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Conserved domains on  [gi|1167103369|gb|OPZ61124|]
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HTH-type transcriptional regulator CatM [Deltaproteobacteria bacterium ADurb.Bin510]

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];
1-288 1.04e-47

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


:

Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 159.65  E-value: 1.04e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   1 MELYQIRTFVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAGAQLLVKARAILNGLEDFAA 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369  81 TAASLNASPQAILTVGLNTDPQVLKIDQLVDLCQNTNPRLSFNFISTNSPVVLKGLHSGEFDAGFVFGPCSLAELTCEPL 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 161 TEIELKLVAPHSWHdriqgrslaeLARLPWVMPPGEcpysmllkaefarlglepevrltadqepILKSLVTAGHGLSLLP 240
Cdd:COG0583   161 GEERLVLVASPDHP----------LARRAPLVNSLE----------------------------ALLAAVAAGLGIALLP 202

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1167103369 241 SFELKPE---DSLSV--WDGPGFKLALSFVCRLSRSQQPELMAFKQVLKRLWA 288
Cdd:COG0583   203 RFLAADElaaGRLVAlpLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-288 1.04e-47

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 159.65  E-value: 1.04e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   1 MELYQIRTFVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAGAQLLVKARAILNGLEDFAA 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369  81 TAASLNASPQAILTVGLNTDPQVLKIDQLVDLCQNTNPRLSFNFISTNSPVVLKGLHSGEFDAGFVFGPCSLAELTCEPL 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 161 TEIELKLVAPHSWHdriqgrslaeLARLPWVMPPGEcpysmllkaefarlglepevrltadqepILKSLVTAGHGLSLLP 240
Cdd:COG0583   161 GEERLVLVASPDHP----------LARRAPLVNSLE----------------------------ALLAAVAAGLGIALLP 202

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1167103369 241 SFELKPE---DSLSV--WDGPGFKLALSFVCRLSRSQQPELMAFKQVLKRLWA 288
Cdd:COG0583   203 RFLAADElaaGRLVAlpLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-284 2.33e-30

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: 115.41  E-value: 2.33e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   1 MELYQIRTFVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAGAQLLVKARAILNGLEDFAA 80
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369  81 TAASLNASPQAILTVGLNTDPQVLKIDQLVDLCQNTNPRLSFNFISTNSPVVLKGLHSGEFDAGFVFGPCSLAELTCEPL 160
Cdd:NF040786   81 EFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 161 TEIELKLVAP--HSWHDRIQ-GRSLAELARLPWVM-PPGECPYSMLLKAeFARLGLEPE----VRLTADQEPIlKSLVTA 232
Cdd:NF040786  161 YKDRLVLITPngTEKYRMLKeEISISELQKEPFIMrEEGSGTRKEAEKA-LKSLGISLEdlnvVASLGSTEAI-KQSVEA 238

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1167103369 233 GHGLSLLPSFELKPEDS---LSVWDGPGFKLALSF--VCRLSRSQQPELMAFKQVLK 284
Cdd:NF040786  239 GLGISVISELAAEKEVErgrVLIFPIPGLPKNRDFylVYNKNRQLSPTAEAFLQFVK 295
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 93-288 2.11e-25

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: 100.06  E-value: 2.11e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369  93 LTVGLNTDPQVLKIDQLVDLCQNTNPRLSFNFISTNSPVVLKGLHSGEFDAGFVFGPCSLAELTCEPLTEIELKLVAP-- 170
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAPpd 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 171 HSWHDRiQGRSLAELARLPWVMPPGECPYSMLLKAEFARLGLEPEVRLTADQEPILKSLVTAGHGLSLLPSFELKPE--- 247
Cdd:pfam03466  84 HPLARG-EPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARElad 162

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1167103369 248 DSLSV--WDGPGFKLALSFVCRLSRSQQPELMAFKQVLKRLWA 288
Cdd:pfam03466 163 GRLVAlpLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 118-283 2.61e-25

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: 99.60  E-value: 2.61e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 118 PRLSFNFISTNSPVVLKGLHSGEFDAGFVFGPCSLAELTCEPLTEIELKLVAP--HSWHDRiQGRSLAELARLPWVMPPG 195
Cdd:cd05466    27 PGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPpdHPLAKR-KSVTLADLADEPLILFER 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 196 ECPYSMLLKAEFARLGLEPEVRLTADQEPILKSLVTAGHGLSLLPSFELKPEDSLSV----WDGPGFKLALSFVCRLSRS 271
Cdd:cd05466   106 GSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELADGGLvvlpLEDPPLSRTIGLVWRKGRY 185

                         170
                  ....*....|..
gi 1167103369 272 QQPELMAFKQVL 283
Cdd:cd05466   186 LSPAARAFLELL 197
PRK12680 PRK12680
LysR family transcriptional regulator;
1-256 1.73e-21

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 92.38  E-value: 1.73e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   1 MELYQIRTFVKVAETG-SITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGME-LSPAGAQLLVKARAILNGLEDF 78
Cdd:PRK12680    1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369  79 AATAASLNASPQAILTVGLNTDPQVLKIDQLVDLCQNTNPRLSFNFISTNSPVVLKGLHSGEFDAGFV--FGPCSLAELT 156
Cdd:PRK12680   81 RTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVstAGGEPSAGIA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 157 CePLTEIELKLVAP--HSWHDRIQGRSLAELARLPWVMPPGEC-PYSMLLKAeFARLGLEPEVRLTADQEPILKSLVTAG 233
Cdd:PRK12680  161 V-PLYRWRRLVVVPrgHALDTPRRAPDMAALAEHPLISYESSTrPGSSLQRA-FAQLGLEPSIALTALDADLIKTYVRAG 238

                         250       260
                  ....*....|....*....|....
gi 1167103369 234 HGLSLLPSFELKPEDS-LSVWDGP 256
Cdd:PRK12680  239 LGVGLLAEMAVNANDEdLRAWPAP 262
 
Name Accession Description Interval E-value
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
1-288 1.04e-47

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 159.65  E-value: 1.04e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   1 MELYQIRTFVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAGAQLLVKARAILNGLEDFAA 80
Cdd:COG0583     1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369  81 TAASLNASPQAILTVGLNTDPQVLKIDQLVDLCQNTNPRLSFNFISTNSPVVLKGLHSGEFDAGFVFGPCSLAELTCEPL 160
Cdd:COG0583    81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 161 TEIELKLVAPHSWHdriqgrslaeLARLPWVMPPGEcpysmllkaefarlglepevrltadqepILKSLVTAGHGLSLLP 240
Cdd:COG0583   161 GEERLVLVASPDHP----------LARRAPLVNSLE----------------------------ALLAAVAAGLGIALLP 202

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1167103369 241 SFELKPE---DSLSV--WDGPGFKLALSFVCRLSRSQQPELMAFKQVLKRLWA 288
Cdd:COG0583   203 RFLAADElaaGRLVAlpLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLREALA 255
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 1-284 2.33e-30

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: 115.41  E-value: 2.33e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   1 MELYQIRTFVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAGAQLLVKARAILNGLEDFAA 80
Cdd:NF040786    1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369  81 TAASLNASPQAILTVGLNTDPQVLKIDQLVDLCQNTNPRLSFNFISTNSPVVLKGLHSGEFDAGFVFGPCSLAELTCEPL 160
Cdd:NF040786   81 EFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 161 TEIELKLVAP--HSWHDRIQ-GRSLAELARLPWVM-PPGECPYSMLLKAeFARLGLEPE----VRLTADQEPIlKSLVTA 232
Cdd:NF040786  161 YKDRLVLITPngTEKYRMLKeEISISELQKEPFIMrEEGSGTRKEAEKA-LKSLGISLEdlnvVASLGSTEAI-KQSVEA 238

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1167103369 233 GHGLSLLPSFELKPEDS---LSVWDGPGFKLALSF--VCRLSRSQQPELMAFKQVLK 284
Cdd:NF040786  239 GLGISVISELAAEKEVErgrVLIFPIPGLPKNRDFylVYNKNRQLSPTAEAFLQFVK 295
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 93-288 2.11e-25

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: 100.06  E-value: 2.11e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369  93 LTVGLNTDPQVLKIDQLVDLCQNTNPRLSFNFISTNSPVVLKGLHSGEFDAGFVFGPCSLAELTCEPLTEIELKLVAP-- 170
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVAPpd 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 171 HSWHDRiQGRSLAELARLPWVMPPGECPYSMLLKAEFARLGLEPEVRLTADQEPILKSLVTAGHGLSLLPSFELKPE--- 247
Cdd:pfam03466  84 HPLARG-EPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVARElad 162

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1167103369 248 DSLSV--WDGPGFKLALSFVCRLSRSQQPELMAFKQVLKRLWA 288
Cdd:pfam03466 163 GRLVAlpLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLREALA 205
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 118-283 2.61e-25

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: 99.60  E-value: 2.61e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 118 PRLSFNFISTNSPVVLKGLHSGEFDAGFVFGPCSLAELTCEPLTEIELKLVAP--HSWHDRiQGRSLAELARLPWVMPPG 195
Cdd:cd05466    27 PGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPpdHPLAKR-KSVTLADLADEPLILFER 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 196 ECPYSMLLKAEFARLGLEPEVRLTADQEPILKSLVTAGHGLSLLPSFELKPEDSLSV----WDGPGFKLALSFVCRLSRS 271
Cdd:cd05466   106 GSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELADGGLvvlpLEDPPLSRTIGLVWRKGRY 185

                         170
                  ....*....|..
gi 1167103369 272 QQPELMAFKQVL 283
Cdd:cd05466   186 LSPAARAFLELL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
3-61 2.23e-22

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 87.44  E-value: 2.23e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1167103369   3 LYQIRTFVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAG 61
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAG 59
PRK12680 PRK12680
LysR family transcriptional regulator;
1-256 1.73e-21

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 92.38  E-value: 1.73e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   1 MELYQIRTFVKVAETG-SITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGME-LSPAGAQLLVKARAILNGLEDF 78
Cdd:PRK12680    1 MTLTQLRYLVAIADAElNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLEsVTPAGVEVIERARAVLSEANNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369  79 AATAASLNASPQAILTVGLNTDPQVLKIDQLVDLCQNTNPRLSFNFISTNSPVVLKGLHSGEFDAGFV--FGPCSLAELT 156
Cdd:PRK12680   81 RTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVstAGGEPSAGIA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 157 CePLTEIELKLVAP--HSWHDRIQGRSLAELARLPWVMPPGEC-PYSMLLKAeFARLGLEPEVRLTADQEPILKSLVTAG 233
Cdd:PRK12680  161 V-PLYRWRRLVVVPrgHALDTPRRAPDMAALAEHPLISYESSTrPGSSLQRA-FAQLGLEPSIALTALDADLIKTYVRAG 238

                         250       260
                  ....*....|....*....|....
gi 1167103369 234 HGLSLLPSFELKPEDS-LSVWDGP 256
Cdd:PRK12680  239 LGVGLLAEMAVNANDEdLRAWPAP 262
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 1-242 7.65e-20

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 87.13  E-value: 7.65e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   1 MELYQIRTFVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAGAQLLVKARAILNGLEDFAA 80
Cdd:PRK09906    1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369  81 TAASLnASPQAILTVG------LNTDPQVLKIDQLvdlcqnTNPRLSFNFISTNSPVVLKGLHSGEFDAGFVFGPC---- 150
Cdd:PRK09906   81 RARKI-VQEDRQLTIGfvpsaeVNLLPKVLPMFRL------RHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVysde 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 151 -SLAELTCEPLTEIeLKLVAPHSWHDRIqgrSLAELARLPWVMPPGEcpYSMLL----KAEFARLGLEPEVRLTADQEPI 225
Cdd:PRK09906  154 iDYLELLDEPLVVV-LPVDHPLAHEKEI---TAAQLDGVNFISTDPA--YSGSLapiiKAWFAQHNSQPNIVQVATNILV 227

                         250
                  ....*....|....*..
gi 1167103369 226 LKSLVTAGHGLSLLPSF 242
Cdd:PRK09906  228 TMNLVGMGLGCTIIPGY 244
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 1-241 3.25e-18

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 82.70  E-value: 3.25e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   1 MELYQIRTFVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAGAQLLVKARAILNGLEdfaa 80
Cdd:PRK11242    1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLE---- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369  81 taaslnASPQAILTVG--------LNTDPQVLK--IDQLVDLCQNTNPRLSFNFISTNSPVVLKGLHSGEFDAGFVFGPC 150
Cdd:PRK11242   77 ------AGRRAIHDVAdlsrgslrLAMTPTFTAylIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPV 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 151 SLAELTCEPLTEIELKLV--APHSWHDRIQGRSLAELARLPWVMPPGECPYSMLLKAEFARLGLEPEVRLTADQEPILKS 228
Cdd:PRK11242  151 HSPEIEAQPLFTETLALVvgRHHPLAARRKALTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLE 230

                         250
                  ....*....|...
gi 1167103369 229 LVTAGHGLSLLPS 241
Cdd:PRK11242  231 IVRRGRLATLLPA 243
PRK09791 PRK09791
LysR family transcriptional regulator;
1-240 5.74e-18

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 82.12  E-value: 5.74e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   1 MELYQIRTFVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAGAQLLVKARAILNGL----E 76
Cdd:PRK09791    5 VKIHQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELraaqE 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369  77 DFAATAASLNASpqaiLTVGLNTDPQVLKIDQLVDLCQNTNPRLSFNFISTNSPVVLKGLHSGEFDAGF-VFGPCSL-AE 154
Cdd:PRK09791   85 DIRQRQGQLAGQ----INIGMGASIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTInTYYQGPYdHE 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 155 LTCEPLTEIELKLVAPHSwHDRIQGRSLAELARLPWVMPPGECPYSMLLKAEFARLGLEPEVRLTADQEPILKSLVTAGH 234
Cdd:PRK09791  161 FTFEKLLEKQFAVFCRPG-HPAIGARSLKQLLDYSWTMPTPHGSYYKQLSELLDDQAQTPQVGVVCETFSACISLVAKSD 239


                  ....*.
gi 1167103369 235 GLSLLP 240
Cdd:PRK09791  240 FLSILP 245
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
6-76 1.44e-16

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 78.31  E-value: 1.44e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1167103369   6 IRTFVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAGAQLLVKARAILNGLE 76
Cdd:PRK10094    7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLE 77
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
 108-241 3.04e-15

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: 72.54  E-value: 3.04e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 108 QLVDLCQNTNPRLSFNFISTNSPVVLKGLHSGEFDAGFVFGPCSLAELTCEPLTEIELKLVAPHSW----HDRIqgrSLA 183
Cdd:cd08414    17 RLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALPADHplaaRESV---SLA 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 184 ELARLPWVM-PPGECP-YSMLLKAEFARLGLEPEVRLTADQEPILKSLVTAGHGLSLLPS 241
Cdd:cd08414    94 DLADEPFVLfPREPGPgLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPA 153
PRK10341 PRK10341
transcriptional regulator TdcA;
9-246 3.69e-15

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 74.13  E-value: 3.69e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   9 FVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAGAQLLVKARAILNGLEDFAATAASLNAS 88
Cdd:PRK10341   15 FQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGMSSE 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369  89 PQAILTVGLNTDPQVLKIDQLVDLCQNTNPRLSFNFISTNSPVVLKGLHSGEFDagFVFGPCS----LAELTCEPLTEIE 164
Cdd:PRK10341   95 AVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLD--FAIGTLSnemkLQDLHVEPLFESE 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 165 LKLVAPHSwHDRIQGRSLAELARLPWVMPPGECPYSMLLKAEFARLGLEPEVRLTADQEPILKSLVTAGHGLSLLPSFEL 244
Cdd:PRK10341  173 FVLVASKS-RTCTGTTTLESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNADFLTVIPCDMT 251


                  ..
gi 1167103369 245 KP 246
Cdd:PRK10341  252 SP 253
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 17-171 1.11e-14

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 72.57  E-value: 1.11e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369  17 SITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAGAQLLVKARAILNGLEDfaATAASLNASPQAILTVG 96
Cdd:PRK11139   22 SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQLAE--ATRKLRARSAKGALTVS 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369  97 LntdPQVLKIDQLVdlcqntnPRLS-FN---------FISTNSPVvlkGLHSGEFDAGFVFGPCSLAELTCEPL-TEIEL 165
Cdd:PRK11139  100 L---LPSFAIQWLV-------PRLSsFNeahpdidvrLKAVDRLE---DFLRDDVDVAIRYGRGNWPGLRVEKLlDEYLL 166


                  ....*.
gi 1167103369 166 KLVAPH 171
Cdd:PRK11139  167 PVCSPA 172
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 1-240 1.42e-14

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 72.41  E-value: 1.42e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   1 MELYQIRTFVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAGAQLLVKARAILNGLEDfAA 80
Cdd:PRK11233    1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQ-AQ 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369  81 TAasLNASPQAI---LTVGL--NTDPQVLKIdQLVDLCQNTNPR----LSFNFISTNSPVVLkglhSGEFDAGFVFGPCS 151
Cdd:PRK11233   80 LA--VHNVGQALsgqVSIGLapGTAASSLTM-PLLQAVRAEFPGivlyLHENSGATLNEKLM----NGQLDMAVIYEHSP 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 152 LAELTCEPLTEIELKLVAPHSWHDriQGRSLAELARLPWVMPPgecPYSMLLK---AEFARLGLEPEVRLTADQEPILKS 228
Cdd:PRK11233  153 VAGLSSQPLLKEDLFLVGTQDCPG--QSVDLAAVAQMNLFLPR---DYSAVRLrvdEAFSLRRLTAKVIGEIESIATLTA 227

                         250
                  ....*....|..
gi 1167103369 229 LVTAGHGLSLLP 240
Cdd:PRK11233  228 AIASGMGVTVLP 239
PRK09986 PRK09986
LysR family transcriptional regulator;
3-240 5.86e-14

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 70.52  E-value: 5.86e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   3 LYQIRTFVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAGAQLLVKARAIlngledFAATA 82
Cdd:PRK09986    9 LKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRL------LDNAE 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369  83 ASLNASPQ---------AILTVGLNTDPQVLKIDQLVdLCQNTNPRLSFNFISTNSPVVLkgLHSGEFDAGF--VFGPCS 151
Cdd:PRK09986   83 QSLARVEQigrgeagriEIGIVGTALWGRLRPAMRHF-LKENPNVEWLLRELSPSMQMAA--LERRELDAGIwrMADLEP 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 152 LAELTCEPLTEiELKLVAPHSWHDRIQGRS--LAELARLPWV-MPPGECPYSMLLKAEFARLGLEPEVRLTADQEPILKS 228
Cdd:PRK09986  160 NPGFTSRRLHE-SAFAVAVPEEHPLASRSSvpLKALRNEYFItLPFVHSDWGKFLQRVCQQAGFSPQIIRQVNEPQTVLA 238

                         250
                  ....*....|..
gi 1167103369 229 LVTAGHGLSLLP 240
Cdd:PRK09986  239 MVSMGIGITLLP 250
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
 109-240 7.46e-14

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: 68.78  E-value: 7.46e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 109 LVDLCQNTNPRLSFNFISTNSPVVLKGLHSGEFDAGFVFGPCSLAELTCEPLTEIELKLVAPHSW-HDRIQGRSLAELAR 187
Cdd:cd08433    18 LLRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGPADApLPRGAPVPLAELAR 97

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1167103369 188 LPWVMPPGECPYSMLLKAEFARLGLEPEVRLTADQEPILKSLVTAGHGLSLLP 240
Cdd:cd08433    98 LPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILP 150
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 1-247 7.92e-13

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 67.38  E-value: 7.92e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   1 MELYQIRTFVKVAETG-SITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSA-RGMELSPAGAQLLVKARAILNGLEDF 78
Cdd:PRK12683    1 MNFQQLRIIREAVRQNfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGkRLTGLTEPGKELLQIVERMLLDAENL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369  79 AATAASLNASPQAILTVGlNTDPQVlkidqlvdlcQNTNPRLSFNFISTNSPVVLKgLHSGefdagfvfGPCSLAELT-- 156
Cdd:PRK12683   81 RRLAEQFADRDSGHLTVA-TTHTQA----------RYALPKVVRQFKEVFPKVHLA-LRQG--------SPQEIAEMLln 140

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 157 --------CEPLTEIElKLVA-P-HSWH-----------DRIQGRSLAELARLPWVM-PPGECPYSMLLKAeFARLGLEP 214
Cdd:PRK12683  141 geadigiaTEALDREP-DLVSfPyYSWHhvvvvpkghplTGRENLTLEAIAEYPIITyDQGFTGRSRIDQA-FAEAGLVP 218

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1167103369 215 EVRLTADQEPILKSLVTAGHGLSLLPSFELKPE 247
Cdd:PRK12683  219 DIVLTALDADVIKTYVELGMGVGIVAAMAYDPQ 251
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
1-247 2.82e-12

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 65.77  E-value: 2.82e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   1 MELYQIRTFVKVAETG-SITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSA-RGMELSPAGAQLLVKARAILNGLEDF 78
Cdd:PRK12684    1 MNLHQLRFVREAVRQNfNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGkRLRGLTEPGRIILASVERILQEVENL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369  79 AATAASLNASPQAILTVG-LNTD-----PQVLK--IDQLVDLcqntnpRLSfnfISTNSPV-VLKGLHSGEFDAGFVFGP 149
Cdd:PRK12684   81 KRVGKEFAAQDQGNLTIAtTHTQaryalPAAIKefKKRYPKV------RLS---ILQGSPTqIAEMVLHGQADLAIATEA 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 150 CSLA-ELTCEPLTEIELKLVAPHSwHDRIQGR--SLAELARLPWVMppgecpY-------SMLLKAeFARLGLEPEVRLT 219
Cdd:PRK12684  152 IADYkELVSLPCYQWNHCVVVPPD-HPLLERKplTLEDLAQYPLIT------YdfafagrSKINKA-FALRGLKPDIVLE 223

                         250       260
                  ....*....|....*....|....*...
gi 1167103369 220 ADQEPILKSLVTAGHGLSLLPSFELKPE 247
Cdd:PRK12684  224 AIDADVIKTYVELGLGVGIVADMAFDPE 251
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 118-247 5.81e-12

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: 63.28  E-value: 5.81e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 118 PRLSFNFISTNSPVVLKGLHSGEFDAGFVFGPCSLAELTCEPLTEIELKLVAP--HSWHDRiQGRSLAELARLPWVM-PP 194
Cdd:cd08420    27 PEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVPpdHPLAGR-KEVTAEELAAEPWILrEP 105

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1167103369 195 GecpyS---MLLKAEFARLGLEPE---VRLTADQEPILKSLVTAGHGLSLLPSFELKPE 247
Cdd:cd08420   106 G----SgtrEVFERALAEAGLDGLdlnIVMELGSTEAIKEAVEAGLGISILSRLAVRKE 160
cbl PRK12679
HTH-type transcriptional regulator Cbl;
17-254 2.84e-11

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 62.90  E-value: 2.84e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369  17 SITRAASELNTSQPSVSAHIKALEDEYGLSLF-KRSARGMELSPAGAQLLVKARAILNGLEDFAATAASLNASPQAILTV 95
Cdd:PRK12679   18 NLTEVANMLFTSQSGVSRHIRELEDELGIEIFiRRGKRLLGMTEPGKALLVIAERILNEASNVRRLADLFTNDTSGVLTI 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369  96 GLNTDPQVLKIDQLVDLCQNTNPRLSFNFISTNSPVVLKGLHSGEFDAGfvfgpcslaeLTCEPLTEIELKLVAP-HSWH 174
Cdd:PRK12679   98 ATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIG----------IASERLSNDPQLVAFPwFRWH 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 175 -----------DRIQGRSLAELARLPWVMPPGECPYSMLLKAEFARLGLEPEVRLTADQEPILKSLVTAGHGLSLLP--S 241
Cdd:PRK12679  168 hsllvphdhplTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGLGIGLVAeqS 247

                         250
                  ....*....|...
gi 1167103369 242 FELKPEDSLSVWD 254
Cdd:PRK12679  248 SGEQEESNLIRLD 260
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
 1-247 3.13e-11

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 62.70  E-value: 3.13e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   1 MELYQIRTFVKVAETG-SITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSA-RGMELSPAGAQLLVKARAILNGLEDF 78
Cdd:PRK12682    1 MNLQQLRFVREAVRRNlNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGkRLKGLTEPGKAVLDVIERILREVGNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369  79 AATAASLNASPQAILTVG-LNTD-----PQVLKidQLVDLcqntNPRLSFNfISTNSP-VVLKGLHSGEFDAGFVFGpcS 151
Cdd:PRK12682   81 KRIGDDFSNQDSGTLTIAtTHTQaryvlPRVVA--AFRKR----YPKVNLS-LHQGSPdEIARMVISGEADIGIATE--S 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 152 LA---ELTCEPLTEIELKLVAP--H--SWHDRIqgrSLAELARLPWVM-PPGECPYSMLLKAeFARLGLEPEVRLTADQE 223
Cdd:PRK12682  152 LAddpDLATLPCYDWQHAVIVPpdHplAQEERI---TLEDLAEYPLITyHPGFTGRSRIDRA-FAAAGLQPDIVLEAIDS 227

                         250       260
                  ....*....|....*....|....
gi 1167103369 224 PILKSLVTAGHGLSLLPSFELKPE 247
Cdd:PRK12682  228 DVIKTYVRLGLGVGIVAEMAYRPD 251
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
8-93 2.90e-10

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 60.02  E-value: 2.90e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   8 TFVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAGAQLlvkarailngledFAATAASLNA 87
Cdd:PRK10086   21 TFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRV-------------FWALKSSLDT 87


                  ....*.
gi 1167103369  88 SPQAIL 93
Cdd:PRK10086   88 LNQEIL 93
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 118-241 3.97e-10

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: 57.99  E-value: 3.97e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 118 PRLSFNFISTNSPVVLKGLHSGEFDAGFVF-----GPCSLAELTCEPLTEIELKLVAPHSwhDRIQGR---SLAELARLP 189
Cdd:cd08423    27 PGLEVRLREAEPPESLDALRAGELDLAVVFdypvtPPPDDPGLTRVPLLDDPLDLVLPAD--HPLAGReevALADLADEP 104

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1167103369 190 WVMPPGECPYSMLLKAEFARLGLEPEVRLTADQEPILKSLVTAGHGLSLLPS 241
Cdd:cd08423   105 WIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGVALVPR 156
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 12-77 3.98e-10

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 59.19  E-value: 3.98e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1167103369  12 VAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAGAQLLVKARAILNGLED 77
Cdd:PRK11074   13 VARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQE 78
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 6-247 4.27e-10

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 59.27  E-value: 4.27e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   6 IRTF---VKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAGAQLLVKARAILNG---LEDFA 79
Cdd:PRK11151    3 IRDLeylVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREvkvLKEMA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369  80 ATAASLNASP---QAILTVGlntdPQVLKidQLVDLCQNTNPRLSFNFISTNSPVVLKGLHSGEFDAGFVfgpCSLAElt 156
Cdd:PRK11151   83 SQQGETMSGPlhiGLIPTVG----PYLLP--HIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAIL---ALVKE-- 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 157 CEPLTEIEL-----KLVAP--HSWHDRIQgRSLAELARLPWVM-PPGECPYSMLLKAEFArLGLEPEVRLTADQEPILKS 228
Cdd:PRK11151  152 SEAFIEVPLfdepmLLAVYedHPWANRDR-VPMSDLAGEKLLMlEDGHCLRDQAMGFCFE-AGADEDTHFRATSLETLRN 229

                         250
                  ....*....|....*....
gi 1167103369 229 LVTAGHGLSLLPSFELKPE 247
Cdd:PRK11151  230 MVAAGSGITLLPALAVPNE 248
cysB PRK12681
HTH-type transcriptional regulator CysB;
1-83 4.47e-10

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 59.53  E-value: 4.47e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   1 MELYQIRTFVKVAETG-SITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGM-ELSPAGAQLLVKARAILNGLEDF 78
Cdd:PRK12681    1 MKLQQLRYIVEVVNHNlNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLtQVTPAGEEIIRIAREILSKVESI 80


                  ....*
gi 1167103369  79 AATAA 83
Cdd:PRK12681   81 KSVAG 85
rbcR CHL00180
LysR transcriptional regulator; Provisional
 3-172 7.80e-10

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 58.49  E-value: 7.80e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   3 LYQIRTFVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAGAQLLVKARAILNGLEDFAATA 82
Cdd:CHL00180    7 LDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRAL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369  83 ASLNASPQAILTVGLNTD------PQVLKIdqlvdLCQN-TNPRLSFNFISTNSpvVLKGLHSGEFDAGFVFG--PCSLA 153
Cdd:CHL00180   87 EDLKNLQRGTLIIGASQTtgtylmPRLIGL-----FRQRyPQINVQLQVHSTRR--IAWNVANGQIDIAIVGGevPTELK 159

                         170       180
                  ....*....|....*....|
gi 1167103369 154 E-LTCEPLTEIELKLVAPHS 172
Cdd:CHL00180  160 KiLEITPYVEDELALIIPKS 179
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 3-192 1.77e-09

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 57.39  E-value: 1.77e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   3 LYQIRTFVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAGAQLLVKARAILNGLED----F 78
Cdd:PRK10837    5 LRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEieqlF 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369  79 AATAASLNASpqAILTVGLNTDPQVLKidqlvdLCQNTNPRLSFNFISTNSPVVLKGLHSGEFDAGFVFGPCSLAELTCE 158
Cdd:PRK10837   85 REDNGALRIY--ASSTIGNYILPAMIA------RYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPELISE 156

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1167103369 159 PLTEIELKLVAPHSwHDRIQGR-SLAELARLPWVM 192
Cdd:PRK10837  157 PWLEDELVVFAAPD-SPLARGPvTLEQLAAAPWIL 190
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 118-247 7.50e-09

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: 54.62  E-value: 7.50e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 118 PRLSFNFISTNSPVVLKGLHSGEFDAGFVFGPCSLAELTCEPLTEIELK-LVAPHSWHDRIQGRSLAELARLPWVMPPGE 196
Cdd:cd08426    27 PGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIRVHSRQPAPIGaVVPPGHPLARQPSVTLAQLAGYPLALPPPS 106

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1167103369 197 CPYSMLLKAEFARLGLEPEVRLTADQEPILKSLVTAGHGLSLLPSFELKPE 247
Cdd:cd08426   107 FSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTELAVRRE 157
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 1-142 7.64e-09

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 55.42  E-value: 7.64e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   1 MELYQIRTFVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAGAQLLVKARAILNgLEDFAA 80
Cdd:PRK15092   11 LDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILR-FNDEAC 89

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1167103369  81 TaaSLNASP-QAILTVGLNTDPQVLKIDQLVDLCQNTNPRLSFNFISTNSPVVLKGLHSGEFD 142
Cdd:PRK15092   90 S--SLMYSNlQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVD 150
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
 114-240 8.33e-09

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: 54.08  E-value: 8.33e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 114 QNTNPRLSFNFISTNSPVVLKGLHSGEFDAGFVFGPCSLAELTCEPLTEIELKLVAP--H--SWHDRIqgrSLAELARLP 189
Cdd:cd08434    23 RKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPkdHplAGRDSV---DLAELADEP 99

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1167103369 190 WV-MPPGecpYSM--LLKAEFARLGLEPEVRLTADQEPILKSLVTAGHGLSLLP 240
Cdd:cd08434   100 FVlLSPG---FGLrpIVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILP 150
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
5-100 1.71e-08

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 54.59  E-value: 1.71e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   5 QIRTFVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSaRGMELSPAGAQLLVKARAIlNGLE-DFAATAA 83
Cdd:PRK13348    6 QLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-RPCRPTPAGQRLLRHLRQV-ALLEaDLLSTLP 83

                          90
                  ....*....|....*..
gi 1167103369  84 SLNASPQAiLTVGLNTD 100
Cdd:PRK13348   84 AERGSPPT-LAIAVNAD 99
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 118-262 2.15e-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: 2.15e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 118 PRLSFNFISTNSPVVLKGLHSGEFDAGFVFGP------CSLAELTCEPLTeielKLVAP-HSWHDRiQGRSLAELARLPW 190
Cdd:cd08436    27 PGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPerrppgLASRELAREPLV----AVVAPdHPLAGR-RRVALADLADEPF 101

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1167103369 191 VMPPGECPYSMLLKAEFARLGLEPEVRLTADQEPILKSLVTAGHGLSLLPSFELKPEDSL---SVWDGPGFKLAL 262
Cdd:cd08436   102 VDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLPASVAARLPGLaalPLEPAPRRRLYL 176
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
 118-240 2.38e-08

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: 52.93  E-value: 2.38e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 118 PRLSFNFISTNSPVVLKGLHSGEFDAGFVFGPCSLAELTCEPLTEIELKLVAPHSwhDRIQGR---SLAELARLPWVM-- 192
Cdd:cd08412    27 PGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARLPPYVWLPAD--HPLAGKdevSLADLAAEPLILld 104

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1167103369 193 -PPGECpYSMLLkaeFARLGLEPEVRL-TADQEpILKSLVTAGHGLSLLP 240
Cdd:cd08412   105 lPHSRE-YFLSL---FAAAGLTPRIAYrTSSFE-AVRSLVANGLGYSLLN 149
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 132-283 2.55e-08

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: 52.91  E-value: 2.55e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 132 VLKGLHSGEFDAGFVFGPCSLAELTCEPLTEIELKLVAP--HSWHDRiQGRSLAELARLPWVMPPGECPYSMLLKAEFAR 209
Cdd:cd08440    41 VIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPkdHPLARR-RSVTWAELAGYPLIALGRGSGVRALIDRALAA 119

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1167103369 210 LGLEPEVRLTADQEPILKSLVTAGHGLSLLPSFELKPEDSLS-VW---DGPGFKLALSFVCRLSRSQQPELMAFKQVL 283
Cdd:cd08440   120 AGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLADHPGlVArplTEPVVTRTVGLIRRRGRSLSPAAQAFLDLL 197
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
 118-257 2.70e-08

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: 52.95  E-value: 2.70e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 118 PRLSFNFISTNSPVVLKGLHSGEFDAGFVFGPCSLAELTCEPLTEIELKLVAPHswHDRIQGR---SLAELARLPWVMPP 194
Cdd:cd08415    27 PDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLPP--GHPLARKdvvTPADLAGEPLISLG 104

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1167103369 195 GECPYSMLLKAEFARLGLEPEVRLTADQEPILKSLVTAGHGLSLLpsfelkpeDSLSVWDGPG 257
Cdd:cd08415   105 RGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIV--------DPLTAAGYAG 159
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
 3-144 4.80e-08

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 53.07  E-value: 4.80e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   3 LYQIRTFVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSaRGmELSP--AGAQLLVKARAILNGLEDFAA 80
Cdd:PRK11013    6 LRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERV-RG-RLHPtvQGLRLFEEVQRSYYGLDRIVS 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1167103369  81 TAASLNASPQAILTVG-LNTDPQVLkidqLVDLCQN---TNPRLSFNFISTNSPVVLKGLHSGEFDAG 144
Cdd:PRK11013   84 AAESLREFRQGQLSIAcLPVFSQSL----LPGLCQPflaRYPDVSLNIVPQESPLLEEWLSAQRHDLG 147
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
 118-214 5.21e-07

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: 49.19  E-value: 5.21e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 118 PRLSFNFISTNSPVVLKGLHSGEFDagFVFG----PCSLAELTCEPLTEIELKLVAPHSwHDRIQGR--SLAELARLPWV 191
Cdd:cd08435    27 PRLTVRVVEGTSDELLEGLRAGELD--LAIGrladDEQPPDLASEELADEPLVVVARPG-HPLARRArlTLADLADYPWV 103

                          90       100
                  ....*....|....*....|...
gi 1167103369 192 MPPGECPYSMLLKAEFARLGLEP 214
Cdd:cd08435   104 LPPPGTPLRQRLEQLFAAAGLPL 126
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
 101-240 1.02e-06

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: 48.33  E-value: 1.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 101 PQVLkidQLVDLCQNTNPRLSFNFISTNSPVVLKGLHSGEFDAGFVFGPCSL-AELTCEPLTEIELKLVAPHSwHDRIQG 179
Cdd:cd08451    14 PLVP---GLIRRFREAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARsDGLVLELLLEEPMLVALPAG-HPLARE 89

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1167103369 180 R--SLAELARLPWVMPPGECPYSML--LKAEFARLGLEPEVRLTADQEPILKSLVTAGHGLSLLP 240
Cdd:cd08451    90 RsiPLAALADEPFILFPRPVGPGLYdaIIAACRRAGFTPRIGQEAPQMASAINLVAAGLGVSIVP 154
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
1-96 2.37e-06

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 48.22  E-value: 2.37e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   1 ME-LYQIRTFVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAGAQLLVKARAILNGLEDFA 79
Cdd:PRK10632    1 MErLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVH 80

                          90
                  ....*....|....*..
gi 1167103369  80 ATAASLNASPQAILTVG 96
Cdd:PRK10632   81 EQLYAFNNTPIGTLRIG 97
PRK09801 PRK09801
LysR family transcriptional regulator;
6-96 4.79e-06

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 47.34  E-value: 4.79e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   6 IRTFVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAGAQLLVKARAILNGLEDFAATAASL 85
Cdd:PRK09801   11 LQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQI 90

                          90
                  ....*....|.
gi 1167103369  86 NASPQAILTVG 96
Cdd:PRK09801   91 KTRPEGMIRIG 101
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
5-100 5.51e-06

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 46.69  E-value: 5.51e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   5 QIRTFVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSaRGMELSPAGAQLLVKARAiLNGLEDFAATAAS 84
Cdd:PRK03635    6 QLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVRT-QPCRPTEAGQRLLRHARQ-VRLLEAELLGELP 83

                          90
                  ....*....|....*.
gi 1167103369  85 LNASPQAILTVGLNTD 100
Cdd:PRK03635   84 ALDGTPLTLSIAVNAD 99
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
6-73 9.64e-06

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 46.16  E-value: 9.64e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1167103369   6 IRTFVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAGAQLLVKARAILN 73
Cdd:PRK03601    6 LKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGERLLPYAETLMN 73
nhaR PRK11062
transcriptional activator NhaR; Provisional
 9-67 1.00e-05

transcriptional activator NhaR; Provisional


Pssm-ID: 182938 [Multi-domain]  Cd Length: 296  Bit Score: 46.16  E-value: 1.00e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1167103369   9 FVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAGaQLLVK 67
Cdd:PRK11062   12 FWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELG-ELVFR 69
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
 129-240 1.05e-05

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: 45.43  E-value: 1.05e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 129 SPVVLKGLHSGEFDAGFVFGPCSL---AELTCEPLTEIELKLVAPHSWHD-RIQGRSLAELARLPWVMPPGECPYSM--L 202
Cdd:cd08453    38 SDVQLEALLAGEIDAGIVIPPPGAsapPALAYRPLLSEPLVLAVPAAWAAeGGAPLALAAVAAEPLVIFPRRIAPAFhdA 117

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1167103369 203 LKAEFARLGLEPEVRLTADQEPILKSLVTAGHGLSLLP 240
Cdd:cd08453   118 VTGYYRAAGQTPRIAQEAIQMQTIISLVSAGMGVALVP 155
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
 136-240 1.60e-05

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


Pssm-ID: 176110 [Multi-domain]  Cd Length: 201  Bit Score: 44.65  E-value: 1.60e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 136 LHSGEFDagFVFGPCS----LAELTCEPLTEIELKLVApHSWHDRIQGRSLAELARLPWVMP-PGECPYSMLLKAeFARL 210
Cdd:cd08418    45 LRDGRLD--FAIGTLPdemyLKELISEPLFESDFVVVA-RKDHPLQGARSLEELLDASWVLPgTRMGYYNNLLEA-LRRL 120

                          90       100       110
                  ....*....|....*....|....*....|
gi 1167103369 211 GLEPEVRLTADQEPILKSLVTAGHGLSLLP 240
Cdd:cd08418   121 GYNPRVAVRTDSIVSIINLVEKADFLTILS 150
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
3-76 3.57e-05

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 44.66  E-value: 3.57e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1167103369   3 LYQIRT-----FVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAGAQLLVKARAILNGLE 76
Cdd:PRK10082    8 LHNIETkwlydFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLE 86
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
 135-240 5.94e-05

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: 43.09  E-value: 5.94e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 135 GLHSGEFDAGFVFGPCSLAELTCEPLTEIELKLVA--PHSWHDRIQGRSLAELARLPWVMPPGECPYSMLLKAEFARLGL 212
Cdd:cd08425    45 ALADDRLDLGIAFAPVRSPDIDAQPLFDERLALVVgaTHPLAQRRTALTLDDLAAEPLALLSPDFATRQHIDRYFQKQGI 124

                          90       100
                  ....*....|....*....|....*...
gi 1167103369 213 EPEVRLTADQEPILKSLVTAGHGLSLLP 240
Cdd:cd08425   125 KPRIAIEANSISAVLEVVRRGRLATILP 152
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
1-72 1.78e-04

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 42.31  E-value: 1.78e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1167103369   1 MELYQIRTFVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAGAQLLVKARAIL 72
Cdd:PRK15421    2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVL 73
ModE COG2005
DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];
11-80 2.23e-04

DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];


Pssm-ID: 441608 [Multi-domain]  Cd Length: 118  Bit Score: 40.19  E-value: 2.23e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1167103369  11 KVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSA-----RGMELSPAGAQLLVKARAILNGLEDFAA 80
Cdd:COG2005    29 AIDETGSISAAAKAMGMSYKRAWDLIDAMNNLLGEPLVERQTggkggGGARLTPEGRRLLALYRRLEAEAQRALA 103
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 133-240 3.25e-04

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: 40.71  E-value: 3.25e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 133 LKGLHSGEFDAGFVFGPCSLAELTCEPLteIELKLVA------PHSWHDRIqgrSLAELARLPWVM-PPGECPY-SMLLK 204
Cdd:cd08447    42 IEALESGRIDLGLLRPPFARPGLETRPL--VREPLVAavpaghPLAGAERL---TLEDLDGQPFIMySPTEARYfHDLVV 116

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1167103369 205 AEFARLGLEPEVRLTADQEPILKSLVTAGHGLSLLP 240
Cdd:cd08447   117 RLFASAGVQPRYVQYLSQIHTMLALVRAGLGVALVP 152
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
 138-240 4.83e-04

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: 40.23  E-value: 4.83e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 138 SGEFDAGFVFGPCSLAELTCEPLTEIELKLVAP--HSW--HDRIqgrSLAELARLPWVMPPGECPYSMLLKAEFARLGLE 213
Cdd:cd08438    47 NGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPrgHPLagRKTV---SLADLADEPFILFNEDFALHDRIIDACQQAGFT 123

                          90       100
                  ....*....|....*....|....*..
gi 1167103369 214 PEVRLTADQEPILKSLVTAGHGLSLLP 240
Cdd:cd08438   124 PNIAARSSQWDFIAELVAAGLGVALLP 150
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 1-95 5.89e-04

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 40.74  E-value: 5.89e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369   1 MELYQIRTFVKVAETGSITRAASELNTSQPSVSAHIKALEDEYGLSLFKRSARGMELSPAGAQLLVKARAILNGLEDFAA 80
Cdd:PRK14997    2 TDLNDFAWFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQD 81

                          90
                  ....*....|....*
gi 1167103369  81 TAASLNASPQAILTV 95
Cdd:PRK14997   82 AIAALQVEPRGIVKL 96
PBP2_YofA_SoxR_like cd08442
The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, ...
 133-240 6.63e-03

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: 36.82  E-value: 6.63e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1167103369 133 LKGLHSGEFDAGFVFGPCSLAELTCEPLTEIELKLVAPhswHDRIQGRSLAELARLPWVMPPGECPYSMLLKAEFARLGL 212
Cdd:cd08442    42 IQAVLEGRLDGAFVAGPVEHPRLEQEPVFQEELVLVSP---KGHPPVSRAEDLAGSTLLAFRAGCSYRRRLEDWLAEEGV 118

                          90       100
                  ....*....|....*....|....*....
gi 1167103369 213 EPEVRLT-ADQEPILKSlVTAGHGLSLLP 240
Cdd:cd08442   119 SPGKIMEfGSYHAILGC-VAAGMGIALLP 146
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
30-78 7.17e-03

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 37.11  E-value: 7.17e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1167103369  30 PS-VSAHIKALEDEYGLSLFKRSARGMELSPAGAQLLVKARAILNGLEDF 78
Cdd:PRK11716    5 PStLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQL 54
 
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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