtLTSTLLYSEELVLVIPKNHPLNETSFVSFRELVGLSR 188
Cdd:cd08446   23 FLTARPdvTVSLHNMTKDEQIEALRAGRIHIGFGRfYPVEPD-IAVENVAQERLYLAVPKSHPLAARPAVSLADLRNEPL 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 189 IMVSCSCRESIKIycERLGLsLSEANIETKSS------ISLLSLVYNGHGVAIIP-----LSLVDFVnndtlsIVRIIDP 257
Cdd:cd08446  102 ILFPRGGRPSFAD--EVLGL-FRRAGVEPRVAqevedvVAALALVAAGFGVCIVPesvaaLRWPGVV------FRPLADA 172

                        170
                 ....*....|....
gi 446345343 258 TSRQDINLIHFDDK 271
Cdd:cd08446  173 EAKVPLSCIYRKDD 186
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 104-284 3.34e-04

The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold; MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. 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: 176128  Cd Length: 198  Bit Score: 40.78  E-value: 3.34e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 104 YLTPYIMKFQQHYPNIVVKIIE--SEVAVNQIVDKNIDIGITRSAQ--IPDTLTSTLLYSEELVLVIPKNHPLNETSFVS 179
Cdd:cd08437   14 YFPKLAKDLIKTGLMIQIDTYEggSAELLEQLLQGDLDIALLGSLTplENSALHSKIIKTQHFMIIVSKDHPLAKAKKVN 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 180 FRELVGLSRIMVScscrESIKIYCERLGLSlSEANIETKS-----SISLL-SLVYNGHGVAIiplsLVDFV--NNDTLSI 251
Cdd:cd08437   94 FADLKKENFILLN----EHFVHPKAFDSLC-QQANFQPNIvyrtnDIHILkSMVRENVGIGF----LTDIAvkPDDHLVA 164

                        170       180       190
                 ....*....|....*....|....*....|....
gi 446345343 252 VRIID-PTSRQDINLIHFDDKFLSFAARIFMQKL 284
Cdd:cd08437  165 IPLLDnEQPTFYISLAHRKDQLLTPAQKKLLDLL 198
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 105-242 7.38e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mechanisms. In Escherichia coli and Salmonella enterica serovar Typhimurium, MetJ and MetR regulate the expression of methionine biosynthetic genes. The MetJ repressor negatively regulates the E. coli met genes, except for metH. Several of these genes are also under the positive control of MetR with homocysteine as a co-inducer. In Bacillus subtilis, the met genes are controlled by S-box termination-antitermination system. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176132  Cd Length: 198  Bit Score: 39.86  E-value: 7.38e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 105 LTPYIMKFQQHYPNIVVKIIeSEV---AVNQIVDKNIDIGITRSAQIPDTLTSTLLYSEELVLVIPKNHPLNETSFVSFR 181
Cdd:cd08441   15 LMPVLDQFRERWPDVELDLS-SGFhfdPLPALLRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAPDHPLAAKEFITPE 93

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446345343 182 ELVGlsrimvscscrESIKIY---CERLGLS---LSEANIETKS------SISLLSLVYNGHGVAIIPLSLVD 242
Cdd:cd08441   94 DLAD-----------ETLITYpveRERLDVFrhfLQPAGIEPKRrrtvelTLMILQLVASGRGVAALPNWAVR 155
PBP2_PnbR cd08469
The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is ...
 103-172 2.13e-03

The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold; PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176158  Cd Length: 221  Bit Score: 38.54  E-value: 2.13e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446345343 103 TYLTPYIMKFQQHYPNI--VVKIIESEVAVNQIVDKNIDIGITRSAQIPDTLTSTLLYSEELVLVIPKNHPL 172
Cdd:cd08469   13 VLLPALVRRLETEAPGIdlRIRPVTRLDLAEQLDLGRIDLVIGIFEQIPPRFRRRTLFDEDEVWVMRKDHPA 84
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 104-281 3.27e-03

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


Pssm-ID: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 37.81  E-value: 3.27e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 104 YLTPYIMKFQQHYPNIVVKIIESEVAVNqIVDKNIDIGItRSAQIPD-TLTSTLLYSEELVLV----------IPKnHP- 171
Cdd:cd08422   15 HLAPLLAEFLARYPDVRLELVLSDRLVD-LVEEGFDLAI-RIGELPDsSLVARRLGPVRRVLVaspaylarhgTPQ-TPe 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343 172 -LNETSFVSFRELVGLSRIMVSC-SCRESIKIycerlglslsEANIETKSSISLLSLVYNGHGVAIIPLSLV-DFVNNDT 248
Cdd:cd08422   92 dLARHRCLGYRLPGRPLRWRFRRgGGEVEVRV----------RGRLVVNDGEALRAAALAGLGIALLPDFLVaEDLASGR 161

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 446345343 249 LsiVRIID--PTSRQDINLIHFDDKFLSFAARIFM 281
Cdd:cd08422  162 L--VRVLPdwRPPPLPIYAVYPSRRHLPAKVRAFI 194
PRK11482 PRK11482
DNA-binding transcriptional regulator;
21-172 3.76e-03

DNA-binding transcriptional regulator;


Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 38.16  E-value: 3.76e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446345343  21 AAEVLGISQPTLSQQIRVLEGELDTPLFHRVGRGIKMTEAGKLLFDkgkFIMQQFDDVYNEIfELKGV--KRGVITIGGL 98
Cdd:PRK11482  49 AAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHE---YISQGLESILGAL-DITGSydKQRTITIATT 124

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446345343  99 LEDLTYLTPYIMK-FQQHYPNIVVKIIESEVAVNQIVDKNIDIGITRSAQIPDTLTSTLLYSEELVLVIPKNHPL 172
Cdd:PRK11482 125 PSVGALVMPVIYQaIKTHYPQLLLRNIPISDAENQLSQFQTDLIIDTHSCSNRTIQHHVLFTDNVVLVCRQGHPL 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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