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Conserved domains on  [gi|694074312|ref|WP_032420147|]
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LysR family transcriptional regulator [Klebsiella pneumoniae]

Protein Classification

LysR family transcriptional regulator( domain architecture ID 10444078)

LysR family transcriptional regulator negatively or positively regulates the transcription of specific genes

Gene Ontology:  GO:0003700|GO:0003677|GO:0005829
PubMed:  8257110|19047729
SCOP:  4000316

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
94-290 8.22e-68

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: 209.69  E-value: 8.22e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  94 KISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVPQ 173
Cdd:cd08440    1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPK 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 174 QSPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPALCKTQMASL 253
Cdd:cd08440   81 DHPLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLADHP 160
                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 694074312 254 GAVCIPLSDPPIEKCVGAIHAGHLPLSKAAQALLDTL 290
Cdd:cd08440  161 GLVARPLTEPVVTRTVGLIRRRGRSLSPAAQAFLDLL 197
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
6-64 1.13e-19

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


:

Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 80.51  E-value: 1.13e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 694074312    6 KQLRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGE 64
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
 
Name Accession Description Interval E-value
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
94-290 8.22e-68

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: 209.69  E-value: 8.22e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  94 KISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVPQ 173
Cdd:cd08440    1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPK 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 174 QSPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPALCKTQMASL 253
Cdd:cd08440   81 DHPLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLADHP 160
                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 694074312 254 GAVCIPLSDPPIEKCVGAIHAGHLPLSKAAQALLDTL 290
Cdd:cd08440  161 GLVARPLTEPVVTRTVGLIRRRGRSLSPAAQAFLDLL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
3-291 3.98e-61

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 194.70  E-value: 3.98e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   3 MSVKQLRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGELFLPMARQLLADWDNVEE 82
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  83 AMRQSFTLQRGKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPL 162
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 163 AVDRFVAIVPQQSPLAKKKQLTwqelltldfitlqrpsavrlmleealarsgrqldvalesHQLVTVGRMVASGLGGSAV 242
Cdd:COG0583  161 GEERLVLVASPDHPLARRAPLV---------------------------------------NSLEALLAAVAAGLGIALL 201
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 694074312 243 PALCKTQMASLGA-VCIPLSDPPIEKCVGAIHAGHLPLSKAAQALLDTLK 291
Cdd:COG0583  202 PRFLAADELAAGRlVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLR 251
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
3-291 1.77e-47

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: 160.86  E-value: 1.77e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   3 MSVKQLRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGELFLPMARQLLADWDNVEE 82
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  83 AMRQSFTLQRGKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPL 162
Cdd:NF040786  81 EFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 163 AVDRFVAIVPQQSPLAKKKQLTW--QELLTLDFITLQRPSAVRLMLEEALARSG---RQLDVALESHQLVTVGRMVASGL 237
Cdd:NF040786 161 YKDRLVLITPNGTEKYRMLKEEIsiSELQKEPFIMREEGSGTRKEAEKALKSLGislEDLNVVASLGSTEAIKQSVEAGL 240
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 694074312 238 GGSAVPALCKTQMASLGAV-CIPLSDPPIEKCVGAIHAGHLPLSKAAQALLDTLK 291
Cdd:NF040786 241 GISVISELAAEKEVERGRVlIFPIPGLPKNRDFYLVYNKNRQLSPTAEAFLQFVK 295
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
92-291 1.50e-38

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: 134.72  E-value: 1.50e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   92 RGKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIV 171
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  172 PQQSPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPA-LCKTQM 250
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRsAVAREL 160
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 694074312  251 ASLGAVCIPLSDPPIEKCVGAIHAGHLPLSKAAQALLDTLK 291
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLR 201
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
3-261 1.49e-35

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 129.50  E-value: 1.49e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   3 MSVKQLRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGELFLPMARQLLADWDNVEE 82
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  83 AMRQSFTLQRgKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPL 162
Cdd:PRK09906  81 RARKIVQEDR-QLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLEL 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 163 AVDRFVAIVPQQSPLAKKKQLTWQELLTLDFITLQRPSAVRL--MLEEALARSGRQLDVALESHQLVTVGRMVASGLGGS 240
Cdd:PRK09906 160 LDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYSGSLapIIKAWFAQHNSQPNIVQVATNILVTMNLVGMGLGCT 239
                        250       260
                 ....*....|....*....|.
gi 694074312 241 AVPALCKTQMASlGAVCIPLS 261
Cdd:PRK09906 240 IIPGYMNNFNTG-QVVFRPLA 259
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
6-64 1.13e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 80.51  E-value: 1.13e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 694074312    6 KQLRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGE 64
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
6-107 2.11e-11

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 63.07  E-value: 2.11e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   6 KQLRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRsTRKVTLTQEGELFLPMARQLladwdnveeAMR 85
Cdd:PRK13348   5 KQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQV---------ALL 74
                         90       100
                 ....*....|....*....|..
gi 694074312  86 QSFTLQRGKISVAAMPSFAANV 107
Cdd:PRK13348  75 EADLLSTLPAERGSPPTLAIAV 96
 
Name Accession Description Interval E-value
PBP2_LTTR_like_4 cd08440
TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
94-290 8.22e-68

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: 209.69  E-value: 8.22e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  94 KISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVPQ 173
Cdd:cd08440    1 RVRVAALPSLAATLLPPVLAAFRRRHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEFEPLLRDPFVLVCPK 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 174 QSPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPALCKTQMASL 253
Cdd:cd08440   81 DHPLARRRSVTWAELAGYPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAGLGVAVLPALALPLADHP 160
                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 694074312 254 GAVCIPLSDPPIEKCVGAIHAGHLPLSKAAQALLDTL 290
Cdd:cd08440  161 GLVARPLTEPVVTRTVGLIRRRGRSLSPAAQAFLDLL 197
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
3-291 3.98e-61

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


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 194.70  E-value: 3.98e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   3 MSVKQLRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGELFLPMARQLLADWDNVEE 82
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  83 AMRQSFTLQRGKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPL 162
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPPDPGLVARPL 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 163 AVDRFVAIVPQQSPLAKKKQLTwqelltldfitlqrpsavrlmleealarsgrqldvalesHQLVTVGRMVASGLGGSAV 242
Cdd:COG0583  161 GEERLVLVASPDHPLARRAPLV---------------------------------------NSLEALLAAVAAGLGIALL 201
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 694074312 243 PALCKTQMASLGA-VCIPLSDPPIEKCVGAIHAGHLPLSKAAQALLDTLK 291
Cdd:COG0583  202 PRFLAADELAAGRlVALPLPDPPPPRPLYLVWRRRRHLSPAVRAFLDFLR 251
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
3-291 1.77e-47

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: 160.86  E-value: 1.77e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   3 MSVKQLRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGELFLPMARQLLADWDNVEE 82
Cdd:NF040786   1 MNLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLDLWEKLEE 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  83 AMRQSFTLQRGKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPL 162
Cdd:NF040786  81 EFDRYGKESKGVLRIGASTIPGQYLLPELLKKFKEKYPNVRFKLMISDSIKVIELLLEGEVDIGFTGTKLEKKRLVYTPF 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 163 AVDRFVAIVPQQSPLAKKKQLTW--QELLTLDFITLQRPSAVRLMLEEALARSG---RQLDVALESHQLVTVGRMVASGL 237
Cdd:NF040786 161 YKDRLVLITPNGTEKYRMLKEEIsiSELQKEPFIMREEGSGTRKEAEKALKSLGislEDLNVVASLGSTEAIKQSVEAGL 240
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 694074312 238 GGSAVPALCKTQMASLGAV-CIPLSDPPIEKCVGAIHAGHLPLSKAAQALLDTLK 291
Cdd:NF040786 241 GISVISELAAEKEVERGRVlIFPIPGLPKNRDFYLVYNKNRQLSPTAEAFLQFVK 295
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
94-290 8.62e-45

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: 150.44  E-value: 8.62e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  94 KISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVPQ 173
Cdd:cd05466    1 TLRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPP 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 174 QSPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPALCKTQMASL 253
Cdd:cd05466   81 DHPLAKRKSVTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAGLGIALLPESAVEELADG 160
                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 694074312 254 GAVCIPLSDPPIEKCVGAIHAGHLPLSKAAQALLDTL 290
Cdd:cd05466  161 GLVVLPLEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
92-291 1.50e-38

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: 134.72  E-value: 1.50e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   92 RGKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIV 171
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  172 PQQSPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPA-LCKTQM 250
Cdd:pfam03466  81 PPDHPLARGEPVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRPRVVLEVNSLEALLQLVAAGLGIALLPRsAVAREL 160
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 694074312  251 ASLGAVCIPLSDPPIEKCVGAIHAGHLPLSKAAQALLDTLK 291
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYLVWRKGRPLSPAVRAFIEFLR 201
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
3-261 1.49e-35

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 129.50  E-value: 1.49e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   3 MSVKQLRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGELFLPMARQLLADWDNVEE 82
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAKL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  83 AMRQSFTLQRgKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPL 162
Cdd:PRK09906  81 RARKIVQEDR-QLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEIDYLEL 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 163 AVDRFVAIVPQQSPLAKKKQLTWQELLTLDFITLQRPSAVRL--MLEEALARSGRQLDVALESHQLVTVGRMVASGLGGS 240
Cdd:PRK09906 160 LDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISTDPAYSGSLapIIKAWFAQHNSQPNIVQVATNILVTMNLVGMGLGCT 239
                        250       260
                 ....*....|....*....|.
gi 694074312 241 AVPALCKTQMASlGAVCIPLS 261
Cdd:PRK09906 240 IIPGYMNNFNTG-QVVFRPLA 259
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
3-264 2.32e-35

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 128.92  E-value: 2.32e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   3 MSVKQLRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGELFLPMARQLLADWDNVEE 82
Cdd:PRK11242   1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRR 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  83 AMRQSFTLQRGKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPL 162
Cdd:PRK11242  81 AIHDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQPL 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 163 AVDRFVAIVPQQSPLAKK-KQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSA 241
Cdd:PRK11242 161 FTETLALVVGRHHPLAARrKALTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRGRLATL 240
                        250       260
                 ....*....|....*....|...
gi 694074312 242 VPALCKTQMASLgaVCIPLsDPP 264
Cdd:PRK11242 241 LPAAIAREHDGL--CAIPL-DPP 260
rbcR CHL00180
LysR transcriptional regulator; Provisional
4-242 1.11e-34

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 127.44  E-value: 1.11e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   4 SVKQLRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGELFLPMARQLLADWDNVEEA 83
Cdd:CHL00180   6 TLDQLRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELLLRYGNRILALCEETCRA 85
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  84 MRQSFTLQRGKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGI---AFEPSPNHNLLFT 160
Cdd:CHL00180  86 LEDLKNLQRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIvggEVPTELKKILEIT 165
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 161 PLAVDRFVAIVPQQSPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSG---RQLDVALESHQLVTVGRMVASGL 237
Cdd:CHL00180 166 PYVEDELALIIPKSHPFAKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGidsKRFKIEMELNSIEAIKNAVQSGL 245

                 ....*
gi 694074312 238 GGSAV 242
Cdd:CHL00180 246 GAAFV 250
PBP2_LysR_opines_like cd08415
The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the ...
97-290 1.83e-34

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: 123.83  E-value: 1.83e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  97 VAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVPQQSP 176
Cdd:cd08415    4 IAALPALALSLLPRAIARFRARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGLESEPLASGRAVCVLPPGHP 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 177 LAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPALCKTQMASLGAV 256
Cdd:cd08415   84 LARKDVVTPADLAGEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIVDPLTAAGYAGAGLV 163
                        170       180       190
                 ....*....|....*....|....*....|....
gi 694074312 257 CIPLsDPPIEKCVGAIHAGHLPLSKAAQALLDTL 290
Cdd:cd08415  164 VRPF-RPAIPFEFALVRPAGRPLSRLAQAFIDLL 196
PBP2_GltC_like cd08434
The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA ...
94-290 7.96e-32

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: 116.87  E-value: 7.96e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  94 KISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVPQ 173
Cdd:cd08434    1 TVRLGFLHSLGTSLVPDLIRAFRKEYPNVTFELHQGSTDELLDDLKNGELDLALCSPVPDEPDIEWIPLFTEELVLVVPK 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 174 QSPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPALckTQMASL 253
Cdd:cd08434   81 DHPLAGRDSVDLAELADEPFVLLSPGFGLRPIVDELCAAAGFTPKIAFEGEEDSTIAGLVAAGLGVAILPEM--TLLNPP 158
                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 694074312 254 GAVCIPLSDPPIEKCVGAIHAGHLPLSKAAQALLDTL 290
Cdd:cd08434  159 GVKKIPIKDPDAERTIGLAWLKDRYLSPAARRFKDFV 195
PRK09986 PRK09986
LysR family transcriptional regulator;
2-264 7.00e-31

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 117.13  E-value: 7.00e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   2 RMSVKQLRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGELFLPMARQLLADWDNVE 81
Cdd:PRK09986   6 RIDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAEQSL 85
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  82 EAMRQSFTLQRGKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGI--AFEPSPNHNLLF 159
Cdd:PRK09986  86 ARVEQIGRGEAGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIwrMADLEPNPGFTS 165
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 160 TPLAVDRFVAIVPQQSPLAKKKQLTWQELLTLDFITLQ-RPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLG 238
Cdd:PRK09986 166 RRLHESAFAVAVPEEHPLASRSSVPLKALRNEYFITLPfVHSDWGKFLQRVCQQAGFSPQIIRQVNEPQTVLAMVSMGIG 245
                        250       260
                 ....*....|....*....|....*.
gi 694074312 239 GSAVPALCKtQMASLGAVCIPLSDPP 264
Cdd:PRK09986 246 ITLLPDSYA-QIPWPGVVFRPLKERI 270
PBP2_Nac cd08433
The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) ...
99-290 2.01e-29

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: 110.76  E-value: 2.01e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  99 AMPSFAANVLPEAL-KAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVPQQSPL 177
Cdd:cd08433    5 GLPPSAASVLAVPLlRAVRRRYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLSTEPLLEEDLFLVGPADAPL 84
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 178 AKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPALCKTQMASLGAVC 257
Cdd:cd08433   85 PRGAPVPLAELARLPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAGLGYTILPASAVAAEVAAGRLV 164
                        170       180       190
                 ....*....|....*....|....*....|....
gi 694074312 258 I-PLSDPPIEKCVGAIHAGHLPLSKAAQALLDTL 290
Cdd:cd08433  165 AaPIVDPALTRTLSLATPRDRPLSPAALAVRDLL 198
PBP2_LTTR_like_1 cd08421
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
95-290 3.37e-29

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


Pssm-ID: 176113  Cd Length: 198  Bit Score: 109.92  E-value: 3.37e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  95 ISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVPQQ 174
Cdd:cd08421    2 VRLLANTSAIVEFLPEDLASFLAAHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLETRPYRTDRLVVVVPRD 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 175 SPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVP-ALCKTQMASL 253
Cdd:cd08421   82 HPLAGRASVAFADTLDHDFVGLPAGSALHTFLREAAARLGRRLRLRVQVSSFDAVCRMVAAGLGIGIVPeSAARRYARAL 161
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 694074312 254 GAVCIPLSDP----PIEKCVGAIHAghlpLSKAAQALLDTL 290
Cdd:cd08421  162 GLRVVPLDDAwarrRLLLCVRSFDA----LPPAARALVDHL 198
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
94-290 1.64e-28

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: 108.35  E-value: 1.64e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  94 KISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHdVIN-EQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVP 172
Cdd:cd08420    1 TLRIGASTTIGEYLLPRLLARFRKRYPEVRVSLT-IGNtEEIAERVLDGEIDLGLVEGPVDHPDLIVEPFAEDELVLVVP 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 173 QQSPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSG---RQLDVALESHQLVTVGRMVASGLGGSAVPALC-KT 248
Cdd:cd08420   80 PDHPLAGRKEVTAEELAAEPWILREPGSGTREVFERALAEAGldgLDLNIVMELGSTEAIKEAVEAGLGISILSRLAvRK 159
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 694074312 249 QMASLGAVCIPLSDPPIEKCVGAIHAGHLPLSKAAQALLDTL 290
Cdd:cd08420  160 ELELGRLVALPVEGLRLTRPFSLIYHKDKYLSPAAEAFLEFL 201
PRK12682 PRK12682
transcriptional regulator CysB-like protein; Reviewed
3-238 2.89e-27

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 183679 [Multi-domain]  Cd Length: 309  Bit Score: 107.77  E-value: 2.89e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   3 MSVKQLRAFL-AVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVT-LTQEGELFLPMARQLLADWDNV 80
Cdd:PRK12682   1 MNLQQLRFVReAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKRLKgLTEPGKAVLDVIERILREVGNI 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  81 EEAMRQsFTLQR-GKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLF 159
Cdd:PRK12682  81 KRIGDD-FSNQDsGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATESLADDPDLA 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 160 TPLAVD-RFVAIVPQQSPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLG 238
Cdd:PRK12682 160 TLPCYDwQHAVIVPPDHPLAQEERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEAIDSDVIKTYVRLGLG 239
PBP2_LTTR_aromatics_like cd08414
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
95-290 5.05e-27

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: 104.13  E-value: 5.05e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  95 ISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVPQQ 174
Cdd:cd08414    2 LRIGFVGSALYGLLPRLLRRFRARYPDVELELREMTTAEQLEALRAGRLDVGFVRPPPDPPGLASRPLLREPLVVALPAD 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 175 SPLAKKKQLTWQELLTLDFITLQRPSAVRL--MLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPAlCKTQMAS 252
Cdd:cd08414   82 HPLAARESVSLADLADEPFVLFPREPGPGLydQILALCRRAGFTPRIVQEASDLQTLLALVAAGLGVALVPA-SVARLQR 160
                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 694074312 253 LGAVCIPLSDPPIEKCVGAIHAGHLPlSKAAQALLDTL 290
Cdd:cd08414  161 PGVVYRPLADPPPRSELALAWRRDNA-SPALRAFLELA 197
PBP2_LTTR_like_3 cd08436
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
95-290 4.96e-23

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: 93.43  E-value: 4.96e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  95 ISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGI-AFEPSPNHNLLFTPLAVDRFVAIVPQ 173
Cdd:cd08436    2 LAIGTITSLAAVDLPELLARFHRRHPGVDIRLRQAGSDDLLAAVREGRLDLAFvGLPERRPPGLASRELAREPLVAVVAP 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 174 QSPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPALCKTQMASL 253
Cdd:cd08436   82 DHPLAGRRRVALADLADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARGLGVALLPASVAARLPGL 161
                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 694074312 254 gaVCIPLSDPPIEKcVGAIHAGHLPlSKAAQALLDTL 290
Cdd:cd08436  162 --AALPLEPAPRRR-LYLAWSAPPP-SPAARAFLELL 194
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
28-188 2.11e-22

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 93.73  E-value: 2.11e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  28 NLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGELFLPMARQLLADWDNVEEAMRQSFTLQRGKI----SVAAMPSF 103
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELslfcSVTAAYSH 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 104 aanvLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEP-SPNHNLLFTPLAVDRFVAIVPQQSP----LA 178
Cdd:PRK11716  82 ----LPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPeTLPASVAFSPIDEIPLVLIAPALPCpvrqQL 157
                        170
                 ....*....|
gi 694074312 179 KKKQLTWQEL 188
Cdd:PRK11716 158 SQEKPDWSRI 167
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
3-290 2.37e-22

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 94.36  E-value: 2.37e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   3 MSVKQLRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGELFLPMARQLLADWDNVEE 82
Cdd:PRK11233   1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  83 AMRQSFTLQRGKISVAAMPSFAANVLP-EALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTP 161
Cdd:PRK11233  81 AVHNVGQALSGQVSIGLAPGTAASSLTmPLLQAVRAEFPGIVLYLHENSGATLNEKLMNGQLDMAVIYEHSPVAGLSSQP 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 162 LAVDRFVAIVPQQSPlakKKQLTWQELLTLDFItLQRP-SAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGS 240
Cdd:PRK11233 161 LLKEDLFLVGTQDCP---GQSVDLAAVAQMNLF-LPRDySAVRLRVDEAFSLRRLTAKVIGEIESIATLTAAIASGMGVT 236
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 694074312 241 AVP-----ALCKTQMASLGAVCIPLSDPPIEKCVgaihAGHLPLSKAAQALLDTL 290
Cdd:PRK11233 237 VLPesaarSLCGAVNGWMARITTPSMSLSLSLNL----SARLPLSPQAQAVKEIL 287
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
3-221 2.64e-22

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 94.34  E-value: 2.64e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   3 MSVKQLRAFL-AVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVT-LTQEGELFLPMARQLLADWDNV 80
Cdd:PRK12683   1 MNFQQLRIIReAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLLDAENL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  81 EEAMRQSFTLQRGKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEP-SPNHNLLF 159
Cdd:PRK12683  81 RRLAEQFADRDSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEAlDREPDLVS 160
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 694074312 160 TPLAVDRFVAIVPQQSPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVAL 221
Cdd:PRK12683 161 FPYYSWHHVVVVPKGHPLTGRENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLVPDIVL 222
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
94-290 2.55e-21

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: 89.29  E-value: 2.55e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  94 KISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNL---LFTPLAVDrfvAI 170
Cdd:cd08426    1 RVRVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIrvhSRQPAPIG---AV 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 171 VPQQSPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPALCKTQM 250
Cdd:cd08426   78 VPPGHPLARQPSVTLAQLAGYPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAGGGISLLTELAVRRE 157
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 694074312 251 ASLGAVC-IPLSDP-PIEKCVGAIHAGHLPLSKAAQALLDTL 290
Cdd:cd08426  158 IRRGQLVaVPLADPhMNHRQLELQTRAGRQLPAAASAFLQLL 199
PBP2_PAO1_like cd08412
The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator ...
95-289 3.97e-21

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: 88.76  E-value: 3.97e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  95 ISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVPQQ 174
Cdd:cd08412    2 LRIGCFSTLAPYYLPGLLRRFREAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAFEPLARLPPYVWLPAD 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 175 SPLAKKKQLTWQELLTLDFITLQRPSAVRLMLeEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPALCKTQMASLG 254
Cdd:cd08412   82 HPLAGKDEVSLADLAAEPLILLDLPHSREYFL-SLFAAAGLTPRIAYRTSSFEAVRSLVANGLGYSLLNDRPYRPWSYDG 160
                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 694074312 255 A--VCIPLSDPPIEKCVGAIHAGHLPLSKAAQALLDT 289
Cdd:cd08412  161 KrlVRRPLADPVPPLRLGLAWRRGARLTRAARAFVDF 197
PBP2_LTTR_like_6 cd08423
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
97-290 9.58e-21

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: 87.65  E-value: 9.58e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  97 VAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFE-----PSPNHNLLFTPLAVDRFVAIV 171
Cdd:cd08423    4 VGAFPTAAAALLPPALAALRARHPGLEVRLREAEPPESLDALRAGELDLAVVFDypvtpPPDDPGLTRVPLLDDPLDLVL 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 172 PQQSPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPALCKTQMA 251
Cdd:cd08423   84 PADHPLAGREEVALADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAGLGVALVPRLALGARP 163
                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 694074312 252 SlGAVCIPLSDPPIEKcVGAIHAGHLPLSKAAQALLDTL 290
Cdd:cd08423  164 P-GVVVRPLRPPPTRR-IYAAVRAGAARRPAVAAALEAL 200
PBP2_CidR cd08438
The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains ...
107-290 1.16e-20

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: 87.23  E-value: 1.16e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 107 VLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVPQQSPLAKKKQLTWQ 186
Cdd:cd08438   14 LFAPLLAAFRQRYPNIELELVEYGGKKVEQAVLNGELDVGITVLPVDEEEFDSQPLCNEPLVAVLPRGHPLAGRKTVSLA 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 187 ELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPALCKTQMASLGAVCIPLSDPPIE 266
Cdd:cd08438   94 DLADEPFILFNEDFALHDRIIDACQQAGFTPNIAARSSQWDFIAELVAAGLGVALLPRSIAQRLDNAGVKVIPLTDPDLR 173
                        170       180
                 ....*....|....*....|....
gi 694074312 267 KCVGAIHAGHLPLSKAAQALLDTL 290
Cdd:cd08438  174 WQLALIWRKGRYLSHAARAWLALL 197
PRK11013 PRK11013
DNA-binding transcriptional regulator LysR; Provisional
1-295 5.09e-20

DNA-binding transcriptional regulator LysR; Provisional


Pssm-ID: 236819 [Multi-domain]  Cd Length: 309  Bit Score: 88.13  E-value: 5.09e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   1 MRMSVKQLRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEG-ELFLPMARQL--LADW 77
Cdd:PRK11013   2 AAVSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFERVRGRLHPTVQGlRLFEEVQRSYygLDRI 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  78 DNVEEAMRQsftLQRGKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVhdVINEQVI--EMVREGRVEMGIAFEPSPNH 155
Cdd:PRK11013  82 VSAAESLRE---FRQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNI--VPQESPLleEWLSAQRHDLGLTETLHTPA 156
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 156 NLLFTPLAVDRFVAIVPQQSPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVAS 235
Cdd:PRK11013 157 GTERTELLTLDEVCVLPAGHPLAAKKVLTPDDFAGENFISLSRTDSYRQLLDQLFAEHGVKRRMVVETHSAASVCAMVRA 236
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 694074312 236 GLGGSAVPALCKTQMASLGAVCIPLS-DPPIEkcVGAIHAGHLPLSKAAQALLDTLKGFLP 295
Cdd:PRK11013 237 GVGVSIVNPLTALDYAGSGLVVRRFSiSVPFT--VSLIRPLHRPASALVDAFSEHLQQQAP 295
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
3-277 5.87e-20

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 87.72  E-value: 5.87e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   3 MSVKQLRaFL--AVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVT-LTQEGELFLPMARQLLADWDN 79
Cdd:PRK12684   1 MNLHQLR-FVreAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVEN 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  80 VEEAMRQSFTLQRGKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEP-SPNHNLL 158
Cdd:PRK12684  80 LKRVGKEFAAQDQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATEAiADYKELV 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 159 FTPLAVDRFVAIVPQQSPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLG 238
Cdd:PRK12684 160 SLPCYQWNHCVVVPPDHPLLERKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGLKPDIVLEAIDADVIKTYVELGLG 239
                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 694074312 239 GSAVpalckTQMAslgavciplSDPPIEKCVGAIHAGHL 277
Cdd:PRK12684 240 VGIV-----ADMA---------FDPERDRNLRAIDAGHL 264
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
6-64 1.13e-19

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


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 80.51  E-value: 1.13e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 694074312    6 KQLRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGE 64
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
1-288 1.23e-18

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 83.97  E-value: 1.23e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   1 MRMSVKQLRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGELFLPMARQLLADWDNV 80
Cdd:PRK10837   1 MHITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEI 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  81 EeamrQSFTLQRGKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFT 160
Cdd:PRK10837  81 E----QLFREDNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGPCHSPELISE 156
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 161 PLAVDRFVAIVPQQSPLAKKKqLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGS 240
Cdd:PRK10837 157 PWLEDELVVFAAPDSPLARGP-VTLEQLAAAPWILRERGSGTREIVDYLLLSHLPRFELAMELGNSEAIKHAVRHGLGIS 235
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 694074312 241 AVPA-LCKTQMAS--LGAVCIPLsdPPIEKCVGAIHAGHLPLSKAAQALLD 288
Cdd:PRK10837 236 CLSRrVIADQLQAgtLVEVAVPL--PRLMRTLYRIHHRQKHLSNALQRFLS 284
cysB PRK12681
HTH-type transcriptional regulator CysB;
3-195 2.89e-18

HTH-type transcriptional regulator CysB;


Pssm-ID: 183678 [Multi-domain]  Cd Length: 324  Bit Score: 83.41  E-value: 2.89e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   3 MSVKQLRAFLAVA-HTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVT-LTQEGELFLPMARQLLADWDNV 80
Cdd:PRK12681   1 MKLQQLRYIVEVVnHNLNVSATAEGLYTSQPGISKQVRMLEDELGIQIFARSGKHLTqVTPAGEEIIRIAREILSKVESI 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  81 EeAMRQSFTLQ-RGKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSpnHnlLF 159
Cdd:PRK12681  81 K-SVAGEHTWPdKGSLYIATTHTQARYALPPVIKGFIERYPRVSLHMHQGSPTQIAEAAAKGNADFAIATEAL--H--LY 155
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 694074312 160 TPLAV------DRFVaIVPQQSPLAKKKQLTWQELLTLDFIT 195
Cdd:PRK12681 156 DDLIMlpcyhwNRSV-VVPPDHPLAKKKKLTIEELAQYPLVT 196
PBP2_OccR cd08457
The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the ...
97-290 2.98e-18

The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176146 [Multi-domain]  Cd Length: 196  Bit Score: 81.00  E-value: 2.98e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  97 VAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVPQQSP 176
Cdd:cd08457    4 IAAMPALANGFLPRFLAAFLRLRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFLIETRSLPAVVAVPMGHP 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 177 LAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPALCKTQMASLGAV 256
Cdd:cd08457   84 LAQLDVVSPQDLAGERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREGLGIAIIDPATAIGLPLDGIV 163
                        170       180       190
                 ....*....|....*....|....*....|....
gi 694074312 257 CIPLsDPPIEKCVGAIHAGHLPLSKAAQALLDTL 290
Cdd:cd08457  164 IRPF-DTFIDAGFLVVRAANGPPSTMVDRFIDEF 196
PRK09791 PRK09791
LysR family transcriptional regulator;
1-183 4.45e-18

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 82.50  E-value: 4.45e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   1 MRMSVK--QLRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGELFLPMARQLLADWD 78
Cdd:PRK09791   1 MAFQVKihQIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELR 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  79 NVEEAMRQSFTLQRGKISVAAMPSFAANVLPEALKAFRDRYAGVNVTvhdVINEQVIEMV---REGRVEMGI-AFEPSP- 153
Cdd:PRK09791  81 AAQEDIRQRQGQLAGQINIGMGASIARSLMPAVISRFHQQHPQVKVR---IMEGQLVSMInelRQGELDFTInTYYQGPy 157
                        170       180       190
                 ....*....|....*....|....*....|
gi 694074312 154 NHNLLFTPLAVDRFVAIVPQQSPLAKKKQL 183
Cdd:PRK09791 158 DHEFTFEKLLEKQFAVFCRPGHPAIGARSL 187
PBP2_LTTR_like_2 cd08427
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
94-290 6.04e-18

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


Pssm-ID: 176118 [Multi-domain]  Cd Length: 195  Bit Score: 79.93  E-value: 6.04e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  94 KISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNH--NLLFTPLAVDRFVAIV 171
Cdd:cd08427    1 RLRLGAIATVLTGLLPRALARLRRRHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPPFPLpkDLVWTPLVREPLVLIA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 172 PQQSPLAkkkqlTWQELL-TLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPALCKTQM 250
Cdd:cd08427   81 PAELAGD-----DPRELLaTQPFIRYDRSAWGGRLVDRFLRRQGIRVREVMELDSLEAIAAMVAQGLGVAIVPDIAVPLP 155
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 694074312 251 ASLGAVCIPLSDPPIEKCVGAIHAGHLPLSKAAQALLDTL 290
Cdd:cd08427  156 AGPRVRVLPLGDPAFSRRVGLLWRRSSPRSRLIQALLEAL 195
PBP2_LysR cd08456
The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine ...
95-290 5.21e-17

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


Pssm-ID: 176145 [Multi-domain]  Cd Length: 196  Bit Score: 77.46  E-value: 5.21e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  95 ISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVPQQ 174
Cdd:cd08456    2 LRIAVLPALSQSFLPRAIKAFLQRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGIERERLLRIDGVCVLPPG 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 175 SPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPALCKTQMASLG 254
Cdd:cd08456   82 HRLAVKKVLTPSDLEGEPFISLARTDGTRQRVDALFEQAGVKRRIVVETSYAATICALVAAGVGVSVVNPLTALDYAAAG 161
                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 694074312 255 AVCIPLsDPPIEKCVGAIHAGHLPLSKAAQALLDTL 290
Cdd:cd08456  162 LVVRRF-SPAVPFEVSLIRPKHRPSSALVAAFSACL 196
PBP2_OxyR cd08411
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a ...
93-264 4.29e-16

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


Pssm-ID: 176103 [Multi-domain]  Cd Length: 200  Bit Score: 74.87  E-value: 4.29e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  93 GKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVP 172
Cdd:cd08411    1 GPLRLGVIPTIAPYLLPRLLPALRQAYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLEEEPLFDEPFLLAVP 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 173 QQSPLAKKKQLTWQELLTLDFitlqrpsavrLMLEE-------ALA---RSGRQLDVALESHQLVTVGRMVASGLGGSAV 242
Cdd:cd08411   81 KDHPLAKRKSVTPEDLAGERL----------LLLEEghclrdqALElcrLAGAREQTDFEATSLETLRQMVAAGLGITLL 150
                        170       180
                 ....*....|....*....|....
gi 694074312 243 PALCKTQMASLGA--VCIPLSDPP 264
Cdd:cd08411  151 PELAVPSEELRGDrlVVRPFAEPA 174
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
94-290 5.49e-16

The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176111  Cd Length: 197  Bit Score: 74.47  E-value: 5.49e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  94 KISVAAMpSFAANVLPEALKAFRDRYAGVNVTVhDVIN-EQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVP 172
Cdd:cd08419    1 RLRLAVV-STAKYFAPRLLGAFCRRHPGVEVSL-RVGNrEQVLERLADNEDDLAIMGRPPEDLDLVAEPFLDNPLVVIAP 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 173 QQSPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPALCKTQMAS 252
Cdd:cd08419   79 PDHPLAGQKRIPLERLAREPFLLREPGSGTRLAMERFFAEHGVTLRVRMELGSNEAIKQAVMAGLGLSVLSLHTLALELA 158
                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 694074312 253 LGAVCI-PLSDPPIEKCVGAIHAGHLPLSKAAQALLDTL 290
Cdd:cd08419  159 TGRLAVlDVEGFPIRRQWYVVHRKGKRLSPAAQAFLDFL 197
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
3-291 1.26e-15

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 75.45  E-value: 1.26e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   3 MSVKQLRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGELFLPMARQLLADWDNVEE 82
Cdd:PRK11151   1 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLREVKVLKE 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  83 AMRQSFTLQRGKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGI-AF--EPSPnhnLLF 159
Cdd:PRK11151  81 MASQQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAIlALvkESEA---FIE 157
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 160 TPLAVDRFVAIVPQQSPLAKKKQ-----LTWQELLTLDFITLQRPSAVRLMLEealarSGRQLDVALESHQLVTVGRMVA 234
Cdd:PRK11151 158 VPLFDEPMLLAVYEDHPWANRDRvpmsdLAGEKLLMLEDGHCLRDQAMGFCFE-----AGADEDTHFRATSLETLRNMVA 232
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 694074312 235 SGLGGSAVPALCKTQMASLGAVC-IPLSDPPIEKCVGAIHAGHLPLSKAAQALLDTLK 291
Cdd:PRK11151 233 AGSGITLLPALAVPNERKRDGVCyLPCIKPEPRRTIGLVYRPGSPLRSRYEQLAEAIR 290
cbl PRK12679
HTH-type transcriptional regulator Cbl;
3-238 2.49e-15

HTH-type transcriptional regulator Cbl;


Pssm-ID: 183676 [Multi-domain]  Cd Length: 316  Bit Score: 74.85  E-value: 2.49e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   3 MSVKQLRAFLAVAHT-LNFAHASERLNLSQPALSLTIKGLEEALGGTL-LQRSTRKVTLTQEGELFLPMARQLLADWDNV 80
Cdd:PRK12679   1 MNFQQLKIIREAARQdYNLTEVANMLFTSQSGVSRHIRELEDELGIEIfIRRGKRLLGMTEPGKALLVIAERILNEASNV 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  81 EEaMRQSFTLQ-RGKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLF 159
Cdd:PRK12679  81 RR-LADLFTNDtSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQLV 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 160 T-PLAVDRFVAIVPQQSPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLG 238
Cdd:PRK12679 160 AfPWFRWHHSLLVPHDHPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALGLG 239
PBP2_BudR cd08451
The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is ...
107-264 1.30e-14

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: 70.67  E-value: 1.30e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 107 VLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEmgIAF-EPSPNH--NLLFTPLAVDRFVAIVPQQSPLAKKKQL 183
Cdd:cd08451   15 LVPGLIRRFREAYPDVELTLEEANTAELLEALREGRLD--AAFvRPPVARsdGLVLELLLEEPMLVALPAGHPLARERSI 92
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 184 TWQELLTLDFITLQRPSAVRLM--LEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPAlCKTQMASLGAVCIPLS 261
Cdd:cd08451   93 PLAALADEPFILFPRPVGPGLYdaIIAACRRAGFTPRIGQEAPQMASAINLVAAGLGVSIVPA-SMRQLQAPGVVYRPLA 171

                 ...
gi 694074312 262 DPP 264
Cdd:cd08451  172 GAP 174
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
8-184 3.66e-14

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 71.57  E-value: 3.66e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   8 LRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGE-LFLPMARQLladwDNVEEAMRQ 86
Cdd:PRK10086  19 LHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKrVFWALKSSL----DTLNQEILD 94
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  87 SFTLQ-RGKISVAAMPSFAANVLPEALKAFRDRYAGVNVTV---HDVINEQviemvREGrVEMGIAFEPSPNHNLLFTPL 162
Cdd:PRK10086  95 IKNQElSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTIltgNENVNFQ-----RAG-IDLAIYFDDAPSAQLTHHFL 168
                        170       180
                 ....*....|....*....|...
gi 694074312 163 AVDrfvAIVPQQSP-LAKKKQLT 184
Cdd:PRK10086 169 MDE---EILPVCSPeYAERHALT 188
PBP2_GbpR cd08435
The C-terminal substrate binding domain of galactose-binding protein regulator contains the ...
94-290 5.56e-14

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


Pssm-ID: 176126 [Multi-domain]  Cd Length: 201  Bit Score: 69.22  E-value: 5.56e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  94 KISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNH--NLLFTPLAVDRFVAIV 171
Cdd:cd08435    1 TVRVGAVPAAAPVLLPPAIARLLARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLADDEQppDLASEELADEPLVVVA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 172 PQQSPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQL-DVALESHQLVTVGRMVASGLGGSAVPALCKTQM 250
Cdd:cd08435   81 RPGHPLARRARLTLADLADYPWVLPPPGTPLRQRLEQLFAAAGLPLpRNVVETASISALLALLARSDMLAVLPRSVAEDE 160
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 694074312 251 ASLGA-VCIPLSDPPIEKCVGAIHAGHLPLSKAAQALLDTL 290
Cdd:cd08435  161 LRAGVlRELPLPLPTSRRPIGITTRRGGPLSPAARALLDAL 201
PBP2_HcaR cd08450
The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in ...
100-261 5.89e-14

The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold; HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176141 [Multi-domain]  Cd Length: 196  Bit Score: 68.94  E-value: 5.89e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 100 MPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVPQQSPLAK 179
Cdd:cd08450    7 LPGAEVQWLPEVLPILREEHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGIDYQLLLKEPLIVVLPADHRLAG 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 180 KKQLTWQELLTLDFITLQRPSAV-RLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPALCKTQMASlGAVCI 258
Cdd:cd08450   87 REKIPPQDLAGENFISPAPTAPVlQQVIENYAAQHNIQPNIIQEADNLLSAMSLVASTLGCALLPLYANNLLPP-SVVAR 165

                 ...
gi 694074312 259 PLS 261
Cdd:cd08450  166 PLS 168
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
8-124 7.29e-14

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 70.26  E-value: 7.29e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   8 LRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGELFLPMARQLLadwDNVEEAMRQS 87
Cdd:PRK11139  11 LRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIF---DQLAEATRKL 87
                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 694074312  88 FTLQR-GKISVAAMPSFAANVLPEALKAFRDRYAGVNV 124
Cdd:PRK11139  88 RARSAkGALTVSLLPSFAIQWLVPRLSSFNEAHPDIDV 125
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
8-193 7.34e-14

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 70.61  E-value: 7.34e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   8 LRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGELFLPMARQlladWDNVEEAMrqs 87
Cdd:PRK10094   7 LRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARD----WLSWLESM--- 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  88 ftlqrgkisvaampsfaanvlPEALKAFRDryaGVNVTVHDVINeqviemvregrvemgiafepspnhNLLFTPLAVDRF 167
Cdd:PRK10094  80 ---------------------PSELQQVND---GVERQVNIVIN------------------------NLLYNPQAVAQL 111
                        170       180       190
                 ....*....|....*....|....*....|..
gi 694074312 168 VAIVPQQSPLAK---KKQL---TWQELLTLDF 193
Cdd:PRK10094 112 LAWLNERYPFTQfhiSRQIymgVWDSLLYEGF 143
PBP2_LTTR_aromatics_like_2 cd08448
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
107-290 9.82e-14

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


Pssm-ID: 176139 [Multi-domain]  Cd Length: 197  Bit Score: 68.45  E-value: 9.82e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 107 VLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVPQQSPLAKKKQLTWQ 186
Cdd:cd08448   14 GLPRILRAFRAEYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAGLSARLLHREPFVCCLPAGHPLAARRRIDLR 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 187 ELLTLDFITLQR---PSAVRLMLeeAL-ARSGRQLDVALESHQLVTVGRMVASGLGGSAVP-ALCKTQMAslGAVCIPLS 261
Cdd:cd08448   94 ELAGEPFVLFSRevsPDYYDQII--ALcMDAGFHPKIRHEVRHWLTVVALVAAGMGVALVPrSLARAGLA--GVRFLPLK 169
                        170       180       190
                 ....*....|....*....|....*....|
gi 694074312 262 DPPIE-KCVGAIHAGHlpLSKAAQALLDTL 290
Cdd:cd08448  170 GATQRsELYAAWKASA--PNPALQAFLAAL 197
PRK12680 PRK12680
LysR family transcriptional regulator;
3-238 2.51e-13

LysR family transcriptional regulator;


Pssm-ID: 183677 [Multi-domain]  Cd Length: 327  Bit Score: 69.27  E-value: 2.51e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   3 MSVKQLRAFLAVAHT-LNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKV-TLTQEGELFLPMARQLLADWDNV 80
Cdd:PRK12680   1 MTLTQLRYLVAIADAeLNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLeSVTPAGVEVIERARAVLSEANNI 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  81 EEAMRQSFTLQRGKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGI----AFEPSPNhn 156
Cdd:PRK12680  81 RTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIvstaGGEPSAG-- 158
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 157 lLFTPLAVDRFVAIVPQQSPLAKKKQ------LTWQELLTLDFITlqRPSAvrlMLEEALARSGRQLDVALESHQLVTVG 230
Cdd:PRK12680 159 -IAVPLYRWRRLVVVPRGHALDTPRRapdmaaLAEHPLISYESST--RPGS---SLQRAFAQLGLEPSIALTALDADLIK 232

                 ....*...
gi 694074312 231 RMVASGLG 238
Cdd:PRK12680 233 TYVRAGLG 240
PBP2_Nitroaromatics_like cd08417
The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved ...
96-235 4.69e-13

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


Pssm-ID: 176109 [Multi-domain]  Cd Length: 200  Bit Score: 66.47  E-value: 4.69e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  96 SVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVPQQS 175
Cdd:cd08417    3 RIAASDYLEALLLPPLLARLRQEAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRSQPLFEDRFVCVARKDH 82
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 176 PLAkKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVAS 235
Cdd:cd08417   83 PLA-GGPLTLEDYLAAPHVLVSPRGRGHGLVDDALAELGLSRRVALTVPHFLAAPALVAG 141
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
3-162 4.90e-13

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 68.16  E-value: 4.90e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   3 MSVKQLRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGELFLPMARQLLADWD-NVE 81
Cdd:PRK10082  11 IETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLEsNLA 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  82 EAMRQSFTLQRgKISVAAMPSFAANVLPEALKAFRDRYAGVnVTVHDVinEQVIEMVREGRVEMGIAFEpspNHNLLFTP 161
Cdd:PRK10082  91 ELRGGSDYAQR-KIKIAAAHSLSLGLLPSIISQMPPLFTWA-IEAIDV--DEAVDKLREGQSDCIFSFH---DEDLLEAP 163

                 .
gi 694074312 162 L 162
Cdd:PRK10082 164 F 164
PBP2_XapR cd08449
The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved ...
95-290 1.22e-12

The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold; In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176140 [Multi-domain]  Cd Length: 197  Bit Score: 65.37  E-value: 1.22e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  95 ISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEP--SPNHNLLFTPLAVDRFVAIVP 172
Cdd:cd08449    2 LNIGMVGSVLWGGLGPALRRFKRQYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFAdtLNDPPLASELLWREPMVVALP 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 173 QQSPLAKKKQLTWQELLTLDFITLQRP-SAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPAlCKTQMA 251
Cdd:cd08449   82 EEHPLAGRKSLTLADLRDEPFVFLRLAnSRFADFLINCCLQAGFTPQITQEVVEPQTLMALVAAGFGVALVPE-SYARLP 160
                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 694074312 252 SLGAVCIPLSdPPIEKCVGAIHAgHLPLSKAAQALLDTL 290
Cdd:cd08449  161 WPGVRFIPLK-QAISADLYAVYH-PDSATPVIQAFLALL 197
PBP2_CysB_like cd08413
The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains ...
94-223 2.84e-12

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


Pssm-ID: 176105 [Multi-domain]  Cd Length: 198  Bit Score: 64.18  E-value: 2.84e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  94 KISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNH-NLLFTPLAVDRFVAIVP 172
Cdd:cd08413    1 QLTIATTHTQARYVLPPVIAAFRKRYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDDHpDLVTLPCYRWNHCVIVP 80
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 694074312 173 QQSPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALES 223
Cdd:cd08413   81 PGHPLADLGPLTLEDLAQYPLITYDFGFTGRSSIDRAFARAGLEPNIVLTA 131
PBP2_AlsR cd08452
The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which ...
107-263 1.82e-11

The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold; AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176143 [Multi-domain]  Cd Length: 197  Bit Score: 62.13  E-value: 1.82e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 107 VLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVPQQSPLAKKKQLTWQ 186
Cdd:cd08452   14 FLPPIVREYRKKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALHIETVQSSPCVLALPKQHPLASKEEITIE 93
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 694074312 187 ELLTLDFITLQRPSAVRLMLE--EALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPAlCKTQMASLGAVCIPLSDP 263
Cdd:cd08452   94 DLRDEPIITVAREAWPTLYDEiiQLCEQAGFRPKIVQEATEYQTVIGLVSAGIGVTFVPS-SAKKLFNLEVAYRKIDQI 171
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
6-107 2.11e-11

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 63.07  E-value: 2.11e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   6 KQLRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRsTRKVTLTQEGELFLPMARQLladwdnveeAMR 85
Cdd:PRK13348   5 KQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQRLLRHLRQV---------ALL 74
                         90       100
                 ....*....|....*....|..
gi 694074312  86 QSFTLQRGKISVAAMPSFAANV 107
Cdd:PRK13348  75 EADLLSTLPAERGSPPTLAIAV 96
PBP2_IlvR cd08453
The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved ...
106-263 4.59e-11

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: 60.84  E-value: 4.59e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 106 NVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNH---NLLFTPLAVDRFVAIVPQQSPLAKKKQ 182
Cdd:cd08453   13 SVLPELVRRFREAYPDVELQLREATSDVQLEALLAGEIDAGIVIPPPGASappALAYRPLLSEPLVLAVPAAWAAEGGAP 92
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 183 LTWQELLTLDFITLQRPSAVRL--MLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPAlCKTQMASLGAVCIPL 260
Cdd:cd08453   93 LALAAVAAEPLVIFPRRIAPAFhdAVTGYYRAAGQTPRIAQEAIQMQTIISLVSAGMGVALVPA-SLRNLARPGVVYREL 171

                 ...
gi 694074312 261 SDP 263
Cdd:cd08453  172 ADP 174
PRK10341 PRK10341
transcriptional regulator TdcA;
6-295 7.93e-11

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 61.80  E-value: 7.93e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   6 KQLRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGELFLPMARQLLADWDNVEEAMR 85
Cdd:PRK10341  10 QHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEIN 89
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  86 QSFTLQRGKISVaAMPSFAA-NVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAF---EPSPnHNLLFTP 161
Cdd:PRK10341  90 GMSSEAVVDVSF-GFPSLIGfTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTlsnEMKL-QDLHVEP 167
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 162 LAVDRFVAIVPQQSPLAKKKQLtwQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSA 241
Cdd:PRK10341 168 LFESEFVLVASKSRTCTGTTTL--ESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNADFLTV 245
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 694074312 242 VPALCKTQMASLGAVCIPLSDP-PIEKcVGAIHAGHLPLSKAAQALLDTLKGFLP 295
Cdd:PRK10341 246 IPCDMTSPFGSNQFITIPIEETlPVAQ-YAAVWSKNYRIKKAASVLVELAKEYSS 299
PRK15421 PRK15421
HTH-type transcriptional regulator MetR;
3-243 1.39e-10

HTH-type transcriptional regulator MetR;


Pssm-ID: 185319 [Multi-domain]  Cd Length: 317  Bit Score: 60.80  E-value: 1.39e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   3 MSVKQLRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGELFLPMARQLLAdwdNVEE 82
Cdd:PRK15421   2 IEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLP---QISQ 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  83 AMRQSFTLQRGKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPL 162
Cdd:PRK15421  79 ALQACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPM 158
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 163 AVDRFVAIVPQQSPLAKKKQLTWQELL--TLDFITLQRPsavRL-MLEEALARSGRQLDVALESHQLVTVgRMVASGLGG 239
Cdd:PRK15421 159 FDYEVRLVLAPDHPLAAKTRITPEDLAseTLLIYPVQRS---RLdVWRHFLQPAGVSPSLKSVDNTLLLI-QMVAARMGI 234

                 ....
gi 694074312 240 SAVP 243
Cdd:PRK15421 235 AALP 238
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
8-243 7.84e-10

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 58.50  E-value: 7.84e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   8 LRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGELFLPMARQLLAdwDNVEEAMRQS 87
Cdd:PRK15092  16 LRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILR--FNDEACSSLM 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  88 FTLQRGKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNllftplavdrf 167
Cdd:PRK15092  94 YSNLQGVLTIGASDDTADTILPFLLNRVSSVYPKLALDVRVKRNAFMMEMLESQEVDLAVTTHRPSSFP----------- 162
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 168 vAIVPQQSPL----AKKKQLTWQELLTLdfITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVP 243
Cdd:PRK15092 163 -ALNLRTSPTlwycAAEYVLQKGEPIPL--VLLDEPSPFRDMALATLNAAGIPWRIAYVASTLSAVRAAVKAGLGVTARP 239
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
6-73 5.92e-09

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 55.94  E-value: 5.92e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 694074312   6 KQLRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRsTRKVTLTQEGELFLPMARQL 73
Cdd:PRK03635   5 KQLEALAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-TQPCRPTEAGQRLLRHARQV 71
PBP2_Cbl cd08444
The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is ...
95-238 6.93e-09

The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold; Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonation enzyme. Both Cbl and CysB require expression of the tau and ssu genes. Like many other members of the LTTR family, the Cbl is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176135  Cd Length: 198  Bit Score: 54.82  E-value: 6.93e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  95 ISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNH-NLLFTPLAVDRFVAIVPQ 173
Cdd:cd08444    2 LTIATTHTQARYALPWVVQAFKEQFPNVHLVLHQGSPEEIASMLANGQADIGIATEALENHpELVSFPYYDWHHHIIVPV 81
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 694074312 174 QSPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLG 238
Cdd:cd08444   82 GHPLESITPLTIETIAKWPIITYHGGFTGRSRIDRAFSRAELTPNIVLSALDADVIKTYVGLGMG 146
PBP2_LTTR_aromatics_like_1 cd08447
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
107-264 1.04e-08

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: 54.19  E-value: 1.04e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 107 VLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVPQQSPLAKKKQLTWQ 186
Cdd:cd08447   14 FLPRLLAAARAALPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFARPGLETRPLVREPLVAAVPAGHPLAGAERLTLE 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 187 ELLTLDFITLQrPSAVRL---MLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPAlCKTQMASLGAVCIPLSDP 263
Cdd:cd08447   94 DLDGQPFIMYS-PTEARYfhdLVVRLFASAGVQPRYVQYLSQIHTMLALVRAGLGVALVPA-SASRLRFEGVVFRPLDLP 171

                 .
gi 694074312 264 P 264
Cdd:cd08447  172 R 172
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
13-98 1.45e-08

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 54.95  E-value: 1.45e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  13 AVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGELFLPMARQLLADWDNVEEAMRQSFTLQR 92
Cdd:PRK11074  12 AVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQETRRQCQQVANGWR 91

                 ....*.
gi 694074312  93 GKISVA 98
Cdd:PRK11074  92 GQLSIA 97
PBP2_CynR cd08425
The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, ...
93-264 1.83e-08

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: 53.49  E-value: 1.83e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  93 GKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVP 172
Cdd:cd08425    1 GSLRLAMTPTFTAYLIGPLIDRFHARYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDAQPLFDERLALVVG 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 173 QQSPLAKKKQ-LTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPALCKTQMA 251
Cdd:cd08425   81 ATHPLAQRRTaLTLDDLAAEPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVRRGRLATILPDAIAREQP 160
                        170
                 ....*....|...
gi 694074312 252 SLGAVCIplsDPP 264
Cdd:cd08425  161 GLCAVAL---EPP 170
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
11-153 1.96e-08

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 54.61  E-value: 1.96e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  11 FLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGELFLPMARQLLADWDNVEEAMRQSFTL 90
Cdd:PRK14997  10 FVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQAAQDAIAALQVE 89
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 694074312  91 QRGKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVhDVINEQViEMVREGrVEMGIAFEPSP 153
Cdd:PRK14997  90 PRGIVKLTCPVTLLHVHIGPMLAKFMARYPDVSLQL-EATNRRV-DVVGEG-VDVAIRVRPRP 149
PBP2_Chlorocatechol cd08446
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
93-244 2.05e-08

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


Pssm-ID: 176137 [Multi-domain]  Cd Length: 198  Bit Score: 53.44  E-value: 2.05e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  93 GKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVP 172
Cdd:cd08446    1 GELDVGYFGSAILDTVPRLLRAFLTARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFYPVEPDIAVENVAQERLYLAVP 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 694074312 173 QQSPLAKKKQLTWQELLTLDFI---TLQRPSAVRLMLeEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPA 244
Cdd:cd08446   81 KSHPLAARPAVSLADLRNEPLIlfpRGGRPSFADEVL-GLFRRAGVEPRVAQEVEDVVAALALVAAGFGVCIVPE 154
PBP2_BenM_CatM_CatR cd08445
The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in ...
107-265 1.66e-07

The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold; This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes of the ortho-pathway required for benzoate catabolism: muconate lactonizing enzyme I, muconolactone isomerase, and catechol 1,2-dioxygenase. CatR normally responds to benzoate and cis,cis-muconate, an inducer molecule, to activate transcription of the catBCA operon, whose gene products convert benzoate to catechol. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176136  Cd Length: 203  Bit Score: 50.69  E-value: 1.66e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 107 VLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMG---IAFE-PSPNHNLLFTplavDRFVAIVPQQSPLAKKKQ 182
Cdd:cd08445   15 LLPELIRRFRQAAPDVEIELIEMTTVQQIEALKEGRIDVGfgrLRIEdPAIRRIVLRE----EPLVVALPAGHPLAQEKA 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 183 -LTWQELLTLDFITL---QRPSAVRLMLeEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPAlCKTQMASLGAVCI 258
Cdd:cd08445   91 pLTLAQLADEPLILYpasPRPSFADQVL-SLFRDHGLRPRVIQEVRELQTALGLVAAGEGVTLVPA-SVQRLRRDDVVYR 168

                 ....*..
gi 694074312 259 PLSDPPI 265
Cdd:cd08445  169 PLLDPDA 175
PBP2_CysB cd08443
The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 ...
94-245 1.96e-07

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


Pssm-ID: 176134  Cd Length: 198  Bit Score: 50.25  E-value: 1.96e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  94 KISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNH-NLLFTPLAVDRFVAIVP 172
Cdd:cd08443    1 SLYVATTHTQARYVLPPVIKGFIERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHDYdDLITLPCYHWNRCVVVK 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 694074312 173 QQSPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPAL 245
Cdd:cd08443   81 RDHPLADKQSISIEELATYPIVTYTFGFTGRSELDTAFNRAGLTPNIVLTATDADVIKTYVRLGLGVGVIASM 153
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
5-124 3.82e-07

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 50.53  E-value: 3.82e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   5 VKQLRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGELFLPMARQLLADWDNVEEAM 84
Cdd:PRK10632   4 LKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQL 83
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 694074312  85 RQSFTLQRGKISVAAMPSFAANVLPEALKAFRDRYAGVNV 124
Cdd:PRK10632  84 YAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSV 123
PBP2_DntR_NahR_LinR_like cd08459
The C-terminal substrate binding domain of LysR-type transcriptional regulators that are ...
108-235 5.64e-07

The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate of the oxidative degradation of the aromatic ring in soil bacteria. LinR positively regulates expression of the genes (linD and linE) encoding enzymes for gamma-hexachlorocyclohexane (a haloorganic insecticide) degradation. Expression of linD and linE are induced by their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ) and chlorohydroquinone (CHQ). The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176148 [Multi-domain]  Cd Length: 201  Bit Score: 49.11  E-value: 5.64e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 108 LPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVPQQSPLAKKKqLTWQE 187
Cdd:cd08459   15 LPRLLAALREVAPGVRIETVRLPVDELEEALESGEIDLAIGYLPDLGAGFFQQRLFRERYVCLVRKDHPRIGST-LTLEQ 93
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 694074312 188 LLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVAS 235
Cdd:cd08459   94 FLAARHVVVSASGTGHGLVEQALREAGIRRRIALRVPHFLALPLIVAQ 141
PBP2_TdcA cd08418
The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is ...
94-291 7.02e-07

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: 48.89  E-value: 7.02e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  94 KISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPS--PNHNLLFTPLAVDRFVAIV 171
Cdd:cd08418    1 KVSIGVSSLIAHTLMPAVINRFKEQFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDemYLKELISEPLFESDFVVVA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 172 PQQSPLAKKKQLtwQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVP-ALCKTQM 250
Cdd:cd08418   81 RKDHPLQGARSL--EELLDASWVLPGTRMGYYNNLLEALRRLGYNPRVAVRTDSIVSIINLVEKADFLTILSrDMGRGPL 158
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 694074312 251 ASLGAVCIPLSDPPIEKCVGAIHAGHLPLSKAAQALLDTLK 291
Cdd:cd08418  159 DSFRLITIPVEEPLPSADYYLIYRKKSRLTPLAEQLVELFR 199
PBP2_IlvY cd08430
The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates ...
96-245 8.75e-07

The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic bindin; In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-independent manner. 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: 176121  Cd Length: 199  Bit Score: 48.34  E-value: 8.75e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  96 SVAAMPSFaanvLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEP-SPNHNLLFTPLAVDRFVAIVPQQ 174
Cdd:cd08430    7 SVTASYSF----LPPILERFRAQHPQVEIKLHTGDPADAIDKVLNGEADIAIAARPdKLPARLAFLPLATSPLVFIAPNI 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 175 SPLAKKKQ----LTWQElltLDFItlqrpsavrlMLEEALARsgRQLDVALESHQLV-----TVG------RMVASGLGG 239
Cdd:cd08430   83 ACAVTQQLsqgeIDWSR---LPFI----------LPERGLAR--ERLDQWFRRRGIKpniyaQVAgheaivSMVALGCGV 147

                 ....*.
gi 694074312 240 SAVPAL 245
Cdd:cd08430  148 GIVPEL 153
PBP2_MleR cd08437
The substrate binding domain of LysR-type transcriptional regulator MleR which required for ...
94-290 1.37e-06

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


Pssm-ID: 176128  Cd Length: 198  Bit Score: 48.10  E-value: 1.37e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  94 KISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSP-NHNLLFTP-LAVDRFVAIV 171
Cdd:cd08437    1 KLRFGLPPIIGNYYFPKLAKDLIKTGLMIQIDTYEGGSAELLEQLLQGDLDIALLGSLTPlENSALHSKiIKTQHFMIIV 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 172 PQQSPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPALCKTQMA 251
Cdd:cd08437   81 SKDHPLAKAKKVNFADLKKENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSMVRENVGIGFLTDIAVKPDD 160
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 694074312 252 SLgaVCIPLSD-PPIEKCVGAIHAGHLPLSKAAQALLDTL 290
Cdd:cd08437  161 HL--VAIPLLDnEQPTFYISLAHRKDQLLTPAQKKLLDLL 198
PRK09801 PRK09801
LysR family transcriptional regulator;
6-140 2.16e-06

LysR family transcriptional regulator;


Pssm-ID: 182085 [Multi-domain]  Cd Length: 310  Bit Score: 48.49  E-value: 2.16e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312   6 KQLRAFLAVAHTLNFAHASERLNLSQPALSLTIKGLEEALGGTLLQRSTRKVTLTQEGELFLPMARQLLADWDNVEEAMR 85
Cdd:PRK09801   9 KDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVT 88
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 694074312  86 QSFTLQRGKISVAAMPSFAANVLPEALKAFRDRYAgvNVTVHDVINEQVIEMVRE 140
Cdd:PRK09801  89 QIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYP--ELQVHFELFDRQIDLVQD 141
PBP2_NocR cd08458
The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the ...
95-281 5.28e-06

The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the catabolism of nopaline, contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator NocR, which is involved in the catabolism of nopaline. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. 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: 176147  Cd Length: 196  Bit Score: 46.24  E-value: 5.28e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  95 ISVAAMPSFAANVLPEALKAFRDRYAGVNVTVhDVINE-QVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVPQ 173
Cdd:cd08458    2 LRVACYTAPALSFMSGVIQTFIADRPDVSVYL-DTVPSqTVLELVSLQHYDLGISILAGDYPGLTTEPVPSFRAVCLLPP 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 174 QSPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPALCKTQMASL 253
Cdd:cd08458   81 GHRLEDKETVHATDLEGESLICLSPVSLLRMQTDAALDSCGVHCNRRIESSLALNLCDLVSRGMGVGIVDPFTADYYSAN 160
                        170       180
                 ....*....|....*....|....*...
gi 694074312 254 GAVCIPLSdPPIEKCVGAIHAGHLPLSK 281
Cdd:cd08458  161 PVIQRSFD-PVVPYHFAIVLPTDSPPPR 187
PBP2_DntR_like_2 cd08464
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
108-266 1.24e-04

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


Pssm-ID: 176153 [Multi-domain]  Cd Length: 200  Bit Score: 42.22  E-value: 1.24e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 108 LPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIV-PQQSPLakKKQLTWQ 186
Cdd:cd08464   15 APPLLAALRAEAPGVRLVFRQVDPFNVGDMLDRGEIDLAIGVFGELPAWLKREVLYTEGYACLFdPQQLSL--SAPLTLE 92
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 187 ELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPALCKTQMASLGAVCipLSDPPIE 266
Cdd:cd08464   93 DYVARPHVLVSYRGGLRGFVDDALAELGRSRRVVASTPHFAALPALLRGTPLIATVPARLARAWAAALGLR--ASPPPLD 170
PBP2_MdcR cd08416
The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which ...
131-263 2.73e-04

The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold; This family includes the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate- binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176108  Cd Length: 199  Bit Score: 41.18  E-value: 2.73e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 131 NEQVIEMVREGRVE-MGIAF-EPSPNHNLLFTPLAVDRFVAIVPQQSPLAKKKQLTWQELLTLDFITLQRPSAVRLMLEE 208
Cdd:cd08416   38 NKDLLKKLKDGELDaILVATpEGLNDPDFEVVPLFEDDIFLAVPATSPLAASSEIDLRDLKDEKFVTLSEGFATYRGFDE 117
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 694074312 209 ALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPALCKTQMASlGAVCIPLSDP 263
Cdd:cd08416  118 AFEIAGFEPNVVMRVNDIFSLMSMVSGGVGYALLPGRIADVYED-KVQLIPLAEP 171
PBP2_SyrM cd08467
The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates ...
94-266 4.07e-04

The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold; Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. 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: 176156 [Multi-domain]  Cd Length: 200  Bit Score: 40.50  E-value: 4.07e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  94 KISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVPQ 173
Cdd:cd08467    1 GFTLAMPDYAEVALLPRLAPRLRERAPGLDLRLCPIGDDLAERGLEQGTIDLAVGRFAVPPDGLVVRRLYDDGFACLVRH 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 174 QSPLAkKKQLTWQELLTLDFITLQRPSAVRLMLEEALARSGRQLDVALESHQLVTVGRMVASGLGGSAVPALCKTQMASL 253
Cdd:cd08467   81 GHPAL-AQEWTLDDFATLRHVAIAPPGRLFGGIYKRLENLGLKRNVAIAVSSFLTAAATVAATDLIATVPRRVATQVAAM 159
                        170
                 ....*....|...
gi 694074312 254 GAVCIplSDPPIE 266
Cdd:cd08467  160 LPLRV--VPPPVD 170
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
93-238 2.46e-03

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


Pssm-ID: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 38.19  E-value: 2.46e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312  93 GKISVAAMPSFAANVLPEALKAFRDRYAGVNVTVHdvINEQVIEMVREGrVEMGIAFEPSPNHNLLFTPLAVDRF--VAi 170
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELV--LSDRLVDLVEEG-FDLAIRIGELPDSSLVARRLGPVRRvlVA- 76
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 694074312 171 vpqqSP--LAKK-KQLTWQELLTLDFITLQRPSAVRLMLeeaLARSGRQLDVALEShQLVT-----VGRMVASGLG 238
Cdd:cd08422   77 ----SPayLARHgTPQTPEDLARHRCLGYRLPGRPLRWR---FRRGGGEVEVRVRG-RLVVndgeaLRAAALAGLG 144
PBP2_MetR cd08441
The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which ...
111-243 5.32e-03

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


Pssm-ID: 176132  Cd Length: 198  Bit Score: 37.16  E-value: 5.32e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694074312 111 ALKAFRDRYAGVNVTVHDVINEQVIEMVREGRVEMGIAFEPSPNHNLLFTPLAVDRFVAIVPQQSPLAKKKQLTWQELLT 190
Cdd:cd08441   18 VLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGIAYEPLFDYEVVLVVAPDHPLAAKEFITPEDLAD 97
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 694074312 191 LDFIT----LQRPSAVRLMLEEALARSGRQLDVALESHQLvtvgRMVASGLGGSAVP 243
Cdd:cd08441   98 ETLITypveRERLDVFRHFLQPAGIEPKRRRTVELTLMIL----QLVASGRGVAALP 150
 
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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