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Conserved domains on  [gi|489182735|ref|WP_003092181|]
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MULTISPECIES: transcriptional regulator MetR [Pseudomonas]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444080)

LysR family transcriptional regulator MetR regulates the expression of methionine biosynthetic genes, metA, metE, metF, and metH

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 93-290 4.60e-119

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: 340.31  E-value: 4.60e-119
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  93 RLHMAIECHSCFQWLMPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPLFTYEALLAVAN 172
Cdd:cd08441    1 RLRIAVECHSCFDWLMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 173 QHALAGRPYVVPEDLERETLITYPVERDRLDVFTRFLDPADVEPAQVRIAELTVMMMQLVASGRGVCCLPNWALHEYSSR 252
Cdd:cd08441   81 DHPLAAKEFITPEDLADETLITYPVERERLDVFRHFLQPAGIEPKRRRTVELTLMILQLVASGRGVAALPNWAVREYLDQ 160

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 489182735 253 GYVTARRLGEKGLYCTLFAAIRTDMFDAPFMRDFLLTA 290
Cdd:cd08441  161 GLVVARPLGEEGLWRTLYAAVRTEDADQPYLQDFLELA 198
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
4-62 2.11e-18

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 77.43  E-value: 2.11e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 489182735    4 LRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAG 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
 
Name Accession Description Interval E-value
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 93-290 4.60e-119

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: 340.31  E-value: 4.60e-119
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  93 RLHMAIECHSCFQWLMPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPLFTYEALLAVAN 172
Cdd:cd08441    1 RLRIAVECHSCFDWLMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 173 QHALAGRPYVVPEDLERETLITYPVERDRLDVFTRFLDPADVEPAQVRIAELTVMMMQLVASGRGVCCLPNWALHEYSSR 252
Cdd:cd08441   81 DHPLAAKEFITPEDLADETLITYPVERERLDVFRHFLQPAGIEPKRRRTVELTLMILQLVASGRGVAALPNWAVREYLDQ 160

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 489182735 253 GYVTARRLGEKGLYCTLFAAIRTDMFDAPFMRDFLLTA 290
Cdd:cd08441  161 GLVVARPLGEEGLWRTLYAAVRTEDADQPYLQDFLELA 198
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-305 5.66e-100

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 296.16  E-value: 5.66e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   1 MLELRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLRTAe 80
Cdd:PRK15421   1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQA- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  81 rdLARLAGGTAGRLHMAIECHSCFQWLMPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVP 160
Cdd:PRK15421  80 --LQACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSP 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 161 LFTYEALLAVANQHALAGRPYVVPEDLERETLITYPVERDRLDVFTRFLDPADVEPaQVRIAELTVMMMQLVASGRGVCC 240
Cdd:PRK15421 158 MFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSP-SLKSVDNTLLLIQMVAARMGIAA 236

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489182735 241 LPNWALHEYSSRGYVTARRLGEkGLYCTLFAAIRTDMFDAPFMRDFLLTAKDTSFATLEGVSAAK 305
Cdd:PRK15421 237 LPHWVVESFERQGLVVTKTLGE-GLWSRLYAAVRDGEQRQPVTEAFIRSARNHACDHLPFVKSAE 300
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
2-287 3.63e-54

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 176.98  E-value: 3.63e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   2 LELRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLRTAER 81
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  82 DLARLAGGTAGRLHMAIECHSCFQWLMPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPL 161
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 162 FTYEALLAVANQHALAGRPYVVPEdleretlitypverdrldvftrfldpadvepaqvriaelTVMMMQLVASGRGVCCL 241
Cdd:COG0583  161 GEERLVLVASPDHPLARRAPLVNS---------------------------------------LEALLAAVAAGLGIALL 201

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 489182735 242 PNWALHEYSSRGYVTARRLGEKGLYCTLFAAIRTDMFDAPFMRDFL 287
Cdd:COG0583  202 PRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFL 247
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-287 3.11e-37

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: 131.64  E-value: 3.11e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   91 AGRLHMAIECHSCFQWLMPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPLFTYEALLAV 170
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  171 ANQHALAGRPYVVPEDLERETLITYPVERDRLDVFTRFLDPADVEPAQVRIAELTVMMMQLVASGRGVCCLPNWALHEYS 250
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 489182735  251 SRGYVTARRLGEKGLYCTLFAAIRTDMFDAPFMRDFL 287
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFI 197
TF_pcaQ TIGR02424
pca operon transcription factor PcaQ; Members of this family are LysR-family transcription ...
 2-197 2.65e-21

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: 91.70  E-value: 2.65e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735    2 LELRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLRTAER 81
Cdd:TIGR02424   3 IKFRHLQCFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGTPLFERDRRGIRLTRYGELFLRHAGASLAALRQGVA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   82 DLARLAGGTAGRLHMAIeCHSCFQWLMP-TIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVV--TADPVELPGITY 158
Cdd:TIGR02424  83 SLSQLGEGEGPTVRIGA-LPTVAARLMPeVVKRFLARAPRLRVRIMTGPNAYLLDQLRVGALDLVVgrLGAPETMQGLSF 161

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 489182735  159 VPLFTYEALLAVANQHALAGRPYVVPEDLERetlitYPV 197
Cdd:TIGR02424 162 EHLYNEPVVFVVRAGHPLLAAPSLPVASLAD-----YPV 195
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
4-62 2.11e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 77.43  E-value: 2.11e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 489182735    4 LRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAG 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 3-289 3.15e-16

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: 77.27  E-value: 3.15e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   3 ELRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLRTAERD 82
Cdd:NF040786   2 NLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  83 LARLAGGTAGRLHMAIechSCF--QWLMPTI-DQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYV 159
Cdd:NF040786  82 FDRYGKESKGVLRIGA---STIpgQYLLPELlKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYT 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 160 PLFTYEALLAVANQHAlagRPYVVPEDLERETLITYP-VERD-----RLdVFTRFLDPADVEPAQVRI-AEL--TVMMMQ 230
Cdd:NF040786 159 PFYKDRLVLITPNGTE---KYRMLKEEISISELQKEPfIMREegsgtRK-EAEKALKSLGISLEDLNVvASLgsTEAIKQ 234

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 489182735 231 LVASGRGVCCLPNWALHEYSSRGYVtarrlgekglyctLFAAIRtdmfDAPFMRDFLLT 289
Cdd:NF040786 235 SVEAGLGISVISELAAEKEVERGRV-------------LIFPIP----GLPKNRDFYLV 276
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 2-104 4.34e-12

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: 65.53  E-value: 4.34e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   2 LELRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLRTAER 81
Cdd:NF041036   1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMD 80

                         90       100
                 ....*....|....*....|...
gi 489182735  82 DLARLaggtAGRLHMAIECHSCF 104
Cdd:NF041036  81 ELKSF----KGRQRLSICCTPTF 99
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-98 3.04e-11

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 62.90  E-value: 3.04e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   1 MLELRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLRTAE 80
Cdd:PRK10094   1 MFDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMP 80

                         90
                 ....*....|....*...
gi 489182735  81 RDLARLAGGTAGRLHMAI 98
Cdd:PRK10094  81 SELQQVNDGVERQVNIVI 98
 
Name Accession Description Interval E-value
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 93-290 4.60e-119

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: 340.31  E-value: 4.60e-119
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  93 RLHMAIECHSCFQWLMPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPLFTYEALLAVAN 172
Cdd:cd08441    1 RLRIAVECHSCFDWLMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 173 QHALAGRPYVVPEDLERETLITYPVERDRLDVFTRFLDPADVEPAQVRIAELTVMMMQLVASGRGVCCLPNWALHEYSSR 252
Cdd:cd08441   81 DHPLAAKEFITPEDLADETLITYPVERERLDVFRHFLQPAGIEPKRRRTVELTLMILQLVASGRGVAALPNWAVREYLDQ 160

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 489182735 253 GYVTARRLGEKGLYCTLFAAIRTDMFDAPFMRDFLLTA 290
Cdd:cd08441  161 GLVVARPLGEEGLWRTLYAAVRTEDADQPYLQDFLELA 198
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-305 5.66e-100

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 296.16  E-value: 5.66e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   1 MLELRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLRTAe 80
Cdd:PRK15421   1 MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQA- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  81 rdLARLAGGTAGRLHMAIECHSCFQWLMPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVP 160
Cdd:PRK15421  80 --LQACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSP 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 161 LFTYEALLAVANQHALAGRPYVVPEDLERETLITYPVERDRLDVFTRFLDPADVEPaQVRIAELTVMMMQLVASGRGVCC 240
Cdd:PRK15421 158 MFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSP-SLKSVDNTLLLIQMVAARMGIAA 236

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489182735 241 LPNWALHEYSSRGYVTARRLGEkGLYCTLFAAIRTDMFDAPFMRDFLLTAKDTSFATLEGVSAAK 305
Cdd:PRK15421 237 LPHWVVESFERQGLVVTKTLGE-GLWSRLYAAVRDGEQRQPVTEAFIRSARNHACDHLPFVKSAE 300
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
2-287 3.63e-54

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 176.98  E-value: 3.63e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   2 LELRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLRTAER 81
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  82 DLARLAGGTAGRLHMAIECHSCFQWLMPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPL 161
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 162 FTYEALLAVANQHALAGRPYVVPEdleretlitypverdrldvftrfldpadvepaqvriaelTVMMMQLVASGRGVCCL 241
Cdd:COG0583  161 GEERLVLVASPDHPLARRAPLVNS---------------------------------------LEALLAAVAAGLGIALL 201

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 489182735 242 PNWALHEYSSRGYVTARRLGEKGLYCTLFAAIRTDMFDAPFMRDFL 287
Cdd:COG0583  202 PRFLAADELAAGRLVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFL 247
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 91-287 3.11e-37

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: 131.64  E-value: 3.11e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   91 AGRLHMAIECHSCFQWLMPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPLFTYEALLAV 170
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  171 ANQHALAGRPYVVPEDLERETLITYPVERDRLDVFTRFLDPADVEPAQVRIAELTVMMMQLVASGRGVCCLPNWALHEYS 250
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 489182735  251 SRGYVTARRLGEKGLYCTLFAAIRTDMFDAPFMRDFL 287
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFI 197
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 93-287 9.67e-30

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: 111.54  E-value: 9.67e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  93 RLHMAIECHSCFQWLMPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPLFTYEALLAVAN 172
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 173 QHALAGRPYVVPEDLERETLITYPVERDRLDVFTRFLDPADVEPAQVRIAELTVMMMQLVASGRGVCCLPNWALHEYSSR 252
Cdd:cd05466   81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELADG 160

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 489182735 253 GyVTARRLGEKGLYCTLFAAIRTDMFDAPFMRDFL 287
Cdd:cd05466  161 G-LVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFL 194
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 4-193 1.70e-23

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 97.61  E-value: 1.70e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   4 LRHLKTLHALR--EA----DSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLR 77
Cdd:PRK11139   2 SRRLPPLNALRafEAaarhLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  78 TAERDLarLAGGTAGRLhmAIECHSCF--QWLMPTIDQFRDAWPEVELDLASGFSfapLPALARGDLDLVVTADPVELPG 155
Cdd:PRK11139  82 EATRKL--RARSAKGAL--TVSLLPSFaiQWLVPRLSSFNEAHPDIDVRLKAVDR---LEDFLRDDVDVAIRYGRGNWPG 154

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 489182735 156 ITYVPLFTyEALLAVANQHALAGR-PYVVPEDLERETLI 193
Cdd:PRK11139 155 LRVEKLLD-EYLLPVCSPALLNGGkPLKTPEDLARHTLL 192
PRK09986 PRK09986
LysR family transcriptional regulator;
2-242 1.18e-22

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 95.17  E-value: 1.18e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   2 LELRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQlrtAER 81
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDN---AEQ 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  82 DLAR---LAGGTAGRLHMAIECHSCFQWLMPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVV--TADPVELPGI 156
Cdd:PRK09986  84 SLARveqIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIwrMADLEPNPGF 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 157 TYVPLFTYEALLAVANQHALAGRPYVVPEDLERETLITYP-VERDrldvFTRFLDPADVE----PAQVRIAELTVMMMQL 231
Cdd:PRK09986 164 TSRRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPfVHSD----WGKFLQRVCQQagfsPQIIRQVNEPQTVLAM 239

                        250
                 ....*....|.
gi 489182735 232 VASGRGVCCLP 242
Cdd:PRK09986 240 VSMGIGITLLP 250
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 2-244 2.81e-22

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 94.07  E-value: 2.81e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   2 LELRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLRTAER 81
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  82 dLARLAGGTAGRLHMAIECHSCFQWLMPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPL 161
Cdd:PRK09906  81 -RARKIVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLEL 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 162 FTYEALLAVANQHALAGRPYVVPEDLERETLITYPVERDRL--DVFTRFLDPADVEPAQVRIAELTVMMMQLVASGRGVC 239
Cdd:PRK09906 160 LDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYSGSlaPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMGLGCT 239


                 ....*
gi 489182735 240 CLPNW 244
Cdd:PRK09906 240 IIPGY 244
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 104-287 1.43e-21

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: 89.87  E-value: 1.43e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 104 FQWLMPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPLFTYEALLAVANQHALAGRPYVV 183
Cdd:cd08414   12 YGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALPADHPLAARESVS 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 184 PEDLERETLITYPVERDRL--DVFTRFLDPADVEPAQVRIAELTVMMMQLVASGRGVCCLPNWALHeYSSRGyVTARRLG 261
Cdd:cd08414   92 LADLADEPFVLFPREPGPGlyDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPASVAR-LQRPG-VVYRPLA 169

                        170       180
                 ....*....|....*....|....*.
gi 489182735 262 EKGLYCTLFAAIRTDmFDAPFMRDFL 287
Cdd:cd08414  170 DPPPRSELALAWRRD-NASPALRAFL 194
TF_pcaQ TIGR02424
pca operon transcription factor PcaQ; Members of this family are LysR-family transcription ...
 2-197 2.65e-21

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: 91.70  E-value: 2.65e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735    2 LELRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLRTAER 81
Cdd:TIGR02424   3 IKFRHLQCFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGTPLFERDRRGIRLTRYGELFLRHAGASLAALRQGVA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   82 DLARLAGGTAGRLHMAIeCHSCFQWLMP-TIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVV--TADPVELPGITY 158
Cdd:TIGR02424  83 SLSQLGEGEGPTVRIGA-LPTVAARLMPeVVKRFLARAPRLRVRIMTGPNAYLLDQLRVGALDLVVgrLGAPETMQGLSF 161

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 489182735  159 VPLFTYEALLAVANQHALAGRPYVVPEDLERetlitYPV 197
Cdd:TIGR02424 162 EHLYNEPVVFVVRAGHPLLAAPSLPVASLAD-----YPV 195
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-193 4.83e-21

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 90.79  E-value: 4.83e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   1 MLeLRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLRTAE 80
Cdd:PRK11242   1 ML-LRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGR 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  81 RDLARLAGGTAGRLHMAIechscfqwlMPT---------IDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPV 151
Cdd:PRK11242  80 RAIHDVADLSRGSLRLAM---------TPTftayligplIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPV 150

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 489182735 152 ELPGITYVPLFTYEALLAVANQHALAGRPYVV-PEDLERETLI 193
Cdd:PRK11242 151 HSPEIEAQPLFTETLALVVGRHHPLAARRKALtLDELADEPLV 193
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 4-195 7.75e-20

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 87.74  E-value: 7.75e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   4 LRHLKTL-HALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPV-RFTSAGLRLLQLADSLLPQLRTAER 81
Cdd:PRK12682   3 LQQLRFVrEAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLkGLTEPGKAVLDVIERILREVGNIKR 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  82 DLARLAGGTAGRLHMAIeCHSCFQWLMP-TIDQFRDAWPEVELDLASGFSFAPLPALARGDLDL-VVTADPVELPGITYV 159
Cdd:PRK12682  83 IGDDFSNQDSGTLTIAT-THTQARYVLPrVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIgIATESLADDPDLATL 161

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 489182735 160 PLFTYEALLAVANQHALAGRPYVVPEDLERETLITY 195
Cdd:PRK12682 162 PCYDWQHAVIVPPDHPLAQEERITLEDLAEYPLITY 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
4-62 2.11e-18

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 77.43  E-value: 2.11e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 489182735    4 LRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAG 62
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
 105-245 1.64e-17

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: 78.96  E-value: 1.64e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 105 QWLMPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPLFTyEALLAV-ANQHALAGRPYVV 183
Cdd:cd08450   13 QWLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGIDYQLLLK-EPLIVVlPADHRLAGREKIP 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489182735 184 PEDLERETLI-TYPVERDRLDVFTRFLDPADVEPAQVRIAELTVMMMQLVASGRGVCCLPNWA 245
Cdd:cd08450   92 PQDLAGENFIsPAPTAPVLQQVIENYAAQHNIQPNIIQEADNLLSAMSLVASTLGCALLPLYA 154
PRK12680 PRK12680
LysR family transcriptional regulator;
2-246 3.16e-17

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 80.44  E-value: 3.16e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   2 LELRHLKTLHALREAD-SLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVR-FTSAGLRLLQLADSLLPQLRTA 79
Cdd:PRK12680   1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  80 ERDLARLAGGTAGRLHMaIECHSCFQWLM-PTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVV--TADPVELPGI 156
Cdd:PRK12680  81 RTYAANQRRESQGQLTL-TTTHTQARFVLpPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIvsTAGGEPSAGI 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 157 TyVPLFTYEALLAVANQHALaGRPYVVPE--DLERETLITYPVERDRLDVFTRFLDPADVEPAQVRIAELTVMMMQLVAS 234
Cdd:PRK12680 160 A-VPLYRWRRLVVVPRGHAL-DTPRRAPDmaALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLIKTYVRA 237

                        250
                 ....*....|..
gi 489182735 235 GRGVCCLPNWAL 246
Cdd:PRK12680 238 GLGVGLLAEMAV 249
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 12-195 3.21e-17

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 80.47  E-value: 3.21e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  12 ALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKpvRF---TSAGLRLLQLADSLLPQLRTAERDLARLAG 88
Cdd:PRK12683  12 AVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGK--RLtglTEPGKELLQIVERMLLDAENLRRLAEQFAD 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  89 GTAGRLHMAIeCHSCFQWLMPTI-DQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPV-ELPGITYVPLFTYEA 166
Cdd:PRK12683  90 RDSGHLTVAT-THTQARYALPKVvRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALdREPDLVSFPYYSWHH 168

                        170       180
                 ....*....|....*....|....*....
gi 489182735 167 LLAVANQHALAGRPYVVPEDLERETLITY 195
Cdd:PRK12683 169 VVVVPKGHPLTGRENLTLEAIAEYPIITY 197
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 4-193 6.98e-17

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 79.30  E-value: 6.98e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   4 LRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLRTAeRDL 83
Cdd:PRK11151   3 IRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVL-KEM 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  84 ARLAGGT-AGRLHMAIeCHSCFQWLMPTI-DQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPL 161
Cdd:PRK11151  82 ASQQGETmSGPLHIGL-IPTVGPYLLPHIiPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFIEVPL 160

                        170       180       190
                 ....*....|....*....|....*....|..
gi 489182735 162 FTYEALLAVANQHALAGRPYVVPEDLERETLI 193
Cdd:PRK11151 161 FDEPMLLAVYEDHPWANRDRVPMSDLAGEKLL 192
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
1-126 8.02e-17

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 79.05  E-value: 8.02e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   1 MLELRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGmQLFVRKTKPVRFTSAGLRLLQLADsllpQLRTAE 80
Cdd:PRK03635   1 MLDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVG-QVLLVRTQPCRPTEAGQRLLRHAR----QVRLLE 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 489182735  81 RDLARLAGGTAG---RLHMAIECHSCFQWLMPTIDQFrDAWPEVELDLA 126
Cdd:PRK03635  76 AELLGELPALDGtplTLSIAVNADSLATWFLPALAPV-LARSGVLLDLV 123
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 3-289 3.15e-16

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: 77.27  E-value: 3.15e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   3 ELRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLRTAERD 82
Cdd:NF040786   2 NLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEEE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  83 LARLAGGTAGRLHMAIechSCF--QWLMPTI-DQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYV 159
Cdd:NF040786  82 FDRYGKESKGVLRIGA---STIpgQYLLPELlKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYT 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 160 PLFTYEALLAVANQHAlagRPYVVPEDLERETLITYP-VERD-----RLdVFTRFLDPADVEPAQVRI-AEL--TVMMMQ 230
Cdd:NF040786 159 PFYKDRLVLITPNGTE---KYRMLKEEISISELQKEPfIMREegsgtRK-EAEKALKSLGISLEDLNVvASLgsTEAIKQ 234

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 489182735 231 LVASGRGVCCLPNWALHEYSSRGYVtarrlgekglyctLFAAIRtdmfDAPFMRDFLLT 289
Cdd:NF040786 235 SVEAGLGISVISELAAEKEVERGRV-------------LIFPIP----GLPKNRDFYLV 276
cbl PRK12679
HTH-type transcriptional regulator Cbl;
12-195 1.19e-15

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 76.00  E-value: 1.19e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  12 ALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVR-FTSAGLRLLQLADSLLPQLRTAERDLARLAGGT 90
Cdd:PRK12679  12 AARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLgMTEPGKALLVIAERILNEASNVRRLADLFTNDT 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  91 AGRLHMAIECHSCFQWLMPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADP-VELPGITYVPLFTYEALLA 169
Cdd:PRK12679  92 SGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERlSNDPQLVAFPWFRWHHSLL 171

                        170       180
                 ....*....|....*....|....*.
gi 489182735 170 VANQHALAGRPYVVPEDLERETLITY 195
Cdd:PRK12679 172 VPHDHPLTQITPLTLESIAKWPLITY 197
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
1-183 1.45e-15

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 75.39  E-value: 1.45e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   1 MLELRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRkTKPVRFTSAGLRLLQladsLLPQLRTAE 80
Cdd:PRK13348   1 MLDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLR----HLRQVALLE 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  81 RDL-ARLAGGTAGR--LHMAIECHSCFQWLMPTIDQFRdAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGIT 157
Cdd:PRK13348  76 ADLlSTLPAERGSPptLAIAVNADSLATWFLPALAAVL-AGERILLELIVDDQDHTFALLERGEVVGCVSTQPKPMRGCL 154

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 489182735 158 YVPLFT--YEALLAVA----------NQHALAGRPYVV 183
Cdd:PRK13348 155 AEPLGTmrYRCVASPAfaaryfaqglTRHSALKAPAVA 192
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
18-180 1.63e-15

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 75.42  E-value: 1.63e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  18 SLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLRTAERDLARLAggTAGRLhmA 97
Cdd:PRK10086  30 SFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQEILDIKNQE--LSGTL--T 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  98 IECHSCFQ--WLMPTIDQFRDAWPEVELDLASGFSFAplpALARGDLDLVVTADPVELPGITYVPLFTyEALLAV----- 170
Cdd:PRK10086 106 VYSRPSIAqcWLVPRLADFTRRYPSISLTILTGNENV---NFQRAGIDLAIYFDDAPSAQLTHHFLMD-EEILPVcspey 181

                        170
                 ....*....|
gi 489182735 171 ANQHALAGRP 180
Cdd:PRK10086 182 AERHALTGNP 191
PRK09791 PRK09791
LysR family transcriptional regulator;
10-168 5.97e-15

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 73.64  E-value: 5.97e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  10 LHALR------EADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLRTAERDL 83
Cdd:PRK09791   7 IHQIRafvevaRQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDI 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  84 ARLAGGTAGRLHMAIEChSCFQWLMP-TIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTadpvelpgiTYVP-- 160
Cdd:PRK09791  87 RQRQGQLAGQINIGMGA-SIARSLMPaVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTIN---------TYYQgp 156

                        170
                 ....*....|.
gi 489182735 161 ---LFTYEALL 168
Cdd:PRK09791 157 ydhEFTFEKLL 167
rbcR CHL00180
LysR transcriptional regulator; Provisional
 4-194 1.15e-13

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 70.05  E-value: 1.15e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   4 LRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLRTAERDL 83
Cdd:CHL00180   7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  84 ARLAGGTAGRLHMAIEcHSCFQWLMP-TIDQFRDAWPE--VELDLASGFSFAplPALARGDLDLVVTAD--PVELPGITY 158
Cdd:CHL00180  87 EDLKNLQRGTLIIGAS-QTTGTYLMPrLIGLFRQRYPQinVQLQVHSTRRIA--WNVANGQIDIAIVGGevPTELKKILE 163

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 489182735 159 VPLFTYEAL-LAVANQHALAGRPYVVPEDLERETLIT 194
Cdd:CHL00180 164 ITPYVEDELaLIIPKSHPFAKLKKIQKEDLYRLNFIT 200
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 106-287 1.78e-13

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: 67.90  E-value: 1.78e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 106 WLMPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPLFTYEALLAVANQHALAGRPYVVPE 185
Cdd:cd08420   14 LLPRLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPPDHPLAGRKEVTAE 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 186 DLERETLITypveRD-----RlDVFTRFLDPADVEPAQVRIA-EL--TVMMMQLVASGRGVCCLPNWALHEYSSRGYVTA 257
Cdd:cd08420   94 ELAAEPWIL----REpgsgtR-EVFERALAEAGLDGLDLNIVmELgsTEAIKEAVEAGLGISILSRLAVRKELELGRLVA 168

                        170       180       190
                 ....*....|....*....|....*....|
gi 489182735 258 RRLGEKGLYCTLFAAIRTDMFDAPFMRDFL 287
Cdd:cd08420  169 LPVEGLRLTRPFSLIYHKDKYLSPAAEAFL 198
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 101-286 4.05e-13

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: 66.79  E-value: 4.05e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 101 HSCFQWLMPT-IDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPLFTYEALLAVANQHALAGR 179
Cdd:cd08434    8 HSLGTSLVPDlIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPKDHPLAGR 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 180 PYVVPEDLERETLITYPVERDRLDVFTRFLDPADVEPaqvRIA----ELTVmMMQLVASGRGVCCLPNWALHEYSSrgyV 255
Cdd:cd08434   88 DSVDLAELADEPFVLLSPGFGLRPIVDELCAAAGFTP---KIAfegeEDST-IAGLVAAGLGVAILPEMTLLNPPG---V 160

                        170       180       190
                 ....*....|....*....|....*....|.
gi 489182735 256 TARRLGEKGLYCTLFAAIRTDMFDAPFMRDF 286
Cdd:cd08434  161 KKIPIKDPDAERTIGLAWLKDRYLSPAARRF 191
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
7-195 6.76e-13

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 67.69  E-value: 6.76e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   7 LKTLHALREAD----SLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVR-FTSAGLRLLQLADSLLPQLRTAER 81
Cdd:PRK12684   3 LHQLRFVREAVrqnfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVENLKR 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  82 DLARLAGGTAGRLHMAIeCHSCFQWLMP-TIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVEL-PGITYV 159
Cdd:PRK12684  83 VGKEFAAQDQGNLTIAT-THTQARYALPaAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATEAIADyKELVSL 161

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 489182735 160 PLFTYEALLAVANQHALAGRPYVVPEDLERETLITY 195
Cdd:PRK12684 162 PCYQWNHCVVVPPDHPLLERKPLTLEDLAQYPLITY 197
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 2-104 4.34e-12

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: 65.53  E-value: 4.34e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   2 LELRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLRTAER 81
Cdd:NF041036   1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMD 80

                         90       100
                 ....*....|....*....|...
gi 489182735  82 DLARLaggtAGRLHMAIECHSCF 104
Cdd:NF041036  81 ELKSF----KGRQRLSICCTPTF 99
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 102-242 6.79e-12

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


Pssm-ID: 176138 [Multi-domain]  Cd Length: 198  Bit Score: 63.43  E-value: 6.79e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 102 SCFQWLMPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPLFTYEALLAVANQHALAGRPY 181
Cdd:cd08447   10 SAYSFLPRLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFARPGLETRPLVREPLVAAVPAGHPLAGAER 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489182735 182 VVPEDLERETLITYPVERDRL--DVFTRFLDPADVEPAQVRIAELTVMMMQLVASGRGVCCLP 242
Cdd:cd08447   90 LTLEDLDGQPFIMYSPTEARYfhDLVVRLFASAGVQPRYVQYLSQIHTMLALVRAGLGVALVP 152
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 107-238 1.03e-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: 62.96  E-value: 1.03e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 107 LMPT-IDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPLFTYEALLAVANQHALAGRPYVVPE 185
Cdd:cd08415   14 LLPRaIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLPPGHPLARKDVVTPA 93

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 489182735 186 DLERETLITYPVE---RDRLDvftRFLDPADVEPaQVRI-AELTVMMMQLVASGRGV 238
Cdd:cd08415   94 DLAGEPLISLGRGdplRQRVD---AAFERAGVEP-RIVIeTQLSHTACALVAAGLGV 146
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 105-287 1.46e-11

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: 62.62  E-value: 1.46e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 105 QWLMPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTAD-----PVELPGITYVPLFTYEALLAVANQHALAGR 179
Cdd:cd08423   13 ALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFDypvtpPPDDPGLTRVPLLDDPLDLVLPADHPLAGR 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 180 PYVVPEDLERETLITYPVERDRLDVFTRFLDPADVEPAQVRIAELTVMMMQLVASGRGVCCLPNWALHEysSRGYVTARR 259
Cdd:cd08423   93 EEVALADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGVALVPRLALGA--RPPGVVVRP 170

                        170       180
                 ....*....|....*....|....*...
gi 489182735 260 LGEKGLYcTLFAAIRTDMFDAPFMRDFL 287
Cdd:cd08423  171 LRPPPTR-RIYAAVRAGAARRPAVAAAL 197
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
 107-262 2.98e-11

The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The C-terminal domain also contains the redox-active cysteines that mediate the redox-dependent conformational switch. Thus, the interaction between the OxyR-tetramer and DNA is notably different between the oxidized and reduced forms. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 61.39  E-value: 2.98e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 107 LMPT-IDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPLFTYEALLAVANQHALAGRPYVVPE 185
Cdd:cd08411   15 LLPRlLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAVPKDHPLAKRKSVTPE 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 186 DLERETLITYPVE---RDR-LDVFTRfldPADVEPAQVRIAELTvMMMQLVASGRGVCCLPNWALH-EYSSRGYVTARRL 260
Cdd:cd08411   95 DLAGERLLLLEEGhclRDQaLELCRL---AGAREQTDFEATSLE-TLRQMVAAGLGITLLPELAVPsEELRGDRLVVRPF 170


                 ..
gi 489182735 261 GE 262
Cdd:cd08411  171 AE 172
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
1-98 3.04e-11

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 62.90  E-value: 3.04e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   1 MLELRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLRTAE 80
Cdd:PRK10094   1 MFDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMP 80

                         90
                 ....*....|....*...
gi 489182735  81 RDLARLAGGTAGRLHMAI 98
Cdd:PRK10094  81 SELQQVNDGVERQVNIVI 98
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 108-269 4.43e-11

The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut. Hence, NAC allows the coupling of sigma70-RNAP dependent operons to the sigma54-RNAP dependent NTR system. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176124  Cd Length: 198  Bit Score: 61.07  E-value: 4.43e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 108 MPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPLFTyEALLAVANQHALAGRPYVVP-ED 186
Cdd:cd08433   16 VPLLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLE-EDLFLVGPADAPLPRGAPVPlAE 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 187 LERETLI---TYPVERDRLDvftRFLDPADVEPaQVRI-AELTVMMMQLVASGRGVCCLPNWALHEYSSRGYVTARRLGE 262
Cdd:cd08433   95 LARLPLIlpsRGHGLRRLVD---EAAARAGLTL-NVVVeIDSVATLKALVAAGLGYTILPASAVAAEVAAGRLVAAPIVD 170


                 ....*..
gi 489182735 263 KGLYCTL 269
Cdd:cd08433  171 PALTRTL 177
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 107-272 6.02e-11

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: 60.79  E-value: 6.02e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 107 LMPT-IDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPLFTYEALLAVANQHALAGRPYVVPE 185
Cdd:cd08426   14 LLPSlIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGAVVPPGHPLARQPSVTLA 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 186 DLERETLITYPVERDRLDVFTRFLDPADVEPAQVRIAELTVMMMQLVASGRGVCCLPNWALHEYSSRGYVTARRLGEKGL 265
Cdd:cd08426   94 QLAGYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTELAVRREIRRGQLVAVPLADPHM 173

                        170
                 ....*....|
gi 489182735 266 ---YCTLFAA 272
Cdd:cd08426  174 nhrQLELQTR 183
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
27-161 7.36e-11

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 61.37  E-value: 7.36e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  27 HLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLRTAERDLARLAGGTAGRLHM-----AIECH 101
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLfcsvtAAYSH 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489182735 102 scfqwLMPTIDQFRDAWPEVELDLASGFsfaplPALA-----RGDLDLVVTADPVELPG------ITYVPL 161
Cdd:PRK11716  82 -----LPPILDRFRAEHPLVEIKLTTGD-----AADAvekvqSGEADLAIAAKPETLPAsvafspIDEIPL 142
PRK10341 PRK10341
transcriptional regulator TdcA;
5-188 1.02e-10

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 61.42  E-value: 1.02e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   5 RHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLRTAERDLA 84
Cdd:PRK10341  10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  85 RLAGGTAGRLHMAIECHSCFQWLMPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVV--TADPVELPGITYVPLF 162
Cdd:PRK10341  90 GMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIgtLSNEMKLQDLHVEPLF 169

                        170       180
                 ....*....|....*....|....*.
gi 489182735 163 TYEALLaVANQhalaGRPYVVPEDLE 188
Cdd:PRK10341 170 ESEFVL-VASK----SRTCTGTTTLE 190
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 103-262 1.62e-10

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: 59.46  E-value: 1.62e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 103 CFQWLMPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPLFTYEALLAVANQHALAGRPYV 182
Cdd:cd08440   11 AATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPKDHPLARRRSV 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 183 VPEDLERETLITYPVERDRLDVFTRFLDPADVEPAQVRIAELTVMMMQLVASGRGVCCLPNWALHEYSSRGyVTARRLGE 262
Cdd:cd08440   91 TWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLADHPG-LVARPLTE 169
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 109-258 1.92e-10

The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176129 [Multi-domain]  Cd Length: 197  Bit Score: 59.11  E-value: 1.92e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 109 PTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPLFTYEALLAVANQHALAGRPYVVPEDLE 188
Cdd:cd08438   17 PLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPRGHPLAGRKTVSLADLA 96

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489182735 189 RETLITYPVE---RDR-LDVFTRfldpADVEPAQV-RIAELTVmMMQLVASGRGVCCLPNWALHEYSSRGYVTAR 258
Cdd:cd08438   97 DEPFILFNEDfalHDRiIDACQQ----AGFTPNIAaRSSQWDF-IAELVAAGLGVALLPRSIAQRLDNAGVKVIP 166
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 4-161 2.55e-10

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 60.08  E-value: 2.55e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   4 LRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLRTAERDL 83
Cdd:PRK11233   3 FRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQLAV 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489182735  84 ARLAGGTAGRLHMAIECHSCFQWL-MPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPL 161
Cdd:PRK11233  83 HNVGQALSGQVSIGLAPGTAASSLtMPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYEHSPVAGLSSQPL 161
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
22-85 3.31e-10

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 59.65  E-value: 3.31e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489182735  22 AAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLRTAERDLAR 85
Cdd:PRK03601  21 AAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMNTWQAAKKEVAH 84
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 1-193 3.88e-10

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 59.62  E-value: 3.88e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   1 MLELRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLL---QLADSLLPQLR 77
Cdd:PRK11013   3 AVSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFeevQRSYYGLDRIV 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  78 TAERDLARLAGGtagrlHMAIECHSCF-QWLMPTIDQ-FRDAWPEVELDLASGFSfaPL--PALARGDLDLVVTADPVEL 153
Cdd:PRK11013  83 SAAESLREFRQG-----QLSIACLPVFsQSLLPGLCQpFLARYPDVSLNIVPQES--PLleEWLSAQRHDLGLTETLHTP 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 489182735 154 PGITYVPLFTYEALLAVANQHALAGRPYVVPEDLERETLI 193
Cdd:PRK11013 156 AGTERTELLTLDEVCVLPAGHPLAAKKVLTPDDFAGENFI 195
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
 114-242 1.24e-09

The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold; The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. 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: 176144 [Multi-domain]  Cd Length: 200  Bit Score: 56.99  E-value: 1.24e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 114 FRDAWPEVELDLASGFSFAPLPALARGDLD--LVVTADPVELP-GITYVPLFTYEALLAVANQHALAGRPYVVPEDLERE 190
Cdd:cd08453   22 FREAYPDVELQLREATSDVQLEALLAGEIDagIVIPPPGASAPpALAYRPLLSEPLVLAVPAAWAAEGGAPLALAAVAAE 101

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 489182735 191 TLITYP--VERDRLDVFTRFLDPADVEPaqvRIAELTVMM---MQLVASGRGVCCLP 242
Cdd:cd08453  102 PLVIFPrrIAPAFHDAVTGYYRAAGQTP---RIAQEAIQMqtiISLVSAGMGVALVP 155
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 113-242 1.86e-09

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: 56.52  E-value: 1.86e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 113 QFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITyVPLFTYEAL-LAVANQHALAGRPYVVPEDLERET 191
Cdd:cd08446   22 AFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFYPVEPDIA-VENVAQERLyLAVPKSHPLAARPAVSLADLRNEP 100

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 489182735 192 LITYPVERDRL--DVFTRFLDPADVEPAQVRIAELTVMMMQLVASGRGVCCLP 242
Cdd:cd08446  101 LILFPRGGRPSfaDEVLGLFRRAGVEPRVAQEVEDVVAALALVAAGFGVCIVP 153
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 18-196 1.93e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 57.64  E-value: 1.93e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  18 SLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLRTAERDLARLAGGTAGRLHMA 97
Cdd:PRK11074  18 SFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQVANGWRGQLSIA 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  98 IECHSCFQWLMPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVV---TADPVelpGITYV--PLFTYEALLAVAN 172
Cdd:PRK11074  98 VDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIgatRAIPV---GGRFAfrDMGMLSWACVVSS 174

                        170       180
                 ....*....|....*....|....
gi 489182735 173 QHALAGRPYVVPEDlereTLITYP 196
Cdd:PRK11074 175 DHPLASMDGPLSDD----ELRPYP 194
PBP2_GcdR_TrpI_HvrB_AmpR_like cd08432
The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, ...
 105-239 5.40e-09

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: 54.89  E-value: 5.40e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 105 QWLMPTIDQFRDAWPEVELDLASGfsfAPLPALARGDLDLVVTADPVELPGITYVPLFTyEALLAVANQHALAGRPYVVP 184
Cdd:cd08432   13 RWLIPRLARFQARHPDIDLRLSTS---DRLVDFAREGIDLAIRYGDGDWPGLEAERLMD-EELVPVCSPALLAGLPLLSP 88

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489182735 185 EDLERETLITypvERDRLDVFTRFLDPADVEPAQVRIA---ELTVMMMQLVASGRGVC 239
Cdd:cd08432   89 ADLARHTLLH---DATRPEAWQWWLWAAGVADVDARRGprfDDSSLALQAAVAGLGVA 143
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 103-242 9.70e-09

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: 54.09  E-value: 9.70e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 103 CFQWLMPT-----IDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPLFTYEALLAVANQHALA 177
Cdd:cd08412    6 CFSTLAPYylpglLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARLPPYVWLPADHPLA 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489182735 178 GRPYVVPEDLERETLITYPVERDRlDVFTRFLDPADVEPaqvRIAELTV---MMMQLVASGRGVCCLP 242
Cdd:cd08412   86 GKDEVSLADLAAEPLILLDLPHSR-EYFLSLFAAAGLTP---RIAYRTSsfeAVRSLVANGLGYSLLN 149
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 107-207 1.15e-08

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: 54.20  E-value: 1.15e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 107 LMPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVV--TADPVELPGITYVPLFTYEALLAVANQHALAGRPYVVP 184
Cdd:cd08435   15 LPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIgrLADDEQPPDLASEELADEPLVVVARPGHPLARRARLTL 94

                         90       100
                 ....*....|....*....|....*..
gi 489182735 185 EDLERETLITYP---VERDRLD-VFTR 207
Cdd:cd08435   95 ADLADYPWVLPPpgtPLRQRLEqLFAA 121
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
 104-242 1.39e-08

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: 53.66  E-value: 1.39e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 104 FQWLMPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPLFTYEALLAVANQHALAGRPYVV 183
Cdd:cd08452   12 YEFLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALHIETVQSSPCVLALPKQHPLASKEEIT 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489182735 184 PEDLERETLITYPVER--DRLDVFTRFLDPADVEPAQVRIAELTVMMMQLVASGRGVCCLP 242
Cdd:cd08452   92 IEDLRDEPIITVAREAwpTLYDEIIQLCEQAGFRPKIVQEATEYQTVIGLVSAGIGVTFVP 152
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 106-282 2.66e-08

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


Pssm-ID: 176133  Cd Length: 193  Bit Score: 52.99  E-value: 2.66e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 106 WLMPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPLFTYEALLAVANQHALAGRpyvvPE 185
Cdd:cd08442   14 RLPPLLAAYHARYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSPKGHPPVSR----AE 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 186 DLERETLITYP---VERDRLDvftRFLDPADVEPAqvRIAELTVM--MMQLVASGRGVCCLPNWALHEYSSRGYVTARRL 260
Cdd:cd08442   90 DLAGSTLLAFRagcSYRRRLE---DWLAEEGVSPG--KIMEFGSYhaILGCVAAGMGIALLPRSVLDSLQGRGSVSIHPL 164

                        170       180
                 ....*....|....*....|..
gi 489182735 261 GEKGLYCTLFAAIRTDMFDAPF 282
Cdd:cd08442  165 PEPFADVTTWLVWRKDSFTAAL 186
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 113-242 2.73e-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: 176127 [Multi-domain]  Cd Length: 194  Bit Score: 52.99  E-value: 2.73e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 113 QFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELP-GITYVPLFTYEALLAVANQHALAGRPYVVPEDLERET 191
Cdd:cd08436   21 RFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRPpGLASRELAREPLVAVVAPDHPLAGRRRVALADLADEP 100

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 489182735 192 LITYPVE---RDRLDvftRFLDPADVEPAQVRIAELTVMMMQLVASGRGVCCLP 242
Cdd:cd08436  101 FVDFPPGtgaRRQVD---RAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLP 151
cysB PRK12681
HTH-type transcriptional regulator CysB;
21-195 5.24e-08

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 53.36  E-value: 5.24e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  21 EAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPV-RFTSAGLRLLQLADSLLPQLRTAERDLARLAGGTAGRLHMAIE 99
Cdd:PRK12681  21 ATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLtQVTPAGEEIIRIAREILSKVESIKSVAGEHTWPDKGSLYIATT 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 100 cHSCFQWLMPT-IDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVEL-PGITYVPLFTYEALLAVANQHALA 177
Cdd:PRK12681 101 -HTQARYALPPvIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAIATEALHLyDDLIMLPCYHWNRSVVVPPDHPLA 179

                        170
                 ....*....|....*...
gi 489182735 178 GRPYVVPEDLERETLITY 195
Cdd:PRK12681 180 KKKKLTIEELAQYPLVTY 197
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 110-238 7.70e-07

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: 48.71  E-value: 7.70e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 110 TIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELP-GITYVPLFTYEALLAVANQHALAGRPYVVPEDLE 188
Cdd:cd08451   19 LIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARSdGLVLELLLEEPMLVALPAGHPLARERSIPLAALA 98

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 489182735 189 RETLITYPVERDRL--DVFTRFLDPADVEPAQVRIAELTVMMMQLVASGRGV 238
Cdd:cd08451   99 DEPFILFPRPVGPGlyDAIIAACRRAGFTPRIGQEAPQMASAINLVAAGLGV 150
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 4-187 1.63e-06

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 48.53  E-value: 1.63e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   4 LRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLRTAErDL 83
Cdd:PRK10837   5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIE-QL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  84 ARLAGGtAGRLHMAiecHSCFQWLMP-TIDQFRDAWPEVELDLASGFSFAPLPALA--RGDLDLVvtADPVELPGITYVP 160
Cdd:PRK10837  84 FREDNG-ALRIYAS---STIGNYILPaMIARYRRDYPQLPLELSVGNSQDVINAVLdfRVDIGLI--EGPCHSPELISEP 157

                        170       180
                 ....*....|....*....|....*..
gi 489182735 161 LFTYEALLAVANQHALAGRPyVVPEDL 187
Cdd:PRK10837 158 WLEDELVVFAAPDSPLARGP-VTLEQL 183
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
2-248 1.61e-05

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 45.82  E-value: 1.61e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   2 LELRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLrtaER 81
Cdd:PRK10082  11 IETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQL---ES 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  82 DLARLAGGT--AGRLHMAIECHSCFQWLMPTI-----DQFRDAWPEVELDLAsgfsfapLPALARGDLDLVVT---ADPV 151
Cdd:PRK10082  88 NLAELRGGSdyAQRKIKIAAAHSLSLGLLPSIisqmpPLFTWAIEAIDVDEA-------VDKLREGQSDCIFSfhdEDLL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 152 ELPgITYVPLFTYEAL-LAVANQHALA----GRPYVVPEDLERETLITYPVERdrldVFTRFldpADVEPAQVRIAELTV 226
Cdd:PRK10082 161 EAP-FDHIRLFESQLFpVCASDEHGEAlfnlAQPHFPLLNYSRNSYMGRLINR----TLTRH---SELSFSTFFVSSMSE 232

                        250       260
                 ....*....|....*....|..
gi 489182735 227 MMMQLVASGRGVCCLPNWALHE 248
Cdd:PRK10082 233 LLKQVALDGCGIAWLPEYAIQQ 254
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
 107-242 1.95e-05

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: 44.57  E-value: 1.95e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 107 LMPTIDQFRDAWPEVELDLasgFSFAP---LPALARGDLDL--VVTADPVELPGITYVPLFTYEALLAVANQHALAGRPY 181
Cdd:cd08449   15 LGPALRRFKRQYPNVTVRF---HELSPeaqKAALLSKRIDLgfVRFADTLNDPPLASELLWREPMVVALPEEHPLAGRKS 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489182735 182 VVPEDLERETLITYPVERDRldvFTRFLDPADVE----PaqvRIAELTV---MMMQLVASGRGVCCLP 242
Cdd:cd08449   92 LTLADLRDEPFVFLRLANSR---FADFLINCCLQagftP---QITQEVVepqTLMALVAAGFGVALVP 153
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 2-73 2.98e-05

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 45.02  E-value: 2.98e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489182735   2 LELRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLL 73
Cdd:PRK15092  11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKIL 82
PBP2_GcdR_like cd08481
The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, ...
 105-242 6.52e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold; GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar 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: 176170 [Multi-domain]  Cd Length: 194  Bit Score: 43.05  E-value: 6.52e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 105 QWLMPTIDQFRDAWPEVELDLASG---FSFaplpalARGDLDLVVTADPVELPGITYVPLFTyEALLAVANQHALAGRPY 181
Cdd:cd08481   13 RWLIPRLPDFLARHPDITVNLVTRdepFDF------SQGSFDAAIHFGDPVWPGAESEYLMD-EEVVPVCSPALLAGRAL 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489182735 182 VVPEDLERETLI---TYPverdrlDVFTRFLDPADVE-PAQVRIA--ELTVMMMQLVASGRGVCCLP 242
Cdd:cd08481   86 AAPADLAHLPLLqqtTRP------EAWRDWFEEVGLEvPTAYRGMrfEQFSMLAQAAVAGLGVALLP 146
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 108-242 6.97e-05

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: 43.02  E-value: 6.97e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 108 MPTI-DQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPLFTYEALLAVANQHALAGRPYVVPED 186
Cdd:cd08448   15 LPRIlRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAGLSARLLHREPFVCCLPAGHPLAARRRIDLRE 94

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489182735 187 LERETLITYP--VERDRLD-VFTRFLDpADVEPA---QVRIAeLTVmmMQLVASGRGVCCLP 242
Cdd:cd08448   95 LAGEPFVLFSreVSPDYYDqIIALCMD-AGFHPKirhEVRHW-LTV--VALVAAGMGVALVP 152
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
 111-258 7.15e-05

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: 42.79  E-value: 7.15e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 111 IDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPLFTYEALLAVANQHALAGRPYVVPEDLERE 190
Cdd:cd08456   19 IKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGIERERLLRIDGVCVLPPGHRLAVKKVLTPSDLEGE 98

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489182735 191 TLITYPVE---RDRLDvftRFLDPADVEPAQVRIAELTVMMMQLVASGRGVCCLPNWALHEYSSRGYVTAR 258
Cdd:cd08456   99 PFISLARTdgtRQRVD---ALFEQAGVKRRIVVETSYAATICALVAAGVGVSVVNPLTALDYAAAGLVVRR 166
PBP2_BenM_CatM_CatR cd08445
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 107-274 7.92e-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: 42.98  E-value: 7.92e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 107 LMPT-IDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPLFTYEALLAVANQHALAGRPYVVP- 184
Cdd:cd08445   15 LLPElIRRFRQAAPDVEIELIEMTTVQQIEALKEGRIDVGFGRLRIEDPAIRRIVLREEPLVVALPAGHPLAQEKAPLTl 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 185 EDLERETLITYPVE-----RDR-LDVFTRfldpADVEPAQVR-IAELTvMMMQLVASGRGVCCLPNWALHeySSRGYVTA 257
Cdd:cd08445   95 AQLADEPLILYPASprpsfADQvLSLFRD----HGLRPRVIQeVRELQ-TALGLVAAGEGVTLVPASVQR--LRRDDVVY 167

                        170
                 ....*....|....*..
gi 489182735 258 RRLGEKGLYCTLFAAIR 274
Cdd:cd08445  168 RPLLDPDATSPIIMSVR 184
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 92-249 8.30e-05

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: 42.81  E-value: 8.30e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  92 GRLHMAieCHSCF--QWLMPTIDQFRDAWPEVELDLasgfSFAP-LPALARGDLDLVVTADPVELPGITYVPLFTYEALL 168
Cdd:cd08422    1 GRLRIS--APVSFgrLHLAPLLAEFLARYPDVRLEL----VLSDrLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 169 aVA-----NQHalaGRPyVVPEDLERETLITYpVERDRLDVFtRFLDPADVEPAQVRIAeLTV----MMMQLVASGRGVC 239
Cdd:cd08422   75 -VAspaylARH---GTP-QTPEDLARHRCLGY-RLPGRPLRW-RFRRGGGEVEVRVRGR-LVVndgeALRAAALAGLGIA 146

                        170
                 ....*....|
gi 489182735 240 CLPNWALHEY 249
Cdd:cd08422  147 LLPDFLVAED 156
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
 107-195 1.19e-04

The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176105 [Multi-domain]  Cd Length: 198  Bit Score: 42.22  E-value: 1.19e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 107 LMPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVEL-PGITYVPLFTYEALLAVANQHALAGRPYVVPE 185
Cdd:cd08413   15 LPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDDhPDLVTLPCYRWNHCVIVPPGHPLADLGPLTLE 94

                         90
                 ....*....|
gi 489182735 186 DLERETLITY 195
Cdd:cd08413   95 DLAQYPLITY 104
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
 107-287 1.27e-04

The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176134  Cd Length: 198  Bit Score: 42.16  E-value: 1.27e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 107 LMPTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVEL-PGITYVPLFTYEALLAVANQHALAGRPYVVPE 185
Cdd:cd08443   15 LPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHDyDDLITLPCYHWNRCVVVKRDHPLADKQSISIE 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 186 DLERETLITYP---VERDRLD-VFTRfldpADVEPAQVRIAELTVMMMQLVASGRGVCCLPNWALHEYSSRGYVTaRRLG 261
Cdd:cd08443   95 ELATYPIVTYTfgfTGRSELDtAFNR----AGLTPNIVLTATDADVIKTYVRLGLGVGVIASMAYDPVDDPDLVI-RDAR 169

                        170       180
                 ....*....|....*....|....*.
gi 489182735 262 EKGLYCTLFAAIRTDMFDAPFMRDFL 287
Cdd:cd08443  170 DLFPWSVTKIAFRRGTFLRSYMYDFI 195
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 109-192 1.63e-04

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: 41.93  E-value: 1.63e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 109 PTIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPLFTYEALLAVANQHALAGRPYVV-PEDL 187
Cdd:cd08425   18 PLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDAQPLFDERLALVVGATHPLAQRRTALtLDDL 97


                 ....*
gi 489182735 188 ERETL 192
Cdd:cd08425   98 AAEPL 102
PBP2_MdcR cd08416
The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which ...
 119-243 4.13e-04

The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold; This family includes the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and 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. 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: 176108  Cd Length: 199  Bit Score: 40.79  E-value: 4.13e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 119 PEVELDLASGFSFAPLPALARGDLDLVVTADPVEL--PGITYVPLFTYEALLAVANQHALAGRPYVVPEDLERETLIT-- 194
Cdd:cd08416   27 PELDIELTLGSNKDLLKKLKDGELDAILVATPEGLndPDFEVVPLFEDDIFLAVPATSPLAASSEIDLRDLKDEKFVTls 106

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 489182735 195 --YPVERDRLDVFtrflDPADVEPAQVRIAELTVMMMQLVASGRGVCCLPN 243
Cdd:cd08416  107 egFATYRGFDEAF----EIAGFEPNVVMRVNDIFSLMSMVSGGVGYALLPG 153
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
 105-180 5.49e-04

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: 40.28  E-value: 5.49e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489182735 105 QWLMPTI-DQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPLFTYEALLAVANQHALAGRP 180
Cdd:cd08417   12 ALLLPPLlARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARKDHPLAGGP 88
PBP2_LTTR_beta_lactamase cd08484
The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase ...
 106-242 5.55e-04

The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase genes, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators, BlaA and AmpR, that are involved in control of the expression of beta-lactamase genes. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. BlaA (a constitutive class A penicillinase) belongs to the LysR family of transcriptional regulators, while BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin-binding protein, but it does not act as a beta-lactamase. AmpR regulates the expression of beta-lactamases in many enterobacterial strains and many other gram-negative bacilli. In contrast to BlaA, AmpR acts an activator only in the presence of the beta-lactam inducer. In the absence of the inducer, AmpR acts as a repressor. 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: 176173 [Multi-domain]  Cd Length: 189  Bit Score: 40.05  E-value: 5.55e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 106 WLMPTIDQFRDAWPEVELDLASGFSFAPlpaLARGDLDLVVTADPVELPGITYVPLFtyEALLAVANQHALAGRpYVVPE 185
Cdd:cd08484   14 WLLPRLAEFRQLHPFIDLRLSTNNNRVD---IAAEGLDFAIRFGEGAWPGTDATRLF--EAPLSPLCTPELARR-LSEPA 87

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 186 DLERETLI-TYpverdRLDVFTRFLDPADVEPAQVR--IAELTVMMMQLVASGRGVCCLP 242
Cdd:cd08484   88 DLANETLLrSY-----RADEWPQWFEAAGVPPPPINgpVFDSSLLMVEAALQGAGVALAP 142
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
 107-255 7.05e-04

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: 39.78  E-value: 7.05e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 107 LMP-TIDQFRDAWPEVELDLASGFSFAPLPALARGDLDLVVTADPVELPGITYVPLFTYEALLAVANQHALAGRPYVVPE 185
Cdd:cd08457   14 FLPrFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIETRSLPAVVAVPMGHPLAQLDVVSPQ 93

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489182735 186 DLERETLIT----YPVeRDRLDVftrFLDPADVEPAQVRIAELTVMMMQLVASGRGVCCLPNWALHEYSSRGYV 255
Cdd:cd08457   94 DLAGERIITlengYLF-RMRVEV---ALGKIGVKRRPIIEVNLSHTALSLVREGLGIAIIDPATAIGLPLDGIV 163
nhaR PRK11062
transcriptional activator NhaR; Provisional
 18-72 1.25e-03

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 39.99  E-value: 1.25e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 489182735  18 SLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSL 72
Cdd:PRK11062  20 SVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKM 74
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 22-125 1.25e-03

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 39.97  E-value: 1.25e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735  22 AAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAGLRLLQLADSLLPQLRTAERDLARLAGGTAGRLHMAIECH 101
Cdd:PRK14997  22 AGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVEPRGIVKLTCPVT 101

                         90       100
                 ....*....|....*....|....
gi 489182735 102 SCFQWLMPTIDQFRDAWPEVELDL 125
Cdd:PRK14997 102 LLHVHIGPMLAKFMARYPDVSLQL 125
PBP2_BlaA cd08487
The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which ...
 106-242 1.27e-03

The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which involved in control of the beta-lactamase gene expression; contains the type 2 periplasmic binding fold; This CD represents the C-terminal substrate binding domain of LysR-type transcriptional regulator, BlaA, that involved in control of the expression of beta-lactamase genes, blaA and blaB. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. The blaA gene is located just upstream of blaB in the opposite direction and regulates the expression of the blaB. BlaA also negatively auto-regulates the expression of its own gene, blaA. BlaA (a constitutive class A penicllinase) belongs to the LysR family of transcriptional regulators, whereas BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin binding protein but it does not act as a beta-lactamase. 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: 176176 [Multi-domain]  Cd Length: 189  Bit Score: 39.07  E-value: 1.27e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 106 WLMPTIDQFRDAWPEVELDLASGFSFAPLpaLARGdLDLVVTADPVELPGITYVPLFtyEALLAVANQHALAgRPYVVPE 185
Cdd:cd08487   14 WLLPRLAEFRQLHPFIELRLRTNNNVVDL--ATEG-LDFAIRFGEGLWPATHNERLL--DAPLSVLCSPEIA-KRLSHPA 87

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 186 DLERETLI-TYpverdRLDVFTRFLDPADVEPAQVR--IAELTVMMMQLVASGRGVCCLP 242
Cdd:cd08487   88 DLINETLLrSY-----RTDEWLQWFEAANMPPIKIRgpVFDSSRLMVEAAMQGAGVALAP 142
PBP2_HvrB cd08483
The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an ...
 106-242 1.41e-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: 38.87  E-value: 1.41e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 106 WLMPTIDQFRDAWPEVELDLASGfsfAPLPALARGDLDLVVTADPVELPGITYVPLfTYEALLAVANQHALAGRPYVVPE 185
Cdd:cd08483   14 WLMPRLGSFWAKHPEIELSLLPS---ADLVDLRPDGIDVAIRYGNGDWPGLESEPL-TAAPFVVVAAPGLLGDRKVDSLA 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735 186 DLERET-------------LITYPVERDRLDVFtrfldpaDVEPAQvriaeltvMMMQLVASGRGVCCLP 242
Cdd:cd08483   90 DLAGLPwlqergtneqrvwLASMGVVPDLERGV-------TFLPGQ--------LVLEAARAGLGLSIQA 144
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-76 7.12e-03

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 37.43  E-value: 7.12e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489182735   1 MLELRHLKTLHALREADSLVEAAERLHLTQSALSHQFKELEERLGMQLFVRKTKPVRFTSAG-------LRLLQLADSLL 73
Cdd:PRK10632   1 MERLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGriyyqgcRRMLHEVQDVH 80


                 ...
gi 489182735  74 PQL 76
Cdd:PRK10632  81 EQL 83
 
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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