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Conserved domains on  [gi|375135155|ref|YP_004995805|]
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LysR family transcriptional regulator [Acinetobacter pittii PHEA-2]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 11426483)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-291 2.84e-44

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 151.17  E-value: 2.84e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155   1 MNINQeqLLMFQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTDEARVLYEKTSQLLIEMNQW 80
Cdd:COG0583    1 MDLRQ--LRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155  81 KQHAHALSTGLEANLTIVIVSELLHTNWTDYICLLESRFPDLQINIVSAPQEDALQMLLDGSAQLALMFEREHlDNREQF 160
Cdd:COG0583   79 EAELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPP-DPGLVA 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155 161 VELKREALIPVISNNHPLAGQNQVTyeqilttrqivvasrdetlkpellfskhywrtDNHHSACLMILRNLGWGVLPQEM 240
Cdd:COG0583  158 RPLGEERLVLVASPDHPLARRAPLV--------------------------------NSLEALLAAVAAGLGIALLPRFL 205

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 375135155 241 FKENPElKNKLKILDLLDFTPRFEYYvdLVWSRESELGAAARFLIEHIRKQ 291
Cdd:COG0583  206 AADELA-AGRLVALPLPDPPPPRPLY--LVWRRRRHLSPAVRAFLDFLREA 253
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-291 2.84e-44

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 151.17  E-value: 2.84e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155   1 MNINQeqLLMFQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTDEARVLYEKTSQLLIEMNQW 80
Cdd:COG0583    1 MDLRQ--LRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155  81 KQHAHALSTGLEANLTIVIVSELLHTNWTDYICLLESRFPDLQINIVSAPQEDALQMLLDGSAQLALMFEREHlDNREQF 160
Cdd:COG0583   79 EAELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPP-DPGLVA 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155 161 VELKREALIPVISNNHPLAGQNQVTyeqilttrqivvasrdetlkpellfskhywrtDNHHSACLMILRNLGWGVLPQEM 240
Cdd:COG0583  158 RPLGEERLVLVASPDHPLARRAPLV--------------------------------NSLEALLAAVAAGLGIALLPRFL 205

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 375135155 241 FKENPElKNKLKILDLLDFTPRFEYYvdLVWSRESELGAAARFLIEHIRKQ 291
Cdd:COG0583  206 AADELA-AGRLVALPLPDPPPPRPLY--LVWRRRRHLSPAVRAFLDFLREA 253
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 118-291 1.59e-20

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: 87.34  E-value: 1.59e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155  118 RFPDLQINIVSAPQEDALQMLLDGSAQLALMFEREHlDNREQFVELKREALIPVISNNHPLAGQNQVTYEQILTTRQIVV 197
Cdd:pfam03466  27 RYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPD-DPGLEARPLGEEPLVLVAPPDHPLARGEPVSLEDLADEPLILL 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155  198 ASR-------DETLKPELLFSKHYWRTDNHHSACLMILRNLGWGVLPQEMFKENPElKNKLKILDLLDFTPRFEYYvdLV 270
Cdd:pfam03466 106 PPGsglrdllDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA-DGRLVALPLPEPPLPRELY--LV 182

                         170       180
                  ....*....|....*....|.
gi 375135155  271 WSRESELGAAARFLIEHIRKQ 291
Cdd:pfam03466 183 WRKGRPLSPAVRAFIEFLREA 203
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-176 3.90e-17

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: 79.58  E-value: 3.90e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155   1 MNINQeqLLMFQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTDEARVLYEKTSQLLiemNQW 80
Cdd:NF040786   1 MNLKQ--LEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEML---DLW 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155  81 KQHAHALSTG---LEANLTI--------VIVSELLhtnwtdyICLLESrFPDLQINIVSAPQEDALQMLLDGSAQLAL-- 147
Cdd:NF040786  76 EKLEEEFDRYgkeSKGVLRIgastipgqYLLPELL-------KKFKEK-YPNVRFKLMISDSIKVIELLLEGEVDIGFtg 147

                        170       180       190
                 ....*....|....*....|....*....|
gi 375135155 148 -MFEREHLdnreQFVELKREALIpVISNNH 176
Cdd:NF040786 148 tKLEKKRL----VYTPFYKDRLV-LITPNG 172
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 118-288 3.74e-16

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 74.94  E-value: 3.74e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155 118 RFPDLQINIVSAPQEDALQMLLDGSAQLALMFEREHLDNREQfVELKREALIPVISNNHPLAGQNQVTYEQIL------- 190
Cdd:cd05466   25 RYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLES-EPLFEEPLVLVVPPDHPLAKRKSVTLADLAdeplilf 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155 191 -----TTRQIVVASRDETLKPELLFskhywRTDNHHSACLMILRNLGWGVLPQEMFKENPElkNKLKILDLLDFTPRFEY 265
Cdd:cd05466  104 ergsgLRRLLDRAFAEAGFTPNIAL-----EVDSLEAIKALVAAGLGIALLPESAVEELAD--GGLVVLPLEDPPLSRTI 176

                        170       180
                 ....*....|....*....|...
gi 375135155 266 YvdLVWSRESELGAAARFLIEHI 288
Cdd:cd05466  177 G--LVWRKGRYLSPAARAFLELL 197
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
3-190 1.40e-12

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 66.75  E-value: 1.40e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155   3 INQEQLLMFQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTDEARVLYEKTSQLLIEMNQWKQ 82
Cdd:PRK10094   2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPS 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155  83 HAHALSTGLEANLTIVIvSELLHTNWT--DYICLLESRFPDLQINIVSAPQEDALQMLLDGSAQLAL-MFEREHLDNREQ 159
Cdd:PRK10094  82 ELQQVNDGVERQVNIVI-NNLLYNPQAvaQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIgVTGTEALANTFS 160

                        170       180       190
                 ....*....|....*....|....*....|.
gi 375135155 160 FVELKREALIPVISNNHPLAGQNQVTYEQIL 190
Cdd:PRK10094 161 LDPLGSVQWRFVMAADHPLANVEEPLTEAQL 191
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 7-146 7.33e-09

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


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 55.69  E-value: 7.33e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155    7 QLLMFQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRkGREPVPTDEARVLYEKTSQLLIEMNQWKQHAHA 86
Cdd:TIGR03298   5 QLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHARQVRLLEAELLAELPG 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155   87 LSTGLEANLTIVIVSELLHTNWTDYICLLESRfPDLQINIVSAPQEDALQMLLDGSAQLA 146
Cdd:TIGR03298  84 LAPGAPTRLTIAVNADSLATWFLPALAPVLAR-EGVLLDLVVEDQDHTAELLRSGEVLGA 142
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 14-74 2.77e-06

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: 47.81  E-value: 2.77e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 375135155  14 VIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTDEARVLYEKTSQLL 74
Cdd:NF041036  12 VAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRIL 72
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-291 2.84e-44

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 151.17  E-value: 2.84e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155   1 MNINQeqLLMFQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTDEARVLYEKTSQLLIEMNQW 80
Cdd:COG0583    1 MDLRQ--LRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155  81 KQHAHALSTGLEANLTIVIVSELLHTNWTDYICLLESRFPDLQINIVSAPQEDALQMLLDGSAQLALMFEREHlDNREQF 160
Cdd:COG0583   79 EAELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPP-DPGLVA 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155 161 VELKREALIPVISNNHPLAGQNQVTyeqilttrqivvasrdetlkpellfskhywrtDNHHSACLMILRNLGWGVLPQEM 240
Cdd:COG0583  158 RPLGEERLVLVASPDHPLARRAPLV--------------------------------NSLEALLAAVAAGLGIALLPRFL 205

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 375135155 241 FKENPElKNKLKILDLLDFTPRFEYYvdLVWSRESELGAAARFLIEHIRKQ 291
Cdd:COG0583  206 AADELA-AGRLVALPLPDPPPPRPLY--LVWRRRRHLSPAVRAFLDFLREA 253
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 118-291 1.59e-20

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: 87.34  E-value: 1.59e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155  118 RFPDLQINIVSAPQEDALQMLLDGSAQLALMFEREHlDNREQFVELKREALIPVISNNHPLAGQNQVTYEQILTTRQIVV 197
Cdd:pfam03466  27 RYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPD-DPGLEARPLGEEPLVLVAPPDHPLARGEPVSLEDLADEPLILL 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155  198 ASR-------DETLKPELLFSKHYWRTDNHHSACLMILRNLGWGVLPQEMFKENPElKNKLKILDLLDFTPRFEYYvdLV 270
Cdd:pfam03466 106 PPGsglrdllDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARELA-DGRLVALPLPEPPLPRELY--LV 182

                         170       180
                  ....*....|....*....|.
gi 375135155  271 WSRESELGAAARFLIEHIRKQ 291
Cdd:pfam03466 183 WRKGRPLSPAVRAFIEFLREA 203
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
6-64 2.19e-17

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 74.34  E-value: 2.19e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 375135155    6 EQLLMFQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTDEAR 64
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-176 3.90e-17

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: 79.58  E-value: 3.90e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155   1 MNINQeqLLMFQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTDEARVLYEKTSQLLiemNQW 80
Cdd:NF040786   1 MNLKQ--LEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEML---DLW 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155  81 KQHAHALSTG---LEANLTI--------VIVSELLhtnwtdyICLLESrFPDLQINIVSAPQEDALQMLLDGSAQLAL-- 147
Cdd:NF040786  76 EKLEEEFDRYgkeSKGVLRIgastipgqYLLPELL-------KKFKEK-YPNVRFKLMISDSIKVIELLLEGEVDIGFtg 147

                        170       180       190
                 ....*....|....*....|....*....|
gi 375135155 148 -MFEREHLdnreQFVELKREALIpVISNNH 176
Cdd:NF040786 148 tKLEKKRL----VYTPFYKDRLV-LITPNG 172
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 118-288 3.74e-16

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


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 74.94  E-value: 3.74e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155 118 RFPDLQINIVSAPQEDALQMLLDGSAQLALMFEREHLDNREQfVELKREALIPVISNNHPLAGQNQVTYEQIL------- 190
Cdd:cd05466   25 RYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLES-EPLFEEPLVLVVPPDHPLAKRKSVTLADLAdeplilf 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155 191 -----TTRQIVVASRDETLKPELLFskhywRTDNHHSACLMILRNLGWGVLPQEMFKENPElkNKLKILDLLDFTPRFEY 265
Cdd:cd05466  104 ergsgLRRLLDRAFAEAGFTPNIAL-----EVDSLEAIKALVAAGLGIALLPESAVEELAD--GGLVVLPLEDPPLSRTI 176

                        170       180
                 ....*....|....*....|...
gi 375135155 266 YvdLVWSRESELGAAARFLIEHI 288
Cdd:cd05466  177 G--LVWRKGRYLSPAARAFLELL 197
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
3-190 1.40e-12

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 66.75  E-value: 1.40e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155   3 INQEQLLMFQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTDEARVLYEKTSQLLIEMNQWKQ 82
Cdd:PRK10094   2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPS 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155  83 HAHALSTGLEANLTIVIvSELLHTNWT--DYICLLESRFPDLQINIVSAPQEDALQMLLDGSAQLAL-MFEREHLDNREQ 159
Cdd:PRK10094  82 ELQQVNDGVERQVNIVI-NNLLYNPQAvaQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIgVTGTEALANTFS 160

                        170       180       190
                 ....*....|....*....|....*....|.
gi 375135155 160 FVELKREALIPVISNNHPLAGQNQVTYEQIL 190
Cdd:PRK10094 161 LDPLGSVQWRFVMAADHPLANVEEPLTEAQL 191
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 8-99 2.56e-12

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 66.12  E-value: 2.56e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155   8 LLMFQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTDEARVLYEKTSQLLIEMNQWKQHAHAL 87
Cdd:PRK11074   7 LEVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQV 86

                         90
                 ....*....|..
gi 375135155  88 STGLEANLTIVI 99
Cdd:PRK11074  87 ANGWRGQLSIAV 98
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 1-74 5.92e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 55.85  E-value: 5.92e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 375135155   1 MNINQEQLLMFQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTDEARVLYEKTSQLL 74
Cdd:PRK10837   1 MHITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALL 74
argP TIGR03298
transcriptional regulator, ArgP family; ArgP used to be known as IciA. ArgP is a positive ...
 7-146 7.33e-09

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


Pssm-ID: 274509 [Multi-domain]  Cd Length: 292  Bit Score: 55.69  E-value: 7.33e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155    7 QLLMFQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRkGREPVPTDEARVLYEKTSQLLIEMNQWKQHAHA 86
Cdd:TIGR03298   5 QLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHARQVRLLEAELLAELPG 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155   87 LSTGLEANLTIVIVSELLHTNWTDYICLLESRfPDLQINIVSAPQEDALQMLLDGSAQLA 146
Cdd:TIGR03298  84 LAPGAPTRLTIAVNADSLATWFLPALAPVLAR-EGVLLDLVVEDQDHTAELLRSGEVLGA 142
rbcR CHL00180
LysR transcriptional regulator; Provisional
 6-74 6.88e-08

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 52.71  E-value: 6.88e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 375135155   6 EQLLMFQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTDEARVLYEKTSQLL 74
Cdd:CHL00180   8 DQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRIL 76
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
2-73 1.06e-07

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 52.28  E-value: 1.06e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 375135155   2 NINQEQLLMFQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRkGREPVPTDEARVLYEKTSQL 73
Cdd:PRK13348   1 MLDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQV 71
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 110-288 1.42e-07

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: 50.95  E-value: 1.42e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155 110 DYICLLESRFPDLQINIVSAPQEDALQMLLDGSAQLAL---MFEREHLDnREQFVElkrEALIPVISNNHPLAGQNQVTY 186
Cdd:cd08420   17 RLLARFRKRYPEVRVSLTIGNTEEIAERVLDGEIDLGLvegPVDHPDLI-VEPFAE---DELVLVVPPDHPLAGRKEVTA 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155 187 EQILT-----------TRQIVvasrdetlkpELLFSKHYWRTDN-HHSACL--------MILRNLGWGVLPQEMFKEnpE 246
Cdd:cd08420   93 EELAAepwilrepgsgTREVF----------ERALAEAGLDGLDlNIVMELgsteaikeAVEAGLGISILSRLAVRK--E 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 375135155 247 LKNK-LKILDLLDFTPRFEYYvdLVWSRESELGAAARFLIEHI 288
Cdd:cd08420  161 LELGrLVALPVEGLRLTRPFS--LIYHKDKYLSPAAEAFLEFL 201
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 11-201 1.45e-07

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 51.88  E-value: 1.45e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155  11 FQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTDEARVLYEKTSQLLIEMNQWKQHAH---AL 87
Cdd:PRK11242   9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRRAIHdvaDL 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155  88 STGleaNLTIVIVSellhtNWTDYIC--LLE---SRFPDLQINIVSAPQEDALQMLLDGSAQLALMFEREHLDNREQfVE 162
Cdd:PRK11242  89 SRG---SLRLAMTP-----TFTAYLIgpLIDafhARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEA-QP 159

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 375135155 163 LKREALIPVISNNHPLAGQNQVTYEQILTTRQIVVASRD 201
Cdd:PRK11242 160 LFTETLALVVGRHHPLAARRKALTLDELADEPLVLLSAE 198
PRK10341 PRK10341
transcriptional regulator TdcA;
6-289 2.73e-07

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 51.02  E-value: 2.73e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155   6 EQLLMFQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTDEARVLYEKTSQLLIEMNQWKQHAH 85
Cdd:PRK10341  10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155  86 ALSTGLEANLTIVIVSELLHTNWTDYICLLESRFPDLQINIVSAPQEDALQMLLDGSAQLALmferEHLDNREQFVELKR 165
Cdd:PRK10341  90 GMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAI----GTLSNEMKLQDLHV 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155 166 EAL-----IPVISNNHPLAGqnqVTYEQILTTRQIVVASRD--------ETLKPELLFSKHYWRTDNHHSACLMILRNLG 232
Cdd:PRK10341 166 EPLfesefVLVASKSRTCTG---TTTLESLKNEQWVLPQTNmgyysellTTLQRNGISIENIVKTDSVVTIYNLVLNADF 242

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 375135155 233 WGVLPQEMFKenPELKNKLKILDLLDFTPRFEYYvdLVWSRESELGAAARFLIEHIR 289
Cdd:PRK10341 243 LTVIPCDMTS--PFGSNQFITIPIEETLPVAQYA--AVWSKNYRIKKAASVLVELAK 295
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
11-151 2.75e-07

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 50.91  E-value: 2.75e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155  11 FQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTDEARVLYEKTSQLLIEMNQWKQHAHALSTG 90
Cdd:PRK10632  10 FAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAFNNT 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 375135155  91 LEANLTIVIVSELLHTNWTDYICLLESRFPDLQINIVSA-PQEDALQMLLD-----GSAQLALMFER 151
Cdd:PRK10632  90 PIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGiPAPDLIADGLDvvirvGALQDSSLFSR 156
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 115-287 3.27e-07

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: 49.85  E-value: 3.27e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155 115 LESRFPDLQINIVSAPQEDALQMLLDGSAQLALMFE---REHLDnREQFVELKREALIPVisnNHPLAGQNQVTYEQ--- 188
Cdd:cd08412   22 FREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDldlPEDIA-FEPLARLPPYVWLPA---DHPLAGKDEVSLADlaa 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155 189 ---ILTTrqiVVASRDETLKpelLFSKHYWRTDNHHSAC------LMILRNLGWGVLPQEMF-KENPELKnKLKILDLLD 258
Cdd:cd08412   98 eplILLD---LPHSREYFLS---LFAAAGLTPRIAYRTSsfeavrSLVANGLGYSLLNDRPYrPWSYDGK-RLVRRPLAD 170

                        170       180
                 ....*....|....*....|....*....
gi 375135155 259 FTPRFEyyVDLVWSRESELGAAARFLIEH 287
Cdd:cd08412  171 PVPPLR--LGLAWRRGARLTRAARAFVDF 197
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 8-189 3.32e-07

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 50.54  E-value: 3.32e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155   8 LLMFQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTDEARVLYEKTSQLLIEMNQWKQHAHAL 87
Cdd:PRK09906   6 LRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKLRARKI 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155  88 STGlEANLTIVIVSELLHTNWTDYICLLESRFPDLQINIVSAPQEDALQMLLDGSAQLALMfeREHLDNRE-QFVELKRE 166
Cdd:PRK09906  86 VQE-DRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFM--RHPVYSDEiDYLELLDE 162

                        170       180
                 ....*....|....*....|...
gi 375135155 167 ALIPVISNNHPLAGQNQVTYEQI 189
Cdd:PRK09906 163 PLVVVLPVDHPLAHEKEITAAQL 185
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 11-126 7.31e-07

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 49.60  E-value: 7.31e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155  11 FQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTDEARVLYEKTSQLLIEMNQWKQHAHALSTG 90
Cdd:PRK14997  10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVE 89

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 375135155  91 LEANLTIVIVSELLHTNWTDYICLLESRFPDLQINI 126
Cdd:PRK14997  90 PRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQL 125
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
3-191 1.33e-06

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 48.86  E-value: 1.33e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155   3 INQEQLLMFQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTDEARVLYEKTSQLLiemnqwKQ 82
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVL------PQ 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155  83 HAHALSTGLEANLTIVIVSELLHT--NW-TDYICLLESRFPDLQINIVSAPQEDALQMLLDGSAQLAL---MFEREHLDN 156
Cdd:PRK15421  76 ISQALQACNEPQQTRLRIAIECHSciQWlTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMtsdILPRSGLHY 155

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 375135155 157 REQFVELKREALIPvisnNHPLAGQNQVTYEQILT 191
Cdd:PRK15421 156 SPMFDYEVRLVLAP----DHPLAAKTRITPEDLAS 186
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
11-79 1.41e-06

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 48.84  E-value: 1.41e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 375135155  11 FQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTDEARVLYEKTSQLLIEMNQ 79
Cdd:PRK10086  22 FEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQ 90
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 14-74 2.77e-06

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: 47.81  E-value: 2.77e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 375135155  14 VIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTDEARVLYEKTSQLL 74
Cdd:NF041036  12 VAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRIL 72
PRK09801 PRK09801
LysR family transcriptional regulator;
14-124 3.22e-06

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 47.72  E-value: 3.22e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155  14 VIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTDEARVLYEKTSQLLIEMNQWKQHAHALSTGLEA 93
Cdd:PRK09801  17 IVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQIKTRPEG 96

                         90       100       110
                 ....*....|....*....|....*....|.
gi 375135155  94 NLTIVIVSELLHTNWTDYICLLESRFPDLQI 124
Cdd:PRK09801  97 MIRIGCSFGFGRSHIAPAITELMRNYPELQV 127
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
3-73 6.86e-06

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 46.69  E-value: 6.86e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 375135155   3 INQEQLLMFQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRkGREPVPTDEARVL---YEKTSQL 73
Cdd:PRK03635   2 LDYKQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLlrhARQVRLL 74
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
 123-284 2.84e-05

The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold; MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176128  Cd Length: 198  Bit Score: 44.25  E-value: 2.84e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155 123 QINIVSAPQEDALQMLLDGSAQLALMFEREHLDNRE-QFVELKREALIPVISNNHPLAGQNQVTYEQILTTRQIVVA--- 198
Cdd:cd08437   30 QIDTYEGGSAELLEQLLQGDLDIALLGSLTPLENSAlHSKIIKTQHFMIIVSKDHPLAKAKKVNFADLKKENFILLNehf 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155 199 ---------SRDETLKPELLFskhywRTDNHHSACLMILRNLGWGVLPQEMFKENPELKnKLKILDllDFTPRFeyYVDL 269
Cdd:cd08437  110 vhpkafdslCQQANFQPNIVY-----RTNDIHILKSMVRENVGIGFLTDIAVKPDDHLV-AIPLLD--NEQPTF--YISL 179

                        170
                 ....*....|....*
gi 375135155 270 VWSRESELGAAARFL 284
Cdd:cd08437  180 AHRKDQLLTPAQKKL 194
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 86-190 6.64e-05

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


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 43.07  E-value: 6.64e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155  86 ALSTGLEANLtiviVSELLHTNWtdyiclleSRFPDLQINIVSAPQEDALQMLLDGSAQLALMFEREHLDnreqfvELKR 165
Cdd:cd08426    5 ATGEGLAAEL----LPSLIARFR--------QRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEP------GIRV 66

                         90       100       110
                 ....*....|....*....|....*....|
gi 375135155 166 EALIP-----VISNNHPLAGQNQVTYEQIL 190
Cdd:cd08426   67 HSRQPapigaVVPPGHPLARQPSVTLAQLA 96
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 96-288 1.07e-04

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: 42.14  E-value: 1.07e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155  96 TIVIVseLLHTNWTDYICLLESRF----PDLQINIVSAPQEDALQMLLDGSAQLALMFEREHLDNREqFVELKREALIPV 171
Cdd:cd08434    1 TVRLG--FLHSLGTSLVPDLIRAFrkeyPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIE-WIPLFTEELVLV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155 172 ISNNHPLAGQNQVTYEQiLTTRQIVVASRDETLKPEL--LFSKHYWRTDnhhSAC----LMILR-----NLGWGVLPqEM 240
Cdd:cd08434   78 VPKDHPLAGRDSVDLAE-LADEPFVLLSPGFGLRPIVdeLCAAAGFTPK---IAFegeeDSTIAglvaaGLGVAILP-EM 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 375135155 241 FKENPElknKLKILDLLDftPRFEYYVDLVWSRESELGAAARFLIEHI 288
Cdd:cd08434  153 TLLNPP---GVKKIPIKD--PDAERTIGLAWLKDRYLSPAARRFKDFV 195
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-189 1.83e-04

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 42.29  E-value: 1.83e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155   1 MNINQEQLLMfQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVP-TDEARVLYEKTSQLLIEMNQ 79
Cdd:PRK12682   1 MNLQQLRFVR-EAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKGlTEPGKAVLDVIERILREVGN 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155  80 WKQHAHALSTGLEANLTIVIVsellHTNwTDY-----ICLLESRFPDLQINIVSA-PQEDAlQMLLDGSAQLALMFEReh 153
Cdd:PRK12682  80 IKRIGDDFSNQDSGTLTIATT----HTQ-ARYvlprvVAAFRKRYPKVNLSLHQGsPDEIA-RMVISGEADIGIATES-- 151

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 375135155 154 LDNREQFVELK--REALIPVISNNHPLAGQNQVTYEQI 189
Cdd:PRK12682 152 LADDPDLATLPcyDWQHAVIVPPDHPLAQEERITLEDL 189
PRK15243 PRK15243
virulence genes transcriptional activator SpvR;
6-82 2.27e-04

virulence genes transcriptional activator SpvR;


Pssm-ID: 185155 [Multi-domain]  Cd Length: 297  Bit Score: 41.96  E-value: 2.27e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 375135155   6 EQLLMFQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTDEARVLYEKTSQLLIEMNQWKQ 82
Cdd:PRK15243   7 KKLKIFITLMETGSFSIATSVLYITRTPLSRVISDLERELKQRLFIRKNGTLIPTEFAQTIYRKVKSHYIFLHALEQ 83
PRK09986 PRK09986
LysR family transcriptional regulator;
3-185 3.99e-04

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 41.25  E-value: 3.99e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155   3 INQEQLLMFQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTDEARVLYEKTSQLLIEMNQWKQ 82
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSLA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155  83 HAHALSTGLEANLTIVIVSELLhtnWTDYICLLeSRFPDLQINIVSAPQEDALQMlldgsaQLALMfEREHLD---NREQ 159
Cdd:PRK09986  87 RVEQIGRGEAGRIEIGIVGTAL---WGRLRPAM-RHFLKENPNVEWLLRELSPSM------QMAAL-ERRELDagiWRMA 155

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 375135155 160 FVE---------LKREALIPVISNNHPLAGQNQVT 185
Cdd:PRK09986 156 DLEpnpgftsrrLHESAFAVAVPEEHPLASRSSVP 190
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 115-185 6.20e-04

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: 40.27  E-value: 6.20e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 375135155 115 LESRFPDLQINIVSAPQEDALQMLLDGSAQLALMFE----REHLDNREQFVELKREALIPVISNNHPLAGQNQVT 185
Cdd:cd08423   22 LRARHPGLEVRLREAEPPESLDALRAGELDLAVVFDypvtPPPDDPGLTRVPLLDDPLDLVLPADHPLAGREEVA 96
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-189 7.58e-04

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 40.41  E-value: 7.58e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155   1 MNINQEQLLMfQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKG-REPVPTDEARVLYEKTSQLLIEMNQ 79
Cdd:PRK12683   1 MNFQQLRIIR-EAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGkRLTGLTEPGKELLQIVERMLLDAEN 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155  80 WKQHAHALSTGLEANLTIVIVsellHTN----WTDYICLLESRFPDLQINIVSAPQEDALQMLLDGSAQLALMFERehLD 155
Cdd:PRK12683  80 LRRLAEQFADRDSGHLTVATT----HTQaryaLPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEA--LD 153

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 375135155 156 NREQFVELK----REALIpvISNNHPLAGQNQVTYEQI 189
Cdd:PRK12683 154 REPDLVSFPyyswHHVVV--VPKGHPLTGRENLTLEAI 189
PRK12680 PRK12680
LysR family transcriptional regulator;
1-178 8.18e-04

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 40.38  E-value: 8.18e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155   1 MNINQEQLLMFQAVIETGSFSAAARKLGKVPsAVSMSIANLEIDLDLTLFDRKGR--EPVpTDEARVLYEKTSQLLIEMN 78
Cdd:PRK12680   1 MTLTQLRYLVAIADAELNITLAAARVHATQP-GLSKQLKQLEDELGFLLFVRKGRslESV-TPAGVEVIERARAVLSEAN 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155  79 QWKQHAHALSTGLEANLTIVIVSELLHTNWTDYICLLESRFPDLQINIVSAPQEDALQMLLDGSAQLALMFEREHLDNRE 158
Cdd:PRK12680  79 NIRTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAG 158

                        170       180
                 ....*....|....*....|
gi 375135155 159 QFVELKREALIPVISNNHPL 178
Cdd:PRK12680 159 IAVPLYRWRRLVVVPRGHAL 178
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
 118-204 8.39e-04

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


Pssm-ID: 176132  Cd Length: 198  Bit Score: 39.86  E-value: 8.39e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155 118 RFPDLQINIVSAPQEDALQMLLDGSAQLALMFEREHLDNREqFVELKREALIPVISNNHPLAGQNQVTYEQIlttrqivv 197
Cdd:cd08441   25 RWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGIA-YEPLFDYEVVLVVAPDHPLAAKEFITPEDL-------- 95


                 ....*..
gi 375135155 198 asRDETL 204
Cdd:cd08441   96 --ADETL 100
PRK11482 PRK11482
DNA-binding transcriptional regulator;
2-72 1.37e-03

DNA-binding transcriptional regulator;


Pssm-ID: 183159 [Multi-domain]  Cd Length: 317  Bit Score: 39.71  E-value: 1.37e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 375135155   2 NINQEQLLMFQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTDEARVLYEKTSQ 72
Cdd:PRK11482  28 NIDLNLLTIFEAVYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHEYISQ 98
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 118-288 1.60e-03

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


Pssm-ID: 176113  Cd Length: 198  Bit Score: 38.66  E-value: 1.60e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155 118 RFPDLQINIVSAPQEDALQMLLDGSAQLALMFEREHLDNREQFVeLKREALIPVISNNHPLAGQNQVTYEQILT------ 191
Cdd:cd08421   25 AHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLETRP-YRTDRLVVVVPRDHPLAGRASVAFADTLDhdfvgl 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155 192 ------TRQIV-VASR-DETLKPELlfskhywRTDNHHSACLMILRNLGWGVLPQEMFKE-NPELknKLKILDLLDFTPR 262
Cdd:cd08421  104 pagsalHTFLReAAARlGRRLRLRV-------QVSSFDAVCRMVAAGLGIGIVPESAARRyARAL--GLRVVPLDDAWAR 174

                        170       180
                 ....*....|....*....|....*.
gi 375135155 263 FEYYvdLVWSRESELGAAARFLIEHI 288
Cdd:cd08421  175 RRLL--LCVRSFDALPPAARALVDHL 198
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 19-68 1.88e-03

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 39.06  E-value: 1.88e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 375135155  19 SFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTDEARVLYE 68
Cdd:PRK11139  22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFL 71
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 105-289 1.94e-03

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


Pssm-ID: 176110 [Multi-domain]  Cd Length: 201  Bit Score: 38.49  E-value: 1.94e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155 105 HTNWTDYICLLESRFPDLQINIVSAPQEDALQMLLDGSAQLAL-MFEREHLDNREQFVELKREALIPVISNNHPLAG--- 180
Cdd:cd08418   12 HTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIgTLPDEMYLKELISEPLFESDFVVVARKDHPLQGars 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155 181 -QNQVTYEQILTT------RQIVVASRDETLKPELLFskhywRTDNhHSACLMILRNLGW-GVLPQEMFKEnPELKNKLK 252
Cdd:cd08418   92 lEELLDASWVLPGtrmgyyNNLLEALRRLGYNPRVAV-----RTDS-IVSIINLVEKADFlTILSRDMGRG-PLDSFRLI 164

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 375135155 253 ILDLLDFTPRFEYYvdLVWSRESELGAAARFLIEHIR 289
Cdd:cd08418  165 TIPVEEPLPSADYY--LIYRKKSRLTPLAEQLVELFR 199
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 1-185 2.19e-03

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 39.20  E-value: 2.19e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155   1 MNINQEQLLMFQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTDEARVLYEKTSQLLIEMNQW 80
Cdd:PRK11013   2 AAVSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGLRLFEEVQRSYYGLDRI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155  81 KQHAHALSTGLEANLTIVIVSELLHTNWTDYICLLESRFPDLQINIVsaPQEDAL--QMLldgSAQ---LALMfEREHLD 155
Cdd:PRK11013  82 VSAAESLREFRQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIV--PQESPLleEWL---SAQrhdLGLT-ETLHTP 155

                        170       180       190
                 ....*....|....*....|....*....|
gi 375135155 156 NREQFVELKREALIPVISNNHPLAGQNQVT 185
Cdd:PRK11013 156 AGTERTELLTLDEVCVLPAGHPLAAKKVLT 185
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 117-288 2.39e-03

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: 38.31  E-value: 2.39e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155 117 SRFPDLQINIV---SAPQEdalQMLLDGSAQLA---LMFEREHLDnreqFVELKREALIPVISNNHPLAGQNQVTYEQ-- 188
Cdd:cd08438   24 QRYPNIELELVeygGKKVE---QAVLNGELDVGitvLPVDEEEFD----SQPLCNEPLVAVLPRGHPLAGRKTVSLADla 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155 189 ----ILTT------RQIVVASRDETLKPELLFSKHYWrtdnhHSACLMILRNLGWGVLPQEMFKEnpELKNKLKILDLLD 258
Cdd:cd08438   97 depfILFNedfalhDRIIDACQQAGFTPNIAARSSQW-----DFIAELVAAGLGVALLPRSIAQR--LDNAGVKVIPLTD 169

                        170       180       190
                 ....*....|....*....|....*....|
gi 375135155 259 ftPRFEYYVDLVWSRESELGAAARFLIEHI 288
Cdd:cd08438  170 --PDLRWQLALIWRKGRYLSHAARAWLALL 197
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 118-198 2.61e-03

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: 38.28  E-value: 2.61e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155 118 RFPDLQINIVSAPQEDALQMLLDGSAQLALMFEREHLDNREqFVELKREALIPVISNNHPLAGQNQVTYEQILTTRQIVV 197
Cdd:cd08440   25 RHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLE-FEPLLRDPFVLVCPKDHPLARRRSVTWAELAGYPLIAL 103


                 .
gi 375135155 198 A 198
Cdd:cd08440  104 G 104
nhaR PRK11062
transcriptional activator NhaR; Provisional
 2-61 3.69e-03

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 38.45  E-value: 3.69e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155   2 NINQEQLLMFQAVIETGSFSAAARKLGKVPSAVSMSIANLEIDLDLTLFDRKGREPVPTD 61
Cdd:PRK11062   3 HINYNHLYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTE 62
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 118-185 6.31e-03

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: 37.16  E-value: 6.31e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155 118 RFPDLQINIVSAPQEDALQMLLDGSAQLALMFEREHLDN--REQFVELKREALIPVisnNHPLAGQNQVT 185
Cdd:cd08415   25 RHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGleSEPLASGRAVCVLPP---GHPLARKDVVT 91
PBP2_Pa0477 cd08468
The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional ...
 106-203 9.80e-03

The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional regulator Pa0477 related to DntR, contains the type 2 periplasmic binding fold; LysR-type transcriptional regulator Pa0477 is related to DntR, which controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. 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. 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: 176157 [Multi-domain]  Cd Length: 202  Bit Score: 36.65  E-value: 9.80e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375135155 106 TNWTDYICL------LESRFPDLQINIVSAPQEDALQMLLDGSAQLALMFEREHLDNREQFVELK--REALIPVISNNHP 177
Cdd:cd08468    7 TDYTALAVMprlmarLEELAPSVRLNLVHAEQKLPLDALLAGEIDFALGYSHDDGAEPRLIEERDwwEDTYVVIASRDHP 86

                         90       100
                 ....*....|....*....|....*.
gi 375135155 178 LAgqNQVTYEQILTTRQIVVASRDET 203
Cdd:cd08468   87 RL--SRLTLDAFLAERHLVVTPWNED 110
 
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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