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Conserved domains on  [gi|490207574|ref|WP_004105985|]
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MULTISPECIES: LysR family transcriptional regulator [Klebsiella]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444297)

LysR family transcriptional regulator containing an N-terminal helix-turn-helix DNA-binding domain and a C-terminal substrate binding domain; similar to CbbR, AmpR, GalR, YhaJ, and NmcR, which are positive transcriptional regulators of various genes

Gene Ontology:  GO:0003677|GO:0003700|GO:0001216
PubMed:  8257110|19047729
SCOP:  4000316

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Periplasmic_Binding_Protein_Type_2 super family cl21456
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
 99-291 3.67e-56

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


The actual alignment was detected with superfamily member cd08431:

Pssm-ID: 473866 [Multi-domain]  Cd Length: 195  Bit Score: 179.77  E-value: 3.67e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  99 LTIVTEALVPTTDLFPLIEKLATKSN-TQLSIITEVLAGAWERLEQGRADIVVAPDmHFRSSSEINSRKLYSVMSVYVAA 177
Cdd:cd08431    2 LRIAIDTVLPLQPLYPLIAEFYQLNKaTRIRLSEEVLGGTWDALASGRADLVIGAT-GELPPGGVKTRPLGEVEFVFAVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 178 PDHPIHQEPEPLSEVTRVKYRGVAVADTARERPVLTVQLLDKQPRLTVSTIEDKRQALLAGLGVATMPYPLVEQDIAEGR 257
Cdd:cd08431   81 PNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASGE 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 490207574 258 LrvVSPEYSNE---IDIIMAWRRDSMGEAKSWCLREI 291
Cdd:cd08431  161 L--VEKALEDPrppQELFLAWRKDQRGKALAWFVQRL 195
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
9-68 1.57e-15

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 69.34  E-value: 1.57e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574    9 LEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGR 68
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 99-291 3.67e-56

The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. 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: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 179.77  E-value: 3.67e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  99 LTIVTEALVPTTDLFPLIEKLATKSN-TQLSIITEVLAGAWERLEQGRADIVVAPDmHFRSSSEINSRKLYSVMSVYVAA 177
Cdd:cd08431    2 LRIAIDTVLPLQPLYPLIAEFYQLNKaTRIRLSEEVLGGTWDALASGRADLVIGAT-GELPPGGVKTRPLGEVEFVFAVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 178 PDHPIHQEPEPLSEVTRVKYRGVAVADTARERPVLTVQLLDKQPRLTVSTIEDKRQALLAGLGVATMPYPLVEQDIAEGR 257
Cdd:cd08431   81 PNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASGE 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 490207574 258 LrvVSPEYSNE---IDIIMAWRRDSMGEAKSWCLREI 291
Cdd:cd08431  161 L--VEKALEDPrppQELFLAWRKDQRGKALAWFVQRL 195
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 11-288 1.67e-45

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 155.87  E-value: 1.67e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  11 ALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAADKLTTDAEA 90
Cdd:PRK11074   6 SLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQ 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  91 LSRGWETHLTIVTEALVPTTDLFPLIEKL-ATKSNTQLSIITEVLAGAWERLEQGRADIV--------VAPDMHFRSSSE 161
Cdd:PRK11074  86 VANGWRGQLSIAVDNIVRPDRTRQLIVDFyRHFDDVELIIRQEVFNGVWDALADGRVDIAigatraipVGGRFAFRDMGM 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 162 INSRklysvmsvYVAAPDHPIHQEPEPLSEVTRVKYRGVAVADTARERPVLTVQLLDKQPRLTVSTIEDKRQALLAGLGV 241
Cdd:PRK11074 166 LSWA--------CVVSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQRRLVVPDWESAINCLSAGLCV 237

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 490207574 242 ATMPYPLVEQDIAEGRLrvVSPEYSNEI---DIIMAWRRDSMGEAKSWCL 288
Cdd:PRK11074 238 GMVPTHFAKPLINSGKL--VELTLENPFpdsPCCLTWQQNDMSPALAWLL 285
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-278 9.23e-41

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 141.93  E-value: 9.23e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574   7 LTLEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAADKLTT 86
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  87 DAEALSRGWETHLTIVTEALVPTTDLFPLIEKLATK-SNTQLSIITEVLAGAWERLEQGRADIVVAPDMHfrSSSEINSR 165
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARhPGVRLELREGNSDRLVDALLEGELDLAIRLGPP--PDPGLVAR 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 166 KLYSVMSVYVAAPDHPIhqepeplsevtrvkyrgvavadtARERPVltvqlldkqprltVSTIEDKRQALLAGLGVATMP 245
Cdd:COG0583  159 PLGEERLVLVASPDHPL-----------------------ARRAPL-------------VNSLEALLAAVAAGLGIALLP 202

                        250       260       270
                 ....*....|....*....|....*....|....
gi 490207574 246 YPLVEQDIAEGRLRVVS-PEYSNEIDIIMAWRRD 278
Cdd:COG0583  203 RFLAADELAAGRLVALPlPDPPPPRPLYLVWRRR 236
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
9-68 1.57e-15

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 69.34  E-value: 1.57e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574    9 LEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGR 68
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 98-279 8.74e-13

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: 65.77  E-value: 8.74e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574   98 HLTIVTEALVPTTDLFPLIEKLATK-SNTQLSIITEVLAGAWERLEQGRADIVVApdMHFRSSSEINSRKLYSVMSVYVA 176
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERyPDVELELTEGNSEELLDLLLEGELDLAIR--RGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  177 APDHPIHQ-EPEPLSEVTRVKY--RGVAVADTARERPVLTVQLLDKQPRLTVSTIEDKRQALLAGLGVATMPYPLVEQDI 253
Cdd:pfam03466  81 PPDHPLARgEPVSLEDLADEPLilLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180
                  ....*....|....*....|....*..
gi 490207574  254 AEGRLRVVS-PEYSNEIDIIMAWRRDS 279
Cdd:pfam03466 161 ADGRLVALPlPEPPLPRELYLVWRKGR 187
rbcR CHL00180
LysR transcriptional regulator; Provisional
 8-94 3.09e-10

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 60.03  E-value: 3.09e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574   8 TLEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERG-RV--LLEAADKL 84
Cdd:CHL00180   6 TLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGnRIlaLCEETCRA 85

                         90
                 ....*....|
gi 490207574  85 TTDAEALSRG 94
Cdd:CHL00180  86 LEDLKNLQRG 95
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 11-279 2.30e-09

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 57.23  E-value: 2.30e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574   11 ALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRsGHRTKFTNVGRMLLERGR--VLLEA--ADKLTT 86
Cdd:TIGR03298   5 QLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHARqvRLLEAelLAELPG 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574   87 DAEALsrgwETHLTIVTEALVPTTDLFPLIEKLATKSNTQLSIITEVLAGAWERLEQGRAdiVVAPDMHFRSSSEINSRK 166
Cdd:TIGR03298  84 LAPGA----PTRLTIAVNADSLATWFLPALAPVLAREGVLLDLVVEDQDHTAELLRSGEV--LGAVTTEAKPVPGCRVVP 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  167 LYSVMSVYVAAPdhPIHQepeplsevtrvKY--RGVaVADTARERPVLT--------VQLLDKQ-------PRLTVSTIE 229
Cdd:TIGR03298 158 LGAMRYLAVASP--AFAA-----------RYfpDGV-TAAALARAPVIVfnrkddlqDRFLRRLfglpvspPRHYVPSSE 223

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 490207574  230 DKRQALLAGLGVATMPYPLVEQDIAEGRLRVVSPEysNEIDIIM---AWRRDS 279
Cdd:TIGR03298 224 GFVDAARAGLGWGMVPELQAEPHLAAGRLVELAPG--RALDVPLywhHWRLES 274
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 22-195 8.36e-07

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: 49.54  E-value: 8.36e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  22 GSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAADKLTTDAEALSRGWETHLTI 101
Cdd:NF040786  16 KSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDRYGKESKGVLRI 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 102 VTEAlVPTTDLFP--LIEKLATKSNTQLSIITEVLAGAWERLEQGRADIVVAPDMhfRSSSEINSRKLYSVMSVyVAAPD 179
Cdd:NF040786  96 GAST-IPGQYLLPelLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTK--LEKKRLVYTPFYKDRLV-LITPN 171

                        170       180
                 ....*....|....*....|
gi 490207574 180 H----PIHQEPEPLSEVTRV 195
Cdd:NF040786 172 GtekyRMLKEEISISELQKE 191
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 22-84 1.62e-05

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


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 45.50  E-value: 1.62e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490207574  22 GSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAADKL 84
Cdd:NF041036  16 GSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSL 78
 
Name Accession Description Interval E-value
PBP2_HupR cd08431
The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which ...
 99-291 3.67e-56

The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. 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: 176122 [Multi-domain]  Cd Length: 195  Bit Score: 179.77  E-value: 3.67e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  99 LTIVTEALVPTTDLFPLIEKLATKSN-TQLSIITEVLAGAWERLEQGRADIVVAPDmHFRSSSEINSRKLYSVMSVYVAA 177
Cdd:cd08431    2 LRIAIDTVLPLQPLYPLIAEFYQLNKaTRIRLSEEVLGGTWDALASGRADLVIGAT-GELPPGGVKTRPLGEVEFVFAVA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 178 PDHPIHQEPEPLSEVTRVKYRGVAVADTARERPVLTVQLLDKQPRLTVSTIEDKRQALLAGLGVATMPYPLVEQDIAEGR 257
Cdd:cd08431   81 PNHPLAKLDGPLDASAIKQYPAIVVADTSRNLPPRSSGLLEGQDRIRVPTMQAKIDAQVLGLGVGYLPRHLAKPELASGE 160

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 490207574 258 LrvVSPEYSNE---IDIIMAWRRDSMGEAKSWCLREI 291
Cdd:cd08431  161 L--VEKALEDPrppQELFLAWRKDQRGKALAWFVQRL 195
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 11-288 1.67e-45

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 155.87  E-value: 1.67e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  11 ALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAADKLTTDAEA 90
Cdd:PRK11074   6 SLEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQ 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  91 LSRGWETHLTIVTEALVPTTDLFPLIEKL-ATKSNTQLSIITEVLAGAWERLEQGRADIV--------VAPDMHFRSSSE 161
Cdd:PRK11074  86 VANGWRGQLSIAVDNIVRPDRTRQLIVDFyRHFDDVELIIRQEVFNGVWDALADGRVDIAigatraipVGGRFAFRDMGM 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 162 INSRklysvmsvYVAAPDHPIHQEPEPLSEVTRVKYRGVAVADTARERPVLTVQLLDKQPRLTVSTIEDKRQALLAGLGV 241
Cdd:PRK11074 166 LSWA--------CVVSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQRRLVVPDWESAINCLSAGLCV 237

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 490207574 242 ATMPYPLVEQDIAEGRLrvVSPEYSNEI---DIIMAWRRDSMGEAKSWCL 288
Cdd:PRK11074 238 GMVPTHFAKPLINSGKL--VELTLENPFpdsPCCLTWQQNDMSPALAWLL 285
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
7-278 9.23e-41

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 141.93  E-value: 9.23e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574   7 LTLEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAADKLTT 86
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  87 DAEALSRGWETHLTIVTEALVPTTDLFPLIEKLATK-SNTQLSIITEVLAGAWERLEQGRADIVVAPDMHfrSSSEINSR 165
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARhPGVRLELREGNSDRLVDALLEGELDLAIRLGPP--PDPGLVAR 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 166 KLYSVMSVYVAAPDHPIhqepeplsevtrvkyrgvavadtARERPVltvqlldkqprltVSTIEDKRQALLAGLGVATMP 245
Cdd:COG0583  159 PLGEERLVLVASPDHPL-----------------------ARRAPL-------------VNSLEALLAAVAAGLGIALLP 202

                        250       260       270
                 ....*....|....*....|....*....|....
gi 490207574 246 YPLVEQDIAEGRLRVVS-PEYSNEIDIIMAWRRD 278
Cdd:COG0583  203 RFLAADELAAGRLVALPlPDPPPPRPLYLVWRRR 236
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
10-295 3.54e-30

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 115.67  E-value: 3.54e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  10 EALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAADKLTTDAE 89
Cdd:PRK10094   5 ETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQ 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  90 ALSRGWETHLTIVTEALV--PTTDLFPLIEKLATKSNTQLSIITEVLAGAWERLEQGRADIVVAPDMHFRSSSEINSRKL 167
Cdd:PRK10094  85 QVNDGVERQVNIVINNLLynPQAVAQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIGVTGTEALANTFSLDPL 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 168 YSVMSVYVAAPDHPIHQEPEPLSEVTRVKYRGVAVADTARERPVLTVQLLDKQPRLTVSTIEDKRQALLAGLGVATMPYP 247
Cdd:PRK10094 165 GSVQWRFVMAADHPLANVEEPLTEAQLRRFPAVNIEDSARTLTKRVAWRLPGQKEIIVPDMETKIAAHLAGVGIGFLPKS 244

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 490207574 248 LVEQDIAEGRL--------RVVSPeysneidIIMAWRRDSMGEAKSwclrEIPKLF 295
Cdd:PRK10094 245 LCQSMIDNQQLvsrviptmRPPSP-------LSLAWRKFGSGKAVE----DIVTLF 289
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
9-68 1.57e-15

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 69.34  E-value: 1.57e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574    9 LEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGR 68
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 98-279 8.74e-13

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: 65.77  E-value: 8.74e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574   98 HLTIVTEALVPTTDLFPLIEKLATK-SNTQLSIITEVLAGAWERLEQGRADIVVApdMHFRSSSEINSRKLYSVMSVYVA 176
Cdd:pfam03466   3 RLRIGAPPTLASYLLPPLLARFRERyPDVELELTEGNSEELLDLLLEGELDLAIR--RGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  177 APDHPIHQ-EPEPLSEVTRVKY--RGVAVADTARERPVLTVQLLDKQPRLTVSTIEDKRQALLAGLGVATMPYPLVEQDI 253
Cdd:pfam03466  81 PPDHPLARgEPVSLEDLADEPLilLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180
                  ....*....|....*....|....*..
gi 490207574  254 AEGRLRVVS-PEYSNEIDIIMAWRRDS 279
Cdd:pfam03466 161 ADGRLVALPlPEPPLPRELYLVWRKGR 187
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
7-250 8.70e-12

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 64.65  E-value: 8.70e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574   7 LTLEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEaadKLTT 86
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLP---QISQ 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  87 DAEALSRGWETHLTIVTEALVPTTDLFPLIEKLATK-SNTQLSIITEVLAGAWERLEQGRADIVVAPDMHFRSSSEinsr 165
Cdd:PRK15421  79 ALQACNEPQQTRLRIAIECHSCIQWLTPALENFHKNwPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLH---- 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 166 klYSVMSVY----VAAPDHPIHQE----PEPLSEVTRVKYrgvavadtARERPVLTVQLLDKQPRLTVSTIEDKRQALL- 236
Cdd:PRK15421 155 --YSPMFDYevrlVLAPDHPLAAKtritPEDLASETLLIY--------PVQRSRLDVWRHFLQPAGVSPSLKSVDNTLLl 224

                        250
                 ....*....|....*....
gi 490207574 237 -----AGLGVATMPYPLVE 250
Cdd:PRK15421 225 iqmvaARMGIAALPHWVVE 243
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 9-258 2.60e-11

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 62.94  E-value: 2.60e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574   9 LEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGR----VLLEAADKL 84
Cdd:PRK11139   8 LNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIReifdQLAEATRKL 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  85 ttdaeaLSRGWETHLTIVTEA------LVPTTDLF----PLIEkLATKSNTQLsiitevlagawerLEQGRADIVVAPDM 154
Cdd:PRK11139  88 ------RARSAKGALTVSLLPsfaiqwLVPRLSSFneahPDID-VRLKAVDRL-------------EDFLRDDVDVAIRY 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 155 HFRSSSEINSRKLYS-----VMSVYVAAPDHPIHQePEPLSEVTRVKyrgvavaDTARE--RPVLT---VQLLDKQPRLT 224
Cdd:PRK11139 148 GRGNWPGLRVEKLLDeyllpVCSPALLNGGKPLKT-PEDLARHTLLH-------DDSREdwRAWFRaagLDDLNVQQGPI 219

                        250       260       270
                 ....*....|....*....|....*....|....
gi 490207574 225 VSTIEDKRQALLAGLGVATMPYPLVEQDIAEGRL 258
Cdd:PRK11139 220 FSHSSMALQAAIHGQGVALGNRVLAQPEIEAGRL 253
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 164-266 4.12e-11

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


Pssm-ID: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 60.92  E-value: 4.12e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 164 SRKLYSVMSVYVAAPD----HPIHQEPEPLSEVTRVKYRGVAVADT---ARERPVLTVQLldkQPRLTVSTIEDKRQALL 236
Cdd:cd08422   64 ARRLGPVRRVLVASPAylarHGTPQTPEDLARHRCLGYRLPGRPLRwrfRRGGGEVEVRV---RGRLVVNDGEALRAAAL 140

                         90       100       110
                 ....*....|....*....|....*....|
gi 490207574 237 AGLGVATMPYPLVEQDIAEGRLRVVSPEYS 266
Cdd:cd08422  141 AGLGIALLPDFLVAEDLASGRLVRVLPDWR 170
rbcR CHL00180
LysR transcriptional regulator; Provisional
 8-94 3.09e-10

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 60.03  E-value: 3.09e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574   8 TLEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERG-RV--LLEAADKL 84
Cdd:CHL00180   6 TLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGnRIlaLCEETCRA 85

                         90
                 ....*....|
gi 490207574  85 TTDAEALSRG 94
Cdd:CHL00180  86 LEDLKNLQRG 95
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 11-279 2.30e-09

transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions]


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 57.23  E-value: 2.30e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574   11 ALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRsGHRTKFTNVGRMLLERGR--VLLEA--ADKLTT 86
Cdd:TIGR03298   5 QLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHARqvRLLEAelLAELPG 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574   87 DAEALsrgwETHLTIVTEALVPTTDLFPLIEKLATKSNTQLSIITEVLAGAWERLEQGRAdiVVAPDMHFRSSSEINSRK 166
Cdd:TIGR03298  84 LAPGA----PTRLTIAVNADSLATWFLPALAPVLAREGVLLDLVVEDQDHTAELLRSGEV--LGAVTTEAKPVPGCRVVP 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  167 LYSVMSVYVAAPdhPIHQepeplsevtrvKY--RGVaVADTARERPVLT--------VQLLDKQ-------PRLTVSTIE 229
Cdd:TIGR03298 158 LGAMRYLAVASP--AFAA-----------RYfpDGV-TAAALARAPVIVfnrkddlqDRFLRRLfglpvspPRHYVPSSE 223

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 490207574  230 DKRQALLAGLGVATMPYPLVEQDIAEGRLRVVSPEysNEIDIIM---AWRRDS 279
Cdd:TIGR03298 224 GFVDAARAGLGWGMVPELQAEPHLAAGRLVELAPG--RALDVPLywhHWRLES 274
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 9-188 4.20e-09

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 56.59  E-value: 4.20e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574   9 LEALRVMDAIDRRG-SFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRtkFTNvgrmLLERGRVLLEAADKLTTD 87
Cdd:PRK12683   3 FQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKR--LTG----LTEPGKELLQIVERMLLD 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  88 AEALSRGWET-------HLTIVTE------ALVPT----TDLFPLIE-KLATKSNTQLSiitevlagawERLEQGRADIV 149
Cdd:PRK12683  77 AENLRRLAEQfadrdsgHLTVATThtqaryALPKVvrqfKEVFPKVHlALRQGSPQEIA----------EMLLNGEADIG 146

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 490207574 150 VAPDMhFRSSSEINSRKLYSVMSVYVAAPDHPIHQEPEP 188
Cdd:PRK12683 147 IATEA-LDREPDLVSFPYYSWHHVVVVPKGHPLTGRENL 184
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 9-283 1.69e-08

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 54.78  E-value: 1.69e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574   9 LEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAADKlttdA 88
Cdd:PRK09906   3 LRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEK----A 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  89 EALSRGWETHLTIVTEALVPTTDLFPLIEKLAT----KSNTQLSIITEVLAGAWERLEQGRADI-VVAPDMHfrsSSEIN 163
Cdd:PRK09906  79 KLRARKIVQEDRQLTIGFVPSAEVNLLPKVLPMfrlrHPDTLIELVSLITTQQEEKLRRGELDVgFMRHPVY---SDEID 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 164 SRKLYSVMSVYVAAPDHPIHQEPE-PLSEVTRVKYrgvaVADTARERPVLTVQLLD--KQPRLTVSTIEDKRQALL---- 236
Cdd:PRK09906 156 YLELLDEPLVVVLPVDHPLAHEKEiTAAQLDGVNF----ISTDPAYSGSLAPIIKAwfAQHNSQPNIVQVATNILVtmnl 231

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 490207574 237 --AGLGVATMPYPLVEQDIAEGRLRVVSPEySNEIDIIMAWRRDSMGEA 283
Cdd:PRK09906 232 vgMGLGCTIIPGYMNNFNTGQVVFRPLAGN-VPSIALLMAWKKGEMKPA 279
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 98-278 2.43e-08

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: 52.99  E-value: 2.43e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  98 HLTIVTEALVPTTDLFPLIEKLATKS-NTQLSIITEVLAGAWERLEQGRADIVVApdMHFRSSSEINSRKLYSVMSVYVA 176
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYpGVELSLVEGGSSELLEALLEGELDLAIV--ALPVDDPGLESEPLFEEPLVLVV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 177 APDHPIHQEPE-PLSEVTRVKYrgVAVADTARERPVLTVQLLDK----QPRLTVSTIEDKRQALLAGLGVATMPYPLVeQ 251
Cdd:cd05466   79 PPDHPLAKRKSvTLADLADEPL--ILFERGSGLRRLLDRAFAEAgftpNIALEVDSLEAIKALVAAGLGIALLPESAV-E 155

                        170       180
                 ....*....|....*....|....*...
gi 490207574 252 DIAEGRLRVVSPEYSN-EIDIIMAWRRD 278
Cdd:cd05466  156 ELADGGLVVLPLEDPPlSRTIGLVWRKG 183
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 9-190 5.00e-08

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 53.04  E-value: 5.00e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574   9 LEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGR-VL--LEAADKLT 85
Cdd:PRK11242   3 LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARrALqdLEAGRRAI 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  86 TDAEALSRGwetHLTIvteALVPT-TDLF--PLIEKL-ATKSNTQLSiITEVlagAWERLEQG----RADIVVA-PDMHf 156
Cdd:PRK11242  83 HDVADLSRG---SLRL---AMTPTfTAYLigPLIDAFhARYPGITLT-IREM---SQERIEALladdELDVGIAfAPVH- 151

                        170       180       190
                 ....*....|....*....|....*....|....
gi 490207574 157 rsSSEINSRKLYSVMSVYVAAPDHPIHQEPEPLS 190
Cdd:PRK11242 152 --SPEIEAQPLFTETLALVVGRHHPLAARRKALT 183
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
9-60 5.13e-08

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 53.08  E-value: 5.13e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 490207574   9 LEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSgHR 60
Cdd:PRK10086  16 LSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRS-HR 66
PBP2_CrgA_like_2 cd08471
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 165-265 1.88e-07

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


Pssm-ID: 176160  Cd Length: 201  Bit Score: 50.60  E-value: 1.88e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 165 RKLYSVMSVYVAAPD----HPIHQEPEPLSEVTRVKYRGVAVADTARERPVLTVQLLDKQPRLTVSTIEDKRQALLAGLG 240
Cdd:cd08471   65 TRVGSVRRVVCASPAylarHGTPKHPDDLADHDCIAFTGLSPAPEWRFREGGKERSVRVRPRLTVNTVEAAIAAALAGLG 144

                         90       100
                 ....*....|....*....|....*
gi 490207574 241 VATMPYPLVEQDIAEGRLRVVSPEY 265
Cdd:cd08471  145 LTRVLSYQVAEELAAGRLQRVLEDF 169
PBP2_CrgA_like_4 cd08473
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 158-274 2.07e-07

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


Pssm-ID: 176162 [Multi-domain]  Cd Length: 202  Bit Score: 50.25  E-value: 2.07e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 158 SSSEINSRKLYSVMSVYVAAPD----HPIHQEPEPLSEvtrvkYRGVAVADTAR------ERPVLTVQLLDKQPRLTVST 227
Cdd:cd08473   62 EDSSLVMRVLGQSRQRLVASPAllarLGRPRSPEDLAG-----LPTLSLGDVDGrhswrlEGPDGESITVRHRPRLVTDD 136

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 490207574 228 IEDKRQALLAGLGVATMPYPLVEQDIAEGRLRVVSPEYSNEIDIIMA 274
Cdd:cd08473  137 LLTLRQAALAGVGIALLPDHLCREALRAGRLVRVLPDWTPPRGIVHA 183
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 7-94 2.92e-07

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 50.84  E-value: 2.92e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574   7 LTLEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAAdkltT 86
Cdd:PRK10837   3 ITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQA----V 78


                 ....*...
gi 490207574  87 DAEALSRG 94
Cdd:PRK10837  79 EIEQLFRE 86
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 22-195 8.36e-07

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: 49.54  E-value: 8.36e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  22 GSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAADKLTTDAEALSRGWETHLTI 101
Cdd:NF040786  16 KSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEEFDRYGKESKGVLRI 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 102 VTEAlVPTTDLFP--LIEKLATKSNTQLSIITEVLAGAWERLEQGRADIVVAPDMhfRSSSEINSRKLYSVMSVyVAAPD 179
Cdd:NF040786  96 GAST-IPGQYLLPelLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTK--LEKKRLVYTPFYKDRLV-LITPN 171

                        170       180
                 ....*....|....*....|
gi 490207574 180 H----PIHQEPEPLSEVTRV 195
Cdd:NF040786 172 GtekyRMLKEEISISELQKE 191
PBP2_CrgA_like_5 cd08474
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 175-266 1.01e-06

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


Pssm-ID: 176163 [Multi-domain]  Cd Length: 202  Bit Score: 48.23  E-value: 1.01e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 175 VAAPD----HPIHQEPEPLSEVTRVKYR-----GVAVADTARERPVLTVQLldkQPRLTVSTIEDKRQALLAGLGVATMP 245
Cdd:cd08474   78 VASPAylarHGTPEHPRDLLNHRCIRYRfptsgALYRWEFERGGRELEVDV---EGPLILNDSDLMLDAALDGLGIAYLF 154

                         90       100
                 ....*....|....*....|.
gi 490207574 246 YPLVEQDIAEGRLRVVSPEYS 266
Cdd:cd08474  155 EDLVAEHLASGRLVRVLEDWS 175
PRK12680 PRK12680
LysR family transcriptional regulator;
7-253 3.88e-06

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 47.69  E-value: 3.88e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574   7 LTLEALRVMDAI-DRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTK-FTNVGRMLLERGRVLLEAADKL 84
Cdd:PRK12680   1 MTLTQLRYLVAIaDAELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  85 TTDAEALSRGWETHLTIVTEALVPTTDLFPLIEKLaTKSNTQLSIITEVLA--GAWERLEQGRADIVVAPDMHFRSSSEI 162
Cdd:PRK12680  81 RTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQI-KQAYPQVSVHLQQAAesAALDLLGQGDADIAIVSTAGGEPSAGI 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 163 nSRKLYSVMSVYVAAPDHPIHQ-----EPEPLSEVTRVKYRGVAVADTARERPVLTVQLldkQPRLTVSTIEDK--RQAL 235
Cdd:PRK12680 160 -AVPLYRWRRLVVVPRGHALDTprrapDMAALAEHPLISYESSTRPGSSLQRAFAQLGL---EPSIALTALDADliKTYV 235

                        250       260
                 ....*....|....*....|.
gi 490207574 236 LAGLGV---ATMPYPLVEQDI 253
Cdd:PRK12680 236 RAGLGVgllAEMAVNANDEDL 256
PRK09801 PRK09801
LysR family transcriptional regulator;
12-276 3.89e-06

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 47.72  E-value: 3.89e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  12 LRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAADKLTTDAEAL 91
Cdd:PRK09801  11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  92 SRGWETHLTIVTEALVPTTDLFPLIEKLaTKSNTQLSIITEVLAgawERLEQGRADIvvapDMHFRSSSEINSRKLYSVM 171
Cdd:PRK09801  91 KTRPEGMIRIGCSFGFGRSHIAPAITEL-MRNYPELQVHFELFD---RQIDLVQDNI----DLDIRINDEIPDYYIAHLL 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 172 S----VYVAAPDH-PIHQEPEPLSEVTR-----VKYR----GVAVADTARERPVLTVqlldkQPRLTVSTIEDKRQALLA 237
Cdd:PRK09801 163 TknkrILCAAPEYlQKYPQPQSLQELSRhdclvTKERdmthGIWELGNGQEKKSVKV-----SGHLSSNSGEIVLQWALE 237

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 490207574 238 GLGVATMPYPLVEQDIAEGRLRVVSPEYSNEIDIIMAWR 276
Cdd:PRK09801 238 GKGIMLRSEWDVLPFLESGKLVQVLPEYAQSANIWAVYR 276
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 114-277 4.94e-06

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


Pssm-ID: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 46.44  E-value: 4.94e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 114 PLIEKLATKS-NTQLSIITEVLAGAWERLEQGRADIVVapDMHFRSSSEINSRKLYSVMSVYVAAPDHPIHQEPEPLSEV 192
Cdd:cd08417   17 PLLARLRQEApGVRLRFVPLDRDDLEEALESGEIDLAI--GVFPELPPGLRSQPLFEDRFVCVARKDHPLAGGPLTLEDY 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 193 TRvkYRGVAVADTARERPV----LTVQLLDKQPRLTVSTIedkrQALLAGLG----VATMPYPLVEQDIAEGRLRVVSPE 264
Cdd:cd08417   95 LA--APHVLVSPRGRGHGLvddaLAELGLSRRVALTVPHF----LAAPALVAgtdlIATVPRRLAEALAERLGLRVLPLP 168

                        170
                 ....*....|....
gi 490207574 265 YS-NEIDIIMAWRR 277
Cdd:cd08417  169 FElPPFTVSLYWHP 182
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 22-84 1.62e-05

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


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 45.50  E-value: 1.62e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490207574  22 GSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAADKL 84
Cdd:NF041036  16 GSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSL 78
PBP2_CrgA_like_8 cd08477
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 221-266 2.72e-05

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 8. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176166  Cd Length: 197  Bit Score: 44.14  E-value: 2.72e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 490207574 221 PRLTVSTIEDKRQALLAGLGVATMPYPLVEQDIAEGRLRVVSPEYS 266
Cdd:cd08477  125 GRLTVNSGQALRVAALAGLGIVLQPEALLAEDLASGRLVELLPDYL 170
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 22-274 3.00e-05

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 44.98  E-value: 3.00e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  22 GSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLL---EAADKLTTDAEALSRGweth 98
Cdd:PRK14997  17 GGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLveaQAAQDAIAALQVEPRG---- 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  99 ltiVTEALVPTTDLFPLIEKLATKSNTQLSIITEVLAGAWERLEQGRADIVVAPDMHFR--SSSEINSRKLYSVMSVYVA 176
Cdd:PRK14997  93 ---IVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQLEATNRRVDVVGEGVDVAIRVRPRpfEDSDLVMRVLADRGHRLFA 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 177 APDHpIHQEPEPLSEVTRVKYRGVAVADTareRPVLTVQLLDKQ---------PRLTVSTIEDKRQALLAGLGVATMPYP 247
Cdd:PRK14997 170 SPDL-IARMGIPSAPAELSHWPGLSLASG---KHIHRWELYGPQgaraevhftPRMITTDMLALREAAMAGVGLVQLPVL 245

                        250       260
                 ....*....|....*....|....*..
gi 490207574 248 LVEQDIAEGRLRVVSPEYSNEIDIIMA 274
Cdd:PRK14997 246 MVKEQLAAGELVAVLEEWEPRREVIHA 272
PRK09986 PRK09986
LysR family transcriptional regulator;
1-101 4.04e-05

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 44.33  E-value: 4.04e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574   1 MAKERALTLEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEA 80
Cdd:PRK09986   1 MERLYRIDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDN 80

                         90       100
                 ....*....|....*....|.
gi 490207574  81 ADKLTTDAEALSRGWETHLTI 101
Cdd:PRK09986  81 AEQSLARVEQIGRGEAGRIEI 101
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
22-81 4.23e-05

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 44.37  E-value: 4.23e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  22 GSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAA 81
Cdd:PRK10632  17 GSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEV 76
PBP2_CrgA_like_3 cd08472
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 157-266 4.48e-05

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 3. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176161  Cd Length: 202  Bit Score: 43.65  E-value: 4.48e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 157 RSSSEInSRKLYSVMSVYVAAPD----HPIHQEPEPLSEVTRVKY-----RGVAVADTARERPVLTVQLldkQPRLTVST 227
Cdd:cd08472   58 ADSSLV-ARRLGELRMVTCASPAylarHGTPRHPEDLERHRAVGYfsartGRVLPWEFQRDGEEREVKL---PSRVSVND 133

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 490207574 228 IEDKRQALLAGLGVATMPYPLVEQDIAEGRLRVVSPEYS 266
Cdd:cd08472  134 SEAYLAAALAGLGIIQVPRFMVRPHLASGRLVEVLPDWR 172
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 159-275 6.44e-05

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


Pssm-ID: 176164 [Multi-domain]  Cd Length: 199  Bit Score: 42.93  E-value: 6.44e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 159 SSEINSRKLYSVMSVYVAAPDH-PIHQEPEPLSEVTR----VKYRG-------VAVADTARERPVLTvqlldkqPRLTVS 226
Cdd:cd08475   60 STGLVARRLGTQRMVLCASPAYlARHGTPRTLEDLAEhqciAYGRGgqplpwrLADEQGRLVRFRPA-------PRLQFD 132

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 490207574 227 TIEDKRQALLAGLGVATMPYPLVEQDIAEGRLRVVSPEYSNE-IDIIMAW 275
Cdd:cd08475  133 DGEAIADAALAGLGIAQLPTWLVADHLQRGELVEVLPELAPEgLPIHAVW 182
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 7-260 7.70e-05

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 43.48  E-value: 7.70e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574   7 LTLEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAADKLTT 86
Cdd:PRK15092  11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACS 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  87 -----DAE-ALSRGW--ETHLTIVTEALVPTTDLFPlieKLAtksntqLSIITEVLAGAWERLEQGRADIVV--APDMHF 156
Cdd:PRK15092  91 slmysNLQgVLTIGAsdDTADTILPFLLNRVSSVYP---KLA------LDVRVKRNAFMMEMLESQEVDLAVttHRPSSF 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 157 RSSSEINSRKLYSVMSVYVAAPDHPIH----QEPEPlsevtrvkYRGVAVA--DTARERPVLTvqlldkqprLTVSTIED 230
Cdd:PRK15092 162 PALNLRTSPTLWYCAAEYVLQKGEPIPlvllDEPSP--------FRDMALAtlNAAGIPWRIA---------YVASTLSA 224

                        250       260       270
                 ....*....|....*....|....*....|
gi 490207574 231 KRQALLAGLGVATMPYPLVEQDiaegrLRV 260
Cdd:PRK15092 225 VRAAVKAGLGVTARPVEMMSPD-----LRV 249
PBP2_CrgA_like_7 cd08476
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 160-268 1.46e-04

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


Pssm-ID: 176165  Cd Length: 197  Bit Score: 41.85  E-value: 1.46e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 160 SEINSRKLYSVMSVYVAAPD----HPIHQEPEPLSEVTRVKYRgvaVADTARERP---VLTVQLLDKQPR--LTVSTIED 230
Cdd:cd08476   58 SRLMSRRLGSFRMVLVASPDylarHGTPETPADLAEHACLRYR---FPTTGKLEPwplRGDGGDPELRLPtaLVCNNIEA 134

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 490207574 231 KRQALLAGLGVATMPYPLVEQDIAEGRLRVVSPEYSNE 268
Cdd:cd08476  135 LIEFALQGLGIACLPDFSVREALADGRLVTVLDDYVEE 172
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 233-258 2.57e-04

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


Pssm-ID: 176123 [Multi-domain]  Cd Length: 194  Bit Score: 41.03  E-value: 2.57e-04
                         10        20
                 ....*....|....*....|....*.
gi 490207574 233 QALLAGLGVATMPYPLVEQDIAEGRL 258
Cdd:cd08432  134 QAAVAGLGVALAPRALVADDLAAGRL 159
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 173-260 4.55e-04

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: 40.57  E-value: 4.55e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574 173 VYVAAPDHPIHQEpeplsevtrvkyRGVAVADTARERPVL------TVQLLDK---------QPRLTVSTIEDKRQALLA 237
Cdd:cd08419   74 VVIAPPDHPLAGQ------------KRIPLERLAREPFLLrepgsgTRLAMERffaehgvtlRVRMELGSNEAIKQAVMA 141

                         90       100
                 ....*....|....*....|...
gi 490207574 238 GLGVATMPYPLVEQDIAEGRLRV 260
Cdd:cd08419  142 GLGLSVLSLHTLALELATGRLAV 164
PBP2_TrpI cd08482
The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is ...
 233-258 6.81e-04

The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is involved in control of tryptophan synthesis, contains type 2 periplasmic binding fold; TrpI and indoleglycerol phosphate (InGP), are required to activate transcription of the trpBA, the genes for tryptophan synthase. The trpBA is induced by the InGp substrate, rather than by tryptophan, but the exact mechanism of the activation event is not known. This substrate-binding domain of TrpI 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: 176171 [Multi-domain]  Cd Length: 195  Bit Score: 40.08  E-value: 6.81e-04
                         10        20
                 ....*....|....*....|....*.
gi 490207574 233 QALLAGLGVATMPYPLVEQDIAEGRL 258
Cdd:cd08482  137 EAAVAGLGVAIAPWPLVRDDLASGRL 162
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
35-72 6.85e-04

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 40.57  E-value: 6.85e-04
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 490207574  35 PSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLE 72
Cdd:PRK11716   5 PSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRP 42
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
9-146 2.55e-03

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 38.80  E-value: 2.55e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574   9 LEALrvmDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKfTNVGRMLLERGRV--LLEaADKLTT 86
Cdd:PRK13348   7 LEAL---AAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRPCRP-TPAGQRLLRHLRQvaLLE-ADLLST 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  87 DAEAlSRGWEThLTIVTEALVPTTDLFPLIEKLATKSNTQLSIITEVLAGAWERLEQGRA 146
Cdd:PRK13348  82 LPAE-RGSPPT-LAIAVNADSLATWFLPALAAVLAGERILLELIVDDQDHTFALLERGEV 139
PRK09791 PRK09791
LysR family transcriptional regulator;
9-79 3.51e-03

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 38.59  E-value: 3.51e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490207574   9 LEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLE 79
Cdd:PRK09791   7 IHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILE 77
PBP2_CrgA cd08478
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains ...
 215-258 4.90e-03

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


Pssm-ID: 176167 [Multi-domain]  Cd Length: 199  Bit Score: 37.32  E-value: 4.90e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 490207574 215 QLLDKQPRLTVSTIEDKRQALLAGLGVATMPYPLVEQDIAEGRL 258
Cdd:cd08478  120 NLLKIQPTITASSGETLRQLALSGCGIACLSDFMTDKDIAEGRL 163
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
9-190 5.54e-03

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 37.65  E-value: 5.54e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574   9 LEALRVMDAIDRRG-SFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTkftnvgRMLLERGRVLLEAADKLTTD 87
Cdd:PRK12684   3 LHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRL------RGLTEPGRIILASVERILQE 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490207574  88 AEALSR-GWE------THLTIVTE------ALVPT----TDLFPLIeKLATKSNTQLSIITEVLAgawerleqGRADIVV 150
Cdd:PRK12684  77 VENLKRvGKEfaaqdqGNLTIATThtqaryALPAAikefKKRYPKV-RLSILQGSPTQIAEMVLH--------GQADLAI 147

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 490207574 151 APDmHFRSSSEINSRKLYSVMSVYVAAPDHPIHQEpEPLS 190
Cdd:PRK12684 148 ATE-AIADYKELVSLPCYQWNHCVVVPPDHPLLER-KPLT 185
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 24-79 7.93e-03

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 37.32  E-value: 7.93e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 490207574  24 FAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGR-VLLE 79
Cdd:PRK11151  18 FRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARtVLRE 74
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 217-260 8.50e-03

The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold; The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine and homocysteine, and orf5, a gene of unknown. The topology of this C-terminal domain of HvrB 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: 176172 [Multi-domain]  Cd Length: 190  Bit Score: 36.55  E-value: 8.50e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 490207574 217 LDKQPRLTVSTIEDKRQALLAGLGVATMPYPLVEQDIAEGRLRV 260
Cdd:cd08483  116 PDLERGVTFLPGQLVLEAARAGLGLSIQARALVEPDIAAGRLTV 159
 
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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